| 1. |
Hurtle W,
Bode E,
Kaplan RS,
Garrison J,
Kearney B,
Shoemaker D,
Henchal E,
Norwood D,
( 2003 ) Use of denaturing high-performance liquid chromatography to identify Bacillus anthracis by analysis of the 16S-23S rRNA interspacer region and gyrA gene. PMID : 14532217 : DOI : 10.1128/jcm.41.10.4758-4766.2003 PMC : PMC254356 Abstract >>
Denaturing high-performance liquid chromatography (DHPLC) was evaluated as a method for identifying Bacillus anthracis by analyzing two chromosomal targets, the 16S-23S intergenic spacer region (ISR) and the gyrA gene. The 16S-23S ISR was analyzed by this method with 42 strains of B. anthracis, 36 strains of Bacillus cereus, and 12 strains of Bacillus thuringiensis; the gyrA gene was analyzed by this method with 33 strains of B. anthracis, 27 strains of B. cereus, and 9 strains of B. thuringiensis. Two blind panels of 45 samples each were analyzed to evaluate the potential diagnostic capability of this method. Our results show that DHPLC is an efficient method for the identification of B. anthracis.
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2. |
Pomerantsev AP,
Kalnin KV,
Osorio M,
Leppla SH,
( 2003 ) Phosphatidylcholine-specific phospholipase C and sphingomyelinase activities in bacteria of the Bacillus cereus group. PMID : 14573681 : DOI : 10.1128/iai.71.11.6591-6606.2003 PMC : PMC219565 Abstract >>
Bacillus anthracis is nonhemolytic, even though it is closely related to the highly hemolytic Bacillus cereus. Hemolysis by B. cereus results largely from the action of phosphatidylcholine-specific phospholipase C (PC-PLC) and sphingomyelinase (SPH), encoded by the plc and sph genes, respectively. In B. cereus, these genes are organized in an operon regulated by the global regulator PlcR. B. anthracis contains a highly similar cereolysin operon, but it is transcriptionally silent because the B. anthracis PlcR is truncated at the C terminus. Here we report the cloning, expression, purification, and enzymatic characterization of PC-PLC and SPH from B. cereus and B. anthracis. We also investigated the effects of expressing PlcR on the expression of plc and sph. In B. cereus, PlcR was found to be a positive regulator of plc but a negative regulator of sph. Replacement of the B. cereus plcR gene by its truncated orthologue from B. anthracis eliminated the activities of both PC-PLC and SPH, whereas introduction into B. anthracis of the B. cereus plcR gene with its own promoter did not activate cereolysin expression. Hemolytic activity was detected in B. anthracis strains containing the B. cereus plcR gene on a multicopy plasmid under control of the strong B. anthracis protective antigen gene promoter or in a strain carrying a multicopy plasmid containing the entire B. cereus plc-sph operon. Slight hemolysis and PC-PLC activation were found when PlcR-producing B. anthracis strains were grown under anaerobic-plus-CO(2) or especially under aerobic-plus-CO(2) conditions. Unmodified parental B. anthracis strains did not demonstrate obvious hemolysis under the same conditions.
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3. |
Brown JR,
Gentry D,
Becker JA,
Ingraham K,
Holmes DJ,
Stanhope MJ,
( 2003 ) Horizontal transfer of drug-resistant aminoacyl-transfer-RNA synthetases of anthrax and Gram-positive pathogens. PMID : 12792655 : DOI : 10.1038/sj.embor.embor881 PMC : PMC1326320 Abstract >>
The screening of new antibiotics against several bacterial strains often reveals unexpected occurrences of natural drug resistance. Two examples of this involve specific inhibitors of Staphylococcus aureus isoleucyl-transfer-RNA synthetase 1 (IleRS1) and, more recently, Streptococcus pneumoniae methionyl-tRNA synthetase 1 (MetRS1). In both cases, resistance is due to the presence of a second gene that encodes another synthetase (IleRS2 or MetRS2). Here, we show that both S. pneumoniae MetRS2 and S. aureus IleRS2 have closely related homologues in the Gram-positive bacterium Bacillus anthracis, the causative agent of anthrax. Furthermore, similar to drug-resistant pathogens, strains of B. anthracis and its closest relative, B. cereus, also have wild-type ileS1 and metS1 genes. Clostridium perfringens, the causative agent of gangrene, also has two metS genes, whereas Oceanobacillus iheyensis isolated from deep-sea sediments has a single ileS2-type gene. This study shows the importance of understanding complex evolutionary networks of ancient horizontal gene transfer for the development of novel antibiotics.
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4. |
Kobayashi K,
Kamakura T,
Tanaka T,
Yamaguchi I,
Endo T,
( 1991 ) Nucleotide sequence of the bsr gene and N-terminal amino acid sequence of blasticidin S deaminase from blasticidin S resistant Escherichia coli TK121. PMID : 1368770 : Abstract >>
N/A
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5. |
Hansen BM,
Høiby PE,
Jensen GB,
Hendriksen NB,
( 2003 ) The Bacillus cereus bceT enterotoxin sequence reappraised. PMID : 12798995 : DOI : 10.1016/S0378-1097(03)00249-0 Abstract >>
Bacillus cereus is a known opportunistic human pathogen belonging to the B. cereus group. Establishment of the pathogenesis most likely involves several gene products. One of these gene products, a single gene component named bceT, has been cloned and described from B. cereus B-4ac [Agata et al., Microbiology 141 (1995) 983-988]. However, our sequences of the bceT region from 16 B. cereus group strains showed inconsistency with the published bceT sequence. Only part of the bceT sequence had homology to our sequences. This initiated a more thorough investigation of the bceT sequence. Restriction site search and database searches intimated that the cloned bceT was created by an incidental joining of four DNA fragments during ligation. One of these fragments had 93% homology to an open reading frame (ORF 101) located within the pathogenic island of the Bacillus anthracis pXO1 virulence plasmid. We suggest that the reported enterotoxic activity of the original cloned bceT construct could be due to either the fusion gene or the fragment with homology to ORF 101 in pXO1.
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6. |
Oyama T,
Miyake H,
Kusunoki M,
Nitta Y,
( 2003 ) Crystal structures of beta-amylase from Bacillus cereus var mycoides in complexes with substrate analogs and affinity-labeling reagents. PMID : 12761294 : DOI : 10.1093/jb/mvg061 Abstract >>
The crystal structures of beta-amylase from Bacillus cereus var. mycoides in complexes with five inhibitors were solved. The inhibitors used were three substrate analogs, i.e. glucose, maltose (product), and a synthesized compound, O-alpha-D-glucopyranosyl-(1-->4)-O-alpha-D-glucopyranosyl-(1-->4)-D-xylopyranose (GGX), and two affinity-labeling reagents with an epoxy alkyl group at the reducing end of glucose. For all inhibitors, one molecule was bound at the active site cleft and the non-reducing end glucose of the four inhibitors except GGX was located at subsite 1, accompanied by a large conformational change of the flexible loop (residues 93-97), which covered the bound inhibitor. In addition, another molecule of maltose or GGX was bound about 30 A away from the active site. A large movement of residues 330 and 331 around subsite 3 was also observed upon the binding of GGX at subsites 3 to 5. Two affinity-labeling reagents, alpha-EPG and alpha-EBG, were covalently bound to a catalytic residue (Glu-172). A substrate recognition mechanism for the beta-amylase was discussed based on the modes of binding of these inhibitors in the active site cleft.
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7. |
Todd SJ,
Moir AJ,
Johnson MJ,
Moir A,
( 2003 ) Genes of Bacillus cereus and Bacillus anthracis encoding proteins of the exosporium. PMID : 12754235 : DOI : 10.1128/jb.185.11.3373-3378.2003 PMC : PMC155386 Abstract >>
The exosporium is the outermost layer of spores of Bacillus cereus and its close relatives Bacillus anthracis and Bacillus thuringiensis. For these pathogens, it represents the surface layer that makes initial contact with the host. To date, only the BclA glycoprotein has been described as a component of the exosporium; this paper defines 10 more tightly associated proteins from the exosporium of B. cereus ATCC 10876, identified by N-terminal sequencing of proteins from purified, washed exosporium. Likely coding sequences were identified from the incomplete genome sequence of B. anthracis or B. cereus ATCC 14579, and the precise corresponding sequence from B. cereus ATCC 10876 was defined by PCR and sequencing. Eight genes encode likely structural components (exsB, exsC, exsD, exsE, exsF, exsG, exsJ, and cotE). Several proteins of the exosporium are related to morphogenetic and outer spore coat proteins of B. subtilis, but most do not have homologues in B. subtilis. ExsE is processed from a larger precursor, and the CotE homologue appears to have been C-terminally truncated. ExsJ contains a domain of GXX collagen-like repeats, like the BclA exosporium protein of B. anthracis. Although most of the exosporium genes are scattered on the genome, bclA and exsF are clustered in a region flanking the rhamnose biosynthesis operon; rhamnose is part of the sugar moiety of spore glycoproteins. Two enzymes, alanine racemase and nucleoside hydrolase, are tightly adsorbed to the exosporium layer; they could metabolize small molecule germinants and may reduce the sensitivity of spores to these, limiting premature germination.
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8. |
Ivanova N,
Sorokin A,
Anderson I,
Galleron N,
Candelon B,
Kapatral V,
Bhattacharyya A,
Reznik G,
Mikhailova N,
Lapidus A,
Chu L,
Mazur M,
Goltsman E,
Larsen N,
D'Souza M,
Walunas T,
Grechkin Y,
Pusch G,
Haselkorn R,
Fonstein M,
Ehrlich SD,
Overbeek R,
Kyrpides N,
( 2003 ) Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. PMID : 12721630 : DOI : 10.1038/nature01582 DOI : 10.1038/nature01582 Abstract >>
Bacillus cereus is an opportunistic pathogen causing food poisoning manifested by diarrhoeal or emetic syndromes. It is closely related to the animal and human pathogen Bacillus anthracis and the insect pathogen Bacillus thuringiensis, the former being used as a biological weapon and the latter as a pesticide. B. anthracis and B. thuringiensis are readily distinguished from B. cereus by the presence of plasmid-borne specific toxins (B. anthracis and B. thuringiensis) and capsule (B. anthracis). But phylogenetic studies based on the analysis of chromosomal genes bring controversial results, and it is unclear whether B. cereus, B. anthracis and B. thuringiensis are varieties of the same species or different species. Here we report the sequencing and analysis of the type strain B. cereus ATCC 14579. The complete genome sequence of B. cereus ATCC 14579 together with the gapped genome of B. anthracis A2012 enables us to perform comparative analysis, and hence to identify the genes that are conserved between B. cereus and B. anthracis, and the genes that are unique for each species. We use the former to clarify the phylogeny of the cereus group, and the latter to determine plasmid-independent species-specific markers.
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9. |
Chang YH,
Shangkuan YH,
Lin HC,
Liu HW,
( 2003 ) PCR assay of the groEL gene for detection and differentiation of Bacillus cereus group cells. PMID : 12902235 : DOI : 10.1128/aem.69.8.4502-4510.2003 PMC : PMC169126 Abstract >>
Strains of species in the Bacillus cereus group are potentially enterotoxic. Thus, the detection of all B. cereus group strains is important. As 16S ribosomal DNA sequence analysis cannot adequately differentiate species of the B. cereus group, we explored the potential of the groEL gene as a phylogenetic marker. A phylogenetic analysis of the groEL sequences of 78 B. cereus group strains revealed that the B. cereus group strains were split into two major clusters, one including six B. mycoides and one B. pseudomycoides (cluster II) and the other including two B. mycoides and the rest of the B. cereus group strains (cluster I). Cluster I was further differentiated into two subclusters, Ia and Ib. The sodA gene sequences of representative strains from different clusters were also compared. The phylogenetic tree constructed from the sodA sequences showed substantial similarity to the tree constructed from the groEL sequences. Based on the groEL sequences, a PCR assay for detection and identification of B. cereus group strains was developed. Subsequent restriction fragment length polymorphism (RFLP) analysis verified the PCR amplicons and the differentiation of the B. cereus group strains. RFLP with MboI was identical for all the B. cereus group strains analyzed, while RFLP with MfeI or PstI classified all B. cereus and B. thuringiensis strains into two groups. All cluster II B. mycoides and B. pseudomycoides strains could be discriminated from other B. cereus group bacteria by restriction analysis with TspRI.
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10. |
Ko KS,
Kim JM,
Kim JW,
Jung BY,
Kim W,
Kim IJ,
Kook YH,
( 2003 ) Identification of Bacillus anthracis by rpoB sequence analysis and multiplex PCR. PMID : 12843020 : DOI : 10.1128/jcm.41.7.2908-2914.2003 PMC : PMC165277 Abstract >>
Comparative sequence analysis was performed upon Bacillus anthracis and its closest relatives, B. cereus and B. thuringiensis. Portions of rpoB DNA from 10 strains of B. anthracis, 16 of B. cereus, 10 of B. thuringiensis, 1 of B. mycoides, and 1 of B. megaterium were amplified and sequenced. The determined rpoB sequences (318 bp) of the 10 B. anthracis strains, including five Korean isolates, were identical to those of Ames, Florida, Kruger B, and Western NA strains. Strains of the "B. cereus group" were separated into two subgroups, in which the B. anthracis strains formed a separate clade in the phylogenetic tree. However, B. cereus and B. thuringiensis could not be differentiated. Sequence analysis confirmed the five Korean isolates as B. anthracis. Based on the rpoB sequences determined in the present study, multiplex PCR generating either B. anthracis-specific amplicons (359 and 208 bp) or cap DNA (291 bp) in a virulence plasmid could be used for the rapid differential detection and identification of virulent B. anthracis.
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11. |
Berger BJ,
English S,
Chan G,
Knodel MH,
( 2003 ) Methionine regeneration and aminotransferases in Bacillus subtilis, Bacillus cereus, and Bacillus anthracis. PMID : 12670965 : DOI : 10.1128/jb.185.8.2418-2431.2003 PMC : PMC152626 Abstract >>
The conversion of ketomethiobutyrate to methionine has been previously examined in a number of organisms, wherein the aminotransferases responsible for the reaction have been found to be members of the Ia subfamily (L. C. Berger, J. Wilson, P. Wood, and B. J. Berger, J. Bacteriol. 183:4421-4434, 2001). The genome of Bacillus subtilis has been found to contain no subfamily Ia aminotransferase sequences. Instead, the analogous enzymes in B. subtilis were found to be members of the If subfamily. These putative aspartate aminotransferases, the yugH, ywfG, ykrV, aspB, and patA gene products, have been cloned, expressed, and characterized for methionine regeneration activity. Only YkrV was able to convert ketomethiobutyrate to methionine, and it catalyzed the reaction only when glutamine was used as amino donor. In contrast, subcellular homogenates of B. subtilis and Bacillus cereus utilized leucine, isoleucine, valine, alanine, phenylalanine, and tyrosine as effective amino donors. The two putative branched-chain aminotransferase genes in B. subtilis, ybgE and ywaA, were also cloned, expressed, and characterized. Both gene products effectively transaminated branched-chain amino acids and ketoglutarate, but only YbgE converted ketomethiobutyrate to methionine. The amino donor preference for methionine regeneration by YbgE was found to be leucine, isoleucine, valine, phenylalanine, and tyrosine. The B. subtilis ybgE gene is a member of the family III of aminotransferases and falls in a subfamily designated here IIIa. Examination of B. cereus and Bacillus anthracis genome data found that there were no subfamily IIIa homologues in these organisms. In both B. cereus and B. anthracis, two putative branched-chain aminotransferases and two putative D-amino acid aminotransferases were discovered as members of subfamily IIIb. These four sequences were cloned from B. cereus, expressed, and characterized. Only the gene product from the sequence designated Bc-BCAT2 was found to convert ketomethiobutyrate to methionine, with an amino donor preference of leucine, isoleucine, valine, phenylalanine, and tyrosine. The B. anthracis homologue of Bc-BCAT2 was also cloned, expressed, and characterized and was found to be identical in activity. The aminooxy compound canaline was found to be an uncompetitive inhibitor of B. subtilis YbgE and also inhibited growth of B. subtilis and B. cereus in culture.
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12. |
Contreras-Zentella M,
Mendoza G,
Membrillo-Hernández J,
Escamilla JE,
( 2003 ) A novel double heme substitution produces a functional bo3 variant of the quinol oxidase aa3 of Bacillus cereus. Purification and paratial characterization. PMID : 12805383 : DOI : 10.1074/jbc.M302583200 Abstract >>
A novel bo3-type quinol oxidase was highly purified from Bacillus cereus PYM1, a spontaneous mutant unable to synthesize heme A and therefore spectroscopically detectable cytochromes aa3 and caa3. The purified enzyme contained 12.4 nmol of heme O and 11.5 nmol of heme B mg-1 protein. The enzyme was composed of two subunits with an Mr of 51,000 and 30,000, respectively. Both subunits were immunoreactive to antibodies raised against the B cereus aa3 oxidase. Moreover, amino-terminal sequence analysis of the 30-kDa subunit revealed that the first 19 residues were identical to those from the 30-kDa subunit of the B. cereus aa3 oxidase. The purified bo3 oxidase failed to oxidize ferrrocytochrome c (neither yeast nor horse) but oxidized tetrachlorohydroquinol with an apparent Km of 498 microM, a Vmax of 21 micromol of O2 min-1mg-1, and a calculated turnover of 55 s-1. The quinol oxidase activity with tetrachlorohydroquinol was inhibited by potassium cyanide and 2-n-heptyl 4-hydroxyquinoline-N-oxide with an I50 of 24 and 300 microM, respectively. Our results demonstrate that the bo3 oxidase of this mutant is not the product of a new operon but instead is a cytochrome aa3 apoprotein encoded by the qox operon of the aa3 oxidase of B. cereus wild type promiscuously assembled with hemes B and O replacing heme A, producing a novel bo3 cytochrome. This is the first reported example of an enzymatically active promiscuous oxidase resulting from the simultaneous substitution of its original hemes in the high and low spin sites.
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13. |
Dunn AK,
Klimowicz AK,
Handelsman J,
( 2003 ) Use of a promoter trap to identify Bacillus cereus genes regulated by tomato seed exudate and a rhizosphere resident, Pseudomonas aureofaciens. PMID : 12571047 : DOI : 10.1128/aem.69.2.1197-1205.2003 PMC : PMC143612 Abstract >>
The goal of this study was to identify genes in Bacillus cereus, a bacterium commonly associated with plant seeds and roots, that are affected by compounds originating from a host plant, tomato, or another rhizosphere resident, Pseudomonas aureofaciens. We constructed a B. cereus chromosomal DNA library in a promoter-trap plasmid, pAD123, which contains a promoterless version of the green fluorescent protein (GFP) gene, gfpmut3a. The library was screened by using fluorescence-activated cell sorting for clones showing a change in GFP expression in response to either tomato seed exudate or culture supernatant of P. aureofaciens strain 30-84. We identified two clones carrying genes that were induced by the presence of tomato seed exudate and nine clones carrying genes that were repressed by P. aureofaciens culture supernatant. A clone chosen for further study contained an open reading frame, designated lipA, that encodes a deduced protein with a lipoprotein signal peptide sequence similar to lipoproteins in B. subtilis. Expression of gusA under control of the lipA promoter increased twofold when cells were exposed to tomato seed exudate and in a concentration-dependent manner when exposed to a mixture of amino acids. When the wild type and a 10-fold excess of a lipA mutant were applied together to tomato seeds, 2 days after planting, the wild type displayed medium-dependent culturability, whereas the lipA mutant was unaffected. This study demonstrates the power of a promoter trap to identify genes in a gram-positive bacterium that are regulated by the biotic environment and resulted in the discovery of lipA, a plant-regulated gene in B. cereus.
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14. |
Lee SJ,
Park SY,
Lee JJ,
Yum DY,
Koo BT,
Lee JK,
( 2002 ) Genes encoding the N-acyl homoserine lactone-degrading enzyme are widespread in many subspecies of Bacillus thuringiensis. PMID : 12147491 : DOI : 10.1128/aem.68.8.3919-3924.2002 PMC : PMC124016 Abstract >>
Gram-negative bacteria can communicate with each other by N-acyl homoserine lactones (AHLs), which are quorum-sensing autoinducers. Recently, the aiiA gene (encoding an enzyme catalyzing the degradation of AHL) has been cloned from Bacillus sp. strain 240B1. During investigations in the course of the ongoing Bacillus thuringiensis subsp. morrisoni genome project, an aiiA homologue gene in the genome sequence was found. These results led to consideration of the possibility of the widespread existence of the gene in B. thuringiensis. aiiA homologue genes were found in 16 subspecies of B. thuringiensis, and their sequences were determined. Comparison of the Bacillus sp. strain 240B1 aiiA gene with the B. thuringiensis aiiA homologue genes showed high homologies of 89 to 95% and 90 to 96% in the nucleotide sequence and deduced amino acid sequence, respectively. Among the subspecies of B. thuringiensis having an aiiA gene, the subspecies aizawai, galleriae, kurstaki, kyushuensis, ostriniae, and subtoxicus were shown to degrade AHL. It was observed that recombinant Escherichia coli producing AiiA proteins also had AHL-degrading activity and could also attenuate the plant pathogenicity of Erwinia carotovora. These results indicate that insecticidal B. thuringiensis strains might have potential to compete with gram-negative bacteria in natural ecosystems by autoinducer-degrading activity.
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15. |
Barlass PJ,
Houston CW,
Clements MO,
Moir A,
( 2002 ) Germination of Bacillus cereus spores in response to L-alanine and to inosine: the roles of gerL and gerQ operons. PMID : 12101297 : DOI : 10.1099/00221287-148-7-2089 Abstract >>
Bacillus cereus 569 (ATCC 10876) endospores germinate in response to inosine or L-alanine, the most rapid germination response being elicited by a combination of these germinants. The gerI operon has already been characterized as a homologue of the gerA spore-germination receptor family of operons found in all Bacillus spp. examined; the primary defect in gerI mutant spores is in the inosine germination response, although spores were also slower to germinate in L-alanine. Additional transposon-insertion mutants, from similar Tn917-LTV1 mutagenesis and enrichment experiments, now define two more operons, also members of the family of gerA homologues, important in L-alanine and inosine germination. Transposon insertions were identified in an alanine-specific germination locus, named gerL, which represents an operon of three genes, termed gerLA, gerLB and gerLC. By examining the residual germination response to L-alanine in gerI and gerL mutants, it was deduced that the GerL proteins contribute most strongly to the L-alanine germination response, and that the GerI proteins, required primarily in inosine germination, mediate only much slower germination responses to alanine. The L-alanine germination responses mediated by GerL and GerI proteins differ in their germination rates, temperature optima and germinant concentration dependence. The gerQ locus, again identified by transposon insertion, is a second inosine-related germinant-receptor operon. GerQ and GerI proteins are both required for the germination response to inosine as sole germinant, but GerQ has no role in L-alanine germination. Although near-identical homologues of gerI and gerL operons are evident in the Bacillus anthracis genome sequence, there is no evidence of a close homologue of gerQ.
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16. |
Maruyama R,
Nishizawa M,
Itoi Y,
Ito S,
Inoue M,
( 2002 ) The enzymes with benzil reductase activity conserved from bacteria to mammals. PMID : 11796169 : Abstract >>
The diketone compound, benzil is reduced to (S)-benzoin with living Bacillus cereus cells. Recently, we isolated a gene responsible for benzil reduction, and Escherichia coli cells in which this gene was overexpressed transformed benzil to (S)-benzoin. Although this benzil reductase showed high identity to the short-chain dehydrogenase/reductase (SDR) family, enzymological features were unknown. Here, we demonstrated that many B. cereus strains had benzil reductase activity in vivo, and that the benzil reductases shared 94-100% amino acid identities. Recombinant B. cereus benzil reductase produced optically pure (S)-benzoin with NADPH in vitro, and the ketone group distal to a benzene ring was asymmetrically reduced. B. cereus benzil reductase showed 31% amino acid identity to the yeast open reading frame YIR036C protein and 28-30% to mammalian sepiapterin reductases, sharing the seven residues consensus for the SDR family. We isolated the genes encoding yeast YIR036C protein and gerbil sepiapterin reductase, and both recombinant proteins also reduced benzil to (S)-benzoin in vitro. Green fluorescent protein-tagged B. cereus benzil reductase distributed in the bipolar cytoplasm in B. cereus cells. Asymmetric reduction with B. cereus benzil reductase, yeast YIR036C protein and gerbil sepiapterin reductase will be utilized to produce important chiral compounds.
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17. |
Miles G,
Bayley H,
Cheley S,
( 2002 ) Properties of Bacillus cereus hemolysin II: a heptameric transmembrane pore. PMID : 12070333 : DOI : 10.1110/ps.0204002 PMC : PMC2373656 Abstract >>
The gene encoding hemolysin II (HlyII) was amplified from Bacillus cereus genomic DNA and a truncated mutant, HlyII(DeltaCT), was constructed lacking the 94 amino acid extension at the C terminus. The proteins were produced in an E. coli cell-free in vitro transcription and translation system, and were shown to assemble into SDS-stable oligomers on rabbit erythrocyte membranes and liposomes. The hemolytic activity of HlyII was measured with rabbit erythrocytes yielding an HC(50) value of 1.64 ng mL(-1), which is over 15 times more potent than staphylococcal alpha-hemolysin. HlyII(DeltaCT) was about eight times less potent than HlyII in this assay. Limited proteolysis of the oligomers formed by HlyII and HlyII(DeltaCT) on red cell membranes showed that the C-terminal extension is sensitive to digestion, while HlyII(DeltaCT) is protease resistant and migrates with an electrophoretic mobility similar to that of digested HlyII. HlyII forms moderately anion selective, rectifying pores (I(+80)/I(-80) = 0.57, 1 M KCl, pH 7.4) in planar lipid bilayers of diphytanoylphosphatidylcholine with a unitary conductance of 637 pS (1 M KCl, 5 mM HEPES, pH 7.4) and exhibits no gating over a wide range of applied potentials (-160 to +160 mV). In addition, it was demonstrated that HlyII forms a homoheptameric pore by using gel shift electrophoresis aided by a genetically encoded oligoaspartate tag. Although they share limited primary sequence identity (30%), these data confirm that HlyII is a structural and functional homolog of staphylococcal alpha-hemolysin.
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18. |
Mabuchi N,
Araki Y,
( 2001 ) Cloning and sequencing of two genes encoding chitinases A and B from Bacillus cereus CH. PMID : 11718542 : Abstract >>
Two genes encoding chitinases A and B (chiA and chiB) from Bacillus cereus CH were cloned into Escherichia coli XL1-Blue MRF', by using pBluescript II SK+, and their nucleotide sequences were determined. Open reading frames of the chiA and chiB genes encoded distinct polypeptide chains consisting of 360 and 674 amino acid residues, respectively, with calculated molecular sizes of 39,470 and 74,261 Da, respectively. Comparison of the deduced amino acid sequences with those of other bacterial chitinases revealed that chitinase A consisted of a catalytic domain, while chitinase B consisted of three functional domains, a catalytic domain, a fibronectin type III-like domain, and a cellulose-binding domain. The primary structures of these two proteins were not similar to each other.
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19. |
Dong YH,
Gusti AR,
Zhang Q,
Xu JL,
Zhang LH,
( 2002 ) Identification of quorum-quenching N-acyl homoserine lactonases from Bacillus species. PMID : 11916693 : DOI : 10.1128/aem.68.4.1754-1759.2002 PMC : PMC123891 Abstract >>
A range of gram-negative bacterial species use N-acyl homoserine lactone (AHL) molecules as quorum-sensing signals to regulate different biological functions, including production of virulence factors. AHL is also known as an autoinducer. An autoinducer inactivation gene, aiiA, coding for an AHL lactonase, was cloned from a bacterial isolate, Bacillus sp. strain 240B1. Here we report identification of more than 20 bacterial isolates capable of enzymatic inactivation of AHLs from different sources. Eight isolates showing strong AHL-inactivating enzyme activity were selected for a preliminary taxonomic analysis. Morphological phenotypes and 16S ribosomal DNA sequence analysis indicated that these isolates probably belong to the species Bacillus thuringiensis. Enzymatic analysis with known Bacillus strains confirmed that all of the strains of B. thuringiensis and the closely related species B. cereus and B. mycoides tested produced AHL-inactivating enzymes but B. fusiformis and B. sphaericus strains did not. Nine genes coding for AHL inactivation were cloned either by functional cloning or by a PCR procedure from selected bacterial isolates and strains. Sequence comparison of the gene products and motif analysis showed that the gene products belong to the same family of AHL lactonases.
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20. |
Miyamoto T,
Sayed MA,
Sasahara R,
Sukimoto K,
Umezaki A,
Honjoh K,
Iio M,
Hatano S,
( 2002 ) Cloning and overexpression of Bacillus cereus penicillin-binding protein 3 gene in Escherichia coli. PMID : 11866118 : Abstract >>
The pbp3 gene encoding PBP3 of Bacillus cereus was cloned and sequenced. For this purpose, PBP3 was first purified from B. cereus ts-4, and N-terminal amino acid sequences of the peptides obtained from the protease digests of the protein were analyzed. The B. cereus ts-4 pbp3 gene consisted of an open reading frame of 1,986 bp encoding 662 amino acid residues with a calculated molecular mass of 73,044 Da. The active site-motifs SXXK, SXN, and KTG are present at the positions 393, 452, and 590, respectively, in the deduced amino acid sequence. The pbp3 structural gene was ligated into the pET17 x b expression vector and pET-pbp3 was constructed. A protein was produced by the cells of E. coli carrying pET-pbp3. The produced protein migrated at about 75 kDa in SDS-polyacrylamide gel and strongly reacted with biotinylated ampicillin.
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21. |
Southworth TW,
Guffanti AA,
Moir A,
Krulwich TA,
( 2001 ) GerN, an endospore germination protein of Bacillus cereus, is an Na(+)/H(+)-K(+) antiporter. PMID : 11566988 : DOI : 10.1128/JB.183.20.5896-5903.2001 PMC : PMC99667 Abstract >>
GerN, a Bacillus cereus spore germination protein, exhibits homology to a widely distributed group of putative cation transporters or channel proteins. GerN complemented the Na(+)-sensitive phenotype of an Escherichia coli mutant that is deficient in Na(+)/H(+) antiport activity (strain KNabc). GerN also reduced the concentration of K(+) required to support growth of an E. coli mutant deficient in K(+) uptake (strain TK2420). In a fluorescence-based assay of everted E. coli KNabc membrane vesicles, GerN exhibited robust Na(+)/H(+) antiport activity, with a K(m) for Na(+) estimated at 1.5 mM at pH 8.0 and 25 mM at pH 7.0. Li(+), but not K(+), served as a substrate. GerN-mediated Na(+)/H(+) antiport was further demonstrated in everted vesicles as energy-dependent accumulation of (22)Na(+). GerN also used K(+) as a coupling ion without completely replacing H(+), as indicated by partial inhibition by K(+) of H(+) uptake into right-side-out vesicles loaded with Na(+). K(+) translocation as part of the antiport was supported by the stimulatory effect of intravesicular K(+) on (22)Na(+) uptake by everted vesicles and the dependence of GerN-mediated (86)Rb(+) efflux on the presence of Na(+) in trans. The inhibitory patterns of protonophore and thiocyanate were most consistent with an electrogenic Na(+)/H(+)-K(+) antiport. GerN-mediated Na(+)/H(+)-K(+) antiport was much more rapid than GerN-mediated Na(+)/H(+) antiport.
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22. |
Browne N,
Dowds BC,
( 2002 ) Acid stress in the food pathogen Bacillus cereus. PMID : 11872115 : Abstract >>
The pathogen Bacillus cereus, which is associated with a number of foods including dairy products, was studied for its response to acid stress during the exponential phase. Bacillus cereus was found to adapt to acid stress (pH 4.6) when pre-exposed to a non-lethal, inducing pH of 6.3 or to inducing concentrations of heat, ethanol, salt or hydrogen peroxide. Cells were found to maintain their internal pH at a higher level than the external acid pH and adapted cells had a higher internal pH than unadapted cells. A constitutive acid-sensitive mutant that was also heat- and ethanol-sensitive was found to be capable of high levels of adaptation despite its lack of induction of proteins induced in the wild type by exposure to moderate pH (6.3) values. A number of proteins were found to be underexpressed in the mutant compared with the wild type at pH 6.3, including some with homology to ribosomal proteins and to the sporulation regulator RapK, while one differentially expressed band contained two proteins, one of which was homologous to the competence regulator CodY. The work has implications for the processing of B. cereus-associated foods by acidification. The linked developmental processes of stationary phase, sporulation and possibly competence appear to be involved in the response to acid stress.
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23. |
Browne N,
Dowds BC,
( 2001 ) Heat and salt stress in the food pathogen Bacillus cereus. PMID : 11851817 : Abstract >>
The effects of stresses imposed on bacterial contaminants during food processing and treatment of packaging material were evaluated on the food pathogen Bacillus cereus. Conditions were established which allowed the cells to adapt to heat, ethanol and hydrogen peroxide stresses, but not to osmotic shock. Cross protection between stresses indicated a clear hierarchy of resistance with salt protecting against hydrogen peroxide, which protected against ethanol, which protected against heat shock. The cultures were shown to be most sensitive to heat, ethanol and oxidative stress at mid-exponential phase and to become resistant at stationary phase. Adaptive levels of stressor were found to induce synthesis of general stress and stress-specific proteins and differential accumulation of proteins was demonstrated between heat- or salt-stressed and unstressed cells. Sequencing revealed that a number of glycolytic enzymes were regulated by heat and osmotic shocks and that the chaperone GroEL was induced by heat shock. The implications of the physiological data in designing storage and processing conditions for food are discussed. The identification of stress-regulated proteins reveals a clear role for glycolysis in adaptation to heat shock and osmotic stress.
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24. |
Qi Y,
Patra G,
Liang X,
Williams LE,
Rose S,
Redkar RJ,
DelVecchio VG,
( 2001 ) Utilization of the rpoB gene as a specific chromosomal marker for real-time PCR detection of Bacillus anthracis. PMID : 11472954 : DOI : 10.1128/AEM.67.8.3720-3727.2001 PMC : PMC93078 Abstract >>
The potential use of Bacillus anthracis as a weapon of mass destruction poses a threat to humans, domesticated animals, and wildlife and necessitates the need for a rapid and highly specific detection assay. We have developed a real-time PCR-based assay for the specific detection of B. anthracis by taking advantage of the unique nucleotide sequence of the B. anthracis rpoB gene. Variable region 1 of the rpoB gene was sequenced from 36 Bacillus strains, including 16 B. anthracis strains and 20 other related bacilli, and four nucleotides specific for B. anthracis were identified. PCR primers were selected so that two B. anthracis-specific nucleotides were at their 3' ends, whereas the remaining bases were specific to the probe region. This format permitted the PCR reactions to be performed on a LightCycler via fluorescence resonance energy transfer (FRET). The assay was found to be specific for 144 B. anthracis strains from different geographical locations and did not cross-react with other related bacilli (175 strains), with the exception of one strain. The PCR assay can be performed on isolated DNA as well as crude vegetative cell lysates in less than 1 h. Therefore, the rpoB-FRET assay could be used as a new chromosomal marker for rapid detection of B. anthracis.
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25. |
Bogdanova E,
Minakhin L,
Bass I,
Volodin A,
Hobman JL,
Nikiforov V,
( 2001 ) Class II broad-spectrum mercury resistance transposons in Gram-positive bacteria from natural environments. PMID : 11446519 : Abstract >>
We have studied the mechanisms of the horizontal dissemination of a broad-spectrum mercury resistance determinant among Bacillus and related species. This mer determinant was first described in Bacillus cereus RC607 from Boston Harbor, USA, and was then found in various Bacillus and related species in Japan, Russia and England. We have shown that the mer determinant can either be located at the chromosome, or on a plasmid in the Bacillus species, and is carried by class II mercury resistance transposons: Tn5084 from B. cereus RC607 and B. cereus VKM684 (ATCC10702) and Tn5085 from Exiguobacterium sp. TC38-2b. Tn5085 is identical in nucleotide sequence to TnMERI1, the only other known mer transposon from Bacillus species, but it does not contain an intron like TnMERI1. Tn5085 is functionally active in Escherichia coli. Tn5083, which we have isolated from B. megaterium MK64-1, contains an RC607-like mer determinant, that has lost some mercury resistance genes and possesses a merA gene which is a novel sequence variant that has not been previously described. Tn5083 and Tn5084 are recombinants, and are comprised of fragments from several transposons including Tn5085, and a relative of a putative transposon from B. firmus (which contains similar genes to the cadmium resistance operon of Staphylococcus aureus), as well as others. The sequence data showed evidence for recombination both between transposition genes and between mer determinants.
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26. |
Wang S,
Moyne A,
Thottappilly G,
Wu S,
Locy RD,
Singh NK,
( 2001 ) Purification and characterization of a Bacillus cereus exochitinase. PMID : 11267643 : Abstract >>
Five extracellular chitinases of Bacillus cereus 6E1 were detected by a novel in-gel chitinase assay using carboxymethyl-chitin-remazol brilliant violet 5R (CM-chitin-RBV) as a substrate. The major chitinase activity was associated with a 36-kDa (Chi36) gel band. Chi36 was purified by a one-step, native gel purification procedure derived from the new in-gel chitinase assay. The purified Chi36 has optimal activity at pH 5.8 and retains some enzymatic activity between pH 2.5-8. The temperature optimum for Chi36 was 35 degrees C, but the enzyme was active between 4-70 degrees C. Based on its ability to hydrolyze mainly p-nitrophenyl-(N-acetyl-beta-D-glucosaminide)(2), Chi36 is characterized as a chitobiosidase, a type of exochitinase. The N-terminal amino acid sequence of mature Chi36 was determined (25 amino acids). Alanine is the first N-terminal amino acid residue indicating the cleavage of a signal peptide from a Chi36 precursor to form the mature extracellular Chi36. The N-terminal sequence of Chi36 demonstrated highest similarity with Bacillus circulans WL-12 chitinase D and significant similarity with several other bacterial chitinases.
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27. |
Thackray PD,
Behravan J,
Southworth TW,
Moir A,
( 2001 ) GerN, an antiporter homologue important in germination of Bacillus cereus endospores. PMID : 11133940 : DOI : 10.1128/JB.183.2.476-482.2001 PMC : PMC94902 Abstract >>
A homologue of the grmA spore germination gene of Bacillus megaterium and of a NaH-antiporter gene (napA) of Enterococcus hirae has been identified in Bacillus cereus 569 (ATCC 10876). The putative protein product has 58 and 43% amino acid identity with GrmA and NapA, respectively. Insertional inactivation of this B. cereus gene, named gerN, did not affect vegetative growth or sporulation. The null mutant spores were 30-fold slower to germinate in inosine (5 mM) but germinated almost normally in response to L-alanine (10 mM). The null mutant spores germinated after several hours with inosine as the sole germinant, but germination was asynchronous and the normal order of germination events was perturbed. At a suboptimal germinant concentration (50 microM), inosine germination was completely blocked in the mutant, while the rate of germination in 50 microM L-alanine was reduced to one-third of that of the wild type. The requirement for GerN function in the response to a particular germinant suggests that a germination receptor may have a specifically associated antiporter, which is required at the initiation of germination and which, in the case of the inosine receptor, is GerN. Since germination in suboptimal concentrations of L-alanine shows a delay, additional germination transporters may be required for optimal response at low germinant concentrations.
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28. |
Lund T,
De Buyser ML,
Granum PE,
( 2000 ) A new cytotoxin from Bacillus cereus that may cause necrotic enteritis. PMID : 11069652 : DOI : 10.1046/j.1365-2958.2000.02147.x Abstract >>
A cytotoxin (CytK) has been isolated from a Bacillus cereus strain that caused a severe food poisoning outbreak killing three people. A protein of 34 kDa was highly cytotoxic, and the addition of other secreted proteins gave no synergistic effect. CytK was also necrotic and haemolytic. No known B. cereus enterotoxins were produced by this strain. A DNA sequence from 1.8 kb upstream to 0.2 kb downstream of the toxin gene was sequenced. The deduced amino acid sequence of the toxin showed similarity to Staphylococcus aureus leucocidins, gamma-haemolysin and alpha-haemolysin, Clostridium perfringens beta-toxin and B. cereus haemolysin II, all belonging to a family of beta-barrel channel-forming toxins. There was no sequence similarity between CytK and enterotoxins of B. cereus. The upstream sequence contained a partial sequence of a putative histidine kinase gene. A recognition site for PlcR, which regulates the transcription of enterotoxins HBL and Nhe of B. cereus, was found in the promoter region of the toxin. This new cytotoxin may be responsible for a disease that is similar to, although not as severe as, the necrotic enteritis caused by the beta-toxin of C. perfringens type C.
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29. |
Celandroni F,
Ghelardi E,
Pastore M,
Lupetti A,
Kolstø AB,
Senesi S,
( 2000 ) Characterization of the chemotaxis fli Y and che A genes in Bacillus cereus. PMID : 11034287 : DOI : 10.1111/j.1574-6968.2000.tb09294.x Abstract >>
This paper describes the first identification of chemotaxis genes in Bacillus cereus. We sequenced and studied the genomic organization and the expression of the cheA and fliY genes in two different B. cereus strains, ATCC 14579 and ATCC 10987. While cheA encodes a highly conserved protein acting as the main regulator of the chemotactic response in flagellated eubacteria, fliY, which has been previously described only in B. subtilis, is one of the three genes encoding proteins of the flagellar switch complex. Although the sequences and relative position of cheA and fliY were found to be identical in the two B. cereus strains analyzed, the restriction fragment containing both genes was located differently on the physical maps of B. cereus ATCC 14579 and ATCC 10987. Evidence is shown that the genomic organization and the expression of fliY and cheA in B. cereus differ significantly from that described for B. subtilis, which is considered a model microorganism for chemotaxis in gram-positive bacteria.
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30. |
Klevytska AM,
Zinser G,
Schupp JM,
( 2000 ) vrrB, a hypervariable open reading frame in Bacillus anthracis. PMID : 10869077 : DOI : 10.1128/jb.182.14.3989-3997.2000 PMC : PMC94584 Abstract >>
Bacillus anthracis appears to be the most molecularly homogeneous bacterial species known. Extensive surveys of worldwide isolates have revealed vanishingly small amounts of genomic variation. The biological importance of the resting-stage spore may lead to very low evolutionary rates and, perhaps, to the lack of potentially adaptive genetic variation. In contrast to the overall homogeneity, some gene coding regions contain hypervariability that is translated into protein variation. During marker analysis of diverse strains, we have discovered a novel ca. 750-nucleotide open reading frame (ORF) that contains in-frame, variable-number tandem-repeat sequences. Four distinct variable regions exist within vrrB, giving rise to 11 distinct alleles in eight different length categories among B. anthracis strains. This ORF putatively codes for a 241- to 265-amino-acid protein, rich in glutamine (13.2%), glycine (23.4%), and histidine (23.0%). The variable-region amino acids of the vrrB ORF are strongly hydrophilic. Coupled with putative transmembrane domains flanking the variable regions, this suggests a membrane-anchored cytosolic or extracellular location for the putative protein. Sequence analysis of the complete ORFs from three Bacillus cereus strains shows maintenance of the ORF across species boundaries, including strong conservation of the amino acid sequence and the capacity to vary among strains. The presence of 11 different alleles of the vrrB locus is in stark contrast to the near homogeneity of B. anthracis. Evolution of hypervariable genes can negate the lack of genetic variability in species such as B. anthracis and provide select rapid evolution in other more variable species.
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31. |
Petri R,
( 2000 ) The relationship of nitrate reducing bacteria on the basis of narH gene sequences and comparison of narH and 16S rDNA based phylogeny. PMID : 10879978 : DOI : 10.1016/S0723-2020(00)80045-4 Abstract >>
On the basis of available nitrate reductase gene sequences primer pairs were designed to specifically amplify gene stretches of the beta-subunit of the membrane-bound nitrate reductase (narH). Additional sequences of this gene were amplified and sequenced from pure cultures of reference species and new isolates. The distribution and phylogeny of this gene in denitrifying and nitrate-reducing bacteria was analysed. Comparison of phylogenetic trees based on 16S rDNA sequences with those based on narH sequences revealed highly similar relationships of both genes from most of the bacteria analysed. Since highly conserved functional cysteine clusters within bacterial and archaeal narH sequences support a linear evolution from one common progenitor a long evolutionary history of the respiratory membrane-bound nitrate reductase can be inferred from our phylogenetic data.
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32. |
Morais MC,
Zhang W,
Baker AS,
Zhang G,
Dunaway-Mariano D,
Allen KN,
( 2000 ) The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase: insight into catalysis of phosphorus bond cleavage and catalytic diversification within the HAD enzyme superfamily. PMID : 10956028 : DOI : 10.1021/bi001171j Abstract >>
Phosphonoacetaldehyde hydrolase (phosphonatase) catalyzes the hydrolysis of phosphonoacetaldehyde to acetaldehyde and phosphate using Mg(II) as cofactor. The reaction proceeds via a novel bicovalent catalytic mechanism in which an active-site nucleophile abstracts the phosphoryl group from the Schiff-base intermediate formed from Lys53 and phosphonoacetaldehyde. In this study, the X-ray crystal structure of the Bacillus cereus phosphonatase homodimer complexed with the phosphate (product) analogue tungstate (K(i) = 50 microM) and the Mg(II) cofactor was determined to 3.0 A resolution with an R(cryst) = 0.248 and R(free) = 0.284. Each monomer is made up of an alpha/beta core domain consisting of a centrally located six-stranded parallel beta-sheet surrounded by six alpha-helices. Two flexible, solvated linkers connect to a small cap domain (residues 21-99) that consists of an antiparallel, five-helix bundle. The subunit-subunit interface, formed by the symmetrical packing of the two alpha8 helices from the respective core domains, is stabilized through the hydrophobic effect derived from the desolvation of paired Met171, Trp164, Tyr162, Tyr167, and Tyr176 side chains. The active site is located at the domain-domain interface of each subunit. The Schiff base forming Lys53 is positioned on the cap domain while tungstate and Mg(II) are bound to the core domain. Mg(II) ligands include two oxygens of the tungstate ligand, one oxygen of the carboxylates of Asp12 and Asp186, the backbone carbonyl oxygen of Ala14, and a water that forms a hydrogen bond with the carboxylate of Asp190 and Thr187. The guanidinium group of Arg160 binds tungstate and the proposed nucleophile Asp12, which is suitably positioned for in-line attack at the tungsten atom. The side chains of the core domain residue Tyr128 and the cap domain residues Cys22 and Lys53 are located nearby. The identity of Asp12 as the active-site nucleophile was further evidenced by the observed removal of catalytic activity resulting from Asp12Ala substitution. The similarity of backbone folds observed in phosphonatase and the 2-haloacid dehalogenase of the HAD enzyme superfamily indicated common ancestry. Superposition of the two structures revealed a conserved active-site scaffold having distinct catalytic stations. Analysis of the usage of polar amino acid residues at these stations by the dehalogenases, phosphonatases, phosphatases, and phosphomutases of the HAD superfamily suggests possible ways in which the active site of an ancient enzyme ancestor might have been diversified for catalysis of C-X, P-C, and P-O bond cleavage reactions.
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33. |
Chirakkal H,
Behravan J,
( 2000 ) Mutations in the gerP locus of Bacillus subtilis and Bacillus cereus affect access of germinants to their targets in spores. PMID : 10715007 : DOI : 10.1128/jb.182.7.1987-1994.2000 PMC : PMC101904 Abstract >>
The gerP1 transposon insertion mutation of Bacillus cereus is responsible for a defect in the germination response of spores to both L-alanine and inosine. The mutant is blocked at an early stage, before loss of heat resistance or release of dipicolinate, and the efficiency of colony formation on nutrient agar from spores is reduced fivefold. The protein profiles of alkaline-extracted spore coats and the spore cortex composition are unchanged in the mutant. Permeabilization of gerP mutant spores by coat extraction procedures removes the block in early stages of germination, although a consequence of the permeabilization procedure in both wild type and mutant is that late germination events are not complete. The complete hexacistronic operon that includes the site of insertion has been cloned and sequenced. Four small proteins encoded by the operon (GerPA, GerPD, GerPB, and GerPF) are related in sequence. A homologous operon (yisH-yisC) can be found in the Bacillus subtilis genome sequence; null mutations in yisD and yisF, constructed by integrational inactivation, result in a mutant phenotype similar to that seen in B. cereus, though somewhat less extreme and equally repairable by spore permeabilization. Normal rates of germination, as estimated by loss of heat resistance, are also restored to a gerP mutant by the introduction of a cotE mutation, which renders the spore coats permeable to lysozyme. The B. subtilis operon is expressed solely during sporulation, and is sigma K-inducible. We hypothesize that the GerP proteins are important as morphogenetic or structural components of the Bacillus spore, with a role in the establishment of normal spore coat structure and/or permeability, and that failure to synthesize these proteins during spore formation limits the opportunity for small hydrophilic organic molecules, like alanine or inosine, to gain access to their normal target, the germination receptor, in the spore.
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34. |
Baker AS,
Dunaway-Mariano D,
Morais MC,
( 2000 ) Crystallization and preliminary crystallographic analysis of phosphonoacetaldehyde hydrolase. PMID : 10666607 : DOI : 10.1107/s0907444999015899 Abstract >>
Phosphonoacetaldehyde hydrolase, a C-P bond-cleaving enzyme which utilizes an unusual bicovalent catalytic strategy, has been crystallized by the hanging-drop vapor-diffusion method using PEG 4000 as the precipitant. The crystals belong to the monoclinic system and belong to space group C2, with unit-cell parameters a = 210.5, b = 45.5, c = 64.7 A, beta = 105.0 degrees. The asymmetric unit contains a dimer related by a non-crystallographic dyad. In addition to a 2.7 A native data set, the following data sets have been collected: a 2.4 A data set from crystals complexed with the intermediate analog vinyl sulfonate, a 3.0 A three-wavelength MAD data set from crystals complexed with the product analog WO(4)(2-), as well as several heavy-atom data sets to 3.0 A or better, of which only three have proven useful for MIR calculations. Examination of the native Patterson map revealed NCS that made previously uninterpretable derivative data useful. Independent phase sets were first calculated and refined for the MAD and MIR experiments separately and were then combined. The combined phase set was further improved by solvent flattening, histogram matching and NCS averaging. Interpretation of the resulting electron-density map is currently under way.
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35. |
Fukuoka S,
Chen Y,
( 2000 ) A novel spore peptidoglycan hydrolase of Bacillus cereus: biochemical characterization and nucleotide sequence of the corresponding gene, sleL. PMID : 10692353 : DOI : 10.1128/jb.182.6.1499-1506.2000 PMC : PMC94445 Abstract >>
The exudate of germinated spores of B. cereus IFO 13597 in 0.15 M KCl-50 mM potassium phosphate (pH 7.0) contained a spore-lytic enzyme which has substrate specificity for fragmented spore cortex from wild-type organisms (cortical-fragment-lytic enzyme [CFLE]), in addition to a previously characterized germination-specific hydrolase which acts on intact spore cortex (spore cortex-lytic enzyme [SCLE]) (R. Moriyama, S. Kudoh, S. Miyata, S. Nonobe, A. Hattori, and S. Makino, J. Bacteriol. 178:5330-5332, 1996). CFLE was not capable of degrading isolated cortical fragments from spores of Bacillus subtilis ADD1, which lacks muramic acid delta-lactam. This suggests that CFLE cooperates with SCLE in cortex hydrolysis during germination. CFLE was purified in an active form and identified as a 48-kDa protein which functions as an N-acetylglucosaminidase. Immunochemical studies suggested that the mature enzyme is localized on a rather peripheral region of the dormant spore, probably the exterior of the cortex layer. A gene encoding the enzyme, sleL, was cloned in Escherichia coli, and the nucleotide sequence was determined. The gene encodes a protein of 430 amino acids with a deduced molecular weight of 48,136. The N-terminal region contains a repeated motif common to several peptidoglycan binding proteins. Inspection of the data banks showed no similarity of CFLE with N-acetylglucosaminidases found so far, suggesting that CFLE is a novel type of N-acetylglucosaminidase. The B. subtilis genome sequence contains genes, yaaH and ydhD, which encode putative proteins showing similarity to SleL.
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36. |
Budarina ZI,
Baida G,
( 1999 ) Complete nucleotide sequence and molecular characterization of hemolysin II gene from Bacillus cereus. PMID : 10547438 : DOI : 10.1111/j.1574-6968.1999.tb08771.x Abstract >>
Hemolysin II gene from Bacillus cereus VKM-B771 has been sequenced. The deduced primary translation product consists of 412 amino acid residues which corresponds to the protein with an M(r) of 45.6 kDa. The predicted mature Hly-II protein (residues 32 to 412) is of 42.3 kDa, which is in close agreement with the mini-cell electrophoresis analysis. Hly-II deletion variant lacking 96 C-terminal residues still has hemolytic activity. The protein primary structure analysis revealed no homology with any known Bacillus cytolysins. Significant general homology (31-28% identity) was found between the hemolysin II and Staphylococcus aureus alpha-toxin, gamma-hemolysin (HlgB), and leukocidins (LukF, LukF-R, LukF-PV). The data suggest that hemolysin II belongs to the group of beta-channel forming cytolysins.
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37. |
Dietrich R,
Nibler B,
Prüss BM,
( 1999 ) The hemolytic enterotoxin HBL is broadly distributed among species of the Bacillus cereus group. PMID : 10584001 : PMC : PMC91741 Abstract >>
The prevalence of the hemolytic enterotoxin complex HBL was determined in all species of the Bacillus cereus group with the exception of Bacillus anthracis. hblA, encoding the binding subunit B, was detected by PCR and Southern analysis and was confirmed by partial sequencing of 18 strains. The sequences formed two clusters, one including B. cereus and Bacillus thuringiensis strains and the other one consisting of Bacillus mycoides, Bacillus pseudomycoides, and Bacillus weihenstephanensis strains. From eight B. thuringiensis strains, the enterotoxin gene hblA could be amplified. Seven of them also expressed the complete HBL complex as determined with specific antibodies against the L(1), L(2), and B components. Eleven of 16 B. mycoides strains, all 3 B. pseudomyoides strains, 9 of 15 B. weihenstephanensis strains, and 10 of 23 B. cereus strains carried hblA. While HBL was not expressed in the B. pseudomycoides strains, the molecular assays were in accordance with the immunological assays for the majority of the remaining strains. In summary, the hemolytic enterotoxin HBL seems to be broadly distributed among strains of the B. cereus group and relates neither to a certain species nor to a specific environment. The consequences of this finding for food safety considerations need to be evaluated.
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38. |
Purnelle B,
Rose M,
Gominet M,
Okstad OA,
( 1999 ) Sequence analysis of three Bacillus cereus loci carrying PIcR-regulated genes encoding degradative enzymes and enterotoxin. PMID : 10589720 : DOI : 10.1099/00221287-145-11-3129 DOI : 10.1099/00221287-145-11-3129 Abstract >>
PIcR is a pleiotropic regulator of extracellular virulence factors in the opportunistic human pathogen Bacillus cereus and the entomopathogenic Bacillus thuringiensis, and is induced in cells entering stationary phase. Among the genes regulated by PIcR are: pIcA, encoding phosphatidylinositol-specific phospholipase C (PI-PLC); plc, encoding phosphatidylcholine-preferring phospholipase C (PC-PLC); nhe, encoding the non-haemolytic enterotoxin; hbl, encoding haemolytic enterotoxin BL (HBL); and genes specifying a putative S-layer like surface protein and a putative extracellular RNase. By analysing 37.1 kb of DNA sequence surrounding hbl, plcA and plcR, 28 ORFs were predicted. Three novel genes putatively regulated by PlcR and encoding a neutral protease (NprB), a subtilase family serine protease (Sfp) and a putative cell-wall hydrolase (Cwh) were identified. The corresponding sfp and cwh genes were located in the immediate upstream region of plcA and could both be regulated by a putative PlcR-binding site positioned between the inversely transcribed genes. Similarly, nprB was positioned directly upstream and transcribed in the opposite orientation to plcR. Genes surrounding plcA, plcR and hblCDAB that were lacking an upstream PlcR regulatory sequence did not appear to serve functions apparently related to PlcR and did not exhibit a conserved organization in Bacillus subtilis.
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39. |
Purnelle B,
Rose M,
Gominet M,
Okstad OA,
( 1999 ) Sequence analysis of three Bacillus cereus loci carrying PIcR-regulated genes encoding degradative enzymes and enterotoxin. PMID : 10589720 : DOI : 10.1099/00221287-145-11-3129 DOI : 10.1099/00221287-145-11-3129 Abstract >>
PIcR is a pleiotropic regulator of extracellular virulence factors in the opportunistic human pathogen Bacillus cereus and the entomopathogenic Bacillus thuringiensis, and is induced in cells entering stationary phase. Among the genes regulated by PIcR are: pIcA, encoding phosphatidylinositol-specific phospholipase C (PI-PLC); plc, encoding phosphatidylcholine-preferring phospholipase C (PC-PLC); nhe, encoding the non-haemolytic enterotoxin; hbl, encoding haemolytic enterotoxin BL (HBL); and genes specifying a putative S-layer like surface protein and a putative extracellular RNase. By analysing 37.1 kb of DNA sequence surrounding hbl, plcA and plcR, 28 ORFs were predicted. Three novel genes putatively regulated by PlcR and encoding a neutral protease (NprB), a subtilase family serine protease (Sfp) and a putative cell-wall hydrolase (Cwh) were identified. The corresponding sfp and cwh genes were located in the immediate upstream region of plcA and could both be regulated by a putative PlcR-binding site positioned between the inversely transcribed genes. Similarly, nprB was positioned directly upstream and transcribed in the opposite orientation to plcR. Genes surrounding plcA, plcR and hblCDAB that were lacking an upstream PlcR regulatory sequence did not appear to serve functions apparently related to PlcR and did not exhibit a conserved organization in Bacillus subtilis.
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40. |
Phung LT,
Gupta A,
( 1999 ) Mercury resistance in Bacillus cereus RC607: transcriptional organization and two new open reading frames. PMID : 10559175 : PMC : PMC94184 Abstract >>
The chromosomal mercury resistance determinant of Bacillus cereus RC607 confers resistance to inorganic mercury and to organomercurials. The order of genes in the completed mercury resistance determinant is operator-promoter 1 (O/P1) merR1 merT open reading frame 3 (ORF3) ORF4 merA O/P2 merR2 merB2 merB1. The previously undetermined 1-kb DNA sequence between the merA and merB1 genes includes two significant ORFs, whose predicted protein products are homologous with MerR (the transcriptional regulator) and MerB (the organomercurial lyase enzyme). Two transcriptional start sites (promoters), O/P1 at the beginning of the determinant and O/P2 immediately upstream of the sixth ORF, the newly identified merR2, were mapped by reverse transcriptase (RT) primer extension. A long 6.3-kb mRNA traversing all eight ORFs was shown by RT-PCR. Growth sensitivity measurements in liquid media and cellular mercury volatization assays characterized inducibility and differences in functional activity in B. cereus RC607 and after cloning of the mer determinant into plasmids in Escherichia coli.
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41. |
Milner JL,
Stohl EA,
( 1999 ) Zwittermicin A biosynthetic cluster. PMID : 10521664 : DOI : 10.1016/s0378-1119(99)00315-7 Abstract >>
The goal of this study was to identify the biosynthetic cluster for zwittermicin A, a novel, broad spectrum, aminopolyol antibiotic produced by Bacillus cereus. The nucleotide sequence of 2.7kb of DNA flanking the zwittermicin A self-resistance gene, zmaR, from B. cereus UW85 revealed three open reading frames (ORFs). Of these ORFs, two had sequence similarity to acyl-CoA dehydrogenases and polyketide synthases, respectively. Insertional inactivation demonstrated that orf2 is necessary for zwittermicin A production and that zmaR is necessary for high-level resistance to zwittermicin A but is not required for zwittermicin A production. Expression of ZmaR was temporally associated with zwittermicin A production. The results suggest that zmaR is part of a cluster of genes that is involved in zwittermicin A biosynthesis, representing the first biosynthetic pathway for an aminopolyol antibiotic.
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42. |
Lund T,
( 1999 ) The 105-kDa protein component of Bacillus cereus non-haemolytic enterotoxin (Nhe) is a metalloprotease with gelatinolytic and collagenolytic activity. PMID : 10499286 : DOI : 10.1111/j.1574-6968.1999.tb08699.x Abstract >>
A sequence of 91 amino acids residues, probably starting from the N-terminal of the mature protein, was determined for the 105-kDa protein of the non-haemolytic enterotoxin of Bacillus cereus. The last part of this sequence was similar to parts of the N-terminal portions of two collagenases of Clostridium histolyticum and Clostridium perfringens. Zymography, with intact collagen fibril and gelatin as substrates, showed that the 105-kDa protein had collagenolytic and gelatinolytic activity. The 105-kDa protein also showed activity against a typical collagenase substrate, azocoll, and was inhibited by EDTA and 1,10-phenanthroline. We conclude that the 105-kDa protein is a collagenase.
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43. |
O'Sullivan K,
Granum PE,
( 1999 ) The sequence of the non-haemolytic enterotoxin operon from Bacillus cereus. PMID : 10474188 : DOI : 10.1111/j.1574-6968.1999.tb13736.x Abstract >>
The non-haemolytic enterotoxin from Bacillus cereus has been sequenced. It is composed of three components, non-haemolytic enterotoxin A, B and C of 41.0, 39.8 and 36.5 kDa, respectively. Transcription of the operon seems to be positively regulated by plcR, a gene that also regulates phospholipase C expression. There is substantial similarity between the three proteins of non-haemolytic enterotoxin and between the non-haemolytic enterotoxin and haemolytic enterotoxin proteins.
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44. |
Shinke R,
Nanmori T,
Sarikaya E,
Kage T,
Adachi M,
( 1999 ) Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose. PMID : 10353816 : DOI : 10.1021/bi9829377 Abstract >>
The crystals of beta-amylase from Bacillus cereus belong to space group P21 with the following cell dimensions: a = 57.70 A, b = 92.87 A, c = 65.93 A, and beta =101.95 degrees. The structures of free and maltose-bound beta-amylases were determined by X-ray crystallography at 2.1 and 2.5 A with R-factors of 0.170 and 0.164, respectively. The final model of the maltose-bound form comprises 516 amino acid residues, four maltose molecules, 275 water molecules, one Ca2+, one acetate, and one sulfate ion. The enzyme consists of a core (beta/alpha)8-barrel domain (residues 5-434) and a C-terminal starch-binding domain (residues 435-613). Besides the active site in the core where two maltose molecules are bound in tandem, two novel maltose-binding sites were found in the core L4 region and in the C-terminal domain. The structure of the core domain is similar to that of soybean beta-amylase except for the L4 maltose-binding site, whereas the C-terminal domain has the same secondary structure as domain E of cyclodextrin glucosyltransferase. These two maltose-binding sites are 32-36 A apart from the active site. These results indicate that the ability of B. cereus beta-amylase to digest raw starch can be attributed to the additional two maltose-binding sites.
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45. |
Kolstø AB,
Rishovd AL,
Okstad OA,
( 1999 ) Genome organization is not conserved between Bacillus cereus and Bacillus subtilis. PMID : 10217496 : DOI : 10.1099/13500872-145-3-621 Abstract >>
The opportunistic pathogen Bacillus cereus is the genetically stable member of a group of closely related bacteria including the insect pathogen Bacillus thuringiensis and the mammalian pathogen Bacillus anthracis. Physical maps of B. cereus and B. thuringiensis strains show considerable variations in discrete parts of the chromosome, suggesting that certain genome regions are more prone to rearrangements. B. cereus belongs to the same subgroup of Bacillus species as Bacillus subtilis, by both phenotypic and rRNA sequence classification. The analysis of 80 kb of genome sequence sampled from different regions of the B. cereus ATCC 10987 chromosome is reported. Analysis of the sequence and comparison of the localization of the putative genes with that of B. subtilis orthologues show the following: (1) gene organization is not conserved between B. cereus and B. subtilis; (2) several putative genes are more closely related to genes from other bacteria and archaea than to B. subtilis, or may be absent in B. subtilis 168; (3) B. cereus contains a 155 bp repetitive sequence that is not present in B. subtilis. By hybridization, this repeat is present in all B. cereus and B. thuringiensis strains so far investigated.
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46. |
Tochikubo K,
Yasuda Y,
Kozuka S,
Miyata S,
Moriyama R,
Hattori A,
( 1999 ) Expression of a germination-specific amidase, SleB, of Bacilli in the forespore compartment of sporulating cells and its localization on the exterior side of the cortex in dormant spores. PMID : 10197998 : PMC : PMC93660 Abstract >>
A germination-specific amidase of bacilli is a major spore-lytic enzyme that is synthesized with a putative signal sequence and hydrolyses spore cortex in situ. The sleB gene encoding this amidase in Bacillus subtilis and Bacillus cereus was expressed in the forespore compartment of sporulating cells under the control of sigmaG, as shown by Northern blot and primer extension analyses. The forespore-specific expression of B. subtilis sleB was further indicated by the forespore-specific accumulation of a SleB-green fluorescent protein fusion protein from which a putative secretion signal of SleB was deleted. Immunoelectron microscopy with anti-SleB antiserum and a colloidal gold-immunoglobulin G complex showed that the enzymes from both Bacillus species are located just inside the spore coat layer in the dormant spore, and in the dormant spore, the amidases appear exist in a mature form lacking a signal sequence. These results indicate that SleB is translocated across the forespore's inner membrane by a secretion signal peptide and is deposited in cortex layer synthesized between the forespore inner and outer membranes. The peripheral location of the spore-lytic enzymes in the dormant spore suggests that spore germination is initiated at the exterior of the cortex.
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47. |
Braathen P,
Léonard C,
Mahillon J,
( 1999 ) MIC231, a naturally occurring mobile insertion cassette from Bacillus cereus. PMID : 10320586 : DOI : 10.1046/j.1365-2958.1999.01388.x Abstract >>
Recent dissection of numerous plasmids and transposable elements has given more credence to the modular organization of these genetic and genomic entities. Although many variations on each theme exist, the number of basic functional cassettes is thought to be relatively limited. In this paper, a novel type of mobile cassette is described. A naturally occurring assemblage consisting of two left IS231 ends flanking a D-stereospecific endopeptidase (adp) gene was found in several natural isolates of Bacillus cereus. This 1.9 kb genetic entity was shown to transpose in the presence of IS231A transposase, not only in Escherichia coli but also in Bacillus. The acronym MIC231 is proposed for this mobile insertion cassette trans-activated (teletransposed) by IS231. Using (D-Phe)4 tetrapeptide as substrate, the endopeptidase activity of the MIC231 adp gene could be demonstrated in E. coli and B. subtilis. Interestingly, this D-stereospecific endopeptidase activity was not limited to the original B. cereus isolates but was also detected in all but one of the 69 B. cereus sensu lato strains tested, indicating its important, yet dispensable, biological function. However, inactivation of the MIC231 adp gene in two B. cereus strains did not result in any detectable variation of their activity on (D-Phe)4, suggesting the presence of other distantly related adp gene(s). Thus, although the exact role of MIC231 adp remains elusive, its presence inside a mobile cassette represents the archetype of a novel insertion sequence modular organization.
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48. |
Yamada S,
Venkateswaran K,
( 1999 ) Cloning and nucleotide sequence analysis of gyrB of Bacillus cereus, B. thuringiensis, B. mycoides, and B. anthracis and their application to the detection of B. cereus in rice. PMID : 10103241 : PMC : PMC91211 Abstract >>
As 16S rRNA sequence analysis has proven inadequate for the differentiation of Bacillus cereus from closely related species, we employed the gyrase B gene (gyrB) as a molecular diagnostic marker. The gyrB genes of B. cereus JCM 2152(T), Bacillus thuringiensis IAM 12077(T), Bacillus mycoides ATCC 6462(T), and Bacillus anthracis Pasteur #2H were cloned and sequenced. Oligonucleotide PCR primer sets were designed from within gyrB sequences of the respective bacteria for the specific amplification and differentiation of B. cereus, B. thuringiensis, and B. anthracis. The results from the amplification of gyrB sequences correlated well with results obtained with the 16S rDNA-based hybridization study but not with the results of their phenotypic characterization. Some of the reference strains of both B. cereus (three serovars) and B. thuringiensis (two serovars) were not positive in PCR amplification assays with gyrB primers. However, complete sequencing of 1.2-kb gyrB fragments of these reference strains showed that these serovars had, in fact, lower homology than their originally designated species. We developed and tested a procedure for the specific detection of the target organism in boiled rice that entailed 15 h of preenrichment followed by PCR amplification of the B. cereus-specific fragment. This method enabled us to detect an initial inoculum of 0.24 CFU of B. cereus cells per g of boiled rice food homogenate without extracting DNA. However, a simple two-step filtration step is required to remove PCR inhibitory substances.
|
49. |
Lindbäck T,
Kolsto AB,
( 1999 ) Characterization of the mbl determinant and cloning of the spoIIID gene from Bacillus cereus ATCC 10987. PMID : 10069858 : Abstract >>
To examine the transcriptional start site of the putative Bacillus cereus mbl gene, we have cloned and sequenced the upstream region of the previously reported B. cereus mbl determinant, which showed sequence similarity to the mreB morphogene from Escherichia coli. Primer extension analysis revealed the transcriptional start site of mbl to 259 bp upstream of the putative translational start site and showed that the mbl gene was expressed at 3, 6, and 10 h of growth after inoculation. Antibodies against B. cereus Mbl showed that even though mbl mRNA was present in amounts detectable with Northern blot analysis exclusively in the early logarithmic growth phase, the amount of protein was constant during the cell cycle. Immunogold labeling cryo-transmission electron microscopy indicates that B. cereus Mbl is a cytoplasmic protein. The upstream sequence of mbl revealed two open reading frames, spoIIID and orf1. The amino acid sequence of B. cereus SpoIIID is identical to the SpoIIID sequence from Bacillus thuringiensis. Primer extension showed that mbl is not cotranscribed with spoIIID.
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50. |
Borin S,
Frova G,
Sorlini C,
Fani R,
( 1999 ) A randomly amplified polymorphic DNA marker specific for the Bacillus cereus group is diagnostic for Bacillus anthracis. PMID : 10049896 : PMC : PMC91177 Abstract >>
Aiming to develop a DNA marker specific for Bacillus anthracis and able to discriminate this species from Bacillus cereus, Bacillus thuringiensis, and Bacillus mycoides, we applied the randomly amplified polymorphic DNA (RAPD) fingerprinting technique to a collection of 101 strains of the genus Bacillus, including 61 strains of the B. cereus group. An 838-bp RAPD marker (SG-850) specific for B. cereus, B. thuringiensis, B. anthracis, and B. mycoides was identified. This fragment included a putative (366-nucleotide) open reading frame highly homologous to the ypuA gene of Bacillus subtilis. The restriction analysis of the SG-850 fragment with AluI distinguished B. anthracis from the other species of the B. cereus group.
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51. |
Wang Y,
Wang H,
Yang CH,
Wang Q,
Mei R,
( 2007 ) Two distinct manganese-containing superoxide dismutase genes in Bacillus cereus: their physiological characterizations and roles in surviving in wheat rhizosphere. PMID : 17521361 : DOI : 10.1111/j.1574-6968.2007.00759.x Abstract >>
Rhizosphere inhabitants interact intricately with plant host. Bacillus cereus 905 isolated from wheat rhizosphere colonized wheat rhizosphere with large population size. In this work, the role of superoxide dismutases (SODs) of B. cereus 905 in surviving in wheat rhizosphere was analyzed. Two genes, sodA-1 and sodA-2 encoding two distinct manganese SODs (MnSODs), were isolated from the bacterium. The amino acid sequence similarity between the two peptides is 58.43%. Through homologous recombination, three mutant strains have been created, each lacking either sodA-1, sodA-2 or both. Analysis of these mutant strains revealed differences in transcription and enzymatic activity of SOD. MnSOD2, encoded by sodA-2, plays a more important role in antioxidative stress. MnSOD1, the product of sodA-1 gene, is expressed at lower level. The function of the two MnSODs appears to be essential in colonization of wheat rhizosphere.
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52. |
Fagerlund A,
Brillard J,
Fürst R,
Guinebretière MH,
Granum PE,
( 2007 ) Toxin production in a rare and genetically remote cluster of strains of the Bacillus cereus group. PMID : 17517121 : DOI : 10.1186/1471-2180-7-43 PMC : PMC1888693 Abstract >>
Three enterotoxins are implicated in diarrhoeal food poisoning due to Bacillus cereus: Haemolysin BL (Hbl), Non-haemolytic enterotoxin (Nhe), and Cytotoxin K (CytK). Toxin gene profiling and assays for detection of toxin-producing stains have been used in attempts to evaluate the enterotoxic potential of B. cereus group strains. B. cereus strain NVH 391/98, isolated from a case of fatal enteritis, was genetically remote from other B. cereus group strains. This strain lacked the genes encoding Hbl and Nhe, but contains CytK-1. The high virulence of this strain is thought to be due to the greater cytotoxic activity of CytK-1 compared to CytK-2, and to a high level of cytK expression. To date, only three strains containing cytK-1 have been identified; B. cereus strains NVH 391/98, NVH 883/00, and INRA AF2. A novel gene variant encoding Nhe was identified in these three strains, which had an average of 80% identity in protein sequence with previously identified Nhe toxins. While culture supernatants containing CytK and Nhe from NVH 391/98 and INRA AF2 were highly cytotoxic, NVH 883/00 expressed little or no CytK and Nhe and was non-cytotoxic. Comparative sequence and expression studies indicated that neither the PlcR/PapR quorum sensing system, nor theYvrGH and YvfTU two-component systems, were responsible for the observed difference in toxin production. Additionally, phylogenetic analysis of 13 genes showed that NVH 391/98, NVH 883/00, and INRA AF2 comprise a novel cluster of strains genetically distant from other B. cereus group strains. Due to its divergent sequence, the novel nhe operon had previously not been detected in NVH 391/98 using PCR and several monoclonal antibodies. Thus, toxigenic profiling based on the original nhe sequence will fail to detect the toxin in this group of strains. The observation that strain NVH 883/00 carries cytK-1 but is non-cytotoxic indicates that the detection of this gene variant is not a sufficient criterion for identification of highly cytotoxic strains. The presence of the novel nhe operon and the cytK-1 gene variant in this cluster of strains reflect their phylogenetically remote relationship towards other B. cereus group strains.
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53. |
Fadouloglou VE,
Deli A,
Glykos NM,
Psylinakis E,
Bouriotis V,
Kokkinidis M,
( 2007 ) Crystal structure of the BcZBP, a zinc-binding protein from Bacillus cereus. PMID : 17501983 : DOI : 10.1111/j.1742-4658.2007.05834.x Abstract >>
Bacillus cereus is an opportunistic pathogenic bacterium closely related to Bacillus anthracis, the causative agent of anthrax in mammals. A significant portion of the B. cereus chromosomal genes are common to B. anthracis, including genes which in B. anthracis code for putative virulence and surface proteins. B. cereus thus provides a convenient model organism for studying proteins potentially associated with the pathogenicity of the highly infectious B. anthracis. The zinc-binding protein of B. cereus, BcZBP, is encoded from the bc1534 gene which has three homologues to B. anthracis. The protein exhibits deacetylase activity with the N-acetyl moiety of the N-acetylglucosamine and the diacetylchitobiose and triacetylchitotriose. However, neither the specific substrate of the BcZBP nor the biochemical pathway have been conclusively identified. Here, we present the crystal structure of BcZBP at 1.8 A resolution. The N-terminal part of the 234 amino acid protein adopts a Rossmann fold whereas the C-terminal part consists of two beta-strands and two alpha-helices. In the crystal, the protein forms a compact hexamer, in agreement with solution data. A zinc binding site and a potential active site have been identified in each monomer. These sites have extensive similarities to those found in two known zinc-dependent hydrolases with deacetylase activity, MshB and LpxC, despite a low degree of amino acid sequence identity. The functional implications and a possible catalytic mechanism are discussed.
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54. |
Zhao C,
Luo Y,
Song C,
Liu Z,
Chen S,
Yu Z,
Sun M,
( 2007 ) Identification of three Zwittermicin A biosynthesis-related genes from Bacillus thuringiensis subsp. kurstaki strain YBT-1520. PMID : 17225146 : DOI : 10.1007/s00203-006-0196-3 Abstract >>
Zwittermicin A (ZwA) is a novel, broad-spectrum linear aminopolyol antibiotic produced by some Bacillus cereus and Bacillus thuringiensis. However, only part of its biosynthesis cluster has been identified and characterized from B. cereus UW85. To better understand the biosynthesis cluster of ZwA, a bacterial artificial chromosome (BAC) library of B. thuringiensis subsp. kurstaki strain YBT-1520, a ZwA-producing strain, was constructed. Two BAC clones, 1F8 and 5E2, were obtained by PCR, which overlap the known ZwA biosynthesis cluster of B. cereus UW85. This ZwA biosynthesis cluster is at least 38.6 kb and is located on the chromosome, instead of the plasmid. Partial DNA sequencing revealed both BAC clones carry three new ZwA biosynthesis-related genes, zwa6, zwa5A and zwa5B, which were found at the corresponding location of B. cereus UW85. Putative amino acid sequences of these genes shown that ZWA6 is homologous to a typical carbamoyltransferase from Streptomyces avermitilis, while ZWA5A and ZWA5B are homologs of cysteine synthetase and ornithine cyclodeaminase which jointly synthesize 2,3-diaminopropionate in the viomycin biosynthesis pathway, respectively. The identification of these three genes further supports the hypothesized ZwA biosynthesis pathway.
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55. |
Zigha A,
Rosenfeld E,
Schmitt P,
Duport C,
( 2007 ) The redox regulator Fnr is required for fermentative growth and enterotoxin synthesis in Bacillus cereus F4430/73. PMID : 17259311 : DOI : 10.1128/JB.01701-06 PMC : PMC1855811 Abstract >>
Glucose-grown cells of Bacillus cereus respond to anaerobiosis and low extracellular oxidoreduction potentials (ORP), notably by enhancing enterotoxin production. This response involves the ResDE two-component system. We searched the B. cereus genome for other redox response regulators potentially involved in this adaptive process, and we identified one gene encoding a protein predicted to have an amino acid sequence 58% identical (80% similar) to that of the Bacillus subtilis Fnr redox regulator. The fnr gene of the food-borne pathogen B. cereus F4430/73 has been cloned and partially characterized. We showed that fnr was up-regulated during anaerobic fermentation, especially when fermentation occurred at low ORP (under highly reducing conditions). The expression of fnr was down-regulated in the presence of O(2) and nitrate which, unlike fumarate, stimulated the respiratory pathways. The inactivation of B. cereus fnr abolished fermentative growth but only moderately affected aerobic and anaerobic nitrate respiratory growth. Analyses of glucose by-products and the transcription profiles of key catabolic genes confirmed the strong regulatory impact of Fnr on B. cereus fermentative pathways. More importantly, the fnr mutation strongly decreased the expression of PlcR-dependent hbl and nhe genes, leading to the absence of hemolysin BL (Hbl) and nonhemolytic enterotoxin (Nhe) secretion by the mutant. These data indicate that fnr is essential for both fermentation and toxinogenesis. The results also suggest that both Fnr and the ResDE two-component system belong to a redox regulatory pathway that functions at least partially independently of the pleiotropic virulence gene regulator PlcR to regulate enterotoxin gene expression.
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56. |
Kosinska U,
Carnrot C,
Sandrini MP,
Clausen AR,
Wang L,
Piskur J,
Eriksson S,
Eklund H,
( 2007 ) Structural studies of thymidine kinases from Bacillus anthracis and Bacillus cereus provide insights into quaternary structure and conformational changes upon substrate binding. PMID : 17288553 : DOI : 10.1111/j.1742-4658.2006.05617.x DOI : 10.1111/j.1742-4658.2006.05617.x Abstract >>
Thymidine kinase (TK) is the key enzyme in salvaging thymidine to produce thymidine monophosphate. Owing to its ability to phosphorylate nucleoside analogue prodrugs, TK has gained attention as a rate-limiting drug activator. We describe the structures of two bacterial TKs, one from the pathogen Bacillus anthracis in complex with the substrate dT, and the second from the food-poison-associated Bacillus cereus in complex with the feedback inhibitor dTTP. Interestingly, in contrast with previous structures of TK in complex with dTTP, in this study dTTP occupies the phosphate donor site and not the phosphate acceptor site. This results in several conformational changes compared with TK structures described previously. One of the differences is the way tetramers are formed. Unlike B. anthracis TK, B. cereus TK shows a loose tetramer. Moreover, the lasso-domain is in open conformation in B. cereus TK without any substrate in the active site, whereas in B. anthracis TK the loop conformation is closed and thymidine occupies the active site. Another conformational difference lies within a region of 20 residues that we refer to as phosphate-binding beta-hairpin. The phosphate-binding beta-hairpin seems to be a flexible region of the enzyme which becomes ordered upon formation of hydrogen bonds to the alpha-phosphate of the phosphate donor, dTTP. In addition to descriptions of the different conformations that TK may adopt during the course of reaction, the oligomeric state of the enzyme is investigated.
|
57. |
Kosinska U,
Carnrot C,
Sandrini MP,
Clausen AR,
Wang L,
Piskur J,
Eriksson S,
Eklund H,
( 2007 ) Structural studies of thymidine kinases from Bacillus anthracis and Bacillus cereus provide insights into quaternary structure and conformational changes upon substrate binding. PMID : 17288553 : DOI : 10.1111/j.1742-4658.2006.05617.x DOI : 10.1111/j.1742-4658.2006.05617.x Abstract >>
Thymidine kinase (TK) is the key enzyme in salvaging thymidine to produce thymidine monophosphate. Owing to its ability to phosphorylate nucleoside analogue prodrugs, TK has gained attention as a rate-limiting drug activator. We describe the structures of two bacterial TKs, one from the pathogen Bacillus anthracis in complex with the substrate dT, and the second from the food-poison-associated Bacillus cereus in complex with the feedback inhibitor dTTP. Interestingly, in contrast with previous structures of TK in complex with dTTP, in this study dTTP occupies the phosphate donor site and not the phosphate acceptor site. This results in several conformational changes compared with TK structures described previously. One of the differences is the way tetramers are formed. Unlike B. anthracis TK, B. cereus TK shows a loose tetramer. Moreover, the lasso-domain is in open conformation in B. cereus TK without any substrate in the active site, whereas in B. anthracis TK the loop conformation is closed and thymidine occupies the active site. Another conformational difference lies within a region of 20 residues that we refer to as phosphate-binding beta-hairpin. The phosphate-binding beta-hairpin seems to be a flexible region of the enzyme which becomes ordered upon formation of hydrogen bonds to the alpha-phosphate of the phosphate donor, dTTP. In addition to descriptions of the different conformations that TK may adopt during the course of reaction, the oligomeric state of the enzyme is investigated.
|
58. |
Antwerpen MH,
Schellhase M,
Ehrentreich-Förster E,
Bier F,
Witte W,
Nübel U,
( 2007 ) DNA microarray for detection of antibiotic resistance determinants in Bacillus anthracis and closely related Bacillus cereus. PMID : 17118627 : DOI : 10.1016/j.mcp.2006.10.002 Abstract >>
We developed a multiplex PCR for amplification of ten genes involved in resistance to ciprofloxacin, doxycycline, rifampin, and vancomycin in Bacillus anthracis and closely related Bacillus cereus. Enzymatic labelling of PCR products followed by hybridization to oligonucleotide probes on a DNA microarray enabled simultaneous detection of resistance genes tetK, tetL, tetM, tetO, vanA, and vanB and resistance-mediating point mutations in genes gyrA, gyrB, parC, and rpoB. The presented assay allows detection of clinically relevant antibiotic resistance determinants within 4h and can be used as a time-saving tool supporting conventional culture-based diagnostics.
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59. |
Xu D,
Côté JC,
( 2006 ) Sequence diversity of the Bacillus thuringiensis and B. cereus sensu lato flagellin (H antigen) protein: comparison with H serotype diversity. PMID : 16820457 : DOI : 10.1128/AEM.00328-06 PMC : PMC1489342 Abstract >>
We set out to analyze the sequence diversity of the Bacillus thuringiensis flagellin (H antigen [Hag]) protein and compare it with H serotype diversity. Some other Bacillus cereus sensu lato species and strains were added for comparison. The internal sequences of the flagellin (hag) alleles from 80 Bacillus thuringiensis strains and 16 strains from the B. cereus sensu lato group were amplified and cloned, and their nucleotide sequences were determined and translated into amino acids. The flagellin allele nucleotide sequences for 10 additional strains were retrieved from GenBank for a total of 106 Bacillus species and strains used in this study. These included 82 B. thuringiensis strains from 67 H serotypes, 5 B. cereus strains, 3 Bacillus anthracis strains, 3 Bacillus mycoides strains, 11 Bacillus weihenstephanensis strains, 1 Bacillus halodurans strain, and 1 Bacillus subtilis strain. The first 111 and the last 66 amino acids were conserved. They were referred to as the C1 and C2 regions, respectively. The central region, however, was highly variable and is referred to as the V region. Two bootstrapped neighbor-joining trees were generated: a first one from the alignment of the translated amino acid sequences of the amplified internal sequences of the hag alleles and a second one from the alignment of the V region amino acid sequences, respectively. Of the eight clusters revealed in the tree inferred from the entire C1-V-C2 region amino acid sequences, seven were present in corresponding clusters in the tree inferred from the V region amino acid sequences. With regard to B. thuringiensis, in most cases, different serovars had different flagellin amino acid sequences, as might have been expected. Surprisingly, however, some different B. thuringiensis serovars shared identical flagellin amino acid sequences. Likewise, serovars from the same H serotypes were most often found clustered together, with exceptions. Indeed, some serovars from the same H serotype carried flagellins with sufficiently different amino acid sequences as to be located on distant clusters. Species-wise, B. halodurans, B. subtilis, and B. anthracis formed specific branches, whereas the other four species, all in the B. cereus sensu lato group, B. mycoides, B. weihenstephanensis, B. cereus, and B. thuringiensis, did not form four specific clusters as might have been expected. Rather, strains from any of these four species were placed side by side with strains from the other species. In the B. cereus sensu lato group, B. anthracis excepted, the distribution of strains was not species specific.
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60. |
Lahiri SD,
Zhang G,
Dunaway-Mariano D,
Allen KN,
( 2006 ) Diversification of function in the haloacid dehalogenase enzyme superfamily: The role of the cap domain in hydrolytic phosphoruscarbon bond cleavage. PMID : 17070898 : DOI : 10.1016/j.bioorg.2006.09.007 PMC : PMC1941675 Abstract >>
Phosphonatase functions in the 2-aminoethylphosphonate (AEP) degradation pathway of bacteria, catalyzing the hydrolysis of the C-P bond in phosphonoacetaldehyde (Pald) via formation of a bi-covalent Lys53ethylenamine/Asp12 aspartylphosphate intermediate. Because phosphonatase is a member of the haloacid dehalogenase superfamily, a family predominantly comprised of phosphatases, the question arises as to how this new catalytic activity evolved. The source of general acid-base catalysis for Schiff-base formation and aspartylphosphate hydrolysis was probed using pH-rate profile analysis of active-site mutants and X-ray crystallographic analysis of modified forms of the enzyme. The 2.9 A X-ray crystal structure of the mutant Lys53Arg complexed with Mg2+ and phosphate shows that the equilibrium between the open and the closed conformation is disrupted, favoring the open conformation. Thus, proton dissociation from the cap domain Lys53 is required for cap domain-core domain closure. The likely recipient of the Lys53 proton is a water-His56 pair that serves to relay the proton to the carbonyl oxygen of the phosphonoacetaldehyde (Pald) substrate upon addition of the Lys53. The pH-rate profile analysis of active-site mutants was carried out to test this proposal. The proximal core domain residues Cys22 and Tyr128 were ruled out, and the role of cap domain His56 was supported by the results. The X-ray crystallographic structure of wild-type phosphonatase reduced with NaBH4 in the presence of Pald was determined at 2.4A resolution to reveal N epsilon-ethyl-Lys53 juxtaposed with a sulfate ligand bound in the phosphate site. The position of the C2 of the N-ethyl group in this structure is consistent with the hypothesis that the cap domain N epsilon-ethylenamine-Lys53 functions as a general base in the hydrolysis of the aspartylphosphate bi-covalent enzyme intermediate. Because the enzyme residues proposed to play a key role in P-C bond cleavage are localized on the cap domain, this domain appears to have evolved to support the diversification of the HAD phosphatase core domain for catalysis of hydrolytic P-C bond cleavage.
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61. |
Kovalevskiy OV,
Lebedev AA,
Surin AK,
Solonin AS,
Antson AA,
( 2007 ) Crystal structure of Bacillus cereus HlyIIR, a transcriptional regulator of the gene for pore-forming toxin hemolysin II. PMID : 17097673 : DOI : 10.1016/j.jmb.2006.10.074 PMC : PMC1828608 Abstract >>
Production of Bacillus cereus and Bacillus anthracis toxins is controlled by a number of transcriptional regulators. Here we report the crystal structure of B. cereus HlyIIR, a regulator of the gene encoding the pore-forming toxin hemolysin II. We show that HlyIIR forms a tight dimer with a fold and overall architecture similar to the TetR family of repressors. A remarkable feature of the structure is a large internal cavity with a volume of 550 A(3) suggesting that the activity of HlyIIR is modulated by binding of a ligand, which triggers the toxin production. Virtual ligand library screening shows that this pocket can accommodate compounds with molecular masses of up to 400-500 Da. Based on structural data and previous biochemical evidence, we propose a model for HlyIIR interaction with the DNA.
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62. |
Rasko DA,
Rosovitz MJ,
?kstad OA,
Fouts DE,
Jiang L,
Cer RZ,
Kolstø AB,
Gill SR,
Ravel J,
( 2007 ) Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1. PMID : 17041058 : DOI : 10.1128/JB.01313-06 PMC : PMC1797222 Abstract >>
The plasmids of the members of the Bacillus cereus sensu lato group of organisms are essential in defining the phenotypic traits associated with pathogenesis and ecology. For example, Bacillus anthracis contains two plasmids, pXO1 and pXO2, encoding toxin production and encapsulation, respectively, that define this species pathogenic potential, whereas the presence of a Bt toxin-encoding plasmid defines Bacillus thuringiensis isolates. In this study the plasmids from B. cereus isolates that produce emetic toxin or are linked to periodontal disease were sequenced and analyzed. Two periodontal isolates examined contained almost identical approximately 272-kb plasmids, named pPER272. The emetic toxin-producing isolate contained one approximately 270-kb plasmid, named pCER270, encoding the cereulide biosynthesis gene cluster. Comparative sequence analyses of these B. cereus plasmids revealed a high degree of sequence similarity to the B. anthracis pXO1 plasmid, especially in a putative replication region. These plasmids form a newly defined group of pXO1-like plasmids. However, these novel plasmids do not contain the pXO1 pathogenicity island, which in each instance is replaced by plasmid specific DNA. Plasmids pCER270 and pPER272 share regions that are not found in any other pXO1-like plasmids. Evolutionary studies suggest that these plasmids are more closely related to each other than to other identified B. cereus plasmids. Screening of a population of B. cereus group isolates revealed that pXO1-like plasmids are more often found in association with clinical isolates. This study demonstrates that the pXO1-like plasmids may define pathogenic B. cereus isolates in the same way that pXO1 and pXO2 define the B. anthracis species.
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63. |
Hu X,
Hansen BM,
Hendriksen NB,
Yuan Z,
( 2006 ) Detection and phylogenic analysis of one anthrax virulence plasmid pXO1 conservative open reading frame ubiquitous presented within Bacillus cereus group strains. PMID : 16978581 : DOI : 10.1016/j.bbrc.2006.08.125 Abstract >>
The presence of one of the anthrax virulence plasmid pXO1 conserved fragments was analyzed in 24 Bacillus cereus and B. thuringiensis strains, including 6 B. thuringiensis subspecies, by polymerase chain reactions. Twelve out of 24 strains showed PCR-positive for an ORF101 homologous sequence. Two pXO1-ORF101-like fragments from a B. cereus B-4ac and a commercial B. thuringiensis kurstaki HD1 were cloned, sequenced and expressed in Escherichia coli. Toxicity assays revealed that the product encoded by the pXO1-ORF101-like fragment had no impact on either Vero cells or Chinese Hamster Ovary cells, suggesting that this fragment probably not contribute to enterotoxic activity. Sequence alignment of the pXO1-ORF101 from three Bacillus anthracis and ORF101-like fragments from other 12 B. cereus group isolates indicated high identity (more than 90%) and the presence of subgroup- and strain-specific SNPs among these fragments.
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64. |
Chan YA,
Boyne MT,
Podevels AM,
Klimowicz AK,
Handelsman J,
Kelleher NL,
Thomas MG,
( 2006 ) Hydroxymalonyl-acyl carrier protein (ACP) and aminomalonyl-ACP are two additional type I polyketide synthase extender units. PMID : 16983083 : DOI : 10.1073/pnas.0603748103 PMC : PMC1599966 Abstract >>
Combinatorial biosynthesis of type I polyketide synthases is a promising approach for the generation of new structural derivatives of polyketide-containing natural products. A target of this approach has been to change the extender units incorporated into a polyketide backbone to alter the structure and activity of the natural product. One limitation to these efforts is that only four extender units were known: malonyl-CoA, methylmalonyl-CoA, ethylmalonyl-CoA, and methoxymalonyl-acyl carrier protein (ACP). The chemical attributes of these extender units are quite similar, with the exception of the potential hydrogen bonding interactions by the oxygen of the methoxy moiety. Furthermore, the incorporated extender units are not easily modified by using simple chemical approaches when combinatorial biosynthesis is coupled to semisynthetic chemistry. We recently proposed the existence of two additional extender units, hydroxymalonyl-ACP and aminomalonyl-ACP, involved in the biosynthesis of zwittermicin A. These extender units offer unique possibilities for combinatorial biosynthesis and semisynthetic chemistry because of the introduction of free hydroxyl and amino moieties into a polyketide structure. Here, we present the biochemical and mass spectral evidence for the formation of these extender units. This evidence shows the formation of ACP-linked extender units for polyketide synthesis. Interestingly, aminomalonyl-ACP formation involves enzymology typically found in nonribosomal peptide synthesis.
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65. |
Johnson MJ,
Todd SJ,
Ball DA,
Shepherd AM,
Sylvestre P,
Moir A,
( 2006 ) ExsY and CotY are required for the correct assembly of the exosporium and spore coat of Bacillus cereus. PMID : 16980471 : DOI : 10.1128/JB.00997-06 PMC : PMC1636315 Abstract >>
The exosporium-defective phenotype of a transposon insertion mutant of Bacillus cereus implicated ExsY, a homologue of B. subtilis cysteine-rich spore coat proteins CotY and CotZ, in assembly of an intact exosporium. Single and double mutants of B. cereus lacking ExsY and its paralogue, CotY, were constructed. The exsY mutant spores are not surrounded by an intact exosporium, though they often carry attached exosporium fragments. In contrast, the cotY mutant spores have an intact exosporium, although its overall shape is altered. The single mutants show altered, but different, spore coat properties. The exsY mutant spore coat is permeable to lysozyme, whereas the cotY mutant spores are less resistant to several organic solvents than is the case for the wild type. The exsY cotY double-mutant spores lack exosporium and have very thin coats that are permeable to lysozyme and are sensitive to chloroform, toluene, and phenol. These spore coat as well as exosporium defects suggest that ExsY and CotY are important to correct formation of both the exosporium and the spore coat in B. cereus. Both ExsY and CotY proteins were detected in Western blots of purified wild-type exosporium, in complexes of high molecular weight, and as monomers. Both exsY and cotY genes are expressed at late stages of sporulation.
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66. |
Lu X,
Yuan Y,
Xue XL,
Zhang GP,
Zhou SN,
( 2006 ) Identification of the critical role of Tyr-194 in the catalytic activity of a novel N-acyl-homoserine lactonase from marine Bacillus cereus strain Y2. PMID : 16972128 : DOI : 10.1007/s00284-006-0224-1 Abstract >>
Enzymatic disruption of quorum-sensing (QS) pathways in pathogenic organisms is a promising anti-infection therapeutic strategy. AHL-lactonase, a potent tool for biocontrol, can hydrolyze QS signal molecule N-acyl-homoserine lactones (AHLs) into inactive products, thereby blocking the QS systems. A marine bacterial isolate Y2, identified as a Bacillus cereus subsp., was found capable of inactivating AHLs. The aiiA gene encoding the AHL-degrading enzyme from bacterial strain Y2 was cloned and expressed in Escherichia coli. The 28-kDa recombinant Y2-AiiA protein was purified and showed strong AHL-degrading activity. Sequence comparisons of Y2-aiiA with known AHL-lactonases revealed high identities in the deduced amino-acid sequences. Functional determination of a potential catalytic residue Tyr-194 of AHL-lactonases was performed by site-directed mutagenesis. As judged by AHL-degrading bioassay, substitution of Tyr-194 with Ala resulted in a dramatic decrease of activity compared with wild-type (WT) recombinant Y2-AiiA, although the expression level of the mutated Y2-AiiA protein was equivalent to that of WT Y2-AiiA. These results suggested that the conserved residue Tyr-194 is critical for catalytic function of the novel AHL-lactonase.
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67. |
Valappil SP,
Boccaccini AR,
Bucke C,
Roy I,
( 2007 ) Polyhydroxyalkanoates in Gram-positive bacteria: insights from the genera Bacillus and Streptomyces. PMID : 17016742 : DOI : 10.1007/s10482-006-9095-5 Abstract >>
Gram-positive bacteria, notably Bacillus and Streptomyces, have been used extensively in industry. However, these microorganisms have not yet been exploited for the production of the biodegradable polymers, polyhydroxyalkanoates (PHAs). Although PHAs have many potential applications, the cost of production means that medical applications are currently the main area of use. Gram-negative bacteria, currently the only commercial source of PHAs, have lipopolysaccharides (LPS) which co-purify with the PHAs and cause immunogenic reactions. On the other hand, Gram- positive bacteria lack LPS, a positive feature which justifies intensive investigation into their production of PHAs. This review summarizes currently available knowledge on PHA production by Gram- positive bacteria especially Bacillus and Streptomyces. We hope that this will form the basis of further research into developing either or both as a source of PHAs for medical applications.
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68. |
Nakano Y,
Kimura K,
( 1991 ) Purification and characterization of a repressor for the Bacillus cereus glnRA operon. PMID : 1677938 : Abstract >>
We report the overexpression, purification, and properties of the regulatory protein, GlnR, for glutamine synthetase synthesis of Bacillus cereus. The protein was found to be a dimer with a molecular weight of approximately 30,000, and its subunit molecular weight was 15,000 in agreement with that (15,025) of deduced amino acid sequence of GlnR. The purified GlnR protein bound specifically to the promoter region of the glnRA operon of B. cereus and Bacillus subtilis. The binding of the GlnR protein to the DNA fragment was enhanced by the presence of glutamine synthetase, the product of glnA, of B. cereus or B. subtilis, although the affinity of the GlnR protein for DNA was not affected in the presence of glutamate, glutamine, Mg2+, Mn2+, or ammonia. These results indicate the existence of an interaction between GlnR and glutamine synthetase, and support the hypothesis that the regulation of glnA expression requires both GlnR protein and glutamine synthetase in Bacillus.
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69. |
Duport C,
Zigha A,
Rosenfeld E,
Schmitt P,
( 2006 ) Control of enterotoxin gene expression in Bacillus cereus F4430/73 involves the redox-sensitive ResDE signal transduction system. PMID : 16952956 : DOI : 10.1128/JB.00702-06 PMC : PMC1595479 Abstract >>
In contrast to Bacillus subtilis, the role of the two-component regulatory system ResDE has not yet been investigated in the facultative anaerobe Bacillus cereus. We examined the role of ResDE in the food-borne pathogen B. cereus F4430/73 by constructing resDE and resE mutants. Growth performances, glucose metabolism, and expression of hemolysin BL (Hbl) and nonhemolytic enterotoxin (Nhe) were analyzed in the three strains under distinct oxygenation and extracellular oxidoreduction potential (ORP) conditions. We show that growth and glucose metabolism were only moderately perturbed in both resDE and resE mutants under aerobiosis, microaerobiosis, and anaerobiosis generated under N(2) atmosphere (initial ORP = +45 mV). The major effects of resDE and resE mutations were observed under low-ORP anaerobic conditions generated under hydrogen atmosphere (iORP = -148 mV). These conditions normally favor enterotoxin production in the wild type. The resE mutation was more deleterious to the cells than the resDE mutation, causing growth limitation and strong deregulation of key catabolic genes. More importantly, the resE mutation abolished the production of enterotoxins under all of the conditions examined. The resDE mutation only decreased enterotoxin expression under anaerobiosis, with a more pronounced effect under low-ORP conditions. Thus, the ResDE system was found to exert major control on both fermentative growth and enterotoxin expression, and it is concluded that the ResDE system of B. cereus should be considered an anaerobic redox regulator. The data presented also provide evidence that the ResDE-dependent regulation of enterotoxins might function at least partially independently of the pleiotropic virulence gene regulator PlcR.
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70. |
Zhang R,
Joachimiak G,
Jiang S,
Cipriani A,
Collart F,
Joachimiak A,
( 2006 ) Structure of phage protein BC1872 from Bacillus cereus, a singleton with new fold. PMID : 16596646 : DOI : 10.1002/prot.20910 PMC : PMC2792010 Abstract >>
N/A
|
71. |
Iddar A,
Valverde F,
Assobhei O,
Serrano A,
Soukri A,
( 2005 ) Widespread occurrence of non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase among gram-positive bacteria. PMID : 16562377 : Abstract >>
The non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase (GAPDHN, NADP+-specific, EC 1.2.1.9) is present in green eukaryotes and some Streptococcus strains. The present report describes the results of activity and immunoblot analyses, which were used to generate the first survey of bacterial GAPDHN distribution in a number of Bacillus, Streptococcus and Clostridium strains. Putative gapN genes were identified after PCR amplification of partial 700-bp sequences using degenerate primers constructed from highly conserved protein regions. Alignment of the amino acid sequences of these fragments with those of known sequences from other eukaryotic and prokaryotic GAPDHNs, demonstrated the presence of conserved residues involved in catalytic activity that are not conserved in aldehyde dehydrogenases, a protein family closely linked to GAPDHNs. The results confirm that the basic structural features of the members of the GAPDHN family have been conserved throughout evolution and that no identity exists with phosphorylating GAPDHs. Furthermore, phylogenetic trees generated from multiple sequence alignments suggested a close relationship between plant and bacterial GAPDHN families.
|
72. |
Sorokin A,
Candelon B,
Guilloux K,
Galleron N,
Wackerow-Kouzova N,
Ehrlich SD,
Bourguet D,
Sanchis V,
( 2006 ) Multiple-locus sequence typing analysis of Bacillus cereus and Bacillus thuringiensis reveals separate clustering and a distinct population structure of psychrotrophic strains. PMID : 16461712 : DOI : 10.1128/AEM.72.2.1569-1578.2006 PMC : PMC1392946 DOI : 10.1128/AEM.72.2.1569-1578.2006 PMC : PMC1392946 Abstract >>
We used multilocus sequence typing (MLST) to characterize phylogenetic relationships for a collection of Bacillus cereus group strains isolated from forest soil in the Paris area during a mild winter. This collection contains multiple strains isolated from the same soil sample and strains isolated from samples from different sites. We characterized 115 strains of this collection and 19 other strains based on the sequences of the clpC, dinB, gdpD, panC, purF, and yhfL loci. The number of alleles ranged from 36 to 53, and a total of 93 allelic profiles or sequence types were distinguished. We identified three major strain clusters-C, T, and W-based on the comparison of individual gene sequences or concatenated sequences. Some less representative clusters and subclusters were also distinguished. Analysis of the MLST data using the concept of clonal complexes led to the identification of two, five, and three such groups in clusters C, T, and W, respectively. Some of the forest isolates were closely related to independently isolated psychrotrophic strains. Systematic testing of the strains of this collection showed that almost all the strains that were able to grow at a low temperature (6 degrees C) belonged to cluster W. Most of these strains, including three independently isolated strains, belong to two clonal complexes and are therefore very closely related genetically. These clonal complexes represent strains corresponding to the previously identified species Bacillus weihenstephanensis. Most of the other strains of our collection, including some from the W cluster, are not psychrotrophic. B. weihenstephanensis (cluster W) strains appear to comprise an effectively sexual population, whereas Bacillus thuringiensis (cluster T) and B. cereus (cluster C) have clonal population structures.
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73. |
Sorokin A,
Candelon B,
Guilloux K,
Galleron N,
Wackerow-Kouzova N,
Ehrlich SD,
Bourguet D,
Sanchis V,
( 2006 ) Multiple-locus sequence typing analysis of Bacillus cereus and Bacillus thuringiensis reveals separate clustering and a distinct population structure of psychrotrophic strains. PMID : 16461712 : DOI : 10.1128/AEM.72.2.1569-1578.2006 PMC : PMC1392946 DOI : 10.1128/AEM.72.2.1569-1578.2006 PMC : PMC1392946 Abstract >>
We used multilocus sequence typing (MLST) to characterize phylogenetic relationships for a collection of Bacillus cereus group strains isolated from forest soil in the Paris area during a mild winter. This collection contains multiple strains isolated from the same soil sample and strains isolated from samples from different sites. We characterized 115 strains of this collection and 19 other strains based on the sequences of the clpC, dinB, gdpD, panC, purF, and yhfL loci. The number of alleles ranged from 36 to 53, and a total of 93 allelic profiles or sequence types were distinguished. We identified three major strain clusters-C, T, and W-based on the comparison of individual gene sequences or concatenated sequences. Some less representative clusters and subclusters were also distinguished. Analysis of the MLST data using the concept of clonal complexes led to the identification of two, five, and three such groups in clusters C, T, and W, respectively. Some of the forest isolates were closely related to independently isolated psychrotrophic strains. Systematic testing of the strains of this collection showed that almost all the strains that were able to grow at a low temperature (6 degrees C) belonged to cluster W. Most of these strains, including three independently isolated strains, belong to two clonal complexes and are therefore very closely related genetically. These clonal complexes represent strains corresponding to the previously identified species Bacillus weihenstephanensis. Most of the other strains of our collection, including some from the W cluster, are not psychrotrophic. B. weihenstephanensis (cluster W) strains appear to comprise an effectively sexual population, whereas Bacillus thuringiensis (cluster T) and B. cereus (cluster C) have clonal population structures.
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74. |
Shi N,
Ye S,
Alam A,
Chen L,
Jiang Y,
( 2006 ) Atomic structure of a Na+- and K+-conducting channel. PMID : 16467789 : DOI : 10.1038/nature04508 Abstract >>
Ion selectivity is one of the basic properties that define an ion channel. Most tetrameric cation channels, which include the K+, Ca2+, Na+ and cyclic nucleotide-gated channels, probably share a similar overall architecture in their ion-conduction pore, but the structural details that determine ion selection are different. Although K+ channel selectivity has been well studied from a structural perspective, little is known about the structure of other cation channels. Here we present crystal structures of the NaK channel from Bacillus cereus, a non-selective tetrameric cation channel, in its Na+- and K+-bound states at 2.4 A and 2.8 A resolution, respectively. The NaK channel shares high sequence homology and a similar overall structure with the bacterial KcsA K+ channel, but its selectivity filter adopts a different architecture. Unlike a K+ channel selectivity filter, which contains four equivalent K+-binding sites, the selectivity filter of the NaK channel preserves the two cation-binding sites equivalent to sites 3 and 4 of a K+ channel, whereas the region corresponding to sites 1 and 2 of a K+ channel becomes a vestibule in which ions can diffuse but not bind specifically. Functional analysis using an 86Rb flux assay shows that the NaK channel can conduct both Na+ and K+ ions. We conclude that the sequence of the NaK selectivity filter resembles that of a cyclic nucleotide-gated channel and its structure may represent that of a cyclic nucleotide-gated channel pore.
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75. |
Daffonchio D,
Raddadi N,
Merabishvili M,
Cherif A,
Carmagnola L,
Brusetti L,
Rizzi A,
Chanishvili N,
Visca P,
Sharp R,
Borin S,
( 2006 ) Strategy for identification of Bacillus cereus and Bacillus thuringiensis strains closely related to Bacillus anthracis. PMID : 16461679 : DOI : 10.1128/AEM.72.2.1295-1301.2006 PMC : PMC1392923 Abstract >>
Bacillus cereus strains that are genetically closely related to B. anthracis can display anthrax-like virulence traits (A. R. Hoffmaster et al., Proc. Natl. Acad. Sci. USA 101:8449-8454, 2004). Hence, approaches that rapidly identify these "near neighbors" are of great interest for the study of B. anthracis virulence mechanisms, as well as to prevent the use of such strains for B. anthracis-based bioweapon development. Here, a strategy is proposed for the identification of near neighbors of B. anthracis based on single nucleotide polymorphisms (SNP) in the 16S-23S rRNA intergenic spacer (ITS) containing tRNA genes, characteristic of B. anthracis. By using restriction site insertion-PCR (RSI-PCR) the presence of two SNP typical of B. anthracis was screened in 126 B. cereus group strains of different origin. Two B. cereus strains and one B. thuringiensis strain showed RSI-PCR profiles identical to that of B. anthracis. The sequencing of the entire ITS containing tRNA genes revealed two of the strains to be identical to B. anthracis. The strict relationship with B. anthracis was confirmed by multilocus sequence typing (MLST) of four other independent loci: cerA, plcR, AC-390, and SG-749. The relationship to B. anthracis of the three strains described by MLST was comparable and even higher to that of four B. cereus strains associated with periodontitis in humans and previously reported as the closest known strains to B. anthracis. SNP in ITS containing tRNA genes combined with RSI-PCR provide a very efficient tool for the identification of strains closely related to B. anthracis.
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76. |
Ehling-Schulz M,
Fricker M,
Grallert H,
Rieck P,
Wagner M,
Scherer S,
( 2006 ) Cereulide synthetase gene cluster from emetic Bacillus cereus: structure and location on a mega virulence plasmid related to Bacillus anthracis toxin plasmid pXO1. PMID : 16512902 : DOI : 10.1186/1471-2180-6-20 PMC : PMC1459170 Abstract >>
Cereulide, a depsipeptide structurally related to valinomycin, is responsible for the emetic type of gastrointestinal disease caused by Bacillus cereus. Recently, it has been shown that this toxin is produced by a nonribosomal peptide synthetase (NRPS), but its exact genetic organization and biochemical synthesis is unknown. The complete sequence of the cereulide synthetase (ces) gene cluster, which encodes the enzymatic machinery required for the biosynthesis of cereulide, was dissected. The 24 kb ces gene cluster comprises 7 CDSs and includes, besides the typical NRPS genes like a phosphopantetheinyl transferase and two CDSs encoding enzyme modules for the activation and incorporation of monomers in the growing peptide chain, a CDS encoding a putative hydrolase in the upstream region and an ABC transporter in the downstream part. The enzyme modules responsible for incorporation of the hydroxyl acids showed an unusual structure while the modules responsible for the activation of the amino acids Ala and Val showed the typical domain organization of NRPS. The ces gene locus is flanked by genetic regions with high homology to virulence plasmids of B. cereus, Bacillus thuringiensis and Bacillus anthracis. PFGE and Southern hybridization showed that the ces genes are restricted to emetic B. cereus and indeed located on a 208 kb megaplasmid, which has high similarities to pXO1-like plasmids. The ces gene cluster that is located on a pXO1-like virulence plasmid represents, beside the insecticidal and the anthrax toxins, a third type of B. cereus group toxins encoded on megaplasmids. The ces genes are restricted to emetic toxin producers, but pXO1-like plasmids are also present in emetic-like strains. These data might indicate the presence of an ancient plasmid in B. cereus which has acquired different virulence genes over time. Due to the unusual structure of the hydroxyl acid incorporating enzyme modules of Ces, substantial biochemical efforts will be required to dissect the complete biochemical pathway of cereulide synthesis.
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77. |
Zigha A,
Rosenfeld E,
Schmitt P,
Duport C,
( 2006 ) Anaerobic cells of Bacillus cereus F4430/73 respond to low oxidoreduction potential by metabolic readjustments and activation of enterotoxin expression. PMID : 16470372 : DOI : 10.1007/s00203-006-0090-z Abstract >>
In the present study, a food-borne pathogen strain of Bacillus cereus (F4430/73) was anaerobically grown in controlled-batch conditions under low initial oxidoreduction potential (ORP=-148 mV) using hydrogen gas as reducing agent. Its physiological characteristics, including growth, glucose fermentation capacity and enterotoxin production, were compared with anaerobic conditions generated by nitrogen gas (ORP=+ 45 mV). The results showed that low ORP affected growth mainly during the early stages. Maximal specific rates of growth and glucose consumption were reduced, and drastic changes in time profiles of fermentation product concentration were observed. Production of lactate was promoted at the expense of acetate. Nevertheless, low ORP did not affect final biomass yield. Under both ORP conditions, Non-haemolytic enterotoxin (Nhe) was produced early during the exponential growth phase as a first enterotoxin and Haemolysin BL (Hbl) later during the early stationary growth phase as a second enterotoxin. The major effect of low ORP was the strong stimulation of Hbl production and, to a lesser extent, Nhe production. This control was complex, involving different levels of regulation. We discussed the regulation of enterotoxin expression and the involvement of the pleiotropic regulator PlcR.
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78. |
Alseth I,
Rognes T,
Lindbäck T,
Solberg I,
Robertsen K,
Kristiansen KI,
Mainieri D,
Lillehagen L,
Kolstø AB,
Bjørås M,
( 2006 ) A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus, AlkC and AlkD. PMID : 16468998 : DOI : 10.1111/j.1365-2958.2006.05044.x PMC : PMC1413580 Abstract >>
Soil bacteria are heavily exposed to environmental methylating agents such as methylchloride and may have special requirements for repair of alkylation damage on DNA. We have used functional complementation of an Escherichia coli tag alkA mutant to screen for 3-methyladenine DNA glycosylase genes in genomic libraries of the soil bacterium Bacillus cereus. Three genes were recovered: alkC, alkD and alkE. The amino acid sequence of AlkE is homologous to the E. coli AlkA sequence. AlkC and AlkD represent novel proteins without sequence similarity to any protein of known function. However, iterative and indirect sequence similarity searches revealed that AlkC and AlkD are distant homologues of each other within a new protein superfamily that is ubiquitous in the prokaryotic kingdom. Homologues of AlkC and AlkD were also identified in the amoebas Entamoeba histolytica and Dictyostelium discoideum, but no other eukaryotic counterparts of the superfamily were found. The alkC and alkD genes were expressed in E. coli and the proteins were purified to homogeneity. Both proteins were found to be specific for removal of N-alkylated bases, and showed no activity on oxidized or deaminated base lesions in DNA. B. cereus AlkC and AlkD thus define novel families of alkylbase DNA glycosylases within a new protein superfamily.
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79. |
Ehling-Schulz M,
Guinebretiere MH,
Monthán A,
Berge O,
Fricker M,
Svensson B,
( 2006 ) Toxin gene profiling of enterotoxic and emetic Bacillus cereus. PMID : 16842349 : DOI : 10.1111/j.1574-6968.2006.00320.x Abstract >>
Very different toxins are responsible for the two types of gastrointestinal diseases caused by Bacillus cereus: the diarrhoeal syndrome is linked to nonhemolytic enterotoxin NHE, hemolytic enterotoxin HBL, and cytotoxin K, whereas emesis is caused by the action of the depsipeptide toxin cereulide. The recently identified cereulide synthetase genes permitted development of a molecular assay that targets all toxins known to be involved in food poisoning in a single reaction, using only four different sets of primers. The enterotoxin genes of 49 strains, belonging to different phylogenetic branches of the B. cereus group, were partially sequenced to encompass the molecular diversity of these genes. The sequence alignments illustrated the high molecular polymorphism of B. cereus enterotoxin genes, which is necessary to consider when establishing PCR systems. Primers directed towards the enterotoxin complex genes were located in different CDSs of the corresponding operons to target two toxin genes with one single set of primers. The specificity of the assay was assessed using a panel of B. cereus strains with known toxin profiles and was successfully applied to characterize strains from food and clinical diagnostic labs as well as for the toxin gene profiling of B. cereus isolated from silo tank populations.
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80. |
Psylinakis E,
Boneca IG,
Mavromatis K,
Deli A,
Hayhurst E,
Foster SJ,
Vårum KM,
Bouriotis V,
( 2005 ) Peptidoglycan N-acetylglucosamine deacetylases from Bacillus cereus, highly conserved proteins in Bacillus anthracis. PMID : 15961396 : DOI : 10.1074/jbc.M407426200 Abstract >>
The genomes of Bacillus cereus and its closest relative Bacillus anthracis contain 10 polysaccharide deacetylase homologues. Six of these homologues have been proposed to be peptidoglycan N-acetylglucosamine deacetylases. Two of these genes, namely bc1960 and bc3618, have been cloned and expressed in Escherichia coli, and the recombinant enzymes have been purified to homogeneity and further characterized. Both enzymes were effective in deacetylating cell wall peptidoglycan from the Gram(+) Bacillus cereus and Bacillus subtilis and the Gram(-) Helicobacter pylori as well as soluble chitin substrates and N-acetylchitooligomers. However, the enzymes were not active on acetylated xylan. These results provide insight into the substrate specificity of carbohydrate esterase family 4 enzymes. It was revealed that both enzymes deacetylated only the GlcNAc residue of the synthetic muropeptide N-acetyl-D-glucosamine-(beta-1,4)-N-acetylmuramyl-L-alanine-D-isoglutamine. Analysis of the constituent muropeptides of peptidoglycan from B. subtilis and H. pylori resulting from incubation of the enzymes BC1960 and BC3618 with these polymers and subsequent hydrolysis by Cellosyl and mutanolysin, respectively, similarly revealed that both enzymes deacetylate GlcNAc residues of peptidoglycan. Kinetic analysis toward GlcNAc(2-6) revealed that GlcNAc4 was the favorable substrate for both enzymes. Identification of the sequence of N-acetychitooligosaccharides (GlcNAc(2-4)) following enzymatic deacetylation by using 1H NMR revealed that both enzymes deacetylate all GlcNAc residues of the oligomers except the reducing end ones. Enzymatic deacetylation of chemically acetylated vegetative peptidoglycan from B. cereus by BC1960 and BC3618 resulted in increased resistance to lysozyme digestion. This is the first biochemical study of bacterial peptidoglycan N-acetylglucosamine deacetylases.
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81. |
Shi JS,
Wu QF,
Xu ZH,
Tao WY,
( 2005 ) [Identification of psychrotrophs SYP-A2-3 producing cold-adapted protease from the No. 1 Glacier of China and study on its fermentation conditions]. PMID : 15989272 : Abstract >>
The psychrotrophs SYP-A2-3 producing the cold-adapted protease has been isolated from the bacterial samples collected from the No. 1 Glacier of China and identified as Bacillus cereus according to its morphological and physiochemical characteristics and 16s rDNA gene sequence analysis. It could grow between 0 degree C and 38 degrees C while its optimal growth temperature was 25 degrees C and the optimal temperature for its protease production was 15 degrees C. The cold-adapted protease was identified as neutral metallo-protease, the molecular weight was 34.2 kD shown by SDS-PAGE, the optimal pH and temperature for activity was 7.0-8.5 and 42 degrees C, respectively. Various fermentation conditions of its protease production were also investigated. The results showed that casein was the best nitrogen source while glucose and starch were suitable carbon source for its protease production. The initial pH of fermentation broth ranged from 6.5 to 7.0 was optimal. Under optimized conditions, the protease activity produced by SYP-A2-3 could reach 3800 U/mL and 4800 U/mL conducted in shaking flask and 5 L stirred jar experiment, respectively.
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82. |
Oscáriz JC,
Cintas L,
Holo H,
Lasa I,
Nes IF,
Pisabarro AG,
( 2006 ) Purification and sequencing of cerein 7B, a novel bacteriocin produced by Bacillus cereus Bc7. PMID : 16451187 : DOI : 10.1111/j.1574-6968.2005.00009.x Abstract >>
Cerein 7B is a new bacteriocin produced simultaneously with cerein 7A by Bacillus cereus Bc7 in liquid brain heart infusion cultures. Both bacteriocins are not synergistic. The two peptides have been purified to homogeneity by hydrophobic interaction, cation exchange and reverse-phase liquid chromatography. They can be distinguished by their N-terminal amino acid sequences N-Gly-Trp-Gly-Asp-Val-Leu (7A) and N-Gly-Trp-Trp-Asn-Ser-Trp-Gly-Lys (7B). Pre-cerein 7B is 74 amino acids long and contains an 18 aminoacid double-glycine type leader sequence that is removed to produce the mature bacteriocin. The leader peptide sequence is related to that of sec-independent secretion signals suggesting that cerein 7B belongs to class II sec-independent bacteriocins.
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83. |
Stark W,
Pauptit RA,
Wilson KS,
Jansonius JN,
( 1992 ) The structure of neutral protease from Bacillus cereus at 0.2-nm resolution. PMID : 1633827 : DOI : 10.1111/j.1432-1033.1992.tb17109.x Abstract >>
The crystal structure of the neutral protease from Bacillus cereus has been refined to an R factor of 17.5% at 0.2-nm resolution. The enzyme, an extracellular metalloendopeptidase, consists of two domains and binds one zinc and four calcium ions. The structure is very similar to that of thermolysin, with which the enzyme shares 73% amino-acid sequence identity. The active-site cleft between the two domains is wider in neutral protease than in thermolysin. This suggests the presence of a flexible hinge region between the two domains, which may assist enzyme action. The high-resolution analysis allows detailed examination of possible causes for the difference in thermostability between neutral protease and thermolysin.
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84. |
Bailey-Smith K,
Todd SJ,
Southworth TW,
Proctor J,
Moir A,
( 2005 ) The ExsA protein of Bacillus cereus is required for assembly of coat and exosporium onto the spore surface. PMID : 15901704 : DOI : 10.1128/JB.187.11.3800-3806.2005 PMC : PMC1112046 Abstract >>
The outermost layer of spores of the Bacillus cereus family is a loose structure known as the exosporium. Spores of a library of Tn917-LTV1 transposon insertion mutants of B. cereus ATCC 10876 were partitioned into hexadecane; a less hydrophobic mutant that was isolated contained an insertion in the exsA promoter region. ExsA is the equivalent of SafA (YrbA) of Bacillus subtilis, which is also implicated in spore coat assembly; the gene organizations around both are identical, and both proteins contain a very conserved N-terminal cortex-binding domain of ca. 50 residues, although the rest of the sequence is much less conserved. In particular, unlike SafA, the ExsA protein contains multiple tandem oligopeptide repeats and is therefore likely to have an extended structure. The exsA gene is expressed in the mother cell during sporulation. Spores of an exsA mutant are extremely permeable to lysozyme and are blocked in late stages of germination, which require coat-associated functions. Two mutants expressing differently truncated versions of ExsA were constructed, and they showed the same gross defects in the attachment of exosporium and spore coat layers. The protein profile of the residual exosporium harvested from spores of the three mutants--two expressing truncated proteins and the mutant with the original transposon insertion in the promoter region--showed some differences from the wild type and from each other, but the major exosporium glycoproteins were retained. The exsA gene is extremely important for the normal assembly and anchoring of both the spore coat and exosporium layers in spores of B. cereus.
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85. |
Hosaka T,
Ui S,
Ohtsuki T,
Mimura A,
Ohkuma M,
Kudo T,
( 2001 ) Characterization of the NADH-linked acetylacetoin reductase/2,3-butanediol dehydrogenase gene from Bacillus cereus YUF-4. PMID : 16233036 : Abstract >>
A 1.4-kbp DNA fragment, including the NADH-linked acetylacetoin reductase/2,3-butanediol dehydrogenase (AACRII/BDH) gene from the chromosomal DNA of Bacillus cereus YUF-4, was cloned in Escherichia coli DH5alpha after its insertion into pUC119, and the resulting plasmid was named pAACRII119. The AACRII/BDH gene had an open reading frame consisting of 1047 bp encoding 349 amino acids. The enzyme exhibited not only AACR activity, but also BDH activity. However, the gene was not located in a 2,3-butanediol (BD) operon, as is the case in the BDH gene of Klebsiella pneumoniae and that of K. terrigena. In addition, there was no BD-cycle-related enzyme gene in the region surrounding the AACRII/BDH gene. The AACR and BDH activities in E. coli DH5alpha/pAACRII119 were 200-fold higher than those in the original B. cereus YUF-4. The characteristics of the AACRII/BDH from E. coli DH 5alpha/pAACRII119 are similar to those of the AACRII/BDH from B. cereus YUF-4. The AACRII/BDH was considered to belong to the NAD(P)- and zinc-dependent long-chain alcohol dehydrogenase (group I ADH) family on the basis of the following distinctive characteristics: it possessed 14 strictly conserved residues of microbial group I ADH and consisted of about 350 amino acids. The enzymatic and genetic characteristics of AACRII/BDH were completely different from those of BDHs belonging to the short-chain dehydrogenase/reductase family. These findings indicated that the AACRII/BDH could be considered a new type of BDH.
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86. |
Davison S,
Couture-Tosi E,
Candela T,
Mock M,
Fouet A,
( 2005 ) Identification of the Bacillus anthracis (gamma) phage receptor. PMID : 16166537 : DOI : 10.1128/JB.187.19.6742-6749.2005 PMC : PMC1251577 Abstract >>
Bacillus anthracis, a gram-positive, spore-forming bacterium, is the etiological agent of anthrax. It belongs to the Bacillus cereus group, which also contains Bacillus cereus and Bacillus thuringiensis. Most B. anthracis strains are sensitive to phage gamma, but most B. cereus and B. thuringiensis strains are resistant to the lytic action of phage gamma. Here, we report the identification of a protein involved in the bacterial receptor for the gamma phage, which we term GamR (Gamma phage receptor). It is an LPXTG protein (BA3367, BAS3121) and is anchored by the sortase A. A B. anthracis sortase A mutant is not as sensitive as the parental strain nor as the sortase B and sortase C mutants, whereas the GamR mutant is resistant to the lytic action of the phage. Electron microscopy reveals the binding of the phage to the surface of the parental strain and its absence from the GamR mutant. Spontaneous B. anthracis mutants resistant to the phage harbor mutations in the gene encoding the GamR protein. A B. cereus strain that is sensitive to the phage possesses a protein similar (89% identity) to GamR. B. thuringiensis 97-27, a strain which, by sequence analysis, is predicted to harbor a GamR-like protein, is resistant to the phage but nevertheless displays phage binding.
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87. |
Easterday WR,
Van Ert MN,
Simonson TS,
Wagner DM,
Kenefic LJ,
Allender CJ,
Keim P,
( 2005 ) Use of single nucleotide polymorphisms in the plcR gene for specific identification of Bacillus anthracis. PMID : 15815042 : DOI : 10.1128/JCM.43.4.1995-1997.2005 PMC : PMC1081367 Abstract >>
A TaqMan-minor groove binding assay designed around a nonsense mutation in the plcR gene was used to genotype Bacillus anthracis, B. cereus, and B. thuringiensis isolates. The assay differentiated B. anthracis from these genetic near-neighbors and determined that the nonsense mutation is ubiquitous across 89 globally and genetically diverse B. anthracis strains.
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88. |
Olsen DB,
Hepburn TW,
Lee SL,
Martin BM,
Mariano PS,
Dunaway-Mariano D,
( 1992 ) Investigation of the substrate binding and catalytic groups of the P-C bond cleaving enzyme, phosphonoacetaldehyde hydrolase. PMID : 1605625 : DOI : 10.1016/0003-9861(92)90556-c Abstract >>
Kinetic studies with substrate analogs and group-directed chemical modification agents were carried out for the purpose of identifying the enzyme-substrate interactions required for phosphonoacetaldehyde (P-Ald) binding and catalyzed hydrolysis by P-Ald hydrolase (phosphonatase). Malonic semialdehyde (Ki = 1.6 mM), phosphonoacetate (Ki = 10 mM), phosphonoethanol (Ki = 10 mM), and fluorophosphate (Ki = 20 mM) were found to be competitive inhibitors of the enzyme but not substrates. Thiophosphonoacetaldehyde and acetonyl phosphonate underwent phosphonatase-catalyzed hydrolysis but at 20-fold and 140-fold slower rates, respectively, than did P-Ald. In the presence of NaBH4, acetonyl-phosphonate inactivated phosphonatase at a rate exceeding that of its turnover. Sequence analysis of the radiolabeled tryptic peptide generated from [3-3H]acetonylphosphonate/NaBH4-treated phosphonatase revealed that Schiff base formation had occurred with the catalytic lysine. From the Vm/Km and Vm pH profiles for phosphonatase-catalyzed P-Ald hydrolysis, an optimal pH range of 6-8 was defined for substrate binding and catalysis. The pH dependence of inactivation by acetylation of the active site lysine with acetic anhydride and 2,4-dinitrophenyl acetate evidenced protonation of the active site lysine residue as the cause for activity loss below pH 6. The pH dependence of inactivation of an active site cysteine residue with methyl methanethiol-sulfonate indicated that deprotonation of this residue may be the cause for the loss of enzyme activity above pH 8.
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89. |
Liu G,
Shen Y,
Atreya HS,
Parish D,
Shao Y,
Sukumaran DK,
Xiao R,
Yee A,
Lemak A,
Bhattacharya A,
Acton TA,
Arrowsmith CH,
Montelione GT,
Szyperski T,
( 2005 ) NMR data collection and analysis protocol for high-throughput protein structure determination. PMID : 16027363 : DOI : 10.1073/pnas.0504338102 PMC : PMC1180791 Abstract >>
A standardized protocol enabling rapid NMR data collection for high-quality protein structure determination is presented that allows one to capitalize on high spectrometer sensitivity: a set of five G-matrix Fourier transform NMR experiments for resonance assignment based on highly resolved 4D and 5D spectral information is acquired in conjunction with a single simultaneous 3D 15N,13C(aliphatic),13C(aromatic)-resolved [1H,1H]-NOESY spectrum providing 1H-1H upper distance limit constraints. The protocol was integrated with methodology for semiautomated data analysis and used to solve eight NMR protein structures of the Northeast Structural Genomics Consortium pipeline. The molecular masses of the hypothetical target proteins ranged from 9 to 20 kDa with an average of approximately 14 kDa. Between 1 and 9 days of instrument time were invested per structure, which is less than approximately 10-25% of the measurement time routinely required to date with conventional approaches. The protocol presented here effectively removes data collection as a bottleneck for high-throughput solution structure determination of proteins up to at least approximately 20 kDa, while concurrently providing spectra that are highly amenable to fast and robust analysis.
|
90. |
Slamti L,
Lereclus D,
( 2005 ) Specificity and polymorphism of the PlcR-PapR quorum-sensing system in the Bacillus cereus group. PMID : 15659693 : DOI : 10.1128/JB.187.3.1182-1187.2005 PMC : PMC545710 Abstract >>
The expression of extracellular virulence factors in various species of the Bacillus cereus group is controlled by the plcR and papR genes, which encode a transcriptional regulator and a cell-cell signaling peptide, respectively. A processed form of PapR, presumably a pentapeptide, specifically interacts with PlcR to facilitate its binding to its DNA targets. This activating mechanism is strain specific, with this specificity being determined by the first residue of the pentapeptide. We carried out in vivo complementation assays and compared the PlcR-PapR sequences of 29 strains from the B. cereus group. Our findings suggested that the fifth amino acid of the pentapeptide is also involved in the specificity of activation. We identified four classes of PlcR-PapR pairs, defining four distinct pherotypes in the B. cereus group. We used these findings to look at the evolution of the PlcR-PapR quorum-sensing system with regard to the phylogeny of the species forming the B. cereus group.
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91. |
Ehling-Schulz M,
Vukov N,
Schulz A,
Shaheen R,
Andersson M,
Märtlbauer E,
Scherer S,
( 2005 ) Identification and partial characterization of the nonribosomal peptide synthetase gene responsible for cereulide production in emetic Bacillus cereus. PMID : 15640177 : DOI : 10.1128/AEM.71.1.105-113.2005 PMC : PMC544239 Abstract >>
Cereulide, a depsipeptide structurally related to valinomycin, is responsible for the emetic type of gastrointestinal disease caused by Bacillus cereus. Due to its chemical structure, (D-O-Leu-D-Ala-L-O-Val-L-Val)(3), cereulide might be synthesized nonribosomally. Therefore, degenerate PCR primers targeted to conserved sequence motifs of known nonribosomal peptide synthetase (NRPS) genes were used to amplify gene fragments from a cereulide-producing B. cereus strain. Sequence analysis of one of the amplicons revealed a DNA fragment whose putative gene product showed significant homology to valine activation NRPS modules. The sequences of the flanking regions of this DNA fragment revealed a complete module that is predicted to activate valine, as well as a putative carboxyl-terminal thioesterase domain of the NRPS gene. Disruption of the peptide synthetase gene by insertion of a kanamycin cassette through homologous recombination produced cereulide-deficient mutants. The valine-activating module was highly conserved when sequences from nine emetic B. cereus strains isolated from diverse geographical locations were compared. Primers were designed based on the NRPS sequence, and the resulting PCR assay, targeting the ces gene, was tested by using a panel of 143 B. cereus group strains and 40 strains of other bacterial species showing PCR bands specific for only the cereulide-producing B. cereus strains.
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92. |
Ehling-Schulz M,
Svensson B,
Guinebretiere MH,
Lindbäck T,
Andersson M,
Schulz A,
Fricker M,
Christiansson A,
Granum PE,
Märtlbauer E,
Nguyen-The C,
Salkinoja-Salonen M,
Scherer S,
( 2005 ) Emetic toxin formation of Bacillus cereus is restricted to a single evolutionary lineage of closely related strains. PMID : 15632437 : DOI : 10.1099/mic.0.27607-0 Abstract >>
An in-depth polyphasic approach was applied to study the population structure of the human pathogen Bacillus cereus. To assess the intraspecific biodiversity of this species, which is the causative agent of gastrointestinal diseases, a total of 90 isolates from diverse geographical origin were studied by genetic [M13-PCR, random amplification of polymorphic DNA (RAPD), multilocus sequence typing (MLST)] and phenetic [Fourier transform Infrared (FTIR), protein profiling, biochemical assays] methods. The strain set included clinical strains, isolates from food remnants connected to outbreaks, as well as isolates from diverse food environments with a well documented strain history. The phenotypic and genotypic analysis of the compiled panel of strains illustrated a considerable diversity among B. cereus connected to diarrhoeal syndrome and other non-emetic food strains, but a very low diversity among emetic isolates. Using all typing methods, cluster analysis revealed a single, distinct cluster of emetic B. cereus strains. The isolates belonging to this cluster were neither able to degrade starch nor could they ferment salicin; they did not possess the genes encoding haemolysin BL (Hbl) and showed only weak or no haemolysis. In contrast, haemolytic-enterotoxin-producing B. cereus strains showed a high degree of heterogeneity and were scattered over different clusters when different typing methods were applied. These data provide evidence for a clonal population structure of cereulide-producing emetic B. cereus and indicate that emetic strains represent a highly clonal complex within a potentially panmictic or weakly clonal background population structure of the species. It may have originated only recently through acquisition of specific virulence factors such as the cereulide synthetase gene.
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93. |
Huang CJ,
Chen CY,
( 2005 ) High-level expression and characterization of two chitinases, ChiCH and ChiCW, of Bacillus cereus 28-9 in Escherichia coli. PMID : 15629422 : DOI : 10.1016/j.bbrc.2004.11.140 Abstract >>
Many chitinase genes have been cloned and sequenced from prokaryotes and eukaryotes but overexpression of chitinases in Escherichia coli cells was less reported. ChiCH and ChiCW of Bacillus cereus 28-9 belong to two distinct groups based on their amino acid sequences of catalytic domains, and in addition, domain structures of two enzymes are different. In this study, we established an ideal method for high-level expression of chitinases in E. coli as glutathione-S-transferase fusion proteins using pGEX-6P-1 vector. Both ChiCH and ChiCW were successfully highly expressed in E. coli cells as soluble GST-chitinase fusion proteins, and recombinant native ChiCH and ChiCW could be purified after cleavage with PreScission protease to remove GST tag. Purified chitinases were used for biochemical characterization of kinetics, hydrolysis products, and binding activities. The results indicate that ChiCW is an endo-chitinase and effectively hydrolyzes chitin and chito-multimers to chito-oligomers and the end product chitobiose, and ChiCH is an exo-chitinase and degrades chito-oligomers to produce chitobiose. Furthermore, due to higher affinity of ChiCW toward colloidal chitin than Avicel, C-terminal domain of ChiCW should be classified as a chitin-binding domain not a cellulose-binding domain although that was revealed as a cellulose-binding domain by conserved domain analysis. Therefore, the method of high-level expression of chitinases is helpful to studies and applications of chitinases.
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94. |
Shi X,
Rao NN,
Kornberg A,
( 2004 ) Inorganic polyphosphate in Bacillus cereus: motility, biofilm formation, and sporulation. PMID : 15572452 : DOI : 10.1073/pnas.0407787101 PMC : PMC535361 Abstract >>
Chains of inorganic polyphosphate (poly-P) with hundreds of P(i) residues linked by phosphoanhydride bonds, as in ATP, are found in every bacterial, fungal, plant, and animal cell, in which they perform various functions. In the spore-forming Bacillus cereus, we have identified three principal enzymes and genes involved in the metabolism of poly-P, namely, (i) poly-P kinase (PPK), which synthesizes poly-P reversibly from ATP, (ii) exopolyphosphatase (PPX), which hydrolyzes poly-P to P(i), and (iii) poly-P/AMP phosphotransferase (PAP), which uses poly-P as a donor to convert AMP to ADP, reversibly. In the null mutant of ppk, poly-P levels are reduced to <5% of the WT; in the ppx mutant, the PPK activity is elevated 10-fold, and the accumulation of poly-P is elevated approximately 1,000-fold. All of the null mutants of ppk, ppx, and pap showed defects in motility and biofilm formation, but sporulation efficiency was impaired only in the ppx mutant. These enzymes and genes in B. cereus are nearly identical to those in the very closely related pathogen Bacillus anthracis, and, thus, they may provide attractive targets for the treatment of anthrax.
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95. |
Priest FG,
Barker M,
Baillie LW,
Holmes EC,
Maiden MC,
( 2004 ) Population structure and evolution of the Bacillus cereus group. PMID : 15547268 : DOI : 10.1128/JB.186.23.7959-7970.2004 PMC : PMC529064 Abstract >>
Representative strains of the Bacillus cereus group of bacteria, including Bacillus anthracis (11 isolates), B. cereus (38 isolates), Bacillus mycoides (1 isolate), Bacillus thuringiensis (53 isolates from 17 serovars), and Bacillus weihenstephanensis (2 isolates) were assigned to 59 sequence types (STs) derived from the nucleotide sequences of seven alleles, glpF, gmk, ilvD, pta, pur, pycA, and tpi. Comparisons of the maximum likelihood (ML) tree of the concatenated sequences with individual gene trees showed more congruence than expected by chance, indicating a generally clonal structure to the population. The STs followed two major lines of descent. Clade 1 comprised B. anthracis strains, numerous B. cereus strains, and rare B. thuringiensis strains, while clade 2 included the majority of the B. thuringiensis strains together with some B. cereus strains. Other species were allocated to a third, heterogeneous clade. The ML trees and split decomposition analysis were used to assign STs to eight lineages within clades 1 and 2. These lineages were defined by bootstrap analysis and by a preponderance of fixed differences over shared polymorphisms among the STs. Lineages were named with reference to existing designations: Anthracis, Cereus I, Cereus II, Cereus III, Kurstaki, Sotto, Thuringiensis, and Tolworthi. Strains from some B. thuringiensis serovars were wholly or largely assigned to a single ST, for example, serovar aizawai isolates were assigned to ST-15, serovar kenyae isolates were assigned to ST-13, and serovar tolworthi isolates were assigned to ST-23, while other serovars, such as serovar canadensis, were genetically heterogeneous. We suggest a revision of the nomenclature in which the lineage and clone are recognized through name and ST designations in accordance with the clonal structure of the population.
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96. |
Hirata A,
Adachi M,
Utsumi S,
Mikami B,
( 2004 ) Engineering of the pH optimum of Bacillus cereus beta-amylase: conversion of the pH optimum from a bacterial type to a higher-plant type. PMID : 15449941 : DOI : 10.1021/bi049173h Abstract >>
The optimum pH of Bacillus cereus beta-amylase (BCB, pH 6.7) differs from that of soybean beta-amylase (SBA, pH 5.4) due to the substitution of a few amino acid residues near the catalytic base residue (Glu 380 in SBA and Glu 367 in BCB). To explore the mechanism for controlling the optimum pH of beta-amylase, five mutants of BCB (Y164E, Y164F, Y164H, Y164Q, and Y164Q/T47M/Y164E/T328N) were constructed and characterized with respect to enzymatic properties and X-ray structural crystal analysis. The optimum pH of the four single mutants shifted to 4.2-4.8, approximately 2 pH units and approximately 1 pH unit lower than those of BCB and SBA, respectively, and their k(cat) values decreased to 41-3% of that of the wild-type enzyme. The X-ray crystal analysis of the enzyme-maltose complexes showed that Glu 367 of the wild type is surrounded by two water molecules (W1 and W2) that are not found in SBA. W1 is hydrogen-bonded to both side chains of Glu 367 and Tyr 164. The mutation of Tyr 164 to Glu and Phe resulted in the disruption of the hydrogen bond between Tyr 164 Oeta and W1 and the introduction of two additional water molecules near position 164. In contrast, the triple mutant of BCB with a slightly decreased pH optimum at pH 6.0 has no water molecules (W1 and W2) around Glu 367. These results suggested that a water-mediated hydrogen bond network (Glu 367...W1...Tyr 164...Thr 328) is the primary requisite for the increased pH optimum of wild-type BCB. This strategy is completely different from that of SBA, in which a hydrogen bond network (Glu 380...Thr 340...Glu 178) reduces the optimum pH in a hydrophobic environment.
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97. |
Fagerlund A,
Ween O,
Lund T,
Hardy SP,
Granum PE,
( 2004 ) Genetic and functional analysis of the cytK family of genes in Bacillus cereus. PMID : 15289565 : DOI : 10.1099/mic.0.26975-0 Abstract >>
CytK is a pore-forming toxin of Bacillus cereus that has been linked to a case of necrotic enteritis. PCR products of the expected size were generated with cytK primers in 13 of 29 strains. Six strains were PCR-positive for the related gene hly-II, which encodes haemolysin II, a protein that is 37 % identical to the original CytK. Five of the strains were positive for both genes. The DNA sequences of putative cytK genes from three positive strains were determined, and the deduced amino acid sequences were 89 % identical to that of the original CytK. The authors have designated this new cytK variant cytK-2, and refer to the original cytK as cytK-1. The CytK-2 proteins from these three strains were isolated, and their identity was verified by N-terminal sequencing. blast analysis using the cytK-2 gene sequences revealed very high homology with two cytK-2 sequences in the genomes of B. cereus strains ATCC 14579 and ATCC 10987. The differences between CytK-1 and the CytK-2 proteins were clustered to certain regions of the proteins. The isolated CytK-2 proteins were haemolytic and toxic towards human intestinal Caco-2 cells and Vero cells, although their toxicity was about 20 % of that of CytK-1. Both native and recombinant CytK-2 proteins from B. cereus 1230-88 were able to form pores in planar lipid bilayers, but the majority of the channels observed were of lower conductance than those created by CytK-1. It is likely that CytK-2 toxins contribute to the enterotoxicity of several strains of B. cereus, although not all of the CytK-2 toxins may be as harmful as the CytK-1 originally isolated.
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98. |
Lister SA,
Wetmore DR,
Roche RS,
Codding PW,
( 1996 ) E144S active-site mutant of the Bacillus cereus thermolysin-like neutral protease at 2.8 A resolution. PMID : 15299677 : DOI : 10.1107/S0907444995016684 Abstract >>
The X-ray crystal structure of the Bacillus cereus neutral protease (CNP) active-site mutant E144S, in which the putative general base proposed for the thermolysin-like zinc neutral proteases, Glu144, has been replaced by serine, has been determined to a resolution of 2.8 A. This represents the first crystal structure of an active-site mutant of a zinc neutral protease. The E 144S mutant was crystallized in the hexagonal space group, P6(5)22, with unit-cell dimensions a = b = 76.57, c = 201.91 A. Although the ligands involved in zinc coordination in the active site are identical to those found in the wild-type protein, the mutation results in a modified environment around the zinc ion; particularly with respect to the water molecules. While the structure of the mutant is similar to that of wild type, its protease activity is reduced to 0.16% that of the wild-type CNP and the protein is virtually resistant to autolysis in the presence of calcium. The lowered protease activity of the mutant is consistent with the role proposed for Glu144 as the general base in the catalysis of thermolysin-like neutral proteases [Matthews (1988). Acc. Chem. Res. 21, 333-340]. We suggest that the residual activity of the E144S mutant arises from a water molecule, which is found within hydrogen-bonding distance of Ser144, acting as a general base in the catalytic function of the mutant.
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99. |
Ko KS,
Kim JW,
Kim JM,
Kim W,
Chung SI,
Kim IJ,
Kook YH,
( 2004 ) Population structure of the Bacillus cereus group as determined by sequence analysis of six housekeeping genes and the plcR Gene. PMID : 15322020 : DOI : 10.1128/IAI.72.9.5253-5261.2004 PMC : PMC517475 Abstract >>
The population structure of the Bacillus cereus group (52 strains of B. anthracis, B. cereus, and B. thuringiensis) was investigated by sequencing seven gene fragments (rpoB, gyrB, pycA, mdh, mbl, mutS, and plcR). Most of the strains were classifiable into two large subgroups in six housekeeping gene trees but not in the plcR tree. In addition, several consistent clusters were identified, which were unrelated to species distinction. Moreover, interrelationships among these clusters were incongruent in each gene tree. The incongruence length difference test and split decomposition analyses also showed incongruences between genes, suggesting horizontal gene transfer. The plcR gene was observed to have characteristics that differed from those of the other genes in terms of phylogenetic topology and pattern of sequence diversity. Thus, we suggest that the evolutionary history of the PlcR regulon differs from those of the other chromosomal genes and that recombination of the plcR gene may be frequent. The homogeneity of B. anthracis, which is depicted as an independent lineage in phylogenetic trees, is suggested to be of recent origin or to be due to the narrow taxonomic definition of species.
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100. |
Slamti L,
Perchat S,
Gominet M,
Vilas-Bôas G,
Fouet A,
Mock M,
Sanchis V,
Chaufaux J,
Gohar M,
Lereclus D,
( 2004 ) Distinct mutations in PlcR explain why some strains of the Bacillus cereus group are nonhemolytic. PMID : 15150241 : DOI : 10.1128/JB.186.11.3531-3538.2004 PMC : PMC415780 Abstract >>
Bacillus thuringiensis, Bacillus cereus, and Bacillus anthracis are closely related species belonging to the Bacillus cereus group. B. thuringiensis and B. cereus generally produce extracellular proteins, including phospholipases and hemolysins. Transcription of the genes encoding these factors is controlled by the pleiotropic regulator PlcR. Disruption of plcR in B. cereus and B. thuringiensis drastically reduces the hemolytic, lecithinase, and cytotoxic properties of these organisms. B. anthracis does not produce these proteins due to a nonsense mutation in the plcR gene. We screened 400 B. thuringiensis and B. cereus strains for their hemolytic and lecithinase properties. Eight Hly- Lec- strains were selected and analyzed to determine whether this unusual phenotype was due to a mutation similar to that found in B. anthracis. Sequence analysis of the DNA region including the plcR and papR genes of these strains and genetic complementation of the strains with functional copies of plcR and papR indicated that different types of mutations were responsible for these phenotypes. We also found that the plcR genes of three B. anthracis strains belonging to different phylogenetic groups contained the same nonsense mutation, suggesting that this mutation is a distinctive trait of this species.
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101. |
Hoffmaster AR,
Ravel J,
Rasko DA,
Chapman GD,
Chute MD,
Marston CK,
De BK,
Sacchi CT,
Fitzgerald C,
Mayer LW,
Maiden MC,
Priest FG,
Barker M,
Jiang L,
Cer RZ,
Rilstone J,
Peterson SN,
Weyant RS,
Galloway DR,
Read TD,
Popovic T,
Fraser CM,
( 2004 ) Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. PMID : 15155910 : DOI : 10.1073/pnas.0402414101 PMC : PMC420414 Abstract >>
Bacillus anthracis is the etiologic agent of anthrax, an acute fatal disease among mammals. It was thought to differ from Bacillus cereus, an opportunistic pathogen and cause of food poisoning, by the presence of plasmids pXO1 and pXO2, which encode the lethal toxin complex and the poly-gamma-d-glutamic acid capsule, respectively. This work describes a non-B. anthracis isolate that possesses the anthrax toxin genes and is capable of causing a severe inhalation anthrax-like illness. Although initial phenotypic and 16S rRNA analysis identified this isolate as B. cereus, the rapid generation and analysis of a high-coverage draft genome sequence revealed the presence of a circular plasmid, named pBCXO1, with 99.6% similarity with the B. anthracis toxin-encoding plasmid, pXO1. Although homologues of the pXO2 encoded capsule genes were not found, a polysaccharide capsule cluster is encoded on a second, previously unidentified plasmid, pBC218. A/J mice challenged with B. cereus G9241 confirmed the virulence of this strain. These findings represent an example of how genomics could rapidly assist public health experts responding not only to clearly identified select agents but also to novel agents with similar pathogenic potentials. In this study, we combined a public health approach with genome analysis to provide insight into the correlation of phenotypic characteristics and their genetic basis.
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102. |
Horwood PF,
Burgess GW,
Oakey HJ,
( 2004 ) Evidence for non-ribosomal peptide synthetase production of cereulide (the emetic toxin) in Bacillus cereus. PMID : 15251214 : DOI : 10.1016/j.femsle.2004.06.004 Abstract >>
Little is known about the process whereby the emetic toxin (or cereulide) of Bacillus cereus is produced. Two cereulide-producing strains of B. cereus were cloned and sequenced following polymerase chain reaction (PCR) amplification with primers that were specific for conserved regions of non-ribosomal peptide synthetase (NRPS) genes. The cloned regions of the B. cereus strains were highly homologous to conserved regions of other peptide synthetase nucleotide sequences. Primers were designed for two variable regions of the NRPS gene sequence to ensure specificity for the emetic strains. A total of 86 B. cereus strains of known emetic or non-emetic activity were screened using these primers. All of the emetic strains (n=30) displayed a 188 bp band following amplification and gel electrophoresis. We have developed an improved method of identifying emetic strains of B. cereus and provided evidence that cereulide is produced by peptide synthetases.
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103. |
Zhang G,
Morais MC,
Dai J,
Zhang W,
Dunaway-Mariano D,
Allen KN,
( 2004 ) Investigation of metal ion binding in phosphonoacetaldehyde hydrolase identifies sequence markers for metal-activated enzymes of the HAD enzyme superfamily. PMID : 15109258 : DOI : 10.1021/bi036309n Abstract >>
The 2-haloalkanoic acid dehalogenase (HAD) family, which contains both carbon and phosphoryl transferases, is one of the largest known enzyme superfamilies. HAD members conserve an alpha,beta-core domain that frames the four-loop active-site platform. Each loop contributes one or more catalytic groups, which function in mediating the core chemistry (i.e., group transfer). In this paper, we provide evidence that the number of carboxylate residues on loop 4 and their positions (stations) on the loop are determinants, and therefore reliable sequence markers, for metal ion activation among HAD family members. Using this predictor, we conclude that the vast majority of the HAD members utilize a metal cofactor. Analysis of the minimum requirements for metal cofactor binding was carried out using Mg(II)-activated Bacillus cereus phosphonoacetaldehyde hydrolase (phosphonatase) as an experimental model for metal-activated HAD members. Mg(II) binding occurs via ligation to the loop 1 Asp12 carboxylate and Thr14 backbone carbonyl and to the loop 4 Asp186 carboxylate. The loop 4 Asp190 forms a hydrogen bond to the Mg(II) water ligand. X-ray structure determination of the D12A mutant in the presence of the substrate phosphonoacetaldehyde showed that replacement of the loop 1 Asp, common to all HAD family members, with Ala shifts the position of Mg(II), thereby allowing innersphere coordination to Asp190 and causing a shift in the position of the substrate. Kinetic analysis of the loop 4 mutants showed that Asp186 is essential to cofactor binding while Asp190 simply enhances it. Within the phosphonatase subfamily, Asp186 is stringently conserved, while either position 185 or position 190 is used to position the second loop 4 Asp residue. Retention of a high level of catalytic activity in the G185D/D190G phosphonatase mutant demonstrated the plasticity of the metal binding loop, reflected in the variety of combinations in positioning of two or three Asp residues along the seven-residue motif of the 2700 potential HAD sequences that were examined.
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104. |
De Palmenaer D,
Vermeiren C,
Mahillon J,
( 2004 ) IS231-MIC231 elements from Bacillus cereus sensu lato are modular. PMID : 15228527 : DOI : 10.1111/j.1365-2958.2004.04146.x Abstract >>
Summary IS231A was originally discovered in Bacillus thuringiensis as a typical 1.6 kb insertion sequence (IS) displaying 20 bp inverted repeats (IR) flanking a transposase gene. A first major variation of this canonical organization was found in MIC231A1. This mobile insertion cassette (MIC), delineated by IS231A-related extremities, contained an active d-stereospecific endopeptidase (adp) gene instead of a transposase. Interestingly, it was shown that MIC231A1 can be mobilized in trans by the IS231A transposase. In this paper, we show that this family of IS231-MIC231 elements can be extended to a broad range of related entities displaying higher levels of structural complexity. Several IS231A-like elements contained, upstream of their transposase gene, passenger genes coding for putative antibiotic resistances or regulatory factors. Furthermore, the diversity of the MIC231 elements ranged from empty cassettes to structures carrying up to three passenger genes. Among these, MIC231V carried, in addition to an adp gene, an active fosfomycin resistance determinant. In vivo transposition assays showed that MIC231V is also trans-activated by the IS231A transposase. These results lend further support to the potential contribution of these modular mobile elements to the genome plasticity of the Bacillus cereus/B. thuringiensis group.
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105. |
Candelon B,
Guilloux K,
Ehrlich SD,
Sorokin A,
( 2004 ) Two distinct types of rRNA operons in the Bacillus cereus group. PMID : 14993309 : DOI : 10.1099/mic.0.26870-0 Abstract >>
The Bacillus cereus group includes insecticidal bacteria (B. thuringiensis), food-borne pathogens (B. cereus and B. weihenstephanensis) and B. anthracis, the causative agent of anthrax. The precise number of rRNA operons in 12 strains of the B. cereus group was determined. Most of the tested strains possess 13 operons and the tested psychrotolerant strains contain 14 operons, the highest number ever found in bacteria. The separate clustering of the tested psychrotolerant strains was confirmed by partial sequencing of several genes distributed over the chromosomes. Analysis of regions downstream of the 23S rRNA genes in the type strain B. cereus ATCC 14579 indicates that the rRNA operons can be divided into two classes, I and II, consisting respectively of eight and five operons. Class II operons exhibit multiple tRNA genes downstream of the 5S rRNA gene and a putative promoter sequence in the 23S-5S intergenic region, suggesting that 5S rRNA and the downstream tRNA genes can be transcribed independently of the 16S and 23S genes. Similar observations were made in the recently sequenced genome of B. anthracis strain Ames. The existence of these distinct types of rRNA operons suggests an unknown mechanism for regulation of rRNA and tRNA synthesis potentially related to the pool of amino acids available for protein synthesis.
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106. |
Wetmore DR,
Wong SL,
Roche RS,
( 1992 ) The role of the pro-sequence in the processing and secretion of the thermolysin-like neutral protease from Bacillus cereus. PMID : 1495388 : DOI : 10.1111/j.1365-2958.1992.tb00884.x Abstract >>
The Bacillus cereus cnp gene coding for the thermolysin-like neutral protease (TNP) has been cloned, sequenced, and expressed in Bacillus subtilis. The protease is first produced as a pre-pro-protein (M(r) = 61,000); the pro-peptide is approximately two-thirds of the size of the mature protein. The pro-sequence has been compared with those of six other TNPs, and significant homologies have been found. Additionally, the TNP pro-sequences are shown to be homologous to the pro-sequence of Pseudomonas aeruginosa elastase. A mutant has been constructed from cnp, in which 23 amino acids upstream from the pro-protein processing site have been deleted. This region has no homologous analogue in any of the other TNP pro-sequences. The deletion results in a delay of six to eight hours in detection of active protease in the growth medium, as well as a 75% decrease in maximum protease production. N-terminal analysis of the mutant mature protein demonstrates that the processing site is unaltered by the pro-sequence deletion. The deletion must, therefore, modulate the kinetics of processing and/or secretion of the pro-protein.
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107. |
Lahiri SD,
Zhang G,
Dai J,
Dunaway-Mariano D,
Allen KN,
( 2004 ) Analysis of the substrate specificity loop of the HAD superfamily cap domain. PMID : 15005616 : DOI : 10.1021/bi0356810 Abstract >>
The haloacid dehalogenase (HAD) superfamily includes a variety of enzymes that catalyze the cleavage of substrate C-Cl, P-C, and P-OP bonds via nucleophilic substitution pathways. All members possess the alpha/beta core domain, and many also possess a small cap domain. The active site of the core domain is formed by four loops (corresponding to sequence motifs 1-4), which position substrate and cofactor-binding residues as well as the catalytic groups that mediate the "core" chemistry. The cap domain is responsible for the diversification of chemistry within the family. A tight beta-turn in the helix-loop-helix motif of the cap domain contains a stringently conserved Gly (within sequence motif 5), flanked by residues whose side chains contribute to the catalytic site formed at the domain-domain interface. To define the role of the conserved Gly in the structure and function of the cap domain loop of the HAD superfamily members phosphonoacetaldehyde hydrolase and beta-phosphoglucomutase, the Gly was mutated to Pro, Val, or Ala. The catalytic activity was severely reduced in each mutant. To examine the impact of Gly substitution on loop 5 conformation, the X-ray crystal structure of the Gly50Pro phosphonoacetaldehyde hydrolase mutant was determined. The altered backbone conformation at position 50 had a dramatic effect on the spatial disposition of the side chains of neighboring residues. Lys53, the Schiff Base forming lysine, had rotated out of the catalytic site and the side chain of Leu52 had moved to fill its place. On the basis of these studies, it was concluded that the flexibility afforded by the conserved Gly is critical to the function of loop 5 and that it is a marker by which the cap domain substrate specificity loop can be identified within the amino acid sequence of HAD family members.
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108. |
Nishiwaki H,
Ito K,
Otsuki K,
Yamamoto H,
Komai K,
Matsuda K,
( 2004 ) Purification and functional characterization of insecticidal sphingomyelinase C produced by Bacillus cereus. PMID : 14728687 : DOI : 10.1111/j.1432-1033.2003.03962.x Abstract >>
Bacillus cereus isolated from the larvae of Myrmeleon bore was found to secrete proteins that paralyze and kill German cockroaches, Blattela germanica, when injected. One of these active proteins was purified from the culture broth of B. cereus using anion-exchange and gel-filtration chromatography. The purified toxin, with a molecular mass of 34 kDa, was identified as sphingomyelinase C (EC 3.1.4.12) on the basis of its N-terminal and internal amino-acid sequences. A recombinant sphingomyelinase C expressed in Escherichia coli was as potent as the native protein in killing the cockroaches. Site-directed mutagenesis (His151Ala) that inactivated the sphingomyelinase activity also abolished the insecticidal activity, suggesting that the rapid insect toxicity of sphingomyelinase C results from its phospholipid-degrading activity.
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109. |
Morais MC,
Zhang G,
Zhang W,
Olsen DB,
Dunaway-Mariano D,
Allen KN,
( 2004 ) X-ray crystallographic and site-directed mutagenesis analysis of the mechanism of Schiff-base formation in phosphonoacetaldehyde hydrolase catalysis. PMID : 14670958 : DOI : 10.1074/jbc.M312345200 Abstract >>
Phosphonoacetaldehyde hydrolase (phosphonatase) catalyzes the hydrolytic P-C bond cleavage of phosphonoacetaldehyde (Pald) to form orthophosphate and acetaldehyde. The reaction proceeds via a Schiff-base intermediate formed between Lys-53 and the Pald carbonyl. The x-ray crystal structures of the wild-type phosphonatase complexed with Mg(II) alone or with Mg(II) plus vinylsulfonate (a phosphonoethylenamine analog) were determined to 2.8 and 2.4 A, respectively. These structures were used to determine the identity and positions of active site residues surrounding the Lys-53 ammonium group and the Pald carbonyl. These include Cys-22, His-56, Tyr-128, and Met-49. Site-directed mutagenesis was then employed to determine whether or not these groups participate in catalysis. Based on rate contributions, Tyr-128 and Cys-22 were eliminated as potential catalytic groups. The Lys-53 epsilon-amino group, positioned for reaction with the Pald carbonyl, forms a hydrogen bond with water 120. Water 120 is also within hydrogen bond distance of an imidazole nitrogen of His-56 and the sulfur atom of Met-49. Kinetic constants for mutants indicated that His-56 (1000-fold reduction in k(cat)/K(m) upon Ala substitution) and Met-49 (17,000-fold reduction in k(cat)/K(m) upon Leu substitution) function in catalysis of Schiff-base formation. Based on these results, it is proposed that a network of hydrogen bonds among Lys-53, water 120, His-56, and Met-49 facilitate proton transfer from Lys-53 to the carbinolamine intermediate. Comparison of the vinylsulfonate complex versus unliganded structures indicated that association of the cap and core domains is essential for the positioning of the Lys-53 for attack at the Pald carbonyl and that substrate binding at the core domain stabilizes cap domain binding.
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110. |
Helgason E,
Tourasse NJ,
Meisal R,
Caugant DA,
Kolstø AB,
( 2004 ) Multilocus sequence typing scheme for bacteria of the Bacillus cereus group. PMID : 14711642 : DOI : 10.1128/aem.70.1.191-201.2004 PMC : PMC321270 Abstract >>
In this study we developed a multilocus sequence typing (MLST) scheme for bacteria of the Bacillus cereus group. This group, which includes the species B. cereus, B. thuringiensis, B. weihenstephanensis, and B. anthracis, is known to be genetically very diverse. It is also very important because it comprises pathogenic organisms as well as bacteria with industrial applications. The MLST system was established by using 77 strains having various origins, including humans, animals, food, and soil. A total of 67 of these strains had been analyzed previously by multilocus enzyme electrophoresis, and they were selected to represent the genetic diversity of this group of bacteria. Primers were designed for conserved regions of housekeeping genes, and 330- to 504-bp internal fragments of seven such genes, adk, ccpA, ftsA, glpT, pyrE, recF, and sucC, were sequenced for all strains. The number of alleles at individual loci ranged from 25 to 40, and a total of 53 allelic profiles or sequence types (STs) were distinguished. Analysis of the sequence data showed that the population structure of the B. cereus group is weakly clonal. In particular, all five B. anthracis isolates analyzed had the same ST. The MLST scheme which we developed has a high level of resolution and should be an excellent tool for studying the population structure and epidemiology of the B. cereus group.
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111. |
Emmert EA,
Klimowicz AK,
Thomas MG,
Handelsman J,
( 2004 ) Genetics of zwittermicin a production by Bacillus cereus. PMID : 14711631 : DOI : 10.1128/aem.70.1.104-113.2004 PMC : PMC321298 Abstract >>
Zwittermicin A represents a new chemical class of antibiotic and has diverse biological activities, including suppression of oomycete diseases of plants and potentiation of the insecticidal activity of Bacillus thuringiensis. To identify genes involved in zwittermicin A production, we generated 4,800 transposon mutants of B. cereus UW101C and screened them for zwittermicin A accumulation. Nine mutants did not produce detectable zwittermicin A, and one mutant produced eightfold more than the parent strain. The DNA flanking the transposon insertions in six of the nine nonproducing mutants contains significant sequence similarity to genes involved in peptide and polyketide antibiotic biosynthesis. The mutant that overproduced zwittermicin A contained a transposon insertion immediately upstream from a gene that encodes a deduced protein that is a member of the MarR family of transcriptional regulators. Three genes identified by the mutant analysis mapped to a region that was previously shown to carry the zwittermicin A self-resistance gene, zmaR, and a biosynthetic gene (E. A. Stohl, J. L. Milner, and J. Handelsman, Gene 237:403-411, 1999). Further sequencing of this region revealed genes proposed to encode zwittermicin A precursor biosynthetic enzymes, in particular, those involved in the formation of the aminomalonyl- and hydroxymalonyl-acyl carrier protein intermediates. Additionally, nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) homologs are present, suggesting that zwittermicin A is synthesized by a mixed NRPS/PKS pathway.
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112. |
Grass G,
Schierhorn A,
Sorkau E,
Müller H,
Rücknagel P,
Nies DH,
Fricke B,
( 2004 ) Camelysin is a novel surface metalloproteinase from Bacillus cereus. PMID : 14688099 : DOI : 10.1128/iai.72.1.219-228.2004 PMC : PMC343988 Abstract >>
Bacillus cereus frequently causes food poisoning or nosocomial diseases. Vegetative cells express the novel surface metalloproteinase camelysin (casein-cleaving metalloproteinase) during exponential growth on complex, peptide-rich media. Camelysin is strongly bound to the cell surface and can be solubilized only by detergents or butanol. Camelysin spontaneously migrates from the surface of intact bacterial cells to preformed liposomes. The complete sequence of the camelysin-encoding gene, calY, was determined by reverse PCR on the basis of the N-terminal sequence and some internal tryptic cleavage peptides. The calY gene codes for a polypeptide of 21.569 kDa with a putative signal peptide of 27 amino acids (2.513 kDa) preceding the mature protein (19.056 kDa). Although the predicted amino acid sequence of CalY does not exhibit a typical metalloprotease consensus sequence, high-pressure liquid chromatography-purified camelysin contains one zinc ion per protein molecule. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry and tryptic peptide mass fingerprinting confirmed the identity of this zinc-binding protein as CalY. Disruption of the calY gene results in a strong decrease in the cell-bound proteolytic activity on various substrates.
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113. |
Gueneau de Novoa P,
Williams KP,
( 2004 ) The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts. PMID : 14681369 : DOI : 10.1093/nar/gkh102 PMC : PMC308836 Abstract >>
tmRNA combines tRNA- and mRNA-like properties and ameliorates problems arising from stalled ribosomes. Research on the mechanism, structure and biology of tmRNA is served by the tmRNA website (http://www.indiana.edu/~ tmrna), a collection of sequences, alignments, secondary structures and other information. Because many of these sequences are not in GenBank, a BLAST server has been added; another new feature is an abbreviated alignment for the tRNA-like domain only. Many tmRNA sequences from plastids have been added, five found in public sequence data and another 10 generated by direct sequencing; detection in early-branching members of the green plastid lineage brings coverage to all three primary plastid lineages. The new sequences include the shortest known tmRNA sequence. While bacterial tmRNAs usually have a lone pseudoknot upstream of the mRNA segment and a string of three or four pseudoknots downstream, plastid tmRNAs collectively show loss of pseudoknots at both postions. The pseudoknot-string region is also too short to contain the usual pseudoknot number in another new entry, the tmRNA sequence from a bacterial endosymbiont of insect cells, Tremblaya princeps. Pseudoknots may optimize tmRNA function in free-living bacteria, yet become dispensible when the endosymbiotic lifestyle relaxes selective pressure for fast growth.
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114. |
Kurnasov O,
Jablonski L,
Polanuyer B,
Dorrestein P,
Begley T,
Osterman A,
( 2003 ) Aerobic tryptophan degradation pathway in bacteria: novel kynurenine formamidase. PMID : 14592712 : DOI : 10.1016/S0378-1097(03)00684-0 Abstract >>
While a variety of chemical transformations related to the aerobic degradation of L-tryptophan (kynurenine pathway), and most of the genes and corresponding enzymes involved therein have been predominantly characterized in eukaryotes, relatively little was known about this pathway in bacteria. Using genome comparative analysis techniques we have predicted the existence of the three-step pathway of aerobic L-tryptophan degradation to anthranilate (anthranilate pathway) in several bacteria. Based on the chromosomal gene clustering analysis, we have identified a previously unknown gene encoding for kynurenine formamidase (EC 3.5.1.19) involved with the second step of the anthranilate pathway. This functional prediction was experimentally verified by cloning, expression and enzymatic characterization of recombinant kynurenine formamidase orthologs from Bacillus cereus, Pseudomonas aeruginosa and Ralstonia metallidurans. Experimental verification of the inferred anthranilate pathway was achieved by functional expression in Escherichia coli of the R. metallidurans putative kynBAU operon encoding three required enzymes: tryptophan 2,3-dioxygenase (gene kynA), kynurenine formamidase (gene kynB), and kynureninase (gene kynU). Our data provide the first experimental evidence of the connection between these genes (only one of which, kynU, was previously characterized) and L-tryptophan aerobic degradation pathway in bacteria.
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115. |
Komeda H,
Asano Y,
( 2003 ) Genes for an alkaline D-stereospecific endopeptidase and its homolog are located in tandem on Bacillus cereus genome. PMID : 14612229 : DOI : 10.1016/S0378-1097(03)00665-7 Abstract >>
Alkaline D-peptidase (Adp) from Bacillus cereus DF4-B is a D-stereospecific endopeptidase acting on oligopeptides composed of D-phenylalanine and the primary structure deduced from its gene, adp, shows a similarity with D-stereospecific hydrolases from Ochrobactrum anthropi strains. We have isolated DNA fragments covering the flanking region of adp from DF4-B genome and found an additional gene, adp2, located upstream of adp. The deduced amino acid sequence of Adp2 showed 96% and 85% identity with those of Adp from B. cereus strains AH559 and DF4-B, respectively. The recombinant Adp2 expressed in Escherichia coli was purified to homogeneity and characterized. It had hydrolyzing activity toward (D-Phe)3, (D-Phe)4, and (D-Phe)6 but did not act on (L-Phe)4, D-Phe-NH2, and L-Phe-NH2, some characteristics that are closely related to those of Adp from strain DF4-B. These results indicate that highly homologous genes encoding D-stereospecific endopeptidases are arranged in a tandem manner on the genomic DNA of B. cereus DF4-B.
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116. |
Duong-Ly KC,
Gabelli SB,
Xu W,
Dunn CA,
Schoeffield AJ,
Bessman MJ,
Amzel LM,
( 2011 ) The Nudix hydrolase CDP-chase, a CDP-choline pyrophosphatase, is an asymmetric dimer with two distinct enzymatic activities. PMID : 21531795 : DOI : 10.1128/JB.00089-11 PMC : PMC3133267 Abstract >>
A Nudix enzyme from Bacillus cereus (NCBI RefSeq accession no. NP_831800) catalyzes the hydrolysis of CDP-choline to produce CMP and phosphocholine. Here, we show that in addition, the enzyme has a 3'��5' RNA exonuclease activity. The structure of the free enzyme, determined to a 1.8-? resolution, shows that the enzyme is an asymmetric dimer. Each monomer consists of two domains, an N-terminal helical domain and a C-terminal Nudix domain. The N-terminal domain is placed relative to the C-terminal domain such as to result in an overall asymmetric arrangement with two distinct catalytic sites: one with an "enclosed" Nudix pyrophosphatase site and the other with a more open, less-defined cavity. Residues that may be important for determining the asymmetry are conserved among a group of uncharacterized Nudix enzymes from Gram-positive bacteria. Our data support a model where CDP-choline hydrolysis is catalyzed by the enclosed Nudix site and RNA exonuclease activity is catalyzed by the open site. CDP-Chase is the first identified member of a novel Nudix family in which structural asymmetry has a profound effect on the recognition of substrates.
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117. |
Laouami S,
Messaoudi K,
Alberto F,
Clavel T,
Duport C,
( 2011 ) Lactate dehydrogenase A promotes communication between carbohydrate catabolism and virulence in Bacillus cereus. PMID : 21296961 : DOI : 10.1128/JB.00024-11 PMC : PMC3067659 Abstract >>
The diarrheal potential of a Bacillus cereus strain is essentially dictated by the amount of secreted nonhemolytic enterotoxin (Nhe). Expression of genes encoding Nhe is regulated by several factors, including the metabolic state of the cells. To identify metabolic sensors that could promote communication between central metabolism and nhe expression, we compared four strains of the B. cereus group in terms of metabolic and nhe expression capacities. We performed growth performance measurements, metabolite analysis, and mRNA measurements of strains F4430/73, F4810/72, F837/76, and PA cultured under anoxic and fully oxic conditions. The results showed that expression levels of nhe and ldhA, which encodes lactate dehydrogenase A (LdhA), were correlated in both aerobically and anaerobically grown cells. We examined the role of LdhA in the F4430/73 strain by constructing an ldhA mutant. The ldhA mutation was more deleterious to anaerobically grown cells than to aerobically grown cells, causing growth limitation and strong deregulation of key fermentative genes. More importantly, the ldhA mutation downregulated enterotoxin gene expression under both anaerobiosis and aerobiosis, with a more pronounced effect under anaerobiosis. Therefore, LdhA was found to exert a major control on both fermentative growth and enterotoxin expression, and it is concluded that there is a direct link between fermentative metabolism and virulence in B. cereus. The data presented also provide evidence that LdhA-dependent regulation of enterotoxin gene expression is oxygen independent. This study is the first report to describe a role of a fermentative enzyme in virulence in B. cereus.
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118. |
Sánchez B,
López P,
González-Rodríguez I,
Suárez A,
Margolles A,
Urdaci MC,
( 2011 ) A flagellin-producing Lactococcus strain: interactions with mucin and enteropathogens. PMID : 21323981 : DOI : 10.1111/j.1574-6968.2011.02244.x Abstract >>
Bacillus cereus CH is a probiotic strain used in human nutrition whose adhesion to mucin is dependent on its surface-associated flagellin. Flagellins from the surface of several probiotic Bacillus strains were efficiently extracted with 5 M LiCl and identified by peptide fingerprinting. Based on the proteomic analysis, cloning of the gene coding for the flagellin of B. cereus CH was performed in the lactococcal vector pNZ8110 under the control of a nisin-inducible promoter. The resulting strain, Lactococcus lactis CH, produced a surface-associated flagellin after 6 h of induction with nisin. The recombinant Lactococcus strain adhered strongly to mucin-coated polystyrene plates, whilst inhibiting competitively the adhesion of the pathogens Escherichia coli LMG2092 and Salmonella enterica ssp. enterica LMG15860 to the same molecule. Strain CH could be used in further experimentation for the characterization of the molecular mechanism of action of this probiotic B. cereus CH flagellin.
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119. |
Li GY,
Li J,
Xiao P,
Guo YH,
Mo ZL,
( 2011 ) Detection of type III secretion gene as an indicator for pathogenic Edwardsiella tarda. PMID : 21219368 : DOI : 10.1111/j.1472-765X.2010.02984.x Abstract >>
To differentiate pathogenic and nonpathogenic Edwardsiella tarda strains based on the detection of type III secretion system (T3SS) gene using polymerase chain reaction (PCR). Primers were designed to amplify Edw. tarda T3SS component gene esaV, catalase gene katB, haemolysin gene hlyA and 16S rRNA gene as an internal positive control. Genomic DNAs were extracted using a commercial isolation kit from 36 Edw. tarda strains consisting of 18 pathogenic and 18 nonpathogenic strains, and 50 ng of each DNA was used as the template for PCR amplification. PCR was performed with a thermocycler (TaKaRa TP600) in a 25-�gl volume. Products of esaV were detected in all pathogenic strains, but not in nonpathogenic strains; katB was detected in all pathogenic strains and one of nonpathogenic strains; hlyA was not detected in any strains. The detection of esaV gene can be used for the assessment of pathogenic Edw. tarda strains. The strategy using T3SS gene as the virulence indicator provides a useful tool for the clinical assessment of pathogenic Edw. tarda strains and prediction of edwardsiellosis risk in fish culture environments.
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120. |
Janse I,
Hamidjaja RA,
Bok JM,
van Rotterdam BJ,
( 2010 ) Reliable detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis by using multiplex qPCR including internal controls for nucleic acid extraction and amplification. PMID : 21143837 : DOI : 10.1186/1471-2180-10-314 PMC : PMC3016324 Abstract >>
Several pathogens could seriously affect public health if not recognized timely. To reduce the impact of such highly pathogenic micro-organisms, rapid and accurate diagnostic tools are needed for their detection in various samples, including environmental samples. Multiplex real-time PCRs were designed for rapid and reliable detection of three major pathogens that have the potential to cause high morbidity and mortality in humans: B. anthracis, F. tularensis and Y. pestis. The developed assays detect three pathogen-specific targets, including at least one chromosomal target, and one target from B. thuringiensis which is used as an internal control for nucleic acid extraction from refractory spores as well as successful DNA amplification. Validation of the PCRs showed a high analytical sensitivity, specificity and coverage of diverse pathogen strains. The multiplex qPCR assays that were developed allow the rapid detection of 3 pathogen-specific targets simultaneously, without compromising sensitivity. The application of B. thuringiensis spores as internal controls further reduces false negative results. This ensures highly reliable detection, while template consumption and laboratory effort are kept at a minimum.
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121. |
Tomita M,
Nakai K,
Yamada A,
Taguchi R,
Ikezawa H,
( 1990 ) Secondary structure of sphingomyelinase from Bacillus cereus. PMID : 2127932 : DOI : 10.1093/oxfordjournals.jbchem.a123285 Abstract >>
Of the total of 306 amino acids in the sequence of sphingomyelinase (SMPLC) from Bacillus cereus, almost half (150) are expected to be involved in the formation of loop or turn structure, while 65 and 73 residues may participate in the formation of alpha-helix and beta-structure, respectively. The helix content of SMPLC was calculated to be 0-5%, based on the CD spectra. The addition of divalent metal ions such as Mg2+ or both Ca2+ and Mg2+ had no effect on the CD spectra of SMPLC, although the addition of these metal ions caused the breakdown of membranous SM and specific adsorption of SMPLC onto erythrocyte membranes. A hydropathy study showed that SMPLC has hydrophobic regions at the N-terminal domain which must be responsible for the binding of the enzyme to the membranes. The partial homologies between the amino acid sequences of SMPLC and Clostridium perfringens alpha-toxin (phospholipase C) are discussed.
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122. |
Watanabe K,
Kitamura K,
Iha H,
Suzuki Y,
( 1990 ) Primary structure of the oligo-1,6-glucosidase of Bacillus cereus ATCC7064 deduced from the nucleotide sequence of the cloned gene. PMID : 2120057 : DOI : 10.1111/j.1432-1033.1990.tb19267.x Abstract >>
The gene coding for Bacillus cereus ATCC7064 (mesophile) oligo-1,6-glucosidase was cloned within a 2.8-kb SalI-EcoRI fragment of DNA, using the plasmid pUC19 as a vector and Escherichia coli C600 as a host. E. coli C600 bearing the hybrid plasmid pBCE4 accumulated oligo-1,6-glucosidase in the cytoplasm. The cloned enzyme coincided absolutely with B. cereus oligo-1,6-glucosidase in its Mr (65,000), in its electrophoretic behavior on a polyacrylamide gel with or without sodium dodecyl sulfate, in its isoelectric point (4.5), in the temperature dependence of its stability and activity, and in its antigenic determinants. The nucleotide sequence of B. cereus oligo-1,6-glucosidase gene and its flanking regions was determined with both complementary strands of DNA (each 2838 nucleotides). The gene consisted of an open reading frame of 1674 bp commencing with a ATG start codon and followed by a TAA stop codon. The amino acid sequence deduced from the nucleotide sequence predicted a protein of 558 amino acid residues with a Mr of 66,010. The amino acid composition and Mr were comparable with those of B. cereus oligo-1,6-glucosidase. The predicted N-terminal sequence of 10 amino acid residues agreed completely with that of the cloned ligo-1,6-glucosidase. The deduced amino acid sequence of B. cereus oligo-1,6-glucosidase was 72% and 42% similar to those from Bacillus thermoglucosidasius KP1006 (DSM2542, obligate thermophile) oligo-1,6-glucosidase and from Saccharomyces carlsbergensis CB11 alpha-glucosidase, respectively. Predictions of protein secondary structures along with amino acid sequence alignments demonstrated that B. cereus oligo-1,6-glucosidase may take the similar (alpha/beta)8-barrel super-secondary structure, a barrel of eight parallel beta-strands surrounded by eight alpha-helices, in its N-terminal active site domain as S. carlsbergensis alpha-glucosidase and Aspergillus oryzae alpha-amylase.
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123. |
Fieldhouse RJ,
Turgeon Z,
White D,
Merrill AR,
( 2010 ) Cholera- and anthrax-like toxins are among several new ADP-ribosyltransferases. PMID : 21170356 : DOI : 10.1371/journal.pcbi.1001029 PMC : PMC3000352 Abstract >>
Chelt, a cholera-like toxin from Vibrio cholerae, and Certhrax, an anthrax-like toxin from Bacillus cereus, are among six new bacterial protein toxins we identified and characterized using in silico and cell-based techniques. We also uncovered medically relevant toxins from Mycobacterium avium and Enterococcus faecalis. We found agriculturally relevant toxins in Photorhabdus luminescens and Vibrio splendidus. These toxins belong to the ADP-ribosyltransferase family that has conserved structure despite low sequence identity. Therefore, our search for new toxins combined fold recognition with rules for filtering sequences--including a primary sequence pattern--to reduce reliance on sequence identity and identify toxins using structure. We used computers to build models and analyzed each new toxin to understand features including: structure, secretion, cell entry, activation, NAD+ substrate binding, intracellular target binding and the reaction mechanism. We confirmed activity using a yeast growth test. In this era where an expanding protein structure library complements abundant protein sequence data--and we need high-throughput validation--our approach provides insight into the newest toxin ADP-ribosyltransferases.
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124. |
Derebe MG,
Zeng W,
Li Y,
Alam A,
Jiang Y,
( 2011 ) Structural studies of ion permeation and Ca2+ blockage of a bacterial channel mimicking the cyclic nucleotide-gated channel pore. PMID : 21187429 : DOI : 10.1073/pnas.1013643108 PMC : PMC3021057 Abstract >>
Cyclic nucleotide-gated (CNG) channels play an essential role in the visual and olfactory sensory systems and are ubiquitous in eukaryotes. Details of their underlying ion selectivity properties are still not fully understood and are a matter of debate in the absence of high-resolution structures. To reveal the structural mechanism of ion selectivity in CNG channels, particularly their Ca(2+) blockage property, we engineered a set of mimics of CNG channel pores for both structural and functional analysis. The mimics faithfully represent the CNG channels they are modeled after, permeate Na(+) and K(+) equally well, and exhibit the same Ca(2+) blockage and permeation properties. Their high-resolution structures reveal a hitherto unseen selectivity filter architecture comprising three contiguous ion binding sites in which Na(+) and K(+) bind with different ion-ligand geometries. Our structural analysis reveals that the conserved acidic residue in the filter is essential for Ca(2+) binding but not through direct ion chelation as in the currently accepted view. Furthermore, structural insight from our CNG mimics allows us to pinpoint equivalent interactions in CNG channels through structure-based mutagenesis that have previously not been predicted using NaK or K(+) channel models.
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125. |
Derebe MG,
Sauer DB,
Zeng W,
Alam A,
Shi N,
Jiang Y,
( 2011 ) Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites. PMID : 21187421 : DOI : 10.1073/pnas.1013636108 PMC : PMC3021048 Abstract >>
Selective ion conduction across ion channel pores is central to cellular physiology. To understand the underlying principles of ion selectivity in tetrameric cation channels, we engineered a set of cation channel pores based on the nonselective NaK channel and determined their structures to high resolution. These structures showcase an ensemble of selectivity filters with a various number of contiguous ion binding sites ranging from 2 to 4, with each individual site maintaining a geometry and ligand environment virtually identical to that of equivalent sites in K(+) channel selectivity filters. Combined with single channel electrophysiology, we show that only the channel with four ion binding sites is K(+) selective, whereas those with two or three are nonselective and permeate Na(+) and K(+) equally well. These observations strongly suggest that the number of contiguous ion binding sites in a single file is the key determinant of the channel's selectivity properties and the presence of four sites in K(+) channels is essential for highly selective and efficient permeation of K(+) ions.
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126. |
Palva A,
Vigren G,
Simonen M,
Rintala H,
Laamanen P,
( 1990 ) Nucleotide sequence of the tetracycline resistance gene of pBC16 from Bacillus cereus. PMID : 2109312 : DOI : 10.1093/nar/18.6.1635 PMC : PMC330541 Abstract >>
N/A
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127. |
Rubinson EH,
Gowda AS,
Spratt TE,
Gold B,
Eichman BF,
( 2010 ) An unprecedented nucleic acid capture mechanism for excision of DNA damage. PMID : 20927102 : DOI : 10.1038/nature09428 PMC : PMC4160814 Abstract >>
DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-targeting anticancer compounds. The basis for glycosylase specificity towards N3- and N7-alkylpurines is believed to result from intrinsic instability of the modified bases and not from direct enzyme functional group chemistry. Here we present crystal structures of the recently discovered Bacillus cereus AlkD glycosylase in complex with DNAs containing alkylated, mismatched and abasic nucleotides. Unlike other glycosylases, AlkD captures the extrahelical lesion in a solvent-exposed orientation, providing an illustration for how hydrolysis of N3- and N7-alkylated bases may be facilitated by increased lifetime out of the DNA helix. The structures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats of AlkD distort the DNA backbone to detect non-Watson-Crick base pairs without duplex intercalation.
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128. |
Kim SJ,
Ha BH,
Kim KH,
Hong SK,
Shin KJ,
Suh SW,
Kim EE,
( 2010 ) Dimeric and tetrameric forms of enoyl-acyl carrier protein reductase from Bacillus cereus. PMID : 20800575 : DOI : 10.1016/j.bbrc.2010.08.083 Abstract >>
Enoyl-[acyl carrier protein] reductase (ENR) is an essential enzyme in type II fatty-acid synthesis that catalyzes the last step in each elongation cycle. Thus far FabI, FabL and FabK have been reported to carry out the reaction, with FabI being the most characterized. Some bacteria have more than one ENR, and Bacillus cereus has two (FabI and FabL) reported. Here, we have determined the crystal structures of the later in the apo form and in the ternary complex with NADP(+) and an indole naphthyridinone inhibitor. The two structures are almost identical, except for the three stretches that are disordered in the apo form. The apo form exists as a homo-dimer in both crystal and solution, while the ternary complex forms a homo-tetramer. The three stretches disordered in the apo structure are important in the cofactor and the inhibitor binding as well as in tetramer formation.
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129. |
Hsieh YC,
Wu YJ,
Chiang TY,
Kuo CY,
Shrestha KL,
Chao CF,
Huang YC,
Chuankhayan P,
Wu WG,
Li YK,
Chen CJ,
( 2010 ) Crystal structures of Bacillus cereus NCTU2 chitinase complexes with chitooligomers reveal novel substrate binding for catalysis: a chitinase without chitin binding and insertion domains. PMID : 20685646 : DOI : 10.1074/jbc.M110.149310 PMC : PMC2951234 Abstract >>
Chitinases hydrolyze chitin, an insoluble linear polymer of N-acetyl-d-glucosamine (NAG)(n), into nutrient sources. Bacillus cereus NCTU2 chitinase (ChiNCTU2) predominantly produces chitobioses and belongs to glycoside hydrolase family 18. The crystal structure of wild-type ChiNCTU2 comprises only a catalytic domain, unlike other chitinases that are equipped with additional chitin binding and insertion domains to bind substrates into the active site. Lacking chitin binding and chitin insertion domains, ChiNCTU2 utilizes two dynamic loops (Gly-67-Thr-69 and Ile-106-Val-112) to interact with (NAG)(n), generating novel substrate binding and distortion for catalysis. Gln-109 is crucial for direct binding with substrates, leading to conformational changes of two loops with a maximum shift of ?4.6 ? along the binding cleft. The structures of E145Q, E145Q/Y227F, and E145G/Y227F mutants complexed with (NAG)(n) reveal (NAG)(2), (NAG)(2), and (NAG)(4) in the active site, respectively, implying various stages of reaction: before hydrolysis, E145G/Y227F with (NAG)(4); in an intermediate state, E145Q/Y227F with a boat-form NAG at the -1 subsite, -1-(NAG); after hydrolysis, E145Q with a chair form -1-(NAG). Several residues were confirmed to play catalytic roles: Glu-145 in cleavage of the glycosidic bond between -1-(NAG) and +1-(NAG); Tyr-227 in the conformational change of -1-(NAG); Asp-143 and Gln-225 in stabilizing the conformation of -1-(NAG). Additionally, Glu-190 acts in the process of product release, and Tyr-193 coordinates with water for catalysis. Residues Asp-143, E145Q, Glu-190, and Tyr-193 exhibit multiple conformations for functions. The inhibitors zinc ions and cyclo-(l-His-l-Pro) are located at various positions and confirm the catalytic-site topology. Together with kinetics analyses of related mutants, the structures of ChiNCTU2 and its mutant complexes with (NAG)(n) provide new insights into its substrate binding and the mechanistic action.
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130. |
Pandiani F,
Brillard J,
Bornard I,
Michaud C,
Chamot S,
Nguyen-the C,
Broussolle V,
( 2010 ) Differential involvement of the five RNA helicases in adaptation of Bacillus cereus ATCC 14579 to low growth temperatures. PMID : 20709848 : DOI : 10.1128/AEM.00782-10 PMC : PMC2950441 Abstract >>
Bacillus cereus ATCC 14579 possesses five RNA helicase-encoding genes overexpressed under cold growth conditions. Out of the five corresponding mutants, only the �GcshA, �GcshB, and �GcshC strains were cold sensitive. Growth of the �GcshA strain was also reduced at 30�XC but not at 37�XC. The cold phenotype was restored with the cshA gene for the �GcshA strain and partially for the �GcshB strain but not for the �GcshC strain, suggesting different functions at low temperature.
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131. |
González JM,
Buschiazzo A,
Vila AJ,
( 2010 ) Evidence of adaptability in metal coordination geometry and active-site loop conformation among B1 metallo-beta-lactamases . PMID : 20677753 : DOI : 10.1021/bi100894r Abstract >>
Subclass B1 beta-lactamases are Zn(II)-dependent hydrolases that confer bacterial resistance to most clinically useful beta-lactam antibiotics. The enzyme BcII from Bacillus cereus is a prototypical enzyme that belongs to this group, the first Zn(II)-dependent beta-lactamase to be discovered. Crucial aspects of the BcII catalytic mechanism and metal binding mode have been assessed mostly on the Co(II)-substituted surrogate. Here we report a high-resolution structure of Co(II)-BcII, revealing a metal coordination geometry identical to that of the native zinc enzyme. In addition, a high-resolution structure of the apoenzyme, together with structures with different degrees of metal occupancy and oxidation levels of a conserved Cys ligand, discloses a considerable mobility of two loops containing four metal ligands (namely, regions His116-Arg121 and Gly219-Cys221). This flexibility is expected to assist in the structural rearrangement of the metal sites during catalytic turnover, which, along with the coordination geometry adaptability of Zn(II) ions, grants the interaction with a variety of substrates, a characteristic feature of B1 metallo-beta-lactamases.
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132. |
Chan KG,
Wong CS,
Yin WF,
Sam CK,
Koh CL,
( 2010 ) Rapid degradation of N-3-oxo-acylhomoserine lactones by a Bacillus cereus isolate from Malaysian rainforest soil. PMID : 20376561 : DOI : 10.1007/s10482-010-9438-0 Abstract >>
A bacterial strain, KM1S, was isolated from a Malaysian rainforest soil sample by using a defined enrichment medium that specifically facilitates selection of quorum quenching bacteria. KM1S was clustered closely to Bacillus cereus by 16S ribosomal DNA sequence analysis. It degraded N-3-oxo-hexanoyl homoserine lactone and N-3-oxo-octanoyl homoserine lactone in vitro rapidly at 4.98 and 6.56 microg AHL h(-1) per 10(9) CFU/ml, respectively, as determined by the Rapid Resolution Liquid Chromatography. The aiiA homologue, encoding an autoinducer inactivation enzyme catalyzing the degradation of N-acylhomoserine lactones, of KM1S was amplified and cloned. Sequence analysis indicated the presence of the motif (106)HXDH-59 amino acids-H(169)-21 amino acids-D(191) for N-acylhomoserine lactone lactonases.
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133. |
Røhr AK,
Hersleth HP,
Andersson KK,
( 2010 ) Tracking flavin conformations in protein crystal structures with Raman spectroscopy and QM/MM calculations. PMID : 20187055 : DOI : 10.1002/anie.200907143 Abstract >>
N/A
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134. |
Schiering N,
Kabsch W,
Moore MJ,
Distefano MD,
Walsh CT,
Pai EF,
( 1991 ) Structure of the detoxification catalyst mercuric ion reductase from Bacillus sp. strain RC607. PMID : 2067577 : DOI : 10.1038/352168a0 Abstract >>
Several hundred million tons of toxic mercurials are dispersed in the biosphere. Microbes can detoxify organo-mercurials and mercury salts through sequential action of two enzymes, organomercury lyase and mercuric ion reductase (MerA). The latter, a homodimer with homology to the FAD-dependent disulphide oxidoreductases, catalyses the reaction NADPH + Hg(II)----NADP+ + H+ + Hg(0), one of the very rare enzymic reactions with metal substrates. Human glutathione reductase serves as a reference molecule for FAD-dependent disulphide reductases and between its primary structure and that of MerA from Tn501 (Pseudomonas), Tn21 (Shigella), p1258 (Staphylococcus) and Bacillus, 25-30% of the residues have been conserved. All MerAs have a C-terminal extension about 15 residues long but have very varied N termini. Although the enzyme from Streptomyces lividans has no addition, from Pseudomonas aeruginosa Tn501 and Bacillus sp. strain RC607 it has one and two copies respectively of a domain of 80-85 residues, highly homologous to MerP, the periplasmic component of proteins encoded by the mer operon. These domains can be proteolytically cleaved off without changing the catalytic efficiency. We report here the crystal structure of MerA from the Gram-positive bacterium Bacillus sp. strain RC607. Analysis of its complexes with nicotinamide dinucleotide substrates and the inhibitor Cd(II) reveals how limited structural changes enable an enzyme to accept as substrate what used to be a dangerous inhibitor. Knowledge of the mode of mercury ligation is a prerequisite for understanding this unique detoxification mechanism.
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135. |
Kovalevskiy OV,
Solonin AS,
Antson AA,
( 2010 ) Structural investigation of transcriptional regulator HlyIIR: influence of a disordered region on protein fold and dimerization. PMID : 20225260 : DOI : 10.1002/prot.22700 Abstract >>
B. cereus HlyIIR belongs to the TetR family of dimeric transcriptional regulators. Unlike other members of the TetR family, HlyIIR contains an insert between alpha-helices alpha8 and alpha9, which is located at the subunit-subunit interface. N-terminal segment of this insert (amino acids, Pro161-Ser169) forms a short alpha-helix alpha8* that occupies a complementary cavity on the surface of the adjacent subunit, whereas the C-terminal segment comprising 16 amino acids (Leu170-Glu185) is disordered. To understand whether this disordered segment is important for protein's function, we determined crystal structures of two engineered HlyIIR proteins where this segment was either substituted by a seven-residue flexible Ser-Gly linker or replaced by a cleavable peptide containing proteolytic sites at both ends. Unexpectedly, alteration or proteolytic removal of the disordered segment resulted in changes in protein's conformation and in a remarkable rearrangement at the subunit-subunit interface. X-ray structures of the two engineered proteins revealed an unusual plasticity at the dimerization interface of HlyIIR enabling it to form dimers stabilized by different sets of interactions. Structural comparison indicates that in spite of the flexible nature of the disordered segment, it is critical for maintaining the native structure as it influences the position of alpha8*. The data demonstrate how disordered loops on protein surfaces may affect folding and subunit-subunit interactions.
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136. |
Soufiane B,
Côté JC,
( 2010 ) Bacillus thuringiensis serovars bolivia, vazensis and navarrensis meet the description of Bacillus weihenstephanensis. PMID : 19937033 : DOI : 10.1007/s00284-009-9547-z Abstract >>
The Bacillus cereus sensu lato group comprises six related species: B. cereus, B. anthracis, B. thuringiensis, B. mycoides, B. pseudomycoides and B. weihenstephanensis. Bacillus thuringiensis is a mesophile. It is distinguished from other members of the B. cereus group by the apparition of an inclusion body upon sporulation. B. weihenstephanensis, however, is a psychrotolerant. It grows at 7 degrees C but not at 43 degrees C. It is further characterised by the presence of specific signature sequences on two genes, the 16S rRNA gene (the small subunit ribosomal RNA gene) and cspA (encoding the major cold shock protein). Five B. thuringiensis serovars selected from previous studies, bolivia, vazensis, navarrensis, azorensis and asturiensis were studied here for their capability to grow at 7 degrees C but not at 43 degrees C. Next, their 16S rRNA and cspA genes were analysed for the presence of B. weihenstephanensis-specific signature sequences. Bacillus thuringiensis serovars bolivia, vazensis and navarrensis met the description of B. weihenstephanensis.
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137. |
Budzik JM,
Poor CB,
Faull KF,
Whitelegge JP,
He C,
Schneewind O,
( 2009 ) Intramolecular amide bonds stabilize pili on the surface of bacilli. PMID : 19903875 : DOI : 10.1073/pnas.0910887106 PMC : PMC2785280 Abstract >>
Gram-positive bacteria elaborate pili and do so without the participation of folding chaperones or disulfide bond catalysts. Sortases, enzymes that cut pilin precursors, form covalent bonds that link pilin subunits and assemble pili on the bacterial surface. We determined the x-ray structure of BcpA, the major pilin subunit of Bacillus cereus. The BcpA precursor encompasses 2 Ig folds (CNA(2) and CNA(3)) and one jelly-roll domain (XNA) each of which synthesizes a single intramolecular amide bond. A fourth amide bond, derived from the Ig fold of CNA(1), is formed only after pilin subunits have been incorporated into pili. We report that the domains of pilin precursors have evolved to synthesize a discrete sequence of intramolecular amide bonds, thereby conferring structural stability and protease resistance to pili.
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138. |
Kovalevskiĭ OV,
Antson AA,
Solonin AS,
( N/A ) [Contraction of the disordered loop located within C-terminal domain of the transcriptional regulator HlyIIR causes its structural rearrangement]. PMID : 19334535 : PMC : PMC3145143 Abstract >>
HlyIIR is the negative transcriptional regulator of the hemolysin II gene from Bacillus cereus. Previous X-ray studies showed that HlyIIR contains a disordered loop (a.a. 170-185) located within the C-terminal domain near dimerization interface. To understand the influence of this region on HlyIIR properties and for a potential improvement in the crystallogenesis of the HlyIIR, we constructed a mutant of HlyIIR in which this disordered region is substituted by a single alanine residue. Biochemical analysis of the mutant indicated that it still forms a dimer but the DNA-binding activity is lost. HlyIIR mutant displayed improved crystallization properties and its structure was determined by X-ray crystallography at 2.1 A resolution. Unexpectedly, the structure shows that the HlyIIR mutant forms an alternative dimer with subunits rotated by 160 degrees. Moreover, there are also changes in the conformation of individual subunits. These dramatic structural rearrangements are caused by changes in the conformation of the segment Pro161-Ser169. We conclude that correct conformation of this segment is principal for maintaining the structure and activity of HlyIIR.
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139. |
Ikeda K,
Inoue S,
Amasaki C,
Teshima K,
Ikezawa H,
( 1991 ) Kinetics of the hydrolysis of monodispersed and micellar phosphatidylcholines catalyzed by a phospholipase C from Bacillus cereus. PMID : 1939031 : DOI : 10.1093/oxfordjournals.jbchem.a123547 Abstract >>
The phosphatidylcholine-hydrolyzing phospholipase C, so-called "phospholipase C" (PLC), was isolated from the culture of Bacillus cereus strain IAM 1208. The amino-acid composition and partial N-terminal sequence of the purified enzyme were in good agreement with those expected from the nucleotide sequence for a PLC of strain ATCC 10987 [Johansen et al. (1988) Gene 65, 293-304]. The chain-length dependence of kinetic parameters for the PLC-catalyzed hydrolysis of monodispersed short-chain phosphatidylcholines (diCNPC, N = 3-6) was studied by a pH-stat assay method at 25 degrees C, pH 8.0, and ionic strength 0.2 in the presence of saturating amounts of Zn2+ (0.1 mM). The result was compared with those for snake venom phospholipases A2 [Teshima et al. (1989) J. Biochem. 106, 518-527]. It was found that the interaction of the PLC with the head group of the substrate molecule is very important for the binding. The pH dependences of kinetic parameters for the hydrolysis of monodispersed diC5PC and mixed micelles of diC16PC with Triton X-100 were also studied under the same conditions. An ionizable group, whose pK value is perturbed from 7.77 to 8.30 by substrate binding, was found to be essential to the catalysis. This group was tentatively assigned to His 14 on the basis of the results on X-ray crystallographic and chemical modification studies [Hough et al. (1989) Nature 338, 357-360 and Little (1977) Biochem. J. 167, 399-404].(ABSTRACT TRUNCATED AT 250 WORDS)
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140. |
Chai Y,
Kolter R,
Losick R,
( 2009 ) A widely conserved gene cluster required for lactate utilization in Bacillus subtilis and its involvement in biofilm formation. PMID : 19201793 : DOI : 10.1128/JB.01464-08 PMC : PMC2668416 Abstract >>
We report that catabolism of l-lactate in Bacillus subtilis depends on the previously uncharacterized yvfV-yvfW-yvbY (herein renamed lutABC) operon, which is inferred to encode three iron-sulfur-containing proteins. The operon is under the dual control of a GntR-type repressor (LutR, formerly YvfI) and the master regulator for biofilm formation SinR and is induced during growth in response to l-lactate. Operons with high similarity to lutABC are present in the genomes of a variety of gram-positive and gram-negative bacteria, raising the possibility that LutABC is a widely conserved and previously unrecognized pathway for the utilization of l-lactate or related metabolites.
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141. |
Martínez-Blanch JF,
Sánchez G,
Garay E,
Aznar R,
( 2009 ) Development of a real-time PCR assay for detection and quantification of enterotoxigenic members of Bacillus cereus group in food samples. PMID : 19665814 : DOI : 10.1016/j.ijfoodmicro.2009.07.013 Abstract >>
A highly sensitive real-time PCR (qPCR) procedure, targeting the phosphatidylcholine-specific phospholipase C gene (pc-plc), was developed for specific detection and quantification of strains belonging to Bacillus cereus group. The target region was selected based on the enterotoxigenic profiles of 75 Bacillus strains. The inclusivity and exclusivity of the RTi-PCR assay were assessed with 59 isolates of the B. cereus group, 16 other Bacillus spp., and 4 non-Bacillus strains. The assay was also used to construct calibration curves for different food matrices, and it had a wide quantification range of 6 log units using both serial dilutions of purified DNA and calibrated cell suspensions of B. cereus CECT 148(T). The detection limit for B. cereus in artificially contaminated liquid egg and reconstituted infant formula was about 3CFU per reaction or 60CFU/ml of food, with a relative accuracy of 86.27% to 116.12% in artificially contaminated liquid egg. Naturally contaminated food samples were tested for the presence of B. cereus with the standard method, a conventional PCR and the new developed RTi-PCR assay. Results showed that the new developed RTi-PCR assay is very suitable for detection and quantification of strains of B. cereus group in food samples without an enrichment step.
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142. |
Adelowo OO,
Fagade OE,
( 2009 ) The tetracycline resistance gene tet39 is present in both Gram-negative and Gram-positive bacteria from a polluted river, Southwestern Nigeria. PMID : 19196439 : DOI : 10.1111/j.1472-765X.2008.02523.x Abstract >>
Previous analysis of tet39 suggests it may be present in other bacterial species. Hence, we investigated the host range of tet39 among bacterial from a poultry waste polluted river in Southwestern Nigeria. Thirteen resistant bacterial isolated from the water and sediment of the polluted river was investigated for the presence of tetracycline resistance genes tetA, tetB, tetC, tet39 and the transposon integrase gene of the Tn916/1545 family by PCR. While tetA, tetB, tetC and integrase genes cannot be detected in any of the organisms, tet39 was detected in eight of the tested organisms including three Gram-positive species. Sequence analysis showed the genes have high sequence identities (> or =99%) with tet39 of Acinetobacter sp. LUH5605, the first and only bacterial genus from which the gene has been reported to date. This is a novel observation. This study shows that apart from Acinetobacter, tet39 is present in other bacterial species tested in this study. This study adds to available information on the occurrence and distribution of tet39 among environmental bacteria and suggests that the gene has a broader host range than previously reported.
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143. |
Osman KT,
Du L,
He Y,
Luo Y,
( 2009 ) Crystal structure of Bacillus cereus D-alanyl carrier protein ligase (DltA) in complex with ATP. PMID : 19324056 : DOI : 10.1016/j.jmb.2009.03.040 Abstract >>
D-alanylation of lipoteichoic acids modulates the surface charge and ligand binding of the Gram-positive cell wall. Disruption of the bacterial dlt operon involved in teichoic acid alanylation, as well as inhibition of the DltA (D-alanyl carrier protein ligase) protein, has been shown to render the bacterium more susceptible to conventional antibiotics and host defense responses. The DltA catalyzes the adenylation and thiolation reactions of d-alanine. This enzyme belongs to a superfamily of AMP-forming domains such as the ubiquitous acetyl-coenzyme A synthetase. We have determined the 1.9-A-resolution crystal structure of a DltA protein from Bacillus cereus in complex with ATP. This structure sheds light on the geometry of the bound ATP. The invariant catalytic residue Lys492 appears to be mobile, suggesting a molecular mechanism of catalysis for this superfamily of enzymes. Specific roles are also revealed for two other invariant residues: the divalent cation-stabilizing Glu298 and the beta-phosphate-interacting Arg397. Mutant proteins with a glutamine substitution at position 298 or 397 are inactive.
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144. |
Wieland Brown LC,
Acker MG,
Clardy J,
Walsh CT,
Fischbach MA,
( 2009 ) Thirteen posttranslational modifications convert a 14-residue peptide into the antibiotic thiocillin. PMID : 19196969 : DOI : 10.1073/pnas.0900008106 PMC : PMC2650375 Abstract >>
The thiazolylpeptides are a family of >50 bactericidal antibiotics that block the initial steps of bacterial protein synthesis. Here, we report a biosynthetic gene cluster for thiocillin and establish that it, and by extension the whole class, is ribosomally synthesized. Remarkably, the C-terminal 14 residues of a 52-residue peptide precursor undergo 13 posttranslational modifications to give rise to thiocillin, making this antibiotic the most heavily posttranslationally-modified peptide known to date.
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145. |
Ki JS,
Zhang W,
Qian PY,
( 2009 ) Discovery of marine Bacillus species by 16S rRNA and rpoB comparisons and their usefulness for species identification. PMID : 19166882 : DOI : 10.1016/j.mimet.2009.01.003 Abstract >>
Systematic studies of the Bacillus group have been biased towards terrestrial and pathogenic isolates, and relatively few studies have examined Bacillus species from marine environments. Here we took twenty Bacillus strains from diverse marine environments and sequenced their 16S rRNA. Using molecular comparisons, we separated the strains into thirteen Bacillus genotypes and identified 9 species: B. aquaemaris. B. badius, B. cereus group, B. firmus, B. halmapalus, B. hwajinpoensis, B. litoralis, B. sporothermodurans, B. vietnamensis, and three indistinguishable Bacilli. In addition, we sequenced the DNA-directed RNA polymerase beta subunit (rpoB) gene and assessed its discriminative power in identifying Bacilli. Phylogenetic trees of Bacillus rpoB genes separated each Bacillus according to their taxonomic positions and were supported statistically. The resolution of Bacillus on the rpoB phylogenetic tree was approximately 4.5 times greater than on the 16S rRNA phylogenetic tree. These results demonstrate that the polymorphism of the Bacillus rpoB gene can be used to identify Bacillus species, providing an improved identification scheme for Bacillus species.
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146. |
Alam A,
Jiang Y,
( 2009 ) High-resolution structure of the open NaK channel. PMID : 19098917 : DOI : 10.1038/nsmb.1531 PMC : PMC2615073 Abstract >>
We report the crystal structure of the nonselective cation channel NaK from Bacillus cereus at a resolution of 1.6 A. The structure reveals the intracellular gate in an open state, as opposed to the closed form reported previously, making NaK the only channel for which the three-dimensional structures of both conformations are known. Channel opening follows a conserved mechanism of inner helix bending using a flexible glycine residue, the gating hinge, seen in MthK and most other tetrameric cation channels. Additionally, distinct inter and intrasubunit rearrangements involved in channel gating are seen and characterized for the first time along with inner helix twisting motions. Furthermore, we identify a residue deeper within the cavity of the channel pore, Phe92, which is likely to form a constriction point within the open pore, restricting ion flux through the channel. Mutating this residue to alanine causes a subsequent increase in ion-conduction rates as measured by (86)Rb flux assays. The structures of both the open and closed conformations of the NaK channel correlate well with those of equivalent K(+) channel conformations, namely MthK and KcsA, respectively.
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147. |
Alam A,
Jiang Y,
( 2009 ) Structural analysis of ion selectivity in the NaK channel. PMID : 19098915 : DOI : 10.1038/nsmb.1537 PMC : PMC2615071 Abstract >>
Here we present a detailed characterization of ion binding in the NaK pore using the high-resolution structures of NaK in complex with various cations. These structures reveal four ion binding sites with similar chemical environments but vastly different ion preference. The most nonselective of all is site 3, which is formed exclusively by backbone carbonyl oxygen atoms and resides deep within the selectivity filter. Additionally, four water molecules in combination with four backbone carbonyl oxygen atoms are seen to participate in K(+) and Rb(+) ion chelation, at both the external entrance and the vestibule of the NaK filter, confirming the channel's preference for an octahedral ligand configuration for K(+) and Rb(+) binding. In contrast, Na(+) binding in the NaK filter, particularly at site 4, utilizes a pyramidal ligand configuration that requires the participation of a water molecule in the cavity. Therefore, the ability of the NaK filter to bind both Na(+) and K(+) ions seemingly arises from the ions' ability to use the existing environment in unique ways, rather than from any structural rearrangements of the filter itself.
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148. |
Kevany BM,
Rasko DA,
Thomas MG,
( 2009 ) Characterization of the complete zwittermicin A biosynthesis gene cluster from Bacillus cereus. PMID : 19098220 : DOI : 10.1128/AEM.02518-08 PMC : PMC2643575 Abstract >>
Bacillus cereus UW85 produces the linear aminopolyol antibiotic zwittermicin A (ZmA). This antibiotic has diverse biological activities, such as suppression of disease in plants caused by protists, inhibition of fungal and bacterial growth, and amplification of the insecticidal activity of the toxin protein from Bacillus thuringiensis. ZmA has an unusual chemical structure that includes a d amino acid and ethanolamine and glycolyl moieties, as well as having an unusual terminal amide that is generated from the modification of the nonproteinogenic amino acid beta-ureidoalanine. The diverse biological activities and unusual structure of ZmA have stimulated our efforts to understand how this antibiotic is biosynthesized. Here, we present the identification of the complete ZmA biosynthesis gene cluster from B. cereus UW85. A nearly identical gene cluster is identified on a plasmid from B. cereus AH1134, and we show that this strain is also capable of producing ZmA. Bioinformatics and biochemical analyses of the ZmA biosynthesis enzymes strongly suggest that ZmA is initially biosynthesized as part of a larger metabolite that is processed twice, resulting in the formation of ZmA and two additional metabolites. Additionally, we propose that the biosynthesis gene cluster for the production of the amino sugar kanosamine is contained within the ZmA biosynthesis gene cluster in B. cereus UW85.
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149. |
Lim HM,
Iyer RK,
Pène JJ,
( 1991 ) Site-directed mutagenesis of dicarboxylic acids near the active site of Bacillus cereus 5/B/6 beta-lactamase II. PMID : 1904717 : DOI : 10.1042/bj2760401 PMC : PMC1151105 Abstract >>
An amino acid residue functioning as a general base has been proposed to assist in the hydrolysis of beta-lactam antibiotics by the zinc-containing Bacillus cereus beta-lactamase II [Bicknell & Waley (1985) Biochemistry 24, 6876-6887]. Oligonucleotide-directed mutagenesis of cloned Bacillus cereus 5/B/6 beta-lactamase II was used in an 'in vivo' study to investigate the role of carboxy-group-containing amino acids near the active site of the enzyme. Substitution of asparagine for the wild-type aspartic acid residue at position 81 resulted in fully functional enzyme. An aspartic acid residue at position 90 is essential for beta-lactamase II to confer any detectable ampicillin and cephalosporin C resistance to Escherichia coli. Conversion of Asp90 into Asn90 or Glu90 lead to the synthesis of inactive enzyme, suggesting that the spatial position of the beta-carboxy group of Asp90 is critical for enzyme function.
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150. |
Takenaka S,
Cheng M,
Mulyono N/A,
Koshiya A,
Murakami S,
Aoki K,
( 2009 ) Gene cloning and characterization of arylamine N-acetyltransferase from Bacillus cereus strain 10-L-2. PMID : 19147105 : DOI : 10.1016/j.jbiosc.2008.09.012 Abstract >>
Bacillus cereus strain 10-L-2 synthesizes two arylamine N-acetyltransferases (Nat-a and Nat-b) with broad substrate specificities toward aniline and its derivatives. In southern blot analysis using probes encoding the NH2-terminus of Nat-b and a conserved region of N-acetyltransferases, digested total DNA of strain 10-L-2 showed one positive band. We cloned and sequenced the gene encoding Nat-b. The NH2-terminal amino acid sequence predicted from the open reading frame (768 base pairs) corresponded to that of purified Nat-b. The cloned Nat-b gene was expressed in Escherichia coli. The expressed enzyme (BcNAT) from the recombinant strain was partially purified and characterized. Nat-b from strain 10-L-2 and BcNAT from the recombinant strain were slightly different from each others in substrate specificity and thermo-stability. We examined the biotransformations of 2-aminophenols and phenylenediamines by the whole cells of the recombinant strain. The cells converted these compounds into their corresponding acetanilides. Only one amino group of phenylenediamines was acetylated. The cells utilized 4-nitroacetanilide as an acetyl donor instead of acetyl-CoA. 4-Aminoacetanilide was produced and 4-nitroaniline was released almost stoichiometrically.
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151. |
Senior A,
Moir A,
( 2008 ) The Bacillus cereus GerN and GerT protein homologs have distinct roles in spore germination and outgrowth, respectively. PMID : 18641133 : DOI : 10.1128/JB.00789-08 PMC : PMC2546803 Abstract >>
The GerT protein of Bacillus cereus shares 74% amino acid identity with its homolog GerN. The latter is a Na(+)/H(+)-K(+) antiporter that is required for normal spore germination in inosine. The germination properties of single and double mutants of B. cereus ATCC 10876 reveal that unlike GerN, which is required for all germination responses that involve the GerI germinant receptor, the GerT protein does not have a significant role in germination, although it is required for the residual GerI-mediated inosine germination response of a gerN mutant. In contrast, GerT has a significant role in outgrowth; gerT mutant spores do not outgrow efficiently under alkaline conditions and outgrow more slowly than the wild type in the presence of high NaCl concentrations. The GerT protein in B. cereus therefore contributes to the success of spore outgrowth from the germinated state during alkaline or Na(+) stress.
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152. |
Rubinson EH,
Metz AH,
O'Quin J,
Eichman BF,
( 2008 ) A new protein architecture for processing alkylation damaged DNA: the crystal structure of DNA glycosylase AlkD. PMID : 18585735 : DOI : 10.1016/j.jmb.2008.05.078 PMC : PMC3763988 Abstract >>
DNA glycosylases safeguard the genome by locating and excising chemically modified bases from DNA. AlkD is a recently discovered bacterial DNA glycosylase that removes positively charged methylpurines from DNA, and was predicted to adopt a protein fold distinct from from those of other DNA repair proteins. The crystal structure of Bacillus cereus AlkD presented here shows that the protein is composed exclusively of helical HEAT-like repeats, which form a solenoid perfectly shaped to accommodate a DNA duplex on the concave surface. Structural analysis of the variant HEAT repeats in AlkD provides a rationale for how this protein scaffolding motif has been modified to bind DNA. We report 7mG excision and DNA binding activities of AlkD mutants, along with a comparison of alkylpurine DNA glycosylase structures. Together, these data provide important insight into the requirements for alkylation repair within DNA and suggest that AlkD utilizes a novel strategy to manipulate DNA in its search for alkylpurine bases.
|
153. |
Du L,
He Y,
Luo Y,
( 2008 ) Crystal structure and enantiomer selection by D-alanyl carrier protein ligase DltA from Bacillus cereus. PMID : 18847223 : DOI : 10.1021/bi801363b Abstract >>
Ubiquitous D-alanylation of lipoteichoic acids modulates the surface charge and ligand binding of the gram-positive cell wall. Disruption of the bacterial DltABCD gene involved in teichoic acid alanylation, as well as inhibition of the DltA protein, has been shown to increase a gram-positive bacterium's susceptibility to antibiotics. The DltA D-alanyl carrier protein ligase promotes a two-step process starting with adenylation of D-alanine. We have determined the 2.0 A resolution crystal structure of a DltA protein from Bacillus cereus in complex with the D-alanine adenylate intermediate of the first reaction. Despite the low level of sequence similarity, the DltA structure resembles known structures of adenylation domains such as the acetyl-CoA synthetase. The enantiomer selection appears to be enhanced by the medium-sized side chain of Cys-269. The Ala-269 mutant protein shows marked loss of such selection. The network of noncovalent interactions between the D-alanine adenylate and DltA provides structure-based rationale for aiding the design of tight-binding DltA inhibitors for combating infectious gram-positive bacteria such as the notorious methicillin-resistant Staphylococcus aureus.
|
154. |
Haakensen M,
Ziola B,
( 2008 ) Identification of novel horA-harbouring bacteria capable of spoiling beer. PMID : 18389005 : DOI : 10.1139/w08-007 Abstract >>
An ATP-binding cassette (ABC) multi-drug resistance (MDR) gene was found in 4 Gram-positive bacterial isolates of environmental origin and found capable of spoiling beer. The bacteria isolated were Bacillus cereus, Bacillus licheniformis, Paenibacillus humicus, and Staphylococcus epidermidis; all of which were previously unappreciated as beer-spoilage bacteria. The MDR gene found in these bacteria has less than 37% similarity to known ABC MDR proteins described for Bacillus and Staphylococcus, and this is the first finding of an ABC MDR gene in the genus Paenibacillus. The sequenced region of the gene was translated and compared phylogenetically with the closest GenBank matches of the respective species and the closest GenBank matches overall. The ABC MDR proteins from these isolates were found to cluster among known sequences of HorA, sharing 99.5% identity within the sequenced region. In the beer-spoilage-associated genera Lactobacillus and Pediococcus, the presence of the MDR gene horA correlates with the ability to grow in beer. As the unique horA-harbouring isolates described here are capable of growing in beer, it is likely that the presence of the horA gene likewise confers hop resistance to these organisms.
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155. |
Castiglioni S,
Pomati F,
Miller K,
Burns BP,
Zuccato E,
Calamari D,
Neilan BA,
( 2008 ) Novel homologs of the multiple resistance regulator marA in antibiotic-contaminated environments. PMID : 18771790 : DOI : 10.1016/j.watres.2008.07.004 Abstract >>
Antibiotics are commonly detected in the environment as contaminants. Exposure to antibiotics may induce antimicrobial-resistance, as well as the horizontal transfer of resistance genes in bacterial populations. We selected the resistance gene marA, mediating resistance to multiple antibiotics, and explored its distribution in sediment and water samples from surface and sewage treatment waters. Ciprofloxacin and ofloxacin (fluoroquinolones), sulphamethoxazole (sulphonamide), erythromycin, clarythromycin, and spiramycin (macrolides), lincomycin (lincosamide), and oxytetracycline (tetracycline) were measured in the same samples to determine antibiotic contamination. Bacterial populations from environmental samples were challenged with antibiotics to identify resistant isolates. The gene marA was found in almost all environmental samples and was confirmed by PCR amplification in antibiotic-resistant colonies. 16S rDNA sequencing revealed that the majority of resistant isolates belonged to the Gram-positive genus Bacillus, not previously known to possess the regulator marA. We assayed the incidence of marA in environmental bacterial populations of Escherichia coli and Bacillus by quantitative real-time PCR in correlation with the levels of antibiotics. Phylogenetic analysis indicated the possible lateral acquisition of marA by Bacillus from Gram-negative Enterobacteriaceae revealing a novel marA homolog in Bacillus. Quantitative PCR assays indicate that the frequency of this gene in antropised environments seems to be related to bacterial exposure to water-borne antibiotics.
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156. |
Tsalafouta A,
Psylinakis E,
Kapetaniou EG,
Kotsifaki D,
Deli A,
Roidis A,
Bouriotis V,
Kokkinidis M,
( 2008 ) Purification, crystallization and preliminary X-ray analysis of the peptidoglycan N-acetylglucosamine deacetylase BC1960 from Bacillus cereus in the presence of its substrate (GlcNAc)6. PMID : 18323609 : DOI : 10.1107/S1744309108002510 PMC : PMC2374148 Abstract >>
The peptidoglycan N-acetylglucosamine (GlcNAc) deacetylase BC1960 from Bacillus cereus (EC 3.5.1.33), an enzyme consisting of 275 amino acids, was crystallized in the presence of its substrate (GlcNAc)(6). The crystals belonged to the tetragonal space group P4(1)2(1)2, with unit-cell parameters a = b = 92.7, c = 242.9 A and four molecules in the asymmetric unit. A complete data set was collected at 100 K to a resolution of 2.38 A using synchrotron radiation.
|
157. |
Zhang JT,
Yan JP,
Zheng DS,
Sun YJ,
Yuan ZM,
( 2008 ) Expression of mel gene improves the UV resistance of Bacillus thuringiensis. PMID : 18266703 : DOI : 10.1111/j.1365-2672.2008.03729.x Abstract >>
To improve ultraviolet (UV) resistance of Bacillus thuringiensis for increasing the duration of the Bt product applied in the field, a genetically engineered strain Bt TD841 that produced both melanin and Cry1A protein was constructed, and its UV resistance was evaluated in the laboratory. Melanin quantitative analysis revealed that the recombinant strain Bt TD841 could synthesize 0.15 mg melanin ml(-1) sporulated culture. Atomic force microscopy confirmed the production of diamond crystal and SDS-PAGE results showed the expression of the 130 kDa Cry1A protein. Bioassay results demonstrated that the LC(50) value of Bt TD841 was 3.69 microl ml(-1) against Helicoverpa armigera and the UV resistance of this recombinant was enhanced 9.7-fold compared to its parental strain Bt HC42 after 4-h UV irradiation. Expression of the mel gene can significantly increase UV resistance of B. thuringiensis. This is the first report on genetically engineered Bt strain with co-expression of melanin and the insecticidal crystal proteins gene, and the results may offer a practical solution for improving the photoprotection of Bt products in field application.
|
158. |
Hsueh YH,
Somers EB,
Wong AC,
( 2008 ) Characterization of the codY gene and its influence on biofilm formation in Bacillus cereus. PMID : 18214442 : DOI : 10.1007/s00203-008-0348-8 Abstract >>
The foodborne pathogen Bacillus cereus can form biofilms on various food contact surfaces, leading to contamination of food products. To study the mechanisms of biofilm formation by B. cereus, a Tn5401 library was generated from strain UW101C. Eight thousand mutants were screened in EPS, a low nutrient medium. One mutant (M124), with a disruption in codY, developed fourfold less biofilm than the wild-type, and its defective biofilm phenotype was rescued by complementation. Addition of 0.1% casamino acids to EPS prolonged the duration of biofilms in the wild-type but not codY mutant. When decoyinine, a GTP synthesis inhibitor, was added to EPS, biofilm formation was decreased in the wild-type but not the mutant. The codY mutant produced three times higher protease activity than the wild-type. Zymogram and SDS-PAGE data showed that production of the protease (approximately 130 kDa) was repressed by CodY. Addition of proteinase K to EPS decreased biofilm formation by the wild-type. Using a dpp-lacZ fusion reporter system, it was shown that that the B. cereus CodY can sense amino acids and GTP levels. These data suggest that by responding to amino acids and intracellular GTP levels CodY represses production of an unknown protease and is involved in biofilm formation.
|
159. |
Nord D,
Sjöberg BM,
( 2008 ) Unconventional GIY-YIG homing endonuclease encoded in group I introns in closely related strains of the Bacillus cereus group. PMID : 18032435 : DOI : 10.1093/nar/gkm1016 PMC : PMC2248736 Abstract >>
Several group I introns have been previously found in strains of the Bacillus cereus group at three different insertion sites in the nrdE gene of the essential nrdIEF operon coding for ribonucleotide reductase. Here, we identify an uncharacterized group IA intron in the nrdF gene in 12 strains of the B. cereus group and show that the pre-mRNA is efficiently spliced. The Bacillus thuringiensis ssp. pakistani nrdF intron encodes a homing endonuclease, denoted I-BthII, with an unconventional GIY-(X)8-YIG motif that cleaves an intronless nrdF gene 7 nt upstream of the intron insertion site, producing 2-nt 3' extensions. We also found four additional occurrences of two of the previously reported group I introns in the nrdE gene of 25 sequenced B. thuringiensis and one B. cereus strains, and one non-annotated group I intron at a fourth nrdE insertion site in the B. thuringiensis ssp. Al Hakam sequenced genome. Two strains contain introns in both the nrdE and the nrdF genes. Phylogenetic studies of the nrdIEF operon from 39 strains of the B. cereus group suggest several events of horizontal gene transfer for two of the introns found in this operon.
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160. |
Florek P,
Muchová K,
Pavelcíková P,
Barák I,
( 2008 ) Expression of functional Bacillus SpoIISAB toxin-antitoxin modules in Escherichia coli. PMID : 18096016 : DOI : 10.1111/j.1574-6968.2007.00984.x Abstract >>
SpoIISA and SpoIISB proteins from Bacillus subtilis belong to a recently described bacterial programmed-cell death system. The current work demonstrates that the toxin-antitoxin module is also functional in Escherichia coli cells, where the expression of SpoIISA toxin leads to transient growth arrest coupled with cell lysis, and SpoIISA-induced death can be prevented by coexpression of its cognate antitoxin, SpoIISB. Escherichia coli cells appear to be able to escape the SpoIISA killing by activation of a specific, as yet unidentified protease that cleaves out the cytosolic part of the protein. Analysis of the toxic effects of the transmembrane and cytosolic portions of SpoIISA showed that neither of them separately can function as a toxin; therefore, both parts of the protein have to act in concert to exert the killing. This work also identifies genes encoding putative homologues of SpoIISA and SpoIISB proteins on chromosomes of other Bacilli species. The SpoIISA-like proteins from Bacillus anthracis and Bacillus cereus were shown to manifest the same effect on the viability of E. coli as their homologue from B. subtilis. Moreover, expression of the proposed spoIISB-like gene rescues E. coli cells from death induced by the SpoIISA homologue.
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161. |
Olsen JS,
Skogan G,
Fykse EM,
Rawlinson EL,
Tomaso H,
Granum PE,
Blatny JM,
( 2007 ) Genetic distribution of 295 Bacillus cereus group members based on adk-screening in combination with MLST (Multilocus Sequence Typing) used for validating a primer targeting a chromosomal locus in B. anthracis. PMID : 17997177 : DOI : 10.1016/j.mimet.2007.10.001 Abstract >>
The genetic distribution of 295 Bacillus cereus group members has been investigated by using a modified Multilocus Sequence Typing method (MLST). By comparing the nucleic acid sequence of the adk gene fragment, isolates of B. cereus group members most related to B. anthracis may be easily identified. The genetic distribution, with focus on the B. anthracis close neighbours, was used to evaluate a new primer set for specific identification of B. anthracis. This primer set, BA5510-1/2, targeted the putative B. anthracis specific gene BA5510. Real-time PCR using BA5510-1/2 amplified the target fragment from all B. anthracis strains tested and only two (of 289) non-B. anthracis strains analysed. This is one of the most thoroughly validated chromosomal B. anthracis markers for real-time PCR identification, in which the screened collection contained several very closely related B. anthracis strains.
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162. |
Cardazzo B,
Negrisolo E,
Carraro L,
Alberghini L,
Patarnello T,
Giaccone V,
( 2008 ) Multiple-locus sequence typing and analysis of toxin genes in Bacillus cereus food-borne isolates. PMID : 18083872 : DOI : 10.1128/AEM.01495-07 PMC : PMC2227710 Abstract >>
In the present study we characterized 47 food-borne isolates of Bacillus cereus using multilocus sequence typing (MLST). Newly determined sequences were combined with sequences available in public data banks in order to produce the largest data set possible. Phylogenetic analysis was performed on a total of 296 strains for which MLST sequence information is available, and three main lineages--I, II, and III--within the B. cereus complex were identified. With few exceptions, all food-borne isolates were in group I. The occurrence of horizontal gene transfer (HGT) among various strains was analyzed by several statistical methods, providing evidence of widespread lateral gene transfer within B. cereus. We also investigated the occurrence of toxin-encoding genes, focusing on their evolutionary history within B. cereus. Several patterns were identified, indicating a pivotal role of HGT in the evolution of toxin-encoding genes. Our results indicate that HGT is an important element in shaping the population structure of the B. cereus complex. The results presented here also provide strong evidence of reticulate evolution within the B. cereus complex.
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163. |
Song L,
Kalyanaraman C,
Fedorov AA,
Fedorov EV,
Glasner ME,
Brown S,
Imker HJ,
Babbitt PC,
Almo SC,
Jacobson MP,
Gerlt JA,
( 2007 ) Prediction and assignment of function for a divergent N-succinyl amino acid racemase. PMID : 17603539 : DOI : 10.1038/nchembio.2007.11 Abstract >>
The protein databases contain many proteins with unknown function. A computational approach for predicting ligand specificity that requires only the sequence of the unknown protein would be valuable for directing experiment-based assignment of function. We focused on a family of unknown proteins in the mechanistically diverse enolase superfamily and used two approaches to assign function: (i) enzymatic assays using libraries of potential substrates, and (ii) in silico docking of the same libraries using a homology model based on the most similar (35% sequence identity) characterized protein. The results matched closely; an experimentally determined structure confirmed the predicted structure of the substrate-liganded complex. We assigned the N-succinyl arginine/lysine racemase function to the family, correcting the annotation (L-Ala-D/L-Glu epimerase) based on the function of the most similar characterized homolog. These studies establish that ligand docking to a homology model can facilitate functional assignment of unknown proteins by restricting the identities of the possible substrates that must be experimentally tested.
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164. |
Chowdhary PK,
Alemseghed M,
Haines DC,
( 2007 ) Cloning, expression and characterization of a fast self-sufficient P450: CYP102A5 from Bacillus cereus. PMID : 17945181 : DOI : 10.1016/j.abb.2007.09.010 Abstract >>
CYP102s represent a family of natural self-sufficient fusions of cytochrome P450 and cytochrome P450 reductase found in some bacteria. One member of this family, named CYP102A1 or more traditionally P450BM-3, has been widely studied as a model of human P450 cytochromes. Remarkable detail of P450 structure and function has been revealed using this highly efficient enzyme. The recent rapid expansion of microbial genome sequences has revealed many relatives of CYP102A1, but to date only two from Bacillus subtilis have been characterized. We report here the cloning and expression of CYP102A5, a new member of this family that is very closely related to CYP102A4 from Bacillus anthracis. Characterization of the substrate specificity of CYP102A5 shows that it, like the other CYP102s, will metabolize saturated and unsaturated fatty acids as well as N-acylamino acids. CYP102A5 catalyzes very fast substrate oxidation, showing one of the highest turnover rates for any P450 monooxygenase studied so far. It does so with more specificity than other CYP102s, yielding primarily omega-1 and omega-2 hydroxylated products. Measurement of the rate of electron transfer through the reductase domain reveals that it is significantly faster in CYP102A5 than in CYP102A1, providing a likely explanation for the increased monooxygenation rate. The availability of this new, very fast fusion P450 will provide a great tool for comparative structure-function studies between CYP102A5 and the other characterized CYP102s.
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165. |
Sandrini MP,
Clausen AR,
On SL,
Aarestrup FM,
Munch-Petersen B,
Piskur J,
( 2007 ) Nucleoside analogues are activated by bacterial deoxyribonucleoside kinases in a species-specific manner. PMID : 17615154 : DOI : 10.1093/jac/dkm240 Abstract >>
To investigate the bactericidal activity of antiviral and anticancer nucleoside analogues against a variety of pathogenic bacteria and characterize the activating enzymes, deoxyribonucleoside kinases (dNKs). Several FDA-approved nucleoside analogue drugs were screened for their potential bactericidal activity against several clinical bacterial isolates and type strains. We identified and subcloned the genes coding for putative deoxyribonucleoside kinases in Escherichia coli, Pasteurella multocida, Salmonella enterica, Yersinia enterocolitica, Bacillus cereus, Clostridium perfringens and Listeria monocytogenes. These genes were tested for their ability to increase the susceptibility of a dNK-deficient E. coli strain to various analogues. We overexpressed, purified and characterized the substrate specificity and kinetic properties of the recombinant enzymes from S. enterica and B. cereus. The tested Gram-negative bacteria were susceptible to 3'-azido-3'-deoxythymidine (AZT) in the concentration range 0.032-31.6 microM except for a single E. coli isolate and two Pseudomonas aeruginosa isolates which were resistant to the tested AZT concentrations. Purified recombinant S. enterica thymidine kinase phosphorylated AZT efficiently with a Km of 73.3 microM and k(cat)/Km of 6.6 x 10(4) s(-1) M(-1) and is the activator of this drug in vivo. 2',2'-Difluoro-2'-deoxycytidine (gemcitabine) was a potent antibiotic against Gram-positive bacteria in the concentration range between 0.001 and 1.0 microM. The B. cereus deoxyadenosine kinase had a Km for gemcitabine of 33.5 microM and k(cat)/Km of 5.1 x 10(3) s(-1) M(-1) and activates gemcitabine in vivo. S. enterica and B. cereus are now amongst the first bacteria with a completely characterized set of dNK enzymes. Bacterial dNKs efficiently activate nucleoside analogues in a species-specific manner. Therefore, nucleoside analogues have a potential to be employed as antibiotics in the fight against emerging multiresistant bacteria.
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166. |
Huck JR,
Woodcock NH,
Ralyea RD,
Boor KJ,
( 2007 ) Molecular subtyping and characterization of psychrotolerant endospore-forming bacteria in two New York State fluid milk processing systems. PMID : 17969618 : DOI : 10.4315/0362-028x-70.10.2354 Abstract >>
Psychrotolerant endospore-forming bacteria Bacillus and Paenibacillus spp. are important spoilage organisms in fluid milk. A recently developed rpoB subtyping method was applied to characterize the diversity and phylogenetic relationships among Bacillus and related sporeformers associated with milk processing systems. Milk samples representing the processing continuum from raw milk to pasteurized products were collected from two fluid milk processing plants, held at 6 degrees C up to the code date that had been established by each processing plant (i.e., either 18 or 21 days), and plated for bacterial enumeration throughout storage. Bacterial colonies selected to represent the visible diversity in colony morphology on enumeration plates were examined further. Among 385 bacterial isolates characterized, 35% were Bacillus spp., and 65% were Paenibacillus spp. A total of 92 rpoB allelic types were identified among these isolates, indicating considerable diversity among endospore-forming spoilage organisms present in fluid milk systems. Of the 92 allelic types identified, 19 were isolated from samples collected from both processing plants. The same rpoB allelic types were frequently identified in paired raw milk and packaged product samples, indicating that Bacillus and Paenibacillus spp. can enter dairy processing systems through raw milk. Certain subtypes were found exclusively in pasteurized samples, including those that were temporally independent, suggesting the possibility of in-plant sources for these spoilage organisms, including through the persistence of selected subtypes in processing plants. Development of effective control strategies for the diverse array of psychrotolerant endospore-forming organisms that currently limit the shelf lives of high-temperature short-time fluid milk products will require comprehensive, integrated efforts along the entire milk processing continuum.
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167. |
Godsey MH,
Minasov G,
Shuvalova L,
Brunzelle JS,
Vorontsov II,
Collart FR,
Anderson WF,
( 2007 ) The 2.2 A resolution crystal structure of Bacillus cereus Nif3-family protein YqfO reveals a conserved dimetal-binding motif and a regulatory domain. PMID : 17586767 : DOI : 10.1110/ps.062674007 PMC : PMC2206684 Abstract >>
YqfO of Bacillus cereus is a member of the widespread Nif3 family of proteins, which has been highlighted as an important target for structural genomics. The N- and C-terminal domains are conserved across the family and contain a dimetal-binding motif in a putative active site. YqfO contains an insert in the middle of the protein, present in a minority of bacterial family members. The structure of YqfO was determined at a resolution of 2.2 A and reveals conservation of the putative active site. It also reveals the previously unknown structure of the insert, which despite extremely limited sequence conservation, bears great similarity to PII, CutA, and a number of other trimeric regulatory proteins. Our results suggest that this domain acts as a signal sensor to regulate the still-unknown catalytic activity of the more-conserved domains.
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168. |
Alam A,
Shi N,
Jiang Y,
( 2007 ) Structural insight into Ca2+ specificity in tetrameric cation channels. PMID : 17878296 : DOI : 10.1073/pnas.0707324104 PMC : PMC2000519 Abstract >>
Apparent blockage of monovalent cation currents by the permeating blocker Ca(2+) is a physiologically essential phenomenon relevant to cyclic nucleotide-gated (CNG) channels. The recently determined crystal structure of a bacterial homolog of CNG channel pores, the NaK channel, revealed a Ca(2+) binding site at the extracellular entrance to the selectivity filter. This site is not formed by the side-chain carboxylate groups from the conserved acidic residue, Asp-66 in NaK, conventionally thought to directly chelate Ca(2+) in CNG channels, but rather by the backbone carbonyl groups of residue Gly-67. Here we present a detailed structural analysis of the NaK channel with a focus on Ca(2+) permeability and blockage. Our results confirm that the Asp-66 residue, although not involved in direct chelation of Ca(2+), plays an essential role in external Ca(2+) binding. Furthermore, we give evidence for the presence of a second Ca(2+) binding site within the NaK selectivity filter where monovalent cations also bind, providing a structural basis for Ca(2+) permeation through the NaK pore. Compared with other Ca(2+)-binding proteins, both sites in NaK present a novel mode of Ca(2+) chelation, using only backbone carbonyl oxygen atoms from residues in the selectivity filter. The external site is under indirect control by an acidic residue (Asp-66), making it Ca(2+)-specific. These findings give us a glimpse of the possible underlying mechanisms allowing Ca(2+) to act both as a permeating ion and blocker of CNG channels and raise the possibility of a similar chemistry governing Ca(2+) chelation in Ca(2+) channels.
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169. |
Soufiane B,
Xu D,
Côté JC,
( 2007 ) Flagellin (FliC) protein sequence diversity among Bacillus thuringiensis does not correlate with H serotype diversity. PMID : 17578675 : DOI : 10.1007/s10482-007-9173-3 Abstract >>
In Escherichia coli, the fliC gene encodes flagellin, the protein responsible for eliciting the immunological reaction in H serotyping. Here, the presence of the flagellin fliC gene was studied in 86 Bacillus thuringiensis strains encompassing 67 H serotypes. Nineteen strains from four additional species in the B. cereus sensu lato group, B. cereus, B. anthracis, B. mycoides, and B. weihenstephanensis, were added for comparison purposes. The fliC genes were amplified, cloned and their nucleotide sequences determined and translated into amino acid sequences. A bootstrapped neighbor-joining tree was generated from the alignment of the translated amino acid sequences of the amplicons. Although most B. thuringiensis H serotypes had different flagellin amino acid sequences, some different B. thuringiensis serovars shared identical flagellin amino acid sequences. In addition, although serovars from the same H serotype were sometimes found clustered together, several serovars from the same H serotype carried flagellins with sufficiently different amino acid sequences as to be located on distant clusters. No correlations could be established between flagellin (FliC) protein sequence diversity among B. thuringiensis H serotypes and H serotype diversity. These suggest that the B. thuringiensis fliC gene does not code for the flagellin copy responsible for eliciting the immunological reaction in H serotyping. In a previous study, the authors have shown that the B. thuringiensis hag gene codes for the flagellin copy responsible for eliciting the immunological reaction in H serotyping. It is proposed that the B. thuringiensis fliC gene studied here be renamed and that the so-called hag gene studied before be renamed fliC, both in accordance with the E. coli nomenclature.
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170. |
Liu Y,
Lai Q,
Du J,
Shao Z,
( 2017 ) Genetic diversity and population structure of the Bacillus cereus group bacteria from diverse marine environments. PMID : 28386130 : DOI : 10.1038/s41598-017-00817-1 PMC : PMC5429728 Abstract >>
The phylogenetic diversity of marine bacteria belonged to the Bacillus cereus group has not been well investigated. Here, we present the genetic diversity and population structure of 71 bacteria from diverse marine environments, using a multilocus sequence typing (MLST) approach and the analyses of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) based on some representative genomic sequences. The MLST analysis demonstrated that these isolates were highly diverse and a wide distribution in marine environments and some of them showed niche specificity to some extent. They were assigned to 27 sequence types (STs) with 23 novel STs. Phylogenetic analysis of 82 bacteria containing 11 type strains based on MLST discriminated them as 20 clusters including 10 new ones. Both the dDDH and ANI results supported the proposition that each of 20 clusters represented one independent species, including 10 putative novel species. Values of 98.3% of MLST similarity and 96.2% of ANI were proposed as the standard for the species definition of this group. In summary, the first insight into the phylogenetic diversity of the group bacteria from marine environments will contribute to better understanding of their ecological role and evolution in contrast with terrestrial environments.
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171. |
Fadouloglou VE,
Balomenou S,
Aivaliotis M,
Kotsifaki D,
Arnaouteli S,
Tomatsidou A,
Efstathiou G,
Kountourakis N,
Miliara S,
Griniezaki M,
Tsalafouta A,
Pergantis SA,
Boneca IG,
Glykos NM,
Bouriotis V,
Kokkinidis M,
( 2017 ) Unusual �\-Carbon Hydroxylation of Proline Promotes Active-Site Maturation. PMID : 28333455 : DOI : 10.1021/jacs.6b12209 Abstract >>
The full extent of proline (Pro) hydroxylation has yet to be established, as it is largely unexplored in bacteria. We describe here a so far unknown Pro hydroxylation activity which occurs in active sites of polysaccharide deacetylases (PDAs) from bacterial pathogens, modifying the protein backbone at the C�\ atom of a Pro residue to produce 2-hydroxyproline (2-Hyp). This process modifies with high specificity a conserved Pro, shares with the deacetylation reaction the same active site and one catalytic residue, and utilizes molecular oxygen as source for the hydroxyl group oxygen of 2-Hyp. By providing additional hydrogen-bonding capacity, the Pro��2-Hyp conversion alters the active site and enhances significantly deacetylase activity, probably by creating a more favorable environment for transition-state stabilization. Our results classify this process as an active-site "maturation", which is highly atypical in being a protein backbone-modifying activity, rather than a side-chain-modifying one.
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172. |
Lee C,
Kim MI,
Park J,
Jeon BY,
Yoon SI,
Hong M,
( 2017 ) Crystal structure of the flagellar chaperone FliS from Bacillus cereus and an invariant proline critical for FliS dimerization and flagellin recognition. PMID : 28414127 : DOI : 10.1016/j.bbrc.2017.04.070 Abstract >>
FliS is a cytoplasmic flagellar chaperone for the flagellin, which polymerizes into filaments outside of the flagellated bacteria. Cytoplasmic interaction between FliS and flagellin is critical to retain the flagellin protein in a monomeric form, which is transported from the cytoplasm through the flagellar export apparatus to the extracellular space for filament assembly. Defects in the FliS protein directly diminish bacterial motility, pathogenicity, and viability. Although the overall structure of FliS is known, structural and mutational studies on FliS from other bacterial species are still required to reveal any unresolved biophysical features of FliS itself or functionally critical residues for flagellin recognition. Here, we present the crystal structure of FliS from Bacillus cereus (BcFliS) at 2.0 ? resolution. FliS possesses a highly dynamic N-terminal region, which is appended to the common four-helix bundle structure. An invariant proline residue (Pro17 in B. cereus FliS) was identified in all known FliS sequences between the N-terminal region and the four-helix bundle. The N-terminal proline residue functions as a helix breaker critical for FliS dimerization and flagellin recognition.
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173. |
Yamada A,
Tsukagoshi N,
Udaka S,
Sasaki T,
Makino S,
Nakamura S,
Little C,
Tomita M,
Ikezawa H,
( 1988 ) Nucleotide sequence and expression in Escherichia coli of the gene coding for sphingomyelinase of Bacillus cereus. PMID : 2841128 : DOI : 10.1111/j.1432-1033.1988.tb14186.x Abstract >>
Bacillus cereus secretes phospholipases C, which hydrolyze phosphatidylcholine, sphingomyelin and phosphatidylinositol. A 7.5-kb HindIII fragment of B. cereus DNA cloned into Escherichia coli, with pUC18 as a vector, directed the synthesis of the sphingomyelin-hydrolyzing phospholipase C, sphingomyelinase. Nucleotide sequence analysis of the subfragment revealed that it contained two open reading frames in tandem. The upstream truncated open reading frame corresponds to the carboxy-terminal portion of the phosphatidylcholine-hydrolyzing phospholipase C, and the downstream open reading frame to the entire translational portion of the sphingomyelinase. The two phospholipase C genes form a gene cluster. As inferred from the DNA sequence, the B. cereus sphingomyelinase has a signal peptide of 27 amino acid residues and the mature enzyme comprises 306 amino acid residues, with a molecular mass of 34233 Da. The signal peptide of the enzyme was found to be functional in protein transport across the membrane of E. coli. The enzymatic properties of the sphingomyelinase synthesized in E. coli resemble those of the donor strain sphingomyelinase. The enzymatic activity toward sphingomyelin was enhanced 20-30-fold in the presence of MgCl2, and the adsorption of the enzyme onto erythrocyte membranes was accelerated in the presence of CaCl2.
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174. |
Lyngwi NA,
Nongkhlaw M,
Kalita D,
Joshi SR,
( 2016 ) Bioprospecting of Plant Growth Promoting Bacilli and Related Genera Prevalent in Soils of Pristine Sacred Groves: Biochemical and Molecular Approach. PMID : 27111883 : DOI : 10.1371/journal.pone.0152951 PMC : PMC4844137 Abstract >>
Bacillus spp. and related genera native to soils of the pristine sacred groves from Meghalaya, India were characterized using biochemical and 16S rRNA gene analysis which revealed dominance of Bacillus, Paenibacillus, Lysinibacillus and Viridibacillus in the groves. Biochemical estimation was carried out for in vitro testing of plant growth promoting traits present in these isolates. PCR screening were performed for plant growth-promoting related genes involved in the biosynthesis of acid phosphatase (AcPho), indolepyruvate decarboxylase (ipdC), 1-aminocyclopropane-1-carboxylate deaminase (accd) and siderophore biosynthesis protein (asbA). 76% of the sacred grove isolates gave an amplified fragment for AcPho. Three of the isolates gave an amplified fragment for IpdC gene. Apart from 2 isolates, all the other isolates including the reference strains were positive for the amplification of the accd gene indicating their potential to produce ACC deaminase enzyme. 42% of the isolates gave an amplified fragment for asbA gene indicating the potential ability of these isolates to produce the catechol type siderophore, petrobactin. Overall findings indicated multiple PGP genetic traits present in these isolates which suggested that these isolates are capable of expressing multiple PGP traits. Phylogenetic and sequence analysis of accd and asbA genes from the isolates revealed that asbA genes from Paenibacillus taichungiensis SG3 and Paenibacillus tylopili SG24 indicated the occurrence of intergeneric horizontal transfer between Paenibacillus and Bacillus.
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175. |
Parsons ZD,
Bland JM,
Mullins EA,
Eichman BF,
( 2016 ) A Catalytic Role for C-H/�k Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD. PMID : 27571247 : DOI : 10.1021/jacs.6b07399 PMC : PMC5034759 Abstract >>
DNA glycosylases protect genomic integrity by locating and excising aberrant nucleobases. Substrate recognition and excision usually take place in an extrahelical conformation, which is often stabilized by �k-stacking interactions between the lesion nucleobase and aromatic side chains in the glycosylase active site. Bacillus cereus AlkD is the only DNA glycosylase known to catalyze base excision without extruding the damaged nucleotide from the DNA helix. Instead of contacting the nucleobase itself, the AlkD active site interacts with the lesion deoxyribose through a series of C-H/�k interactions. These interactions are ubiquitous in protein structures, but evidence for their catalytic significance in enzymology is lacking. Here, we show that the C-H/�k interactions between AlkD and the lesion deoxyribose participate in catalysis of glycosidic bond cleavage. This is the first demonstration of a catalytic role for C-H/�k interactions as intermolecular forces important to DNA repair.
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176. |
Wu H,
Wu Q,
Wu G,
Gu Q,
Wei L,
( 2016 ) Cd-Resistant Strains of B. cereus S5 with Endurance Capacity and Their Capacities for Cadmium Removal from Cadmium-Polluted Water. PMID : 27077388 : DOI : 10.1371/journal.pone.0151479 PMC : PMC4831789 Abstract >>
The goal of this study was to identify Cd-resistant bacterial strains with endurance capacity and to evaluate their ability to remove cadmium ions from cadmium-polluted water. The Bacillus cereusS5 strain identified in this study had the closest genetic relationship with B. cereus sp. Cp1 and performed well in the removal of Cd2+ions from solution. The results showed that both the live and dead biomasses of the Cd2+-tolerant B. cereus S5 strain could absorb Cd2+ ions in solution but that the live biomass of the B. cereus S5 strain outperformed the dead biomass at lower Cd2+concentrations. An analysis of the cadmium tolerance genes of B. cereus S5 identified ATPase genes that were associated with cadmium tolerance and involved in the ATP pumping mechanism. The FTIR spectra revealed the presence of amino, carboxyl and hydroxyl groups on the pristine biomass and indicated that the cadmium ion removal ability was related to the structure of the strain. The maximum absorption capacity of the B. cereus S5 strain in viable spore biomass was 70.16 mg/g (dry weight) based on a pseudo-second-order kinetic model fit to the experimental data. The Langmuir and Langmuir-Freundlich isotherm adsorption models fit the cadmium ion adsorption data well, and the kinetic curves indicated that the adsorption rate was second-order. For Cd2+ concentrations (mg/L) of 1-109 mg/L, good removal efficiency (>80%) was achieved using approximately 3.48-10.3 g/L of active spore biomass of the B. cereus S5 strain. A cadmium-tolerant bacteria-activated carbon-immobilized column could be used for a longer duration and exhibited greater treatment efficacy than the control column in the treatment of cadmium-polluted water. In addition, a toxicity assessment using mice demonstrated that the biomass of the B. cereus S5 strain and its fermentation products were non-toxic. Thus, the isolated B. cereus S5 strain can be considered an alternative biological adsorbent for use in emergency responses to severe cadmium pollution and in the routine treatment of trace cadmium pollution.
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177. |
Park SC,
Kim PH,
Lee GS,
Kang SG,
Ko HJ,
Yoon SI,
( 2016 ) Structural and biochemical characterization of the Bacillus cereus 3-hydroxyisobutyrate dehydrogenase. PMID : 27120461 : DOI : 10.1016/j.bbrc.2016.04.126 Abstract >>
The 3-hydroxyisobutyrate dehydrogenase (HIBADH) family catalyzes the NAD(+)- or NADP(+)-dependent oxidation of various �]-hydroxyacid substrates into their cognate semialdehydes for diverse metabolic pathways. Because HIBADH group members exhibit different substrate specificities, the substrate-recognition mode of each enzyme should be individually characterized. In the current study, we report the biochemical and structural analysis of a HIBADH group enzyme from Bacillus cereus (bcHIBADH). bcHIBADH mediates a dehydrogenation reaction on S-3-hydroxyisobutyrate substrate with high catalytic efficiency in an NAD(+)-dependent manner; it also oxidizes l-serine and 3-hydroxypropionate with lower activity. bcHIBADH consists of two domains and is further assembled into a functional dimer rather than a tetramer that has been commonly observed in other prokaryotic HIBADH group members. In the bcHIBADH structure, the interdomain cleft forms a putative active site and simultaneously accommodates both an NAD(+) cofactor and a substrate mimic. Our structure-based comparative analysis highlights structural motifs that are important in the cofactor and substrate recognition of the HIBADH group.
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178. |
Omer H,
Alpha-Bazin B,
Brunet JL,
Armengaud J,
Duport C,
( 2015 ) Proteomics identifies Bacillus cereus EntD as a pivotal protein for the production of numerous virulence factors. PMID : 26500610 : DOI : 10.3389/fmicb.2015.01004 PMC : PMC4595770 Abstract >>
Bacillus cereus is a Gram-positive pathogen that causes a wide variety of diseases in humans. It secretes into the extracellular milieu proteins that may contribute directly or indirectly to its virulence. EntD is a novel exoprotein identified by proteogenomics of B. cereus ATCC 14579. We constructed a �GentD mutant and analyzed the impact of entD disruption on the cellular proteome and exoproteome isolated from early, late, and stationary-phase cultures. We identified 308 and 79 proteins regulated by EntD in the cellular proteome and the exoproteome, respectively. The contribution of these proteins to important virulence-associated functions, including central metabolism, cell structure, antioxidative ability, cell motility, and toxin production, are presented. The proteomic data were correlated with the growth defect, cell morphology change, reduced motility, and reduced cytotoxicity of the �GentD mutant strain. We conclude that EntD is an important player in B. cereus virulence. The function of EntD and the putative EntD-dependent regulatory network are discussed. To our knowledge, this study is the first characterization of an Ent family protein in a species of the B. cereus group.
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179. |
Gao T,
Foulston L,
Chai Y,
Wang Q,
Losick R,
( 2015 ) Alternative modes of biofilm formation by plant-associated Bacillus cereus. PMID : 25828975 : DOI : 10.1002/mbo3.251 PMC : PMC4475387 Abstract >>
The ability to form multicellular communities known as biofilms is a widespread adaptive behavior of bacteria. Members of the Bacillus group of bacteria have been found to form biofilms on plant roots, where they protect against pathogens and promote growth. In the case of the model bacterium Bacillus subtilis the genetic pathway controlling biofilm formation and the production of an extracellular matrix is relatively well understood. However, it is unclear whether other members of this genus utilize similar mechanisms. We determined that a plant-associated strain of Bacillus cereus (905) can form biofilms by two seemingly independent pathways. In one mode involving the formation of floating biofilms (pellicles) B. cereus 905 appears to rely on orthologs of many of the genes known to be important for B. subtilis biofilm formation. We report that B. cereus 905 also forms submerged, surface-associated biofilms and in a manner that resembles biofilm formation by the pathogen Staphylococcus aureus. This alternative mode, which does not rely on B. subtilis-like genes for pellicle formation, takes place under conditions of glucose fermentation and depends on a drop in the pH of the medium.
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180. |
Zhu K,
Hölzel CS,
Cui Y,
Mayer R,
Wang Y,
Dietrich R,
Didier A,
Bassitta R,
Märtlbauer E,
Ding S,
( 2016 ) Probiotic Bacillus cereus Strains, a Potential Risk for Public Health in China. PMID : 27242738 : DOI : 10.3389/fmicb.2016.00718 PMC : PMC4876114 Abstract >>
Bacillus cereus is an important cause of foodborne infectious disease and food poisoning. However, B. cereus has also been used as a probiotic in human medicine and livestock production, with low standards of safety assessment. In this study, we evaluated the safety of 15 commercial probiotic B. cereus preparations from China in terms of mislabeling, toxin production, and transferable antimicrobial resistance. Most preparations were incorrectly labeled, as they contained additional bacterial species; one product did not contain viable B. cereus at all. In total, 18 B. cereus group strains-specifically B. cereus and Bacillus thuringiensis-were isolated. Enterotoxin genes nhe, hbl, and cytK1, as well as the ces-gene were assessed by PCR. Enterotoxin production and cytotoxicity were confirmed by ELISA and cell culture assays, respectively. All isolated B. cereus group strains produced the enterotoxin Nhe; 15 strains additionally produced Hbl. Antimicrobial resistance was assessed by microdilution; resistance genes were detected by PCR and further characterized by sequencing, transformation and conjugation assays. Nearly half of the strains harbored the antimicrobial resistance gene tet(45). In one strain, tet(45) was situated on a mobile genetic element-encoding a site-specific recombination mechanism-and was transferable to Staphylococcus aureus and Bacillus subtilis by electro-transformation. In view of the wide and uncontrolled use of these products, stricter regulations for safety assessment, including determination of virulence factors and transferable antimicrobial resistance genes, are urgently needed.
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181. |
Kim MI,
Hong M,
( 2016 ) Crystal structure of the Bacillus-conserved MazG protein, a nucleotide pyrophosphohydrolase. PMID : 26920050 : DOI : 10.1016/j.bbrc.2016.02.097 Abstract >>
BA1544 from Bacillus anthracis was previously annotated as a transcription factor for the gene cluster ba1554 - ba1558, but has not been experimentally characterized. B. anthracis is an obligate pathogen causing fatal inhalational anthrax, and BA1544 is absolutely conserved in Bacillus species, including Bacillus cereus, Bacillus thuringiensis and Bacillus mycoides, with 100% sequence identity. To address the function of BA1544, we performed structural and biochemical studies, which revealed that BA1544 is a MazG protein. Thus, herein, the protein is defined as Bacillus-conserved MazG (BcMazG). Like other MazG structures, BcMazG assembles into a tetrameric architecture. Each monomer adopts a four-�\-helix bundle that accommodates a metal ion using four acidic residues, and presents one putative substrate-binding site. Enzymatic characterization demonstrated that BcMazG is a nucleoside triphosphate (NTP) pyrophosphohydrolase and prefers adenosine triphosphate as a substrate among canonical NTPs. Moreover, structural comparison of BcMazG with its homologues revealed a potential regulation mechanism whereby the enzymatic activity of BcMazG is regulated by its C-terminal region.
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182. |
Mullins EA,
Shi R,
Parsons ZD,
Yuen PK,
David SS,
Igarashi Y,
Eichman BF,
( 2015 ) The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. PMID : 26524531 : DOI : 10.1038/nature15728 PMC : PMC4896645 Abstract >>
Threats to genomic integrity arising from DNA damage are mitigated by DNA glycosylases, which initiate the base excision repair pathway by locating and excising aberrant nucleobases. How these enzymes find small modifications within the genome is a current area of intensive research. A hallmark of these and other DNA repair enzymes is their use of base flipping to sequester modified nucleotides from the DNA helix and into an active site pocket. Consequently, base flipping is generally regarded as an essential aspect of lesion recognition and a necessary precursor to base excision. Here we present the first, to our knowledge, DNA glycosylase mechanism that does not require base flipping for either binding or catalysis. Using the DNA glycosylase AlkD from Bacillus cereus, we crystallographically monitored excision of an alkylpurine substrate as a function of time, and reconstructed the steps along the reaction coordinate through structures representing substrate, intermediate and product complexes. Instead of directly interacting with the damaged nucleobase, AlkD recognizes aberrant base pairs through interactions with the phosphoribose backbone, while the lesion remains stacked in the DNA duplex. Quantum mechanical calculations revealed that these contacts include catalytic charge-dipole and CH-�k interactions that preferentially stabilize the transition state. We show in vitro and in vivo how this unique means of recognition and catalysis enables AlkD to repair large adducts formed by yatakemycin, a member of the duocarmycin family of antimicrobial natural products exploited in bacterial warfare and chemotherapeutic trials. Bulky adducts of this or any type are not excised by DNA glycosylases that use a traditional base-flipping mechanism. Hence, these findings represent a new model for DNA repair and provide insights into catalysis of base excision.
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183. |
Toda A,
Tsurumura T,
Yoshida T,
Tsumori Y,
Tsuge H,
( 2015 ) Rho GTPase Recognition by C3 Exoenzyme Based on C3-RhoA Complex Structure. PMID : 26067270 : DOI : 10.1074/jbc.M115.653220 PMC : PMC4528107 Abstract >>
C3 exoenzyme is a mono-ADP-ribosyltransferase (ART) that catalyzes transfer of an ADP-ribose moiety from NAD(+) to Rho GTPases. C3 has long been used to study the diverse regulatory functions of Rho GTPases. How C3 recognizes its substrate and how ADP-ribosylation proceeds are still poorly understood. Crystal structures of C3-RhoA complex reveal that C3 recognizes RhoA via the switch I, switch II, and interswitch regions. In C3-RhoA(GTP) and C3-RhoA(GDP), switch I and II adopt the GDP and GTP conformations, respectively, which explains why C3 can ADP-ribosylate both nucleotide forms. Based on structural information, we successfully changed Cdc42 to an active substrate with combined mutations in the C3-Rho GTPase interface. Moreover, the structure reflects the close relationship among Gln-183 in the QXE motif (C3), a modified Asn-41 residue (RhoA) and NC1 of NAD(H), which suggests that C3 is the prototype ART. These structures show directly for the first time that the ARTT loop is the key to target protein recognition, and they also serve to bridge the gaps among independent studies of Rho GTPases and C3.
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184. |
Zhang S,
Liao SA,
Yu X,
Lu H,
Xian JA,
Guo H,
Wang A,
Xie J,
( 2015 ) Microbial diversity of mangrove sediment in Shenzhen Bay and gene cloning, characterization of an isolated phytase-producing strain of SPC09 B. cereus. PMID : 25646962 : DOI : 10.1007/s00253-015-6405-8 Abstract >>
Phytases hydrolyze phytate to release inorganic phosphate, which decreases the requirement for phosphorus in fertilizers for crops and thus reduces environmental pollutants. This study analyzed microbial communities in rhizosphere sediment, collected in September 2012 from Shenzhen Bay, Guangdong, China, using high-throughput pyrosequencing; the results showed that the dominant taxonomic phyla were Chloroflexi, Firmicutes, and Proteobacteria, and the proportion of the beneficial bacteria, Bacillus, was 4.95 %. Twenty-nine culturable, phytase-producing bacteria were isolated, their phosphorus solubilization capacity was analyzed, and they were taxonomically characterized. Their phylogenetic placement was determined using 16S ribosomal RNA (rRNA) gene sequence analysis. The result shows that most of the isolates are members of the order Bacillales, although seven strains of Enterobacteriales, two strains of Pseudomonadales, and one strain of Oceanospirillales were also identified. The phytase gene was cloned from SPC09, Bacillus cereus, which showed the highest phosphorus solubilizing ability among the isolated strains. The gene encoded a primary translation product of 335 amino acids. A construct including the 1005-nt ORF fragment, Bc-phy, was transformed into Escherichia coli. The recombinant phytase was produced and purified, which revealed the temperature optima at 60 �XC and pH optima at 6.5. The assessment by quantitative PCR (qPCR) showed an abundance of bacteria containing the Bc-phy gene; the level was generally higher in the mangrove forest than in the tidal flats and in surface soil compared to bottom soil, and the highest value was obtained in June. Herein, we report on the cloning, characterization, and activity of a novel phytase isolated from a mangrove system.
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185. |
Hwang S,
Aronov A,
Bar-Peled M,
( 2015 ) The Biosynthesis of UDP-D-QuiNAc in Bacillus cereus ATCC 14579. PMID : 26207987 : DOI : 10.1371/journal.pone.0133790 PMC : PMC4514872 Abstract >>
N-acetylquinovosamine (2-acetamido-2,6-di-deoxy-D-glucose, QuiNAc) is a relatively rare amino sugar residue found in glycans of few pathogenic gram-negative bacteria where it can play a role in infection. However, little is known about QuiNAc-related polysaccharides in gram-positive bacteria. In a routine screen for bacillus glycan grown at defined medium, it was surprising to identify a QuiNAc residue in polysaccharides isolated from this gram-positive bacterium. To gain insight into the biosynthesis of these glycans, we report the identification of an operon in Bacillus cereus ATCC 14579 that contains two genes encoding activities not previously described in gram-positive bacteria. One gene encodes a UDP-N-acetylglucosamine C4,6-dehydratase, (abbreviated Pdeg) that converts UDP-GlcNAc to UDP-4-keto-4,6-D-deoxy-GlcNAc (UDP-2-acetamido-2,6-dideoxy-�\-D-xylo-4-hexulose); and the second encodes a UDP-4-reductase (abbr. Preq) that converts UDP-4-keto-4,6-D-deoxy-GlcNAc to UDP-N-acetyl-quinovosamine in the presence of NADPH. Biochemical studies established that the sequential Pdeg and Preq reaction product is UDP-D-QuiNAc as determined by mass spectrometry and one- and two-dimensional NMR experiments. Also, unambiguous evidence for the conversions of the dehydratase product, UDP-�\-D-4-keto-4,6-deoxy-GlcNAc, to UDP-�\-D-QuiNAc was obtained using real-time 1H-NMR spectroscopy and mass spectrometry. The two genes overlap by 4 nucleotides and similar operon organization and identical gene sequences were also identified in a few other Bacillus species suggesting they may have similar roles in the lifecycle of this class of bacteria important to human health. Our results provide new information about the ability of Bacilli to form UDP-QuiNAc and will provide insight to evaluate their role in the biology of Bacillus.
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186. |
Thorsen L,
Kando CK,
Sawadogo H,
Larsen N,
Diawara B,
Ouédraogo GA,
Hendriksen NB,
Jespersen L,
( 2015 ) Characteristics and phylogeny of Bacillus cereus strains isolated from Maari, a traditional West African food condiment. PMID : 25528535 : DOI : 10.1016/j.ijfoodmicro.2014.11.026 Abstract >>
Maari is a spontaneously fermented food condiment made from baobab tree seeds in West African countries. This type of product is considered to be safe, being consumed by millions of people on a daily basis. However, due to the spontaneous nature of the fermentation the human pathogen Bacillus cereus occasionally occurs in Maari. This study characterizes succession patterns and pathogenic potential of B. cereus isolated from the raw materials (ash, water from a drilled well (DW) and potash), seed mash throughout fermentation (0-96h), after steam cooking and sun drying (final product) from two production sites of Maari. Aerobic mesophilic bacterial (AMB) counts in raw materials were of 10(5)cfu/ml in DW, and ranged between 6.5��10(3) and 1.2��10(4)cfu/g in potash, 10(9)-10(10)cfu/g in seed mash during fermentation and 10(7) - 10(9) after sun drying. Fifty three out of total 290 AMB isolates were identified as B. cereus sensu lato by use of ITS-PCR and grouped into 3 groups using PCR fingerprinting based on Escherichia coli phage-M13 primer (M13-PCR). As determined by panC gene sequencing, the isolates of B. cereus belonged to PanC types III and IV with potential for high cytotoxicity. Phylogenetic analysis of concatenated sequences of glpF, gmk, ilvD, pta, pur, pycA and tpi revealed that the M13-PCR group 1 isolates were related to B. cereus biovar anthracis CI, while the M13-PCR group 2 isolates were identical to cereulide (emetic toxin) producing B. cereus strains. The M13-PCR group 1 isolates harboured poly-�^-D-glutamic acid capsule biosynthesis genes capA, capB and capC showing 99-100% identity with the environmental B. cereus isolate 03BB108. Presence of cesB of the cereulide synthetase gene cluster was confirmed by PCR in M13-PCR group 2 isolates. The B. cereus harbouring the cap genes were found in potash, DW, cooking water and at 8h fermentation. The "emetic" type B. cereus were present in DW, the seed mash at 48-72h of fermentation and in the final product, while the remaining isolates (PanC type IV) were detected in ash, at 48-72h fermentation and in the final product. This work sheds light on the succession and pathogenic potential of B. cereus species in traditional West African food condiment and clarifies their phylogenetic relatedness to B. cereus biovar anthracis. Future implementation of GMP and HACCP and development of starter cultures for controlled Maari fermentations will help to ensure a safe product.
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187. |
Napolitano LM,
Bisha I,
De March M,
Marchesi A,
Arcangeletti M,
Demitri N,
Mazzolini M,
Rodriguez A,
Magistrato A,
Onesti S,
Laio A,
Torre V,
( 2015 ) A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels. PMID : 26100907 : DOI : 10.1073/pnas.1503334112 PMC : PMC4500290 Abstract >>
Cyclic nucleotide-gated (CNG) ion channels, despite a significant homology with the highly selective K(+) channels, do not discriminate among monovalent alkali cations and are permeable also to several organic cations. We combined electrophysiology, molecular dynamics (MD) simulations, and X-ray crystallography to demonstrate that the pore of CNG channels is highly flexible. When a CNG mimic is crystallized in the presence of a variety of monovalent cations, including Na(+), Cs(+), and dimethylammonium (DMA(+)), the side chain of Glu66 in the selectivity filter shows multiple conformations and the diameter of the pore changes significantly. MD simulations indicate that Glu66 and the prolines in the outer vestibule undergo large fluctuations, which are modulated by the ionic species and the voltage. This flexibility underlies the coupling between gating and permeation and the poor ionic selectivity of CNG channels.
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188. |
Nakano Y,
Kato C,
Tanaka E,
Kimura K,
Horikoshi K,
( 1989 ) Nucleotide sequence of the glutamine synthetase gene (glnA) and its upstream region from Bacillus cereus. PMID : 2572584 : DOI : 10.1093/oxfordjournals.jbchem.a122834 Abstract >>
We have determined the complete nucleotide sequence of a 2.4 kb chromosomal EcoT22I-NspV fragment, containing the Bacillus cereus glnA gene (structural gene of glutamine synthetase). The deduced amino acid sequence indicates that the glutamine synthetase subunit consists of 444 amino acid residues (50,063 Da). Comparisons are made with reported amino acid sequences of glutamine synthetases from other bacteria. Upstrem of glnA we found an open reading frame of 129 codons (ORF129) preceded by the consensus sequence for a typical promoter. Maxicell experiments showed two polypeptide bands, with molecular weights in good agreement with that of glutamine synthetase and that of ORF129, in addition to vector-coded protein. It is possible that the product of this open reading frame upstream of glnA has a regulatory role in glutamine synthetase expression.
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189. |
Lam YL,
Zeng W,
Derebe MG,
Jiang Y,
( 2015 ) Structural implications of weak Ca2+ block in Drosophila cyclic nucleotide-gated channels. PMID : 26283200 : DOI : 10.1085/jgp.201511431 PMC : PMC4555469 Abstract >>
Calcium permeability and the concomitant calcium block of monovalent ion current ("Ca(2+) block") are properties of cyclic nucleotide-gated (CNG) channel fundamental to visual and olfactory signal transduction. Although most CNG channels bear a conserved glutamate residue crucial for Ca(2+) block, the degree of block displayed by different CNG channels varies greatly. For instance, the Drosophila melanogaster CNG channel shows only weak Ca(2+) block despite the presence of this glutamate. We previously constructed a series of chimeric channels in which we replaced the selectivity filter of the bacterial nonselective cation channel NaK with a set of CNG channel filter sequences and determined that the resulting NaK2CNG chimeras displayed the ion selectivity and Ca(2+) block properties of the parent CNG channels. Here, we used the same strategy to determine the structural basis of the weak Ca(2+) block observed in the Drosophila CNG channel. The selectivity filter of the Drosophila CNG channel is similar to that of most other CNG channels except that it has a threonine at residue 318 instead of a proline. We constructed a NaK chimera, which we called NaK2CNG-Dm, which contained the Drosophila selectivity filter sequence. The high resolution structure of NaK2CNG-Dm revealed a filter structure different from those of NaK and all other previously investigated NaK2CNG chimeric channels. Consistent with this structural difference, functional studies of the NaK2CNG-Dm chimeric channel demonstrated a loss of Ca(2+) block compared with other NaK2CNG chimeras. Moreover, mutating the corresponding threonine (T318) to proline in Drosophila CNG channels increased Ca(2+) block by 16 times. These results imply that a simple replacement of a threonine for a proline in Drosophila CNG channels has likely given rise to a distinct selectivity filter conformation that results in weak Ca(2+) block.
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190. |
Ruiu L,
Falchi G,
Floris I,
Marche MG,
Mura ME,
Satta A,
( 2015 ) Pathogenicity and characterization of a novel Bacillus cereus sensu lato isolate toxic to the Mediterranean fruit fly Ceratitis capitata Wied. PMID : 25659732 : DOI : 10.1016/j.jip.2015.01.010 Abstract >>
The lethal and sub-lethal effects of sporulated cultures of a novel Bacillus cereus sensu lato strain lacking detectable cry genes and identified through morphological and genetic analyses, have been studied on the Mediterranean fruit fly Ceratitis capitata. The lethal effects on young larvae were concentration dependent, with a median lethal concentration (LC50) of 4.48 �� 10(8)spores/g of diet. Sporulated cultures of this strain significantly extended development time and reduced immature survival, and the size of emerging fly adults. Besides spores, the toxicity has been associated to the insoluble extra-spore fraction characterized through a proteomic approach. The profile of the extra-spore protein fraction (ES) showed major protein bands within the 35-65 kDa range. The results of mass spectrometry analysis highlighted the presence of putative virulence factors, including members of protein families previously associated to the insecticidal action of other microbial entomopathogens. These proteins include metalloproteases, peptidases and other enzymes.
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191. |
Nakano S,
Okazaki S,
Ishitsubo E,
Kawahara N,
Komeda H,
Tokiwa H,
Asano Y,
( 2015 ) Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B. PMID : 26370172 : DOI : 10.1038/srep13836 PMC : PMC4570186 Abstract >>
Alkaline D-peptidase from Bacillus cereus DF4-B, called ADP, is a D-stereospecific endopeptidase reacting with oligopeptides containing D-phenylalanine (D-Phe) at N-terminal penultimate residue. ADP has attracted increasing attention because it is useful as a catalyst for synthesis of D-Phe oligopeptides or, with the help of substrate mimetics, L-amino acid peptides and proteins. Structure and functional analysis of ADP is expected to elucidate molecular mechanism of ADP. In this study, the crystal structure of ADP (apo) form was determined at 2.1 ? resolution. The fold of ADP is similar to that of the class C penicillin-binding proteins of type-AmpH. Docking simulations and fragment molecular orbital analyses of two peptides, (D-Phe)4 and (D-Phe)2-(L-Phe)2, with the putative substrate binding sites of ADP indicated that the P1 residue of the peptide interacts with hydrophobic residues at the S1 site of ADP. Furthermore, molecular dynamics simulation of ADP for 50 nsec suggested that the ADP forms large cavity at the active site. Formation of the cavity suggested that the ADP has open state in the solution. For the ADP, having the open state is convenient to bind the peptides having bulky side chain, such as (D-Phe)4. Taken together, we predicted peptide recognition mechanism of ADP.
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192. |
Gwenin VV,
Poornima P,
Halliwell J,
Ball P,
Robinson G,
Gwenin CD,
( 2015 ) Identification of novel nitroreductases from Bacillus cereus and their interaction with the CB1954 prodrug. PMID : 26415543 : DOI : 10.1016/j.bcp.2015.09.013 Abstract >>
Directed enzyme prodrug therapy is a form of cancer chemotherapy in which bacterial prodrug-activating enzymes, or their encoding genes, are directed to the tumour before administration of a prodrug. The prodrug can then be activated into a toxic drug at the tumour site, reducing off-target effects. The bacterial nitroreductases are a class of enzymes used in this therapeutic approach and although very promising, the low turnover rate of prodrug by the most studied nitroreductase enzyme, NfnB from Escherichia coli (NfnB_Ec), is a major limit to this technology. There is a continual search for enzymes with greater efficiency, and as part of the search for more efficient bacterial nitroreductase enzymes, two novel enzymes from Bacillus cereus (strain ATCC 14579) have been identified and shown to reduce the CB1954 (5-(aziridin-1-yl)-2,4-dinitrobenzamide) prodrug to its respective 2'-and 4'-hydroxylamine products. Both enzymes shared features characteristic of the nitro-FMN-reductase superfamily including non-covalently associated FMN, requirement for the NAD(P)H cofactor, homodimeric, could be inhibited by Dicoumarol (3,3'-methylenebis(4-hydroxy-2H-chromen-2-one)), and displayed ping pong bi bi kinetics. Based on the biochemical characteristics and nucleotide alignment with other nitroreductase enzymes, one enzyme was named YdgI_Bc and the other YfkO_Bc. Both B. cereus enzymes had greater turnover for the CB1954 prodrug compared with NfnB_Ec, and in the presence of added NADPH cofactor, YfkO_Bc had superior cell killing ability, and produced mainly the 4'-hydroxylamine product at low prodrug concentration. The YfkO_Bc was identified as a promising candidate for future enzyme prodrug therapy.
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193. |
Guo Y,
Kalathur RC,
Liu Q,
Kloss B,
Bruni R,
Ginter C,
Kloppmann E,
Rost B,
Hendrickson WA,
( 2015 ) Protein structure. Structure and activity of tryptophan-rich TSPO proteins. PMID : 25635100 : DOI : 10.1126/science.aaa1534 PMC : PMC4341906 Abstract >>
Translocator proteins (TSPOs) bind steroids and porphyrins, and they are implicated in many human diseases, for which they serve as biomarkers and therapeutic targets. TSPOs have tryptophan-rich sequences that are highly conserved from bacteria to mammals. Here we report crystal structures for Bacillus cereus TSPO (BcTSPO) down to 1.7 ? resolution, including a complex with the benzodiazepine-like inhibitor PK11195. We also describe BcTSPO-mediated protoporphyrin IX (PpIX) reactions, including catalytic degradation to a previously undescribed heme derivative. We used structure-inspired mutations to investigate reaction mechanisms, and we showed that TSPOs from Xenopus and man have similar PpIX-directed activities. Although TSPOs have been regarded as transporters, the catalytic activity in PpIX degradation suggests physiological importance for TSPOs in protection against oxidative stress.
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194. |
Wang Y,
Moore M,
Levinson HS,
Silver S,
Walsh C,
Mahler I,
( 1989 ) Nucleotide sequence of a chromosomal mercury resistance determinant from a Bacillus sp. with broad-spectrum mercury resistance. PMID : 2536669 : DOI : 10.1128/jb.171.1.83-92.1989 PMC : PMC209558 Abstract >>
A 13.5-kilobase HindIII fragment, bearing an intact mercury resistance (mer) operon, was isolated from chromosomal DNA of broad-spectrum mercury-resistant Bacillus sp. strain RC607 by using as a probe a clone containing the mercury reductase (merA) gene. The new clone, pYW33, expressed broad-spectrum mercury resistance both in Escherichia coli and in Bacillus subtilis, but only in B. subtilis was the mercuric reductase activity inducible. Sequencing of a 1.8-kilobase mercury hypersensitivity-producing fragment revealed four open reading frames (ORFs). ORF1 may code for a regulatory protein (MerR). ORF2 and ORF4 were associated with cellular transport function and the hypersensitivity phenotype. DNA fragments encompassing the merA and the merB genes were sequenced. The predicted Bacillus sp. strain RC607 MerA (mercuric reductase) and MerB (organomercurial lyase) were similar to those predicted from Staphylococcus aureus plasmid pI258 (67 and 73% amino acid identities, respectively); however, only 40% of the amino acid residues of RC607 MerA were identical to those of the mercuric reductase from gram-negative bacteria. A 69-kilodalton polypeptide was isolated and identified as the merA gene product by examination of its amino-terminal sequence.
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195. |
Park H,
Kevany BM,
Dyer DH,
Thomas MG,
Forest KT,
( 2014 ) A polyketide synthase acyltransferase domain structure suggests a recognition mechanism for its hydroxymalonyl-acyl carrier protein substrate. PMID : 25340352 : DOI : 10.1371/journal.pone.0110965 PMC : PMC4207774 Abstract >>
We have previously shown that the acyl transferase domain of ZmaA (ZmaA-AT) is involved in the biosynthesis of the aminopolyol polyketide/nonribosomal peptide hybrid molecule zwittermicin A from cereus UW85, and that it specifically recognizes the precursor hydroxymalonyl-acyl carrier protein (ACP) and transfers the hydroxymalonyl extender unit to a downstream second ACP via a transacylated AT domain intermediate. We now present the X-ray crystal structure of ZmaA-AT at a resolution of 1.7 ?. The structure shows a patch of solvent-exposed hydrophobic residues in the area where the AT is proposed to interact with the precursor ACP. We addressed the significance of the AT/ACP interaction in precursor specificity of the AT by testing whether malonyl- or methylmalonyl-ACP can be recognized by ZmaA-AT. We found that the ACP itself biases extender unit selection. Until now, structural information for ATs has been limited to ATs specific for the CoA-linked precursors malonyl-CoA and (2S)-methylmalonyl-CoA. This work contributes to polyketide synthase engineering efforts by expanding our knowledge of AT/substrate interactions with the structure of an AT domain that recognizes an ACP-linked substrate, the rare hydroxymalonate. Our structure suggests a model in which ACP interaction with a hydrophobic motif promotes secondary structure formation at the binding site, and opening of the adjacent substrate pocket lid to allow extender unit binding in the AT active site.
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196. |
Gilmore MS,
Cruz-Rodz AL,
Leimeister-Wächter M,
Kreft J,
Goebel W,
( 1989 ) A Bacillus cereus cytolytic determinant, cereolysin AB, which comprises the phospholipase C and sphingomyelinase genes: nucleotide sequence and genetic linkage. PMID : 2536680 : DOI : 10.1128/jb.171.2.744-753.1989 PMC : PMC209660 Abstract >>
A cloned cytolytic determinant from the genome of Bacillus cereus GP-4 has been characterized at the molecular level. Nucleotide sequence determination revealed the presence of two open reading frames. Both open reading frames were found by deletion and complementation analysis to be necessary for expression of the hemolytic phenotype by Bacillus subtilis and Escherichia coli hosts. The 5' open reading frame was found to be nearly identical to a recently reported phospholipase C gene derived from a mutant B. cereus strain which overexpresses the respective protein, and it conferred a lecithinase-positive phenotype to the B. subtilis host. The 3' open reading frame encoded a sphingomyelinase. The two tandemly encoded activities, phospholipase C and sphingomyelinase, constitute a biologically functional cytolytic determinant of B. cereus termed cereolysin AB.
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197. |
Raiol T,
De-Souza MT,
Oliveira JV,
Silva HS,
Orem JC,
Cavalcante DA,
Almeida NF,
Telles GP,
Setubal JC,
Brigido MM,
Torres FA,
Stadler PS,
Walter ME,
Moraes LM,
( 2014 ) Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring. PMID : 25301660 : DOI : 10.1128/genomeA.01027-14 PMC : PMC4192392 Abstract >>
A Bacillus cereus strain, FT9, isolated from a hot spring in the midwest region of Brazil, had its entire genome sequenced.
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198. |
Hwang S,
Li Z,
Bar-Peled Y,
Aronov A,
Ericson J,
Bar-Peled M,
( 2014 ) The biosynthesis of UDP-d-FucNAc-4N-(2)-oxoglutarate (UDP-Yelosamine) in Bacillus cereus ATCC 14579: Pat and Pyl, an aminotransferase and an ATP-dependent Grasp protein that ligates 2-oxoglutarate to UDP-4-amino-sugars. PMID : 25368324 : DOI : 10.1074/jbc.M114.614917 PMC : PMC4271244 Abstract >>
Surface glycan switching is often observed when micro-organisms transition between different biotic and abiotic niches, including biofilms, although the advantages of this switching to the organism are not well understood. Bacillus cereus grown in a biofilm-inducing medium has been shown to synthesize an unusual cell wall polysaccharide composed of the repeating subunit ��6)Gal(�\1-2)(2-R-hydroxyglutar-5-ylamido)Fuc2NAc4N(�\1-6)GlcNAc(�]1��, where galactose is linked to the hydroxyglutarate moiety of FucNAc-4-amido-(2)-hydroxyglutarate. The molecular mechanism involved in attaching 2-hydroxyglutarate to 4-amino-FucNAc has not been determined. Here, we show two genes in B. cereus ATCC 14579 encoding enzymes involved in the synthesis of UDP-FucNAc-4-amido-(2)-oxoglutarate (UDP-Yelosamine), a modified UDP-sugar not previously reported to exist. Using mass spectrometry and real time NMR spectroscopy, we show that Bc5273 encodes a C4?-aminotransferase (herein referred to as Pat) that, in the presence of pyridoxal phosphate, transfers the primary amino group of l-Glu to C-4? of UDP-4-keto-6-deoxy-d-GlcNAc to form UDP-4-amino-FucNAc and 2-oxoglutarate. Pat also converts 4-keto-xylose, 4-keto-glucose, and 4-keto-2-acetamido-altrose to their corresponding UDP-4-amino-sugars. Bc5272 encodes a carboxylate-amine ligase (herein referred as Pyl) that, in the presence of ATP and Mg(II), adds 2-oxoglutarate to the 4-amino moiety of UDP-4-amino-FucNAc to form UDP-Yelosamine and ADP. Pyl is also able to ligate 2-oxoglutarate to other 4-amino-sugar derivatives to form UDP-Yelose, UDP-Solosamine, and UDP-Aravonose. Characterizing the metabolic pathways involved in the formation of modified nucleotide sugars provides a basis for understanding some of the mechanisms used by bacteria to modify or alter their cell surface polysaccharides in response to changing growth and environmental challenges.
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199. |
Søborg DA,
Hendriksen NB,
Kroer N,
( 2014 ) Occurrence and expression of bacterial human virulence gene homologues in natural soil bacteria. PMID : 25118010 : DOI : 10.1111/1574-6941.12413 Abstract >>
The presence and in vitro expression of homologues to 22 bacterial human virulence determinants amongst culturable soil bacteria were investigated. About 25% of the bacterial isolates contained virulence gene homologues representing toxin (hblA, cytK2), adhesin (fimH), regulator (phoQ) and resistance (yfbI) determinants in pathogenic bacteria. The homologues of the toxin genes were found in Actinobacteria and Firmicutes (hblA), and in Firmicutes and Alpha- and Gammaproteobacteria (cytK2). The homologues to the type 1 fimbrial adhesin gene, fimH, and the L-Ara4N transferase gene, yfbI, were observed in Actinobacteria, Firmicutes and Gammaproteobacteria. The regulator gene, phoQ, was only found in Gammaproteobacteria. The presence of cytK2 in Alpha- and Gammaproteobacteria, fimH in Actinobacteria and Firmicutes, and hblA in Actinobacteria has not previously been described. A close sequence similarity (84-100%) was observed between the genes of environmental and clinical isolates, and expression assays suggested that the genes in some cases were expressed in vitro. The presence of functional virulence gene homologues underpins their importance for the survival of environmental bacteria. Furthermore, the high degree of sequence conservation to clinical sequences indicates that natural environments may be 'evolutionary cribs' of emerging pathogens.
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200. |
Johnson SL,
Daligault HE,
Davenport KW,
Jaissle J,
Frey KG,
Ladner JT,
Broomall SM,
Bishop-Lilly KA,
Bruce DC,
Gibbons HS,
Coyne SR,
Lo CC,
Meincke L,
Munk AC,
Koroleva GI,
Rosenzweig CN,
Palacios GF,
Redden CL,
Minogue TD,
Chain PS,
( 2015 ) Complete genome sequences for 35 biothreat assay-relevant bacillus species. PMID : 25931591 : DOI : 10.1128/genomeA.00151-15 PMC : PMC4417687 Abstract >>
In 2011, the Association of Analytical Communities (AOAC) International released a list of Bacillus strains relevant to biothreat molecular detection assays. We present the complete and annotated genome assemblies for the 15 strains listed on the inclusivity panel, as well as the 20 strains listed on the exclusivity panel.
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201. |
Zhao S,
Sakai A,
Zhang X,
Vetting MW,
Kumar R,
Hillerich B,
San Francisco B,
Solbiati J,
Steves A,
Brown S,
Akiva E,
Barber A,
Seidel RD,
Babbitt PC,
Almo SC,
Gerlt JA,
Jacobson MP,
( 2014 ) Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. PMID : 24980702 : DOI : 10.7554/eLife.03275 PMC : PMC4113996 Abstract >>
Metabolic pathways in eubacteria and archaea often are encoded by operons and/or gene clusters (genome neighborhoods) that provide important clues for assignment of both enzyme functions and metabolic pathways. We describe a bioinformatic approach (genome neighborhood network; GNN) that enables large scale prediction of the in vitro enzymatic activities and in vivo physiological functions (metabolic pathways) of uncharacterized enzymes in protein families. We demonstrate the utility of the GNN approach by predicting in vitro activities and in vivo functions in the proline racemase superfamily (PRS; InterPro IPR008794). The predictions were verified by measuring in vitro activities for 51 proteins in 12 families in the PRS that represent ?85% of the sequences; in vitro activities of pathway enzymes, carbon/nitrogen source phenotypes, and/or transcriptomic studies confirmed the predicted pathways. The synergistic use of sequence similarity networks3 and GNNs will facilitate the discovery of the components of novel, uncharacterized metabolic pathways in sequenced genomes.
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202. |
Lim HM,
Pène JJ,
( 1989 ) Mutations affecting the catalytic activity of Bacillus cereus 5/B/6 beta-lactamase II. PMID : 2501295 : Abstract >>
Random in vitro mutagenesis of a cloned Bacillus cereus 5/B/6 beta-lactamase II gene was used to select defective genes unable to confer ampicillin or cephalosporin C resistance to Escherichia coli. DNA sequencing of mutant genes identified histidine at position 28 as important to beta-lactamase II function. In addition, the isolation of six identical frameshift mutants established that the carboxyl-terminal end of beta-lactamase II is critical for enzyme function. Random mutagenesis also revealed that His88 (implicated previously as one of 4 residues acting as a zinc ligand) is crucial to enzymatic activity and that a glycine to glutamic acid substitution at position 148 produced a defective beta-lactamase. Oligonucleotide mutagenesis directed at Glu37 and Glu212 suggests that these residues are inconsequential to enzyme function but that histidine at position 28 may be involved in substrate binding or recognition.
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203. |
Hough E,
Hansen LK,
Birknes B,
Jynge K,
Hansen S,
Hordvik A,
Little C,
Dodson E,
Derewenda Z,
( 1989 ) High-resolution (1.5 A) crystal structure of phospholipase C from Bacillus cereus. PMID : 2493587 : DOI : 10.1038/338357a0 Abstract >>
Both the phosphatidylinositol-hydrolysing and the phosphatidylcholine-hydrolysing phospholipases C have been implicated in the generation of second messengers in mammalian cells. The phosphatidylcholine-hydrolysing phospholipase C (PLC) from Bacillus cereus, a monomeric protein containing 245 amino-acid residues, is similar to some of the corresponding mammalian proteins. This, together with the fact that the bacterial enzyme can mimic the action of mammalian PLC in causing, for example, enhanced prostaglandin biosynthesis, suggests that B. cereus PLC can be used as a model for the hitherto poorly characterized mammalian PLCs. We report here the three-dimensional structure of B. cereus PLC at 1.5 A resolution. The enzyme is an all-helix protein belonging to a novel structural class and contains, at least in the crystalline state, three Zn2+ in the active site. We also present preliminary results from a study at 1.9 A resolution of the complex between PLC and inorganic phosphate (Pi) which indicate that the substrate binds directly to the metal ions.
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204. |
Wang J,
Zhang L,
Teng K,
Sun S,
Sun Z,
Zhong J,
( 2014 ) Cerecidins, novel lantibiotics from Bacillus cereus with potent antimicrobial activity. PMID : 24532070 : DOI : 10.1128/AEM.03751-13 PMC : PMC3993178 Abstract >>
Lantibiotics are ribosomally synthesized and posttranslationally modified antimicrobial peptides that are widely produced by Gram-positive bacteria, including many species of the Bacillus group. In the present study, one novel gene cluster coding lantibiotic cerecidins was unveiled in Bacillus cereus strain As 1.1846 through genomic mining and PCR screening. The designated cer locus is different from that of conventional class II lantibiotics in that it included seven tandem precursor cerA genes, one modification gene (cerM), two processing genes (cerT and cerP), one orphan regulator gene (cerR), and two immunity genes (cerF and cerE). In addition, one unprecedented quorum sensing component, comQXPA, was inserted between cerM and cerR. The expression of cerecidins was not detected in this strain of B. cereus, which might be due to repressed transcription of cerM. We constitutively coexpressed cerA genes and cerM in Escherichia coli, and purified precerecidins were proteolytically processed with the endoproteinase GluC and a truncated version of putative serine protease CerP. Thus, two natural variants of cerecidins A1 and A7 were obtained which contained two terminal nonoverlapping thioether rings rarely found in lantibiotics. Both cerecidins A1 and A7 were active against a broad spectrum of Gram-positive bacteria. Cerecidin A7, especially its mutant Dhb13A, showed remarkable efficacy against multidrug-resistant Staphylococcus aureus (MDRSA), vancomycin-resistant Enterococcus faecalis (VRE), and even Streptomyces.
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205. |
Helmann JD,
Wang Y,
Mahler I,
Walsh CT,
( 1989 ) Homologous metalloregulatory proteins from both gram-positive and gram-negative bacteria control transcription of mercury resistance operons. PMID : 2492496 : DOI : 10.1128/jb.171.1.222-229.1989 PMC : PMC209576 Abstract >>
We report the overexpression, purification, and properties of the regulatory protein, MerR, for a chromosomally encoded mercury resistance determinant from Bacillus strain RC607. This protein is similar in sequence to the metalloregulatory proteins encoded by gram-negative resistance determinants found on transposons Tn21 and Tn501 and to a predicted gene product of a Staphylococcus aureus resistance determinant. In vitro DNA-binding and transcription experiments were used to demonstrate those purified Bacillus MerR protein controls transcription from a promoter-operator site similar in sequence to that found in the transposon resistance determinants. The Bacillus MerR protein bound in vitro to its promoter-operator region in both the presence and absence of mercuric ion and functioned as a negative and positive regulator of transcription. The MerR protein bound less tightly to its operator region (ca. 50- to 100-fold) in the presence of mercuric ion; this reduced affinity was largely accounted for by an increased rate of dissociation of the MerR protein from the DNA. Despite this reduced DNA-binding affinity, genetic and biochemical evidence support a model in which the MerR protein-mercuric ion complex is a positive regulator of operon transcription. Although the Bacillus MerR protein bound only weakly to the heterologous Tn501 operator region, the Tn501 and Tn21 MerR proteins bound with high affinity to the Bacillus promoter-operator region and exhibited negative, but not positive, transcriptional control.
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206. |
Erickson BD,
Elkins CA,
Mullis LB,
Heinze TM,
Wagner RD,
Cerniglia CE,
( 2014 ) A metallo-�]-lactamase is responsible for the degradation of ceftiofur by the bovine intestinal bacterium Bacillus cereus P41. PMID : 24972871 : DOI : 10.1016/j.vetmic.2014.05.032 Abstract >>
Ceftiofur is a highly effective veterinary cephalosporin, yet it is rapidly degraded by bacteria in the gut. The goal of this work was to directly determine the mechanism of ceftiofur degradation by the bovine intestinal isolate Bacillus cereus P41. B. cereus P41 was isolated from the feces of a cow that had not been treated with cephalosporins, and was found to rapidly degrade ceftiofur in culture. Analysis of spent culture media by HPLC/UV and HPLC/MS revealed one major metabolite of ceftiofur, with a negative ion m/z of 127. Comparison of ceftiofur, ceftriaxone, and cefpodoxime degradation suggested that the major stable ceftiofur metabolite was the thiofuroic acid group eliminated from the C-3 position of the drug after hydrolysis by �]-lactamase. Genomic DNA from B. cereus P41 was cloned into Escherichia coli, and the transformants were screened for growth in the presence of ceftiofur. DNA sequencing of the plasmid pHSG299-BC-3 insert revealed the presence of a gene encoding a metallo-�]-lactamase. Incubation of ceftiofur with either the E. coli transformant or a commercial B. cereus metallo-�]-lactamase showed degradation of the drug and formation of the same major metabolite produced by B. cereus P41. These data demonstrate that a metallo-�]-lactamase plays a major role in the degradation of ceftiofur by the bovine intestinal bacterium B. cereus P41.
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207. |
Hammerstad M,
Hersleth HP,
Tomter AB,
Røhr AK,
Andersson KK,
( 2014 ) Crystal structure of Bacillus cereus class Ib ribonucleotide reductase di-iron NrdF in complex with NrdI. PMID : 24295378 : DOI : 10.1021/cb400757h DOI : 10.1021/cb400757h Abstract >>
Class Ib ribonucleotide reductases (RNRs) use a dimetal-tyrosyl radical (Y?) cofactor in their NrdF (�]2) subunit to initiate ribonucleotide reduction in the NrdE (�\2) subunit. Contrary to the diferric tyrosyl radical (Fe(III)2-Y?) cofactor, which can self-assemble from Fe(II)2-NrdF and O2, generation of the Mn(III)2-Y? cofactor requires the reduced form of a flavoprotein, NrdIhq, and O2 for its assembly. Here we report the 1.8 ? resolution crystal structure of Bacillus cereus Fe2-NrdF in complex with NrdI. Compared to the previously solved Escherichia coli NrdI-Mn(II)2-NrdF structure, NrdI and NrdF binds similarly in Bacillus cereus through conserved core interactions. This protein-protein association seems to be unaffected by metal ion type bound in the NrdF subunit. The Bacillus cereus Mn(II)2-NrdF and Fe2-NrdF structures, also presented here, show conformational flexibility of residues surrounding the NrdF metal ion site. The movement of one of the metal-coordinating carboxylates is linked to the metal type present at the dimetal site and not associated with NrdI-NrdF binding. This carboxylate conformation seems to be vital for the water network connecting the NrdF dimetal site and the flavin in NrdI. From these observations, we suggest that metal-dependent variations in carboxylate coordination geometries are important for active Y? cofactor generation in class Ib RNRs. Additionally, we show that binding of NrdI to NrdF would structurally interfere with the suggested �\2�]2 (NrdE-NrdF) holoenzyme formation, suggesting the potential requirement for NrdI dissociation before NrdE-NrdF assembly after NrdI-activation. The mode of interactions between the proteins involved in the class Ib RNR system is, however, not fully resolved.
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208. |
Hammerstad M,
Hersleth HP,
Tomter AB,
Røhr AK,
Andersson KK,
( 2014 ) Crystal structure of Bacillus cereus class Ib ribonucleotide reductase di-iron NrdF in complex with NrdI. PMID : 24295378 : DOI : 10.1021/cb400757h DOI : 10.1021/cb400757h Abstract >>
Class Ib ribonucleotide reductases (RNRs) use a dimetal-tyrosyl radical (Y?) cofactor in their NrdF (�]2) subunit to initiate ribonucleotide reduction in the NrdE (�\2) subunit. Contrary to the diferric tyrosyl radical (Fe(III)2-Y?) cofactor, which can self-assemble from Fe(II)2-NrdF and O2, generation of the Mn(III)2-Y? cofactor requires the reduced form of a flavoprotein, NrdIhq, and O2 for its assembly. Here we report the 1.8 ? resolution crystal structure of Bacillus cereus Fe2-NrdF in complex with NrdI. Compared to the previously solved Escherichia coli NrdI-Mn(II)2-NrdF structure, NrdI and NrdF binds similarly in Bacillus cereus through conserved core interactions. This protein-protein association seems to be unaffected by metal ion type bound in the NrdF subunit. The Bacillus cereus Mn(II)2-NrdF and Fe2-NrdF structures, also presented here, show conformational flexibility of residues surrounding the NrdF metal ion site. The movement of one of the metal-coordinating carboxylates is linked to the metal type present at the dimetal site and not associated with NrdI-NrdF binding. This carboxylate conformation seems to be vital for the water network connecting the NrdF dimetal site and the flavin in NrdI. From these observations, we suggest that metal-dependent variations in carboxylate coordination geometries are important for active Y? cofactor generation in class Ib RNRs. Additionally, we show that binding of NrdI to NrdF would structurally interfere with the suggested �\2�]2 (NrdE-NrdF) holoenzyme formation, suggesting the potential requirement for NrdI dissociation before NrdE-NrdF assembly after NrdI-activation. The mode of interactions between the proteins involved in the class Ib RNR system is, however, not fully resolved.
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209. |
Kuppe A,
Evans LM,
McMillen DA,
Griffith OH,
( 1989 ) Phosphatidylinositol-specific phospholipase C of Bacillus cereus: cloning, sequencing, and relationship to other phospholipases. PMID : 2509427 : DOI : 10.1128/jb.171.11.6077-6083.1989 PMC : PMC210474 Abstract >>
The phosphatidylinositol (PI)-specific phospholipase C (PLC) of Bacillus cereus was cloned into Escherichia coli by using monoclonal antibody probes raised against the purified protein. The enzyme is specific for hydrolysis of the membrane lipid PI and PI-glycan-containing membrane anchors, which are important structural components of one class of membrane proteins. The protein expressed in E. coli comigrated with B. cereus PI-PLC in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, as detected by immunoblotting, and conferred PI-PLC activity on the host. This enzyme activity was inhibited by PI-PLC-specific monoclonal antibodies. The nucleotide sequence of the PI-PLC gene suggests that this secreted bacterial protein is synthesized as a larger precursor with a 31-amino-acid N-terminal extension to the mature enzyme of 298 amino acids. From analysis of coding and flanking sequences of the gene, we conclude that the PI-PLC gene does not reside next to the gene cluster of the other two secreted phospholipases C on the bacterial chromosome. The deduced amino acid sequence of the B. cereus PI-PLC contains a stretch of significant similarity to the glycosylphosphatidylinositol-specific PLC of Trypanosoma brucei. The conserved peptide is proposed to play a role in the function of these enzymes.
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210. |
Sen R,
Tripathy S,
Padhi SK,
Mohanty S,
Maiti NK,
( 2014 ) Sequence polymorphism of GroEL gene in natural population of Bacillus and Brevibacillus spp. that showed variation in thermal tolerance capacity and mRNA expression. PMID : 24894903 : DOI : 10.1007/s00284-014-0614-8 Abstract >>
GroEL, a class I chaperonin, plays an important role in the thermal adaptation of the cell and helps to maintain the viability of the cell under heat shock condition. Function of groEL in vivo depends on the maintenance of proper structure of the protein which in turn depends on the nucleotide and amino acid sequence of the gene. In this study, we investigated the changes in nucleotide and amino acid sequences of the partial groEL gene that may affect the thermotolerance capacity as well as mRNA expression of bacterial isolates. Sequences among the same species having differences in the amino acid level were identified as different alleles. The effect of allelic variation on the groEL gene expression was analyzed by comparison and relative quantification in each allele under thermal shock condition by RT-PCR. Evaluation of K a/K s ratio among the strains of same species showed that the groEL gene of all the species had undergone similar functional constrain during evolution. The strains showing similar thermotolerance capacity was found to carry same allele of groEL gene. The isolates carrying allele having amino acid substitution inside the highly ATP/ADP or Mg(2+)-binding region could not tolerate thermal stress and showed lower expression of the groEL gene. Our results indicate that during evolution of these bacterial species the groEL gene has undergone the process of natural selection, and the isolates have evolved with the groEL allelic sequences that help them to withstand the thermal stress during their interaction with the environment.
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211. |
Karsisiotis AI,
Damblon CF,
Roberts GC,
( 2013 ) Solution structures of the Bacillus cereus metallo-�]-lactamase BcII and its complex with the broad spectrum inhibitor R-thiomandelic acid. PMID : 24059435 : DOI : 10.1042/BJ20131003 PMC : PMC3898119 Abstract >>
Metallo-�]-lactamases, enzymes which inactivate �]-lactam antibiotics, are of increasing biological and clinical significance as a source of antibiotic resistance in pathogenic bacteria. In the present study we describe the high-resolution solution NMR structures of the Bacillus cereus metallo-�]-lactamase BcII and of its complex with R-thiomandelic acid, a broad-spectrum inhibitor of metallo-�]-lactamases. This is the first reported solution structure of any metallo-�]-lactamase. There are differences between the solution structure of the free enzyme and previously reported crystal structures in the loops flanking the active site, which are important for substrate and inhibitor binding and catalysis. The binding of R-thiomandelic acid and the roles of active-site residues are defined in detail. Changes in the enzyme structure upon inhibitor binding clarify the role of the mobile �]3-�]4 loop. Comparisons with other metallo-�]-lactamases highlight the roles of individual amino-acid residues in the active site and the �]3-�]4 loop in inhibitor binding and provide information on the basis of structure-activity relationships among metallo-�]-lactamase inhibitors.
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212. |
Kubiak X,
Li de la Sierra-Gallay I,
Chaffotte AF,
Pluvinage B,
Weber P,
Haouz A,
Dupret JM,
Rodrigues-Lima F,
( 2013 ) Structural and biochemical characterization of an active arylamine N-acetyltransferase possessing a non-canonical Cys-His-Glu catalytic triad. PMID : 23770703 : DOI : 10.1074/jbc.M113.468595 PMC : PMC3829337 Abstract >>
Arylamine N-acetyltransferases (NATs), a class of xenobiotic-metabolizing enzymes, catalyze the acetylation of aromatic amine compounds through a strictly conserved Cys-His-Asp catalytic triad. Each residue is essential for catalysis in both prokaryotic and eukaryotic NATs. Indeed, in (HUMAN)NAT2 variants, mutation of the Asp residue to Asn, Gln, or Glu dramatically impairs enzyme activity. However, a putative atypical NAT harboring a catalytic triad Glu residue was recently identified in Bacillus cereus ((BACCR)NAT3) but has not yet been characterized. We report here the crystal structure and functional characterization of this atypical NAT. The overall fold of (BACCR)NAT3 and the geometry of its Cys-His-Glu catalytic triad are similar to those present in functional NATs. Importantly, the enzyme was found to be active and to acetylate prototypic arylamine NAT substrates. In contrast to (HUMAN) NAT2, the presence of a Glu or Asp in the triad of (BACCR)NAT3 did not significantly affect enzyme structure or function. Computational analysis identified differences in residue packing and steric constraints in the active site of (BACCR)NAT3 that allow it to accommodate a Cys-His-Glu triad. These findings overturn the conventional view, demonstrating that the catalytic triad of this family of acetyltransferases is plastic. Moreover, they highlight the need for further study of the evolutionary history of NATs and the functional significance of the predominant Cys-His-Asp triad in both prokaryotic and eukaryotic forms.
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213. |
Fang Z,
Roberts AA,
Weidman K,
Sharma SV,
Claiborne A,
Hamilton CJ,
Dos Santos PC,
( 2013 ) Cross-functionalities of Bacillus deacetylases involved in bacillithiol biosynthesis and bacillithiol-S-conjugate detoxification pathways. PMID : 23758290 : DOI : 10.1042/BJ20130415 Abstract >>
BshB, a key enzyme in bacillithiol biosynthesis, hydrolyses the acetyl group from N-acetylglucosamine malate to generate glucosamine malate. In Bacillus anthracis, BA1557 has been identified as the N-acetylglucosamine malate deacetylase (BshB); however, a high content of bacillithiol (~70%) was still observed in the B. anthracis ?BA1557 strain. Genomic analysis led to the proposal that another deacetylase could exhibit cross-functionality in bacillithiol biosynthesis. In the present study, BA1557, its paralogue BA3888 and orthologous Bacillus cereus enzymes BC1534 and BC3461 have been characterized for their deacetylase activity towards N-acetylglucosamine malate, thus providing biochemical evidence for this proposal. In addition, the involvement of deacetylase enzymes is also expected in bacillithiol-detoxifying pathways through formation of S-mercapturic adducts. The kinetic analysis of bacillithiol-S-bimane conjugate favours the involvement of BA3888 as the B. anthracis bacillithiol-S-conjugate amidase (Bca). The high degree of specificity of this group of enzymes for its physiological substrate, along with their similar pH-activity profile and Zn??-dependent catalytic acid-base reaction provides further evidence for their cross-functionalities.
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214. |
Ganash M,
Phung D,
Sedelnikova SE,
Lindbäck T,
Granum PE,
Artymiuk PJ,
( 2013 ) Structure of the NheA component of the Nhe toxin from Bacillus cereus: implications for function. PMID : 24040335 : DOI : 10.1371/journal.pone.0074748 PMC : PMC3769298 Abstract >>
The structure of NheA, a component of the Bacillus cereus Nhe tripartite toxin, has been solved at 2.05 ? resolution using selenomethionine multiple-wavelength anomalous dispersion (MAD). The structure shows it to have a fold that is similar to the Bacillus cereus Hbl-B and E. coli ClyA toxins, and it is therefore a member of the ClyA superfamily of �\-helical pore forming toxins (�\-PFTs), although its head domain is significantly enlarged compared with those of ClyA or Hbl-B. The hydrophobic �]-hairpin structure that is a characteristic of these toxins is replaced by an amphipathic �]-hairpin connected to the main structure via a �]-latch that is reminiscent of a similar structure in the �]-PFT Staphylococcus aureus �\-hemolysin. Taken together these results suggest that, although it is a member of an archetypal �\-PFT family of toxins, NheA may be capable of forming a �] rather than an �\ pore.
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215. |
Røhr ?K,
Hammerstad M,
Andersson KK,
( 2013 ) Tuning of thioredoxin redox properties by intramolecular hydrogen bonds. PMID : 23936007 : DOI : 10.1371/journal.pone.0069411 PMC : PMC3720550 Abstract >>
Thioredoxin-like proteins contain a characteristic C-x-x-C active site motif and are involved in a large number of biological processes ranging from electron transfer, cellular redox level maintenance, and regulation of cellular processes. The mechanism for deprotonation of the buried C-terminal active site cysteine in thioredoxin, necessary for dissociation of the mixed-disulfide intermediate that occurs under thiol/disulfide mediated electron transfer, is not well understood for all thioredoxin superfamily members. Here we have characterized a 8.7 kD thioredoxin (BC3987) from Bacillus cereus that unlike the typical thioredoxin appears to use the conserved Thr8 side chain near the unusual C-P-P-C active site to increase enzymatic activity by forming a hydrogen bond to the buried cysteine. Our hypothesis is based on biochemical assays and thiolate pKa titrations where the wild type and T8A mutant are compared, phylogenetic analysis of related thioredoxins, and QM/MM calculations with the BC3987 crystal structure as a precursor for modeling of reduced active sites. We suggest that our model applies to other thioredoxin subclasses with similar active site arrangements.
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216. |
Schneewind O,
He C,
Budzik JM,
Hendrickx AP,
Jureller JE,
( 2012 ) Isopeptide bonds of the major pilin protein BcpA influence pilus structure and bundle formation on the surface of Bacillus cereus. PMID : 22624947 : DOI : 10.1111/j.1365-2958.2012.08098.x PMC : PMC3538817 Abstract >>
Bacillus cereus strains elaborate pili on their surface using a mechanism of sortase-mediated cross-linking of major and minor pilus components. Here we used a combination of electron microscopy and atomic force microscopy to visualize these structures. Pili occur as single, double or higher order assemblies of filaments formed from monomers of the major pilin, BcpA, capped by the minor pilin, BcpB. Previous studies demonstrated that within assembled pili, four domains of BcpA - CNA(1), CNA(2), XNA and CNA(3) - each acquire intramolecular lysine-asparagine isopeptide bonds formed via catalytic glutamic acid or aspartic acid residues. Here we showed that mutants unable to form the intramolecular isopeptide bonds in the CNA(2) or CNA(3) domains retain the ability to form pilus bundles. A mutant lacking the CNA(1) isopeptide bond assembled deformed pilin subunits that failed to associate as bundles. X-ray crystallography revealed that the BcpA variant Asp(312) Ala, lacking an aspartyl catalyst, did not generate the isopeptide bond within the jelly-roll structure of XNA. The Asp(312) Ala mutant was also unable to form bundles and promoted the assembly of deformed pili. Thus, structural integrity of the CNA(1) and XNA domains are determinants for the association of pili into higher order bundle structures and determine native pilus structure.
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217. |
Huang Y,
Wei Y,
Huang R,
Du L,
Liang J,
Huang J,
Li M,
( 2012 ) [Gene expression and characterisation of three pullulanases from Bacillus cereus GXBC-3]. PMID : 22803396 : Abstract >>
Exploring excellent new pullulanase genes, and enriching pullulanase theory are of great importance to realize the industrialization of pullulanase. Three genes, pulA, pulB and pulC, encoding pullulanases, were cloned from Bacillus cereus GXBC-3 by bioinformatics analyzing the open reading frame in Bacillus cereus, annotated as putative I and II pullulanases in the GenBank database. Characteristics of these recombinant enzymes were inducible intracellular expressed in Escherichia coli, the results showed PulA was typical II pullulanase. Recombinant PulA could hydrolyze alpha-1,4- and alpha-1,6-glycosidic bonds. Its specific activity was 32.89 U/mg with an optimum temperature of 40 degrees C and optimum pH 6.5 using pullulan as substrate. And for soluble starch substrate, its specific activity was 25.71 U/mg with an optimum temperature of 50 degrees C and optimum pH 7.0. PulB and PulC were I pullulanases and only hydrolyzed alpha-1,6-glycosidic bond. The specific activities, optimum temperature and optimum pH of PulB and PulC for pullulan substrate were 228.54 U/mg, 45 degrees C, 7.0 and 229.65 U/mg, 45 degrees C, 6.5, respectively.
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218. |
Lequette Y,
Garénaux E,
Tauveron G,
Dumez S,
Perchat S,
Slomianny C,
Lereclus D,
Guérardel Y,
Faille C,
( 2011 ) Role played by exosporium glycoproteins in the surface properties of Bacillus cereus spores and in their adhesion to stainless steel. PMID : 21622795 : DOI : 10.1128/AEM.02872-10 PMC : PMC3147369 Abstract >>
Bacillus cereus spores are surrounded by a loose-fitting layer called the exosporium, whose distal part is mainly formed from glycoproteins. The role played by the exosporium glycoproteins of B. cereus ATCC 14579 (BclA and ExsH) was investigated by considering hydrophobicity and charge, as well as the properties of spore adhesion to stainless steel. The absence of BclA increased both the isoelectric point (IEP) and hydrophobicity of whole spores while simultaneously reducing the interaction between spores and stainless steel. However, neither the hydrophobicity nor the charge associated with BclA could explain the differences in the adhesion properties. Conversely, ExsH, another exosporium glycoprotein, did not play a significant role in spore surface properties. The monosaccharide analysis of B. cereus ATCC 14579 showed different glycosylation patterns on ExsH and BclA. Moreover, two specific glycosyl residues, namely, 2-O-methyl-rhamnose (2-Me-Rha) and 2,4-O-methyl-rhamnose (2,4-Me-Rha), were attached to BclA, in addition to the glycosyl residues already reported in B. anthracis.
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219. |
Santos CA,
Almeida FS,
Guimarães AG,
Abrahão WM,
Arantes OM,
Vilas-Bôas GT,
( 2011 ) RE-PCR variability and toxigenic profile of food poisoning, foodborne and soil-associated Bacillus cereus isolates from Brazil. PMID : 21978657 : DOI : 10.1016/j.ijfoodmicro.2011.09.008 Abstract >>
Twenty-three Bacillus cereus isolates from food poisoning outbreaks associated with a diarrheal-type syndrome, fourteen foodborne isolates not associated with food poisoning and fifteen isolates from Brazilian soil samples were analyzed for the presence and genetic diversity (by RE-PCR) of the virulence genes ces (emetic toxin, cereulide), plcR-papR (pleiotropic regulator PlcR and peptide PapR), nheA (a component of the NHE complex), bceT (diarrheal enterotoxin bc-D-ENT), gyrB (B subunit of DNA gyrase), cytK-2 (necrotic enterotoxin cytotoxin K-2), and plcA (phosphatidylcholine-specific phospholipase C). Additionally, these isolates were phenotypically characterized for motility, hemolytic and lecithinase activities, as well as HBL enterotoxin production. The group of isolates associated with food poisoning had the highest occurrence of the phenotypically analyzed factors and the most frequent occurrence and highest genetic diversity of the plcR-papR, nheA, bceT, cytK-2, plcA, and gyrB genes. An analysis of molecular variance (AMOVA), in which all loci were analyzed, demonstrated that the genetic variation intragroup of isolates (92%) was significantly higher than that intergroup (8%) (P<0.05). These results were corroborated by an analysis of the genetic differentiation between the groups, which was low/moderate, the result of a high degree of allele sharing. Our results suggest that B. cereus isolates with the potential to cause food poisoning outbreaks do not have a specific genetic profile characterized by the presence of a particular gene or allele among the genes assessed. On the contrary, different combinations of genes encoding virulence factors may be present in different isolates of B. cereus that potentially cause food poisoning outbreaks.
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220. |
Sauer DB,
Zeng W,
Raghunathan S,
Jiang Y,
( 2011 ) Protein interactions central to stabilizing the K+ channel selectivity filter in a four-sited configuration for selective K+ permeation. PMID : 21933962 : DOI : 10.1073/pnas.1111688108 PMC : PMC3189067 Abstract >>
The structural and functional conversion of the nonselective NaK channel to a K(+) selective channel (NaK2K) allows us to identify two key residues, Tyr and Asp in the filter sequence of TVGYGD, that participate in interactions central to stabilizing the K(+) channel selectivity filter. By using protein crystallography and channel electrophysiology, we demonstrate that the K(+) channel filter exists as an energetically strained structure and requires these key protein interactions working in concert to hold the filter in the precisely defined four-sited configuration that is essential for selective K(+) permeation. Disruption of either interaction, as tested on both the NaK2K and eukaryotic K(v)1.6 channels, can reduce or completely abolish K(+) selectivity and in some cases may also lead to channel inactivation due to conformational changes at the filter. Additionally, on the scaffold of NaK we recapitulate the protein interactions found in the filter of the Kir channel family, which uses a distinct interaction network to achieve similar stabilization of the filter.
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221. |
Pandiani F,
Chamot S,
Brillard J,
Carlin F,
Nguyen-the C,
Broussolle V,
( 2011 ) Role of the five RNA helicases in the adaptive response of Bacillus cereus ATCC 14579 cells to temperature, pH, and oxidative stresses. PMID : 21705526 : DOI : 10.1128/AEM.02974-10 PMC : PMC3165264 Abstract >>
In this study, growth rates and lag times of the five RNA helicase-deleted mutants of Bacillus cereus ATCC 14579 were compared to those of the wild-type strain under thermal, oxidative, and pH stresses. Deletion of cshD and cshE had no impact under any of the tested conditions. Deletion of cshA, cshB, and cshC abolished growth at 12�XC, confirming previous results. In addition, we found that each RNA helicase had a role in a specific temperature range: deletion of cshA reduced growth at all the tested temperatures up to 45�XC, deletion of cshB had impact below 30�XC and over 37�XC, and deletion of cshC led mainly to a cold-sensitive phenotype. Under oxidative conditions, deletion of cshB and cshC reduced growth rate and increased lag time, while deletion of cshA increased lag time only with H(2)O(2) and reduced growth rate at a high diamide concentration. Growth of the �GcshA strain was affected at a basic pH independently of the temperature, while these conditions had a limited effect on �GcshB and �GcshC strain growth. The RNA helicases CshA, CshB, and CshC could participate in a general adaptation pathway to stressful conditions, with a stronger impact at low temperature and a wider role of CshA.
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222. |
Soufiane B,
Sirois M,
Côté JC,
( 2011 ) Mutually exclusive distribution of the sap and eag S-layer genes and the lytB/lytA cell wall hydrolase genes in Bacillus thuringiensis. PMID : 21611767 : DOI : 10.1007/s10482-011-9590-1 Abstract >>
Recently, two Bacillus thuringiensis strains were reported to synthesize parasporal inclusion bodies made not of the expected crystal (Cry) proteins but rather of the surface layer proteins (SLP) Sap (encoded by sap) and EA1 (encoded by eag), respectively. Whether the presence of the sap and eag genes is restricted to these two B. thuringiensis strains or ubiquitous in B. thuringiensis is unknown. We report here the distribution of the sap and eag genes in B. thuringiensis. Strains in the Bacillus cereus group were added for comparison purposes. We show that sap and eag are either present in tandem in 35% of the B. thuringiensis strains analysed and absent in 65% of the strains. When absent, a different tandem, the lytB/lytA cell wall hydrolase genes, is present. The distribution of the sap and eag S-layer and the lytB/lytA cell wall hydrolase genes is not species-specific in B. thuringiensis, B. cereus and Bacillus weihenstephanensis. Bacillus anthracis and Bacillus mycoides harbor sap and eag but not lytB/lytA. The sap, eag and lytB/lytA genes were absent in Bacillus pseudomycoides. Clearly, the distribution of the sap and eag S-layer and the lytB/lytA cell wall hydrolase genes in B. thuringiensis and in the Bacillus cereus group is mutually exclusive. We also showed that two genes involved in cell wall metabolism, csaA and csaB, are present not only upstream of the sap and eag S-layer genes, but also upstream of the lytB/lytA tandem in strains where sap and eag are absent. Bootstrapped neighbor-joining trees were inferred from the translated amino acid sequences of sap, eag and the tandem lytB/lytA, respectively.
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223. |
Holberger LE,
Garza-Sánchez F,
Lamoureux J,
Low DA,
Hayes CS,
( 2012 ) A novel family of toxin/antitoxin proteins in Bacillus species. PMID : 22200572 : DOI : 10.1016/j.febslet.2011.12.020 PMC : PMC3259279 Abstract >>
The C-terminal regions (CT) of Pfam PF04740 proteins share significant sequence identity with the toxic CdiA-CT effector domains of contact-dependent growth inhibition (CDI) systems. In accord with this homology, we find that several PF04740 CT domains inhibit cell growth when expressed in Escherichia coli. This growth inhibition is specifically blocked by antitoxin proteins encoded downstream of each PF04740 gene. The YobL-CT, YxiD-CT and YqcG-CT domains from Bacillus subtilis 168 have cytotoxic RNase activities, which are neutralized by the binding of cognate YobK, YxxD and YqcF antitoxin proteins, respectively. Our results show that PF04740 proteins represent a new family of toxin/antitoxin pairs that are widely distributed in Gram-positive bacteria.
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224. |
Zhang J,
van Hung P,
Hayashi M,
Yoshida S,
Ohkusu K,
Ezaki T,
( 2011 ) DnaJ sequences of Bacillus cereus strains isolated from outbreaks of hospital infection are highly similar to Bacillus anthracis. PMID : 21683265 : DOI : 10.1016/j.diagmicrobio.2011.02.012 Abstract >>
Bacillus cereus is becoming an important nomosomial pathogen because of frequent isolation from blood cultures and from severe systemic infections. To differentiate highly pathogenic outbreak strain of B. cereus from other sources of the Bacillus cereus, we attempted to analyze their dnaJ sequences. Assays indicated that dnaJ sequence similarity of all of 52 blood culture isolates of B. cereus ranged from 92.8% to 100%. The distance between B. anthracis and B. cereus except six outbreak isolates ranged from 3.8% to 6.4%. The dnaJ sequences of six outbreak strains of B. cereus (GTC 02891, GTC 02896, GTC 02916, GTC 02917, GTC 03221, and GTC 03222) were closely related to those of B. anthracis (99.2%-99.5% sequence similarity). Ba813 sequences were only found in the six outbreak strains of B. cereus. The other pathogenic factors of B. anthracis were not found in these six outbreak strains, with the exception of GTC 02891 (cap-positive). The six outbreak strains formed clear �]-hemolytic colonies on a sheep blood agar plate. Our findings suggest that outbreak strains of B. cereus isolated from blood cultures are likely to have the risk of causing serious infection, and dnaJ and Ba813 are important markers to identify such strains. Phylogenetic analysis of dnaJ and MLST revealed that the six outbreak strains of B. cereus are closely related to B. anthracis.
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225. |
Soriano-Maldonado P,
Martínez-Gómez AI,
Andújar-Sánchez M,
Neira JL,
Clemente-Jiménez JM,
Las Heras-Vázquez FJ,
Rodríguez-Vico F,
Martínez-Rodríguez S,
( 2011 ) Biochemical and mutational studies of the Bacillus cereus CECT 5050T formamidase support the existence of a C-E-E-K tetrad in several members of the nitrilase superfamily. PMID : 21705545 : DOI : 10.1128/AEM.00312-11 PMC : PMC3165270 Abstract >>
Formamidases (EC 3.5.1.49) are poorly characterized proteins. In spite of this scarce knowledge, ammonia has been described as playing a central role in the pathogenesis of human pathogens such as Helicobacter pylori, for which formamidase has been shown to participate in the nitrogen metabolic pathway. Sequence analysis has revealed that at least two different groups of formamidases are classified as EC 3.5.1.49: on the one hand, the derivatives of the FmdA-AmdA superfamily, which are the best studied to date, and on the other hand, the derivatives of Helicobacter pylori AmiF. Here we present the cloning, purification, and characterization of a recombinant formamidase from Bacillus cereus CECT 5050T (BceAmiF), the second member of the AmiF subfamily to be characterized, showing new features of the enzyme further supporting its relationship with aliphatic amidases. We also present homology modeling-based mutational studies confirming the importance of the Glu140 and Tyr191 residues in the enzymatic activities of the AmiF family. Moreover, we can conclude that a second glutamate residue is critical in several members of the nitrilase superfamily, meaning that what has consistently been identified as a C-E-K triad is in fact a C-E-E-K tetrad.
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226. |
Huma N,
Shankar P,
Kushwah J,
Bhushan A,
Joshi J,
Mukherjee T,
Raju S,
Purohit HJ,
Kalia VC,
( 2011 ) Diversity and polymorphism in AHL-lactonase gene (aiiA) of Bacillus. PMID : 22031023 : Abstract >>
To explore bacterial diversity for elucidating genetic variability in acylhomoserine lactone (AHL) lactonase structure, we screened 800 bacterial strains. It revealed the presence of a quorum quenching (QQ) AHL-lactonase gene (aiiA) in 42 strains. These 42 strains were identified using rrs (16S rDNA) sequencing as Bacillus strains, predominantly B. cereus. An in silico restriction endonuclease (RE) digestion of 22 AHL lactonase gene (aiiA) sequences (from NCBI database) belonging to 9 different genera, along with 42 aiiA gene sequences from different Bacillus spp. (isolated here) with 14 type II REs, revealed distinct patterns of fragments (nucleotide length and order) with four REs; AluI, DpnII, RsaI, and Tru9I. Our study reflects on the biodiversity of aiiA among Bacillus species. Bacillus sp. strain MBG11 with polymorphism (115Alanine > Valine) may confer increased stability to AHL lactonase, and can be a potential candidate for heterologous expression and mass production. Microbes with ability to produce AHL-lactonases degrade quorum sensing signals such as AHL by opening of the lactone ring. The naturally occurring diversity of QQ molecules provides opportunities to use them for preventing bacterial infections, spoilage of food, and bioremediation.
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227. |
( 1997 ) Insertional inactivation of a Tet(K)/Tet(L) like transporter does not eliminate tetracycline resistance in Bacillus cereus. PMID : 9311114 : DOI : 10.1111/j.1574-6968.1997.tb12641.x Abstract >>
Bacillus cereus ATCC 10987 and ATCC 14579 can be induced to high levels of resistance to tetracycline. The chromosomal B. cereus gene bctl encodes a transmembrane protein with homology to Gram-positive tetracycline efflux proteins and relation to other members of the major facilitator superfamily of transport proteins. A mutant strain containing an insertionally inactivated bctl gene did not show impaired tetracycline resistance. No additional altered phenotype was observed in the mutant. Accumulation studies suggested that the resistance mechanism involves a reduced sensitivity to intracellular tetracycline.
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228. |
( 1997 ) Cloning, sequencing and overexpression of the leucine dehydrogenase gene from Bacillus cereus. PMID : 9188201 : Abstract >>
The L-leucine dehydrogenase gene from Bacillus cereus (DSM 626) was cloned from a partial genomic library and sequenced. The open reading frame has 1101 bp and codes for a protein of 39.9 kDa. The deduced amino acid sequence of the LeuDH from B. cereus shares 70-80% identity with LeuDH's from the thermophilic strains B. stearothermophilus and Thermoactinomyces intermedius. The active protein was overexpressed in Escherichia coli to yield approximately 30% of the total soluble protein.
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229. |
( 1997 ) Probing the roles of active site residues in phosphatidylinositol-specific phospholipase C from Bacillus cereus by site-directed mutagenesis. PMID : 9335537 : DOI : 10.1021/bi971102d Abstract >>
The role of amino acid residues located in the active site pocket of phosphatidylinositol-specific phospholipase C (PI-PLC) from Bacillus cereus[Heinz, D. W., Ryan, M., Bullock, T., & Griffith, O. H. (1995) EMBO J. 14, 3855-3863] was investigated by site-directed mutagenesis, kinetics, and crystal structure analysis. Twelve residues involved in catalysis and substrate binding (His32, Arg69, His82, Gly83, Lys115, Glu117, Arg163, Trp178, Asp180, Asp198, Tyr200, and Asp274) were individually replaced by 1-3 other amino acids, resulting in a total number of 21 mutants. Replacements in the mutants H32A, H32L, R69A, R69E, R69K, H82A, H82L, E117K, R163I, D198A, D198E, D198S, Y200S, and D274S caused essentially complete inactivation of the enzyme. The remaining mutants (G83S, K115E, R163K, W178Y, D180S, Y200F, and D274N) exhibited reduced activities up to 57% when compared with wild-type PI-PLC. Crystal structures determined at a resolution ranging from 2.0 to 2.7 A for six mutants (H32A, H32L, R163K, D198E, D274N, and D274S) showed that significant changes were confined to the site of the respective mutation without perturbation of the rest of the structure. Only in mutant D198E do the side chains of two neighboring arginine residues move across the inositol binding pocket toward the newly introduced glutamic acid. An analysis of these structure-function relationships provides new insight into the catalytic mechanism, and suggests a molecular explanation of some of the substrate stereospecificity and inhibitor binding data available for this enzyme.
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( 1997 ) The refined crystal structure of Bacillus cereus oligo-1,6-glucosidase at 2.0 A resolution: structural characterization of proline-substitution sites for protein thermostabilization. PMID : 9193006 : DOI : 10.1006/jmbi.1997.1018 Abstract >>
The crystal structure of oligo-1,6-glucosidase (dextrin 6-alpha-glucanohydrolase, EC 3.2.1.10) from Bacillus cereus ATCC7064 has been refined to 2.0 A resolution with an R-factor of 19.6% for 43,328 reflections. The final model contains 4646 protein atoms and 221 ordered water molecules with respective root-mean-square deviations of 0.015 A for bond lengths and of 3.166 degrees for bond angles from the ideal values. The structure consists of three domains: the N-terminal domain (residues 1 to 104 and 175 to 480), the subdomain (residues 105 to 174) and the C-terminal domain (residues 481 to 558). The N-terminal domain takes a (beta/alpha)8-barrel structure with additions of an alpha-helix (N alpha6') between the sixth strand Nbeta6 and the sixth helix N alpha6, an alpha-helix (N alpha7') between the seventh strand Nbeta7 and the seventh helix N alpha7 and three alpha-helices (N alpha8', N alpha8" and N alpha8'" between the eighth strand Nbeta8 and the eighth helix N alpha8. The subdomain is composed of an alpha-helix, a three-stranded antiparallel beta-sheet, and long intervening loops. The C-terminal domain has a beta-barrel structure of eight antiparallel beta-strands folded in double Greek key motifs, which is distorted in the sixth strand Cbeta6. Three catalytic residues, Asp199, Glu255 and Asp329, are located at the bottom of a deep cleft formed by the subdomain and a cluster of the two additional alpha-helices N alpha8' and N alpha8" in the (beta/alpha)8-barrel. The refined structure reveals the locations of 21 proline-substitution sites that are expected to be critical to protein thermostabilization from a sequence comparison among three Bacillus oligo-1,6-glucosidases with different thermostability. These sites lie in loops, beta-turns and alpha-helices, in order of frequency, except for Cys515 in the fourth beta-strand Cbeta4 of the C-terminal domain. The residues in beta-turns (Lys121, Glu208, Pro257, Glu290, Pro443, Lys457 and Glu487) are all found at their second positions, and those in alpha-helices (Asn109, Glu175, Thr261 and Ile403) are present at their N1 positions of the first helical turns. Those residues in both secondary structures adopt phi and phi values favorable for proline substitution. Residues preceding the 21 sites are mostly conserved upon proline occurrence at these 21 sites in more thermostable Bacillus oligo-1,6-glucosidases. These structural features with respect to the 21 sites indicate that the sites in beta-turns and alpha-helices have more essential prerequisites for proline substitution to thermostabilize the protein than those in loops. This well supports the previous finding that the replacement at the appropriate positions in beta-turns or alpha-helices is the most effective for protein thermostabilization by proline substitution.
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( 1997 ) Molecular cloning and characterization of the genes encoding the L1 and L2 components of hemolysin BL from Bacillus cereus. PMID : 9098052 : DOI : 10.1128/jb.179.8.2551-2556.1997 PMC : PMC179003 Abstract >>
Hemolysin BL, which is composed of a binding component, B, and two lytic components, L1 and L2, is the enterotoxin responsible for the diarrheal food poisoning syndrome caused by strains of Bacillus cereus. To further characterize the toxin, we sought to clone and sequence the genes encoding the L1 and L2 proteins. A genomic library was screened with polyclonal antibody to the L1 and L2 proteins to identify recombinant clones containing the genes. Five clones reacted with the antibody to L2, but none reacted with the antibody to L1. Southern hybridization analysis with oligonucleotide probes designed from the N-terminal amino acid sequences of the L1 and L2 proteins, in conjunction with immunoblot and nucleotide sequence analysis, revealed that the recombinant plasmid from one of the clones contained two genes, hblC and hblD, which encode L2 and L1, respectively. The two genes are arranged in tandem and are separated by only 37 bases. The gene which encodes the B component of hemolysin BL (hblA) is located immediately downstream from the gene encoding the L1 protein. Northern blot analysis of B. cereus RNA showed a 5.5-kb transcript which hybridized with DNA fragments internal to, or including a portion of, the coding sequences of the B, L1, and L2 genes, suggesting that the clustered genes which encode the components of hemolysin BL are cotranscribed and constitute an operon.
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( 1996 ) An alkaline D-stereospecific endopeptidase with beta-lactamase activity from Bacillus cereus. PMID : 8939979 : DOI : 10.1074/jbc.271.47.30256 Abstract >>
We purified a novel extracellular D-stereospecific endopeptidase, alkaline D-peptidase (D-stereospecific peptide hydrolase, EC 3.4.11.-), to homogeneity from the culture broth of the soil bacterium Bacillus cereus strain DF4-B. The Mr of the enzyme was 37,952, and it was composed of a single polypeptide chain. The optimal pH for activity was approximately 10.3. The enzyme was strictly D-stereospecific toward oligopeptides composed of Dphenylalanine such as (D-Phe)3 and (D-Phe)4. The enzyme also acted to a lesser extent on (D-Phe)6, Boc-(D-Phe)4 (where Boc is tert-butoxycarbonyl), Boc-(D-Phe)4 methyl ester, Boc-(D-Phe)3 methyl ester, Boc-(D-Phe)2, (D-Phe)2, and others, but not upon their corresponding peptides composed of L-Phe, (D-Ala)n (n = 2-5), (D-Val)3, and (D-Leu)2. The mode of action of the enzyme was clarified with synthetic substrates ((D-Phe)2-D-Tyr and D-Tyr-(D-Phe)2) and eight stereoisomers of (Phe)3. The enzyme had beta-lactamase activity toward ampicillin and penicillin G, although carboxypeptidase DD and D-aminopeptidase activities were undetectable. The gene coding for alkaline D-peptidase (adp) was cloned into plasmid pUC118, and a 1164-base pair open reading frame consisting of 388 codons was identified as the adp gene. The predicted polypeptide was similar to carboxypeptidase DD from Streptomyces R61, penicillin-binding proteins from Streptomyces lactamdurans and Bacillus subtilis, and class C beta-lactamases. Thus, the enzyme was categorized as a new "penicillin-recognizing enzyme."
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( 1993 ) Cloning of the beta-amylase gene from Bacillus cereus and characteristics of the primary structure of the enzyme. PMID : 8434930 : PMC : PMC202157 Abstract >>
The gene encoding the beta-amylase of Bacillus cereus BQ10-S1 (SpoII) was cloned into Escherichia coli JM 109. A sequenced DNA fragment of 2,001 bp contains the beta-amylase gene. The N-terminal sequences (AVNGKG MNPDYKAYLMAPLKKI), the C-terminal sequences (SHTSSW), and the amino acid sequences of the five regions in the beta-amylase molecules were determined. The mature beta-amylase contains 514 amino acid residues with a molecular mass of 57,885 Da. The amino acid sequence homology with those of known beta-amylases was 52.7% for Bacillus polymyxa, 52.0% for Bacillus circulans, 43.4% for Clostridium thermosulfurogenes, 31.8% for Arabidopsis thaliana, 31.5% for barley, 29.9% for sweet potato, and 28.9% for soybean. Ten well-conserved regions were found between the N terminus and the area around residue 430, but the C-terminal region of 90 residues has no similarity with those of the plant beta-amylases. The homology search revealed that this C-terminal region has homology with C-terminal regions of the beta-amylase from C. thermosulfurogenes, some bacterial alpha-amylases, cyclodextrin glucanotransferase, and glucoamylase. Some of these sequences are known as the raw-starch-binding domain. These results suggest that B. cereus beta-amylase has an extra domain which has raw-starch-binding ability and that the domain has considerable sequence homology with those of other amylases or related enzymes from a wide variety of microorganisms.
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( 1996 ) A germination-specific spore cortex-lytic enzyme from Bacillus cereus spores: cloning and sequencing of the gene and molecular characterization of the enzyme. PMID : 8752358 : DOI : 10.1128/jb.178.17.5330-5332.1996 PMC : PMC178337 Abstract >>
A gene (sleB) encoding a 24-kDa germination-specific spore cortex-lytic enzyme, probably an N-acetylmuramyl-L-alanine amidase, was cloned from Bacillus cereus, and its nucleotide sequence was determined. It was indicated that the enzyme is produced as a 259-residue protein with a signal sequence of 32 residues and is present in dormant spores in its active form. Sulfhydryl reagents inactivated the enzyme, but mutation of a single cysteine of the protein, Cys-258, to Gly did not cause complete inactivation of the enzyme, suggesting that the residue does not function as the catalytic center of enzyme.
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( 1996 ) Zwittermicin A resistance gene from Bacillus cereus. PMID : 8763956 : DOI : 10.1128/jb.178.14.4266-4272.1996 PMC : PMC178185 Abstract >>
Zwittermicin A is a novel aminopolyol antibiotic produced by Bacillus cereus that is active against diverse bacteria and lower eukaryotes (L.A. Silo-Suh, B.J. Lethbridge, S.J. Raffel, H. He, J. Clardy, and J. Handelsman, Appl. Environ. Microbiol. 60:2023-2030, 1994). To identify a determinant for resistance to zwittermicin A, we constructed a genomic library from B. cereus UW85, which produces zwittermicin A, and screened transformants of Escherichia coli DH5alpha, which is sensitive to zwittermicin A, for resistance to zwittermicin A. Subcloning and mutagenesis defined a genetic locus, designated zmaR, on a 1.2-kb fragment of DNA that conferred zwittermicin A resistance on E. coli. A DNA fragment containing zmaR hybridized to a corresponding fragment of genomic DNA from B. cereus UW85. Corresponding fragments were not detected in mutants of B. cereus UW85 that were sensitive to zwittermicin A, and the plasmids carrying zmaR restored resistance to the zwittermicin A-sensitive mutants, indicating that zmaR was deleted in the zwittermicin A-sensitive mutants and that zmaR is functional in B. cereus. Sequencing of the 1.2-kb fragment of DNA defined an open reading frame, designated ZmaR. Neither the nucleotide sequence nor the predicted protein sequence had significant similarity to sequences in existing databases. Cell extracts from an E. coli strain carrying zmaR contained a 43.5-kDa protein whose molecular mass and N-terminal sequence matched those of the protein predicted by the zmaR sequence. The results demonstrate that we have isolated a gene, zmaR, that encodes a zwIttermicin A resistance determinant that is functional in both B. cereus and E. coli.
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( 1996 ) Cloning, sequencing, and expression of a beta-amylase gene from Bacillus cereus var. mycoides and characterization of its products. PMID : 8987540 : DOI : 10.1271/bbb.60.1255 Abstract >>
The cloned gene was composed of 1638 bp for coding plus promoter like and SD-like sequences ahead of it. The deduced amino acid sequence had high similarity with known beta-amylases. The N-terminal sequence of the cloned beta-amylase seemed to be a signal peptide. The gene was introduced into Bacillus subtilis 1A289 using pHY300PLK as a vector and the expressed protein was recovered from the culture media. The enzyme fraction produced was divided into two components upon the DEAE column chromatography. The amino acid sequence of one fraction (FrI) was the same as the mature enzyme, and the other (FrII) lacked the N-terminal amino acid residue (Ala) of the mature enzyme. The kinetic parameters of the hydrolysis catalyzed by the enzyme component FrI were measured, and the subsite affinities of the enzyme were evaluated. In conclusion, it was shown that the recombinant enzyme was the same as the mature enzyme functionally and proteochemically.
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( 1996 ) Characterisation of a non-haemolytic enterotoxin complex from Bacillus cereus isolated after a foodborne outbreak. PMID : 8768516 : DOI : 10.1111/j.1574-6968.1996.tb08377.x Abstract >>
Three enterotoxic components have been isolated from a strain of Bacillus cereus which was involved in a large food poisoning outbreak in Norway in 1995. The components were purified by chromatography on three different columns. Three proteins of 39, 45 and 105 kDa, respectively, were found to be necessary for maximum cytotoxicity. The amino acid N-terminal sequences of the 39 and 45 kDa proteins were determined. The 45 kDa component was the same protein as the main antigen detected in the Bacillus Diarrhoeal Enterotoxin Visual Immunoassay (Tecra). The 39 kDa protein showed some similarity to the L1 protein of haemolysin BL from B. cereus. Furthermore, the three toxic components were all recognised by a polyclonal antiserum reported to detect enterotoxin from B. cereus. The proteins were different from the B- and L2-components of haemolysin BL, previously suggested to be a primary virulence factor, and had no detectable haemolytic activity.
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( 1996 ) Crystal structure of phosphatidylinositol-specific phospholipase C from Bacillus cereus in complex with glucosaminyl(alpha 1-->6)-D-myo-inositol, an essential fragment of GPI anchors. PMID : 8755729 : DOI : 10.1021/bi9606105 Abstract >>
Numerous proteins on the external surface of the plasma membrane are anchored by glycosylated derivatives of phosphatidylinositol (GPI), rather than by hydrophobic amino acids embedded in the phospholipid bilayer. These GPI anchors are cleaved by phosphatidylinositol-specific phospholipases C (PI-PLCs) to release a water-soluble protein with an exposed glycosylinositol moiety and diacylglycerol, which remains in the membrane. We have previously determined the crystal structure of Bacillus cereus PI-PLC, the enzyme which is widely used to release GPI-anchored proteins from membranes, as free enzyme and also in complex with myo-inositol [Heinz, D.W., Ryan, M. Bullock, T.L., & Griffith, O. H. (1995) EMBO J. 14, 3855-3863]. Here we report the refined 2.2 A crystal structure of this enzyme complexed with a segment of the core of all GPI anchors, glucosaminyl(alpha 1-->6)-D-myo-inositol [GlcN-(alpha 1-->6)Ins ]. The myo-inositol moiety of GlcN(alpha 1-->6)Ins is well-defined and occupies essentially the same position in the active site as does free myo-inositol, which provides convincing evidence that the enzyme utilizes the same catalytic mechanism for cleavage of PI and GPI anchors. The myo-inositol moiety makes several specific hydrogen bonding interactions with active site residues. In contrast, the glucosamine moiety lies exposed to solvent at the entrance of the active site with minimal specific protein contacts. The glucosamine moiety is also less well-defined, suggesting enhanced conformational flexibility. On the basis of the positioning of GlcN(alpha 1-->6)Ins in the active site, it is predicted that the remainder of the GPI-glycan makes little or no specific interactions with B. cereus PI-PLC. This explains why B. cereus PI-PLC can cleave GPI anchors having variable glycan structures.
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( N/A ) [Evidence of the existence of hemolysin II from Bacillus cereus: cloning the genetic determinant of hemolysin II]. PMID : 8283976 : Abstract >>
The hemolysin genetic determinant distinct from cereolysin AB genetic determinant (lecithinase and sphingomyelinase genes) has been cloned in Escherichia coli and Bacillus subtilis cells as an EcoRI fragment (2.9 kb) of Bacillus cereus VKM-B771 chromosome DNA. The hemolytic product encoded by the cloned DNA fragment possessed all the properties of hemolysin II known to date: it was not inhibited by cholesterol, exhibited the Arrhenius effect, and had a relatively long (in comparison with cereolysin) lag period in erythrocyte lysis. The cloned DNA fragment was concluded to contain the gene of hemolysin II from B. cereus. In contrast to previous suggestions that hemolitic activity ascribed to hemolysin II is due to the combined action of sphingomyelinase and lecithinase, the results obtained present convincing evidence that hemolysin II is an independent B. cereus hemolytic factor different from cereolysin AB.
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( 1996 ) Identification and purification of a family of dimeric major cold shock protein homologs from the psychrotrophic Bacillus cereus WSBC 10201. PMID : 8631682 : DOI : 10.1128/jb.178.10.2916-2925.1996 PMC : PMC178029 Abstract >>
Whole-cell protein patterns of a psychrotrophic Bacillus cereus strain from cultures grown at 7 and 30 degrees C were compared. This analysis revealed that at least three major proteins are expressed at a significantly higher rate at 7 degrees C than at 30 degrees C. The most abundant of these cold-induced proteins was a small polypeptide of 7.5 kDa, designated CspA, of B. cereus. In addition, four small proteins very similar in size to CspA were seen on both 7 degrees C and 30 degrees C two-dimensional protein gels. Immunoblot analysis using B. cereus anti-CspA antibodies indicated that the five proteins described above plus an additional sixth protein not visible on silver-stained two-dimensional gels are members of a B. cereus cold shock protein family. This hypothesis was corroborated by cloning and sequencing of the genes encoding five proteins of this family. The protein sequences deduced are highly similar and show homology to small procaryotic cold shock proteins and to the cold shock domain of eucaryotic Y-box proteins. Besides CspA, only one of the additional five CspA homologs was slightly cold inducible. In the presence of 100 mM NaCl, the two purified members of the protein family (CspA and CspE) elute as dimers at an apparent molecular mass of 15 kDa from a gel filtration column. At higher salt concentrations, they dissociate into their monomers. Their ability to bind to the ATTGG motif of single-stranded oligonucleotides was demonstrated by band shift analysis.
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( 1993 ) [Nucleotide sequence of phospholipase C and sphingomyelinase genes from Bacillus cereus BKM-B164]. PMID : 8387306 : Abstract >>
A BamHI-EcoRV DNA fragment, containing tandemly arranged genes for the Bacillus cereus VKM-B164 phosphatidylcholine-specific phospholipase C and sphingomyelinase, has been cloned and sequenced in pUC19 plasmid (EMBL accession No X64141). The obtained gene sequences have been compared with those the B. cereus strains SE-1, IAM-1208 and GP-4 reported previously. Both phospholipase C and sphingomyelinase gene sequences of the VKM-B164 strain were found to be identical to those of the strain SE-1 and to differ from the sequences of GP-4 and IAM-1208 strains, containing another version of the gene sequences.
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( 1993 ) Sphingomyelinase is part of the 'enterotoxin complex' produced by Bacillus cereus. PMID : 8319899 : DOI : 10.1111/j.1574-6968.1993.tb06301.x Abstract >>
The three components of the 'enterotoxin complex' have been purified and the sequence of the first 14-15 amino acids of the proteins determined. Limited homology was found in the N-terminal sequence of the three proteins. The molecular mass of the proteins was determined to be 48, 40 and 34 kDa, respectively. Only the 40-kDa protein was toxic to Vero cells, whilst the 34-kDa protein was found to be hemolytic. The sequence of the first 14 N-terminal amino acids of this protein was identical to the sequence of the sphingomyelinase residues 28-41 (the N-terminal after loss of the signal sequence), except for a change from Gln to Glu in position 33 of the sphingomyelinase sequence.
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( 1993 ) Polypeptide folding of Bacillus cereus ATCC7064 oligo-1,6-glucosidase revealed by 3.0 A resolution X-ray analysis. PMID : 8370659 : DOI : 10.1093/oxfordjournals.jbchem.a124097 Abstract >>
The crystal structure of an oligo-1,6-glucosidase from Bacillus cereus ATCC7064 was determined by the X-ray diffraction method at 3.0 A resolution. The structure was solved by the multiple isomorphous replacement method and refined to a crystallographic R-factor of 0.208, using the molecular dynamics refinement program, X-PLOR. The electron density map revealed the folding of a polypeptide chain consisting of 558 amino acid residues. The molecule can be subdivided into three domains (N-terminal domain, subdomain, and C-terminal domain). The N-terminal domain has an (alpha/beta)8-barrel structure called the TIM-barrel structure. The C-terminal domain is characterized by a beta-barrel structure composed of eight antiparallel beta-strands, while the subdomain has a loop-rich structure with a small alpha-helix and a beta-sheet. The enzyme has a large cleft between the N-terminal domain and the subdomain. The cleft leads from the molecular surface to the molecular center. The bottom of the cleft is at the C-terminal end of the parallel beta-strands of the (alpha/beta)8-barrel. These structural features closely resemble those of alpha-amylases from Aspergillus oryzae and pig pancreas.
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( 1976 ) Isolation of three new antibiotics, thiocillins I, II and III, related to micrococcin P. Studies on antibiotics from the genus Bacillus. VIII. PMID : 819410 : DOI : 10.7164/antibiotics.29.366 Abstract >>
Thiocillins I and II were isolated from the culture broth of Bacillus cereus G-15, and thiocillins II and III from that of Bacillus badius AR-91. Also, the former two were probably produced by Bacillus megatherium I-13. These antibiotics active against Gram-positive bacteria are soluble in a mixture of chloroform and methanol, show characteristic ultraviolet absorptions (maxima at ca. 275 nm and ca. 348 nm), and contain a high content of sulfur, as much as approximately 15%. They are related to each other and also to micrococcin P, but differentiated by chromatographic behaviours.
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( 1994 ) A spore-lytic enzyme released from Bacillus cereus spores during germination. PMID : 8081503 : DOI : 10.1099/00221287-140-6-1403 Abstract >>
The exudate of fully germinated spores of Bacillus cereus IFO 13597 in 0.25 M sodium phosphate buffer, pH 7.0, was found to contain a spore-lytic enzyme. This enzyme was found to cause loss of absorbance in coat-stripped spore suspensions and phase-darkening of the spores but had minimal activity on isolated peptidoglycan substrates. The enzyme was purified in an active form and identified as a 24 kDa protein which is either an amidase or a peptidase. The amino-terminal 19 residues had the following sequence: FSNQVIQRGASGEKVIELQ. The spore-lytic enzyme retained its activity in a medium of a relatively high ionic strength containing a non-ionic surfactant such as nonaethyleneglycol n-dodecyl ether. This activity was optimum at a salt concentration of about 30 mM in assay buffer at neutral pH. In contrast to the enzyme in a spore-bound form, the enzyme in solution was shown to be heat-sensitive and was readily inactivated by thiol reagents.
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( 1994 ) Cloning and sequencing of the sspF (originally 0.3 kb) genes from Bacillus cereus and Bacillus megaterium. PMID : 7959056 : DOI : 10.1016/0378-1119(94)90888-5 Abstract >>
The sspF gene (originally 0.3 kb) of Bacillus cereus and B. megaterium has been cloned and sequenced, and the predicted amino acid sequences of the gene products (SspF) compared to that of B. subtilis SspF. These proteins exhibit an average of 74% sequence identity across species, suggesting they may play some important role in either sporulation or the dormant spore.
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( 1994 ) The gene encoding a new mitogenic factor in a Streptococcus pyogenes strain is distributed only in group A streptococci. PMID : 8063419 : PMC : PMC303059 Abstract >>
We recently cloned a gene encoding a new mitogenic factor (MF) from Streptococcus pyogenes NY-5. In the present study, we determined the distribution of this MF gene (mf) by PCR based upon its sequence. Of 371 streptococcal group A strains isolated from clinical specimens, 370 (99.7%) were positive for mf. The strain that was negative for the MF gene was also negative for the streptolysin O gene (slo). Some streptococcal strains belonging to groups C and G were negative for mf but positive for slo. Group B strains were negative for both. Furthermore, we examined the presence of mf in 54 strains belonging to 28 families and found mf only in group A streptococci. These results indicate that mf is distributed specifically in group A streptococci and the presence of mf in clinical samples strongly suggests infection with group A streptococci.
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248. |
Brown DP,
Ganova-Raeva L,
Green BD,
Wilkinson SR,
Young M,
Youngman P,
( 1994 ) Characterization of spo0A homologues in diverse Bacillus and Clostridium species identifies a probable DNA-binding domain. PMID : 7885226 : DOI : 10.1111/j.1365-2958.1994.tb02176.x Abstract >>
Spo0A is a phosphorylation-activated transcription factor of Bacillus subtilis. It is a member of the response regulator superfamily of bacterial signal transduction proteins and controls many of the changes in gene expression that occur during the transition into stationary phase and during the initiation of sporulation. To identify the domains of Spo0A most critical for determining its structural and functional features, presumptive homologues of the spo0A gene were characterized in a collection of eight Bacillus species and six Clostridium species representing phylogenetically diverse members of these genera. An alignment of the partial or complete DNA sequences of these homologues revealed three regions of especially high conservation in the effector domain. We speculate that the most highly conserved of these corresponds to the recognition helix of a putative helix-turn-helix motif, and, therefore, represents the actual DNA-containing surface of the protein. In the case of homologues identified in Bacillus anthracis and Clostridium acetobutylicum and retrieved by polymerase chain reaction amplification, we confirmed by gene-disruption analysis that the homologue actually is required for initiation of sporulation. Apparent homologues of the B. subtilis spoIVB gene were also discovered immediately upstream from the spo0A homologues in all Bacillus and Clostridium species examined. The discovery of homologues of B. subtilis sporulation genes in these diverse species implies that the gene products required for specifying pathways of sporulation-specific gene activation and for determining key morphogenetic changes may be highly conserved and suggests that an approach similar to that undertaken here might be used as a general strategy to retrieve and compare their gene sequences. Exhaustive efforts to detect a spo0A-like gene in non-endospore formers, including close relatives of Bacillus such as Listeria and Staphylococcus, were uniformly unsuccessful, suggesting that regulation of gene activity during the transition into stationary phase mediated by Spo0A-like proteins may be exclusive to the endospore-forming bacteria.
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Matsuno K,
Miyamoto T,
Yamaguchi K,
Abu Sayed M,
Kajiwara T,
Hatano S,
( 1995 ) Identification of DNA-binding proteins changed after induction of sporulation in Bacillus cereus. PMID : 7766022 : Abstract >>
DNA-binding proteins were extracted from both exponentially growing cells of Bacillus cereus ts-4 and cells that were induced to sporulate at different stages of chromosome replication, by using a double-stranded B. cereus ts-4 DNA-cellulose column. Two-dimensional electrophoresis of the proteins found that the amounts of 17 proteins changed drastically after induction of sporulation at all the stages. For 8 of those proteins, the largest or the smallest amount was found in the cells which were induced to sporulate 40 min after the initiation of chromosome replication, the sensitive stage for sporulation. The N-terminal amino acids of 6 proteins among the selected proteins were sequenced. The sequence obtained from a 59-kDa protein had sequence similarity (> 45%) to GroEL from several bacterial species. In addition, the sequences from 76- and 52-kDa proteins matched deduced amino acid sequences of a Mycobacterium leprae gene showing homology to the bacteria atp operon and the B. subtilis guaB for IMP dehydrogenase, respectively.
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250. |
Just I,
Selzer J,
Jung M,
van Damme J,
Vandekerckhove J,
Aktories K,
( 1995 ) Rho-ADP-ribosylating exoenzyme from Bacillus cereus. Purification, characterization, and identification of the NAD-binding site. PMID : 7819216 : DOI : 10.1021/bi00001a041 Abstract >>
The ADP-ribosyltransferase produced by a pathogenic strain of Bacillus cereus was purified to near homogeneity. The transferase is a 28,000 Da molecular mass enzyme with a pI of 10.3. The specific enzyme activity is 7.0 nmol of ADP-ribose min-1 mg-1 with a Km for NAD of 0.3 microM. Partial amino acid sequence analysis of the exoenzyme reveals no significant homology to Clostridium botulinum C3 nor to Clostridium limosum exoenzyme. The novel exoenzyme selectively modifies the small GTP-binding proteins of the Rho family presumably at the same acceptor amino acid (Asn-41) as determined for C3. Besides cellular Rho, recombinant RhoA and -B are substrates for the exoenzyme. However, recombinant Rac1 and CDC42, although belonging to the Rho family, are not modified. B. cereus exoenzyme was photolabeled with [carbonyl-14C]NAD resulting in inhibition of ADP-ribosyltransferase and NAD-glycohydrolase activity. A glutamic acid residue was identified as part of the NAD-binding site which corresponds to Glu-174 of C3. This glutamic acid is located in a domain which shows high homology with the C-terminal part of C3 exoenzyme, C. limosum exoenzyme, and Staphylococcus aureus EDIN and which probably represents the catalytic site of the transferases. The data indicate that B. cereus exoenzyme is a novel member of the family of C3-like ADP-ribosyltransferases which share the same substrate protein Rho and which have an identical highly conserved catalytic domain.
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251. |
Heinz DW,
Ryan M,
Bullock TL,
Griffith OH,
( 1995 ) Crystal structure of the phosphatidylinositol-specific phospholipase C from Bacillus cereus in complex with myo-inositol. PMID : 7664726 : PMC : PMC394464 Abstract >>
Phosphatidylinositol (PI), once regarded as an obscure component of membranes, is now recognized as an important reservoir of second messenger precursors and as an anchor for membrane enzymes. PI-specific phospholipase C (PI-PLC) is the enzyme that cleaves PI, invoking numerous cellular responses. The crystal structure of PI-PLC from Bacillus cereus (EC 3.1.4.10) has been solved at 2.6 A resolution and refined to a crystallographic R factor of 18.7%. The structure consists of an imperfect (beta alpha)8-barrel similar to that first observed for triose phosphate isomerase and does not resemble any other known phospholipase structure. The active site of the enzyme has been identified by determining the structure of PI-PLC in complex with its inhibitor, myo-inositol, at 2.6 A resolution (R factor = 19.5%). This substrate-like inhibitor interacts with a number of residues highly conserved among prokaryotic PI-PLCs. Residues His32 and His82, which are also conserved between prokaryotic and eukaryotic PI-PLCs, most likely act as general base and acid respectively in a catalytic mechanism analogous to that observed for ribonucleases.
|
252. |
Beecher DJ,
Wong AC,
( 1994 ) Identification and analysis of the antigens detected by two commercial Bacillus cereus diarrheal enterotoxin immunoassay kits. PMID : 7811099 : PMC : PMC202031 Abstract >>
The usefulness of two commercial immunoassays for the detection of diarrheal enterotoxin of Bacillus cereus is unclear because the identity of the enterotoxin(s) has not been proven and the kits detect different proteins. We found that the Bacillus cereus Enterotoxin-Reversed Passive Latex Agglutination kit (Oxoid) detects the L2 component from hemolysin BL, and the Bacillus Diarrhoeal Enterotoxin Visual Immunoassay (Tecra) detects two apparently nontoxic proteins.
|
253. |
Agata N,
Ohta M,
Arakawa Y,
Mori M,
( 1995 ) The bceT gene of Bacillus cereus encodes an enterotoxic protein. PMID : 7773399 : DOI : 10.1099/13500872-141-4-983 Abstract >>
A toxin gene (bceT) on a 2.9 kb DNA fragment of Bacillus cereus B-4ac was cloned and expressed in Escherichia coli, and its nucleotide sequence determined. The DNA fragment contained an open reading frame capable of encoding a polypeptide of 336 amino acids with a molecular mass of 41039 Da. The translated product in E. coli exhibited Vero cell cytotoxicity, and was positive in a vascular permeability assay. It also caused fluid accumulation in a ligated mouse ileal loop and was lethal to mice upon injection. These biological activities are considered characteristic of diarrhoeal enterotoxins. We therefore conclude that this gene, designated bceT, encodes one of the enterotoxic proteins of B. cereus which cause food-borne diarrhoea.
|
254. |
Heinrichs JH,
Beecher DJ,
MacMillan JD,
Zilinskas BA,
( 1993 ) Molecular cloning and characterization of the hblA gene encoding the B component of hemolysin BL from Bacillus cereus. PMID : 7693651 : DOI : 10.1128/jb.175.21.6760-6766.1993 PMC : PMC206798 Abstract >>
Previous evidence suggests that hemolysin BL, which consists of a binding component, B, and two lytic components, L1 and L2, is the enterotoxin responsible for the diarrheal form of gastroenteritis caused by food-borne strains of Bacillus cereus. To prove that hemolysin BL and the enterotoxin are the same requires large amounts of these components free of other B. cereus proteins. For this purpose, we sought to clone the gene encoding the B component and to express it in Escherichia coli. A partial genomic library was constructed and a 29-base, 1,152-fold-degenerate oligonucleotide probe, designed from the N-terminal amino acid sequence of the B component, was used to identify recombinant clones containing the gene. Detection of gene products reactive with a monoclonal antibody specific for the B component and analysis of the nucleotide sequence confirmed that isolated clones, reactive with the oligonucleotide probe, did contain the gene encoding the B component. The protein, expressed in E. coli, apparently from the B. cereus promoter, produces a ring-shaped zone of hemolysis when combined with purified L components from B. cereus, a reaction typical of hemolysin BL. Northern (RNA) blot analysis of B. cereus RNA showed a large (5.1-kb) transcript which hybridized with a 500-bp probe internal to the B-component-coding sequence, suggesting that the hblA gene encoding the B component may be transcribed as part of a polycistronic message, possibly including the structural genes for the two lytic components. Higher levels of expression and disruption of the hblA gene are being pursued to resolve whether hemolysin BL is indeed the enterotoxin.
|
255. |
( 1994 ) In vivo and in vitro effects of mutagenesis of active site tyrosine residues of mercuric reductase. PMID : 7988676 : DOI : 10.1016/0014-5793(94)01180-x Abstract >>
X-ray crystal structure analysis of mercuric reductase suggested that the binding site for Hg2+ consisted of two tyrosine residues, Tyr264 and Tyr605, as well as two cysteine residues, Cys207 and Cys628. We have previously shown that mutagenesis of Tyr605 to Phe lowered the kcat of the enzyme 6-fold, whereas the same mutation of Tyr264 resulted in a reduction of 160-fold [(1993) Biochemistry 32, 7475-7478]. Tyr605 occupies the same position in mercuric reductase as the active site His residue in the related enzyme glutathione reductase. The mutation of Tyr605 of mercuric reductase to a His residue produced a 24-fold decrease in kcat and a 15-fold decrease in Km. The in vivo resistance to Hg2+ of E. coli strains carrying wild type or mutant merA genes correlated with the in vitro measurements of kcat/Km for mercuric reductase activity.
|
256. |
Sloma A,
Gross M,
( 1983 ) Molecular cloning and nucleotide sequence of the type I beta-lactamase gene from Bacillus cereus. PMID : 6308567 : DOI : 10.1093/nar/11.14.4997 PMC : PMC326101 Abstract >>
The gene for the type I beta-lactamase from Bacillus cereus has been cloned in Bacillus subtilis and Escherichia coli. In B. subtilis, penicillinase activity is detected and the enzyme is secreted. In E. coli, the gene confers ampicillin resistance. The cloned insert is 4.3 kb in length and DNA sequencing has revealed the location of the gene, its promoter and signal peptide.
|
257. |
Otnaess AB,
Little C,
Sletten K,
Wallin R,
Johnsen S,
Flengsrud R,
Prydz H,
( 1977 ) Some characteristics of phospholipase C from Bacillus cereus. PMID : 72664 : DOI : 10.1111/j.1432-1033.1977.tb11828.x Abstract >>
N/A
|
258. |
Shoji J,
Kato T,
Yoshimura Y,
Tori K,
( 1981 ) Structural studies on thiocillins I, II and III (studies on antibiotics from the genus Bacillus XXIX). PMID : 7328054 : DOI : 10.7164/antibiotics.34.1126 Abstract >>
Thiocillins I, II and III were compared with micrococcin P1 by analysis of acid hydrolyzates of the native and the reduced antibiotics as well as by means of 1H and 13CNMR spectroscopies. As a result of these studies, the differences of these antibiotics were clarified in their structural units, and the structures of thiocillins I, II and III were assigned on the basis of the proposed structure of micrococcin P1.
|
259. |
Mézes PS,
Yang YQ,
Hussain M,
Lampen JO,
( 1983 ) Bacillus cereus 569/H beta-lactamase I: cloning in Escherichia coli and signal sequence determination. PMID : 6413253 : DOI : 10.1016/0014-5793(83)81006-0 Abstract >>
The gene, penPC, for beta-lactamase I of Bacillus cereus 569/H has been cloned and its expression studied in Escherichia coli. The protein product from the in vitro translation of penPC was shown by gel electrophoresis to have an Mr of 36 000 which is larger than the in vivo products found in B. cereus and E. coli. The DNA sequence of the signal region was determined. It revealed that the smallest known mature form present in B. cereus culture fluids is preceded by 45-48 amino acids in pre-beta-lactamase I, considering that there are 3 initiation codons in the same reading frame, one or more of which might be initiating translation. Unlike the Bacillus licheniformis 749/C beta-lactamase, which has a membrane-bound thioether lipoprotein form, the single Cys residue in the B. cereus beta-lactamase I signal sequence is unmodified and a single processed form of the enzyme is present in E. coli cells carrying penPC.
|
260. |
Baida GE,
Kuzmin NP,
( 1995 ) Cloning and primary structure of a new hemolysin gene from Bacillus cereus. PMID : 7495855 : DOI : 10.1016/0167-4781(95)00150-f Abstract >>
A new hemolysin gene from Bacillus cereus VKM-B164 was cloned in Escherichia coli and sequenced. Deduced protein consists of 219 amino acids and has a molecular mass of 24.4 kDa. It has been concluded that the hemolysin, named 'hemolysin III', is distinct from the B. cereus hemolysins reported previously: cereolysin, sphingomyelinase, cereolysin AB, hemolysin II, and 'cereolysin-like' hemolysin (Honda, T., Shiba, A., Seo, S., Yamamoto, J., Matsuyama, J. and Miwatani, T. (1991) FEMS Microbiol. Lett. 79, 205-210).
|
261. |
Carfi A,
Pares S,
Duée E,
Galleni M,
Duez C,
Frère JM,
Dideberg O,
( 1995 ) The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold. PMID : 7588620 : PMC : PMC394593 Abstract >>
The 3-D structure of Bacillus cereus (569/H/9) beta-lactamase (EC 3.5.2.6), which catalyses the hydrolysis of nearly all beta-lactams, has been solved at 2.5 A resolution by the multiple isomorphous replacement method, with density modification and phase combination, from crystals of the native protein and of a specially designed mutant (T97C). The current model includes 212 of the 227 amino acid residues, the zinc ion and 10 water molecules. The protein is folded into a beta beta sandwich with helices on each external face. To our knowledge, this fold has never been observed. An approximate internal molecular symmetry is found, with a 2-fold axis passing roughly through the zinc ion and suggesting a possible gene duplication. The active site is located at one edge of the beta beta sandwich and near the N-terminal end of a helix. The zinc ion is coordinated by three histidine residues (86, 88 and 149) and a water molecule. A sequence comparison of the relevant metallo-beta-lactamases, based on this protein structure, highlights a few well-conserved amino acid residues. The structure shows that most of these residues are in the active site. Among these, aspartic acid 90 and histidine 210 participate in a proposed catalytic mechanism for beta-lactam hydrolysis.
|
262. |
Mizuno Y,
Ito E,
( 1968 ) Purification and properties of uridine diphosphate N-acetylmuramyl-L-alanyl-D-glutamate:meso-2,6-diaminopimelate ligase. PMID : 4967958 : Abstract >>
N/A
|
263. |
Hussain M,
Carlino A,
Madonna MJ,
Lampen JO,
( 1985 ) Cloning and sequencing of the metallothioprotein beta-lactamase II gene of Bacillus cereus 569/H in Escherichia coli. PMID : 3930467 : PMC : PMC214233 Abstract >>
The structural gene for beta-lactamase II (EC 3.5.2.6), a metallothioenzyme, from Bacillus cereus 569/H (constitutive for high production of the enzyme) was cloned in Escherichia coli, and the nucleotide sequence was determined. This is the first class B beta-lactamase whose primary structure has been reported. The amino acid sequence of the exoenzyme form, deduced from the DNA, indicates that beta-lactamase II, like other secreted proteins, is synthesized as a precursor with a 30-amino acid N-terminal signal peptide. The pre-beta-lactamase II (Mr, 28,060) is processed in E. coli and in B. cereus to a single mature protein (Mr, 24,932) which is totally secreted by B. cereus but in E. coli remains intracellular, probably in the periplasm. The expression of the gene in E. coli RR1 on the multicopy plasmid pRWHO12 was comparable to that in B. cereus, where it is presumably present as a single copy. The three histidine residues that are involved (along with the sole cysteine of the mature protein) in Zn(II) binding and hence in enzymatic activity against beta-lactams were identified. These findings will help to define the secondary structure, mechanism of action, and evolutionary lineage of B. cereus beta-lactamase II and other class B beta-lactamases.
|
264. |
Ambler RP,
Daniel M,
Fleming J,
Hermoso JM,
Pang C,
Waley SG,
( 1985 ) The amino acid sequence of the zinc-requiring beta-lactamase II from the bacterium Bacillus cereus 569. PMID : 3930290 : DOI : 10.1016/0014-5793(85)81024-3 Abstract >>
The amino acid sequence of the zinc-requiring beta-lactamase II from Bacillus cereus strain 569 has been determined. It consists of a single polypeptide chain of 227 residues. It is the only example so far fully characterized of a class B beta-lactamase, and is structurally and mechanistically distinct from both the widely distributed class A beta-lactamases (such as the Escherichia coli RTEM enzyme) and from the chromosomally encoded class C enzymes from Gram-negative bacteria.
|
265. |
Nielsen JB,
Lampen JO,
( 1983 ) Beta-lactamase III of Bacillus cereus 569: membrane lipoprotein and secreted protein. PMID : 6414515 : DOI : 10.1021/bi00289a007 Abstract >>
A third beta-lactamase in Bacillus cereus 569 has been identified and characterized. It corresponds to gamma-penicillinase reported by Pollock [Pollock, M. R. (1956) J. Gen. Microbiol. 15, 154-169] but whose existence has been questioned since then. It will be called beta-lactamase III. It resembles the class A beta-lactamases but is immunologically distinct from the major class A secreted beta-lactamase I of B. cereus. As with several other Gram-positive beta-lactamases it occurs in two forms, membrane bound as a glyceride-cysteine lipoprotein and as a hydrophilic secreted protein formed by cleavage on the carboxyl side of the modified cysteine that is the membrane attachment site. It is produced in all B. cereus 569 strains tested but is absent in B. cereus 5/b. Antibody to beta-lactamase III interacts to varying degrees with all the known class A beta-lactamases, most strongly with that of B. licheniformis 749/C.
|
266. |
Hong CE,
Kim JU,
Lee JW,
Bang KH,
Jo IH,
( 2018 ) Complete Genome Sequence of the Endophytic Bacterium Bacillus cereus PgBE311, Isolated from Panax ginseng. PMID : 30533836 : DOI : 10.1128/MRA.01382-18 PMC : PMC6284724 Abstract >>
Bacillus cereus PgBE311, isolated from the root tissue of a 5-year-old Panax ginseng plant, showed activities against the fungal pathogens Cylindrocarpon destructans and Botrytis cinerea. Here, we report the genome sequence of B. cereus PgBE311. The bacterium contains antibiotic-related gene clusters and has the potential to stimulate plant growth.
|
267. |
Bucher T,
Keren-Paz A,
Hausser J,
Olender T,
Cytryn E,
Kolodkin-Gal I,
( 2019 ) An active �]-lactamase is a part of an orchestrated cell wall stress resistance network of Bacillus subtilis and related rhizosphere species. PMID : 30637927 : DOI : 10.1111/1462-2920.14526 Abstract >>
A hallmark of the Gram-positive bacteria, such as the soil-dwelling bacterium Bacillus subtilis, is their cell wall. Here, we report that d-leucine and flavomycin, biofilm inhibitors targeting the cell wall, activate the �]-lactamase PenP. This �]-lactamase contributes to ampicillin resistance in B. subtilis under all conditions tested. In contrast, both Spo0A, a master regulator of nutritional stress, and the general cell wall stress response, differentially contribute to �]-lactam resistance under different conditions. To test whether �]-lactam resistance and �]-lactamase genes are widespread in other Bacilli, we isolated Bacillus species from undisturbed soils, and found that their genomes can encode up to five �]-lactamases with differentiated activity spectra. Surprisingly, the activity of environmental �]-lactamases and PenP, as well as the general stress response, resulted in a similarly reduced lag phase of the culture in the presence of �]-lactam antibiotics, with little or no impact on the logarithmic growth rate. The length of the lag phase may determine the outcome of the competition between �]-lactams and �]-lactamases producers. Overall, our work suggests that antibiotic resistance genes in B. subtilis and related species are ancient and widespread, and could be selected by interspecies competition in undisturbed soils.
|
268. |
?zdemir F,
Arslan S,
( 2019 ) Molecular Characterization and Toxin Profiles of Bacillus spp. Isolated from Retail Fish and Ground Beef. PMID : 30690739 : DOI : 10.1111/1750-3841.14445 Abstract >>
Bacillus species are common in the environment due to their spore-forming ability and nutritional versatility and cause food contamination. Bacilli play a significant role in foodborne illnesses and food spoilage. In this study, 52 Bacillus isolates from retail fish and ground beef were identified and differentiated based on 16S rRNA, gyrB, and rpoB gene sequencing. The presence of genes encoding emetic toxin (ces), hemolytic enterotoxin hemolysin BL (hbl), nonhemolytic enterotoxin (nhe) and cytotoxin K (cytK1) was assessed in all Bacillus isolates. The ability of the Bacillus isolates to produce several extracellular enzymes that contribute to pathogenicity and food spoilage was investigated. The 16S rRNA, rpoB, and gyrB gene sequence similarities of the Bacillus isolates tested were 96.1%, 83.2%, and 77.5%, respectively. The gyrB gene demonstrated a higher degree of sequence variation than the 16S rRNA and rpoB genes. The prevalence of Bacillus isolates producing at least two of the genes of the HBL and NHE complexes was 23.1% and 15.4%, respectively. Of the B. cereus isolates, 10 (41.7%) possessed two or more enterotoxin genes. None of the isolates carried the ces and cytK1 genes. All isolates were positive for the production of enzymes such as protease, lipase, gelatinase, and DNase. However, only 92.3% of the tested isolates were positive for amylase. In conclusion, our results revealed that the presence of genes involved in toxin production and enzyme production in meat-originated B. cereus and other Bacillus isolates may cause spoilage of food and pose a health risk for consumers. PRACTICAL APPLICATION: Bacillus species can be found in various foods due to their ubiquitous nature. Bacillus spp., especially B. cereus, are associated with food poisoning and other infections in humans. Toxins and many extracellular enzymes produced by Bacillus spp. are the causative agents of foodborne outbreaks, food spoilage, and low-quality food with significantly reduced edibility. This study highlights the characterization of Bacillus spp. and presence of potentially pathogenic Bacillus species in meats.
|
269. |
Loshon CA,
Fliss ER,
Setlow B,
Foerster HF,
Setlow P,
( 1986 ) Cloning and nucleotide sequencing of genes for small, acid-soluble spore proteins of Bacillus cereus, Bacillus stearothermophilus, and "Thermoactinomyces thalpophilus". PMID : 3087949 : DOI : 10.1128/jb.167.1.168-173.1986 PMC : PMC212856 Abstract >>
As found previously with other Bacillus species, spores of B. stearothermophilus and "Thermoactinomyces thalpophilus" contained significant levels of small, acid-soluble spore proteins (SASP) which were rapidly degraded during spore germination and which reacted with antibodies raised against B. megaterium SASP. Genes coding for a B. stearothermophilus and a "T. thalpophilus" SASP as well as for two B. cereus SASP were cloned, their nucleotide sequences were determined, and the amino acid sequences of the SASP coded for were compared. Strikingly, all of the amino acid residues previously found to be conserved in this group of SASP both within and between two other Bacillus species (B. megaterium and B. subtilis) were also conserved in the SASP coded for by the B. cereus genes as well as those coded for by the genes from the more distantly related organisms B. stearothermophilus and "T. thalpophilus." This finding strongly suggests that there is significant selective pressure to conserve SASP primary sequence and thus that these proteins serve some function other than simply amino acid storage.
|
270. |
Madonna MJ,
Zhu YF,
Lampen JO,
( 1987 ) Nucleotide sequence of the beta-lactamase I gene of Bacillus cereus strains 569/H and 5/B. PMID : 3103105 : DOI : 10.1093/nar/15.4.1877 PMC : PMC340593 Abstract >>
N/A
|
271. |
Pauptit RA,
Karlsson R,
Picot D,
Jenkins JA,
Niklaus-Reimer AS,
Jansonius JN,
( 1988 ) Crystal structure of neutral protease from Bacillus cereus refined at 3.0 A resolution and comparison with the homologous but more thermostable enzyme thermolysin. PMID : 3127592 : DOI : 10.1016/0022-2836(88)90623-7 Abstract >>
Neutral protease from Bacillus cereus exhibits a 73% amino acid sequence homology to thermolysin, for which an accurate crystal structure exists. The B. cereus enzyme is, however, markedly less thermostable. The neutral protease was crystallized and diffraction data to 3.0 A resolution were recorded by oscillation photography. The crystal structure was solved by molecular replacement methods using thermolysin as a trial molecule. The solution was improved by rigid-body refinement and model rebuilding into electron density omit-maps. The atomic co-ordinates were refined to R = 21.7% at 3.0 A resolution. Comparison of the resultant model with the thermolysin structure shows that the two enzymes are very similar with a root-mean-square deviation between equivalent C alpha-atoms of 0.88 A. The gamma-turn found in thermolysin is transformed into a beta-turn in the neutral protease by the insertion of a glycine residue. There appear to be no contributions to the enhanced thermostability of thermolysin from additional salt bridges, whereas contributions in the form of extra hydrogen bonding interactions could be important. Other factors that may affect thermostability include the two glycine to alanine exchanges and perturbations in the environment of the double calcium site.
|
272. |
Sidler W,
Niederer E,
Suter F,
Zuber H,
( 1986 ) The primary structure of Bacillus cereus neutral proteinase and comparison with thermolysin and Bacillus subtilis neutral proteinase. PMID : 3092843 : Abstract >>
The complete amino-acid sequence of a neutral proteinase, produced by Bacillus cereus, was determined by protein sequencing. The neutral proteinase consists of 317 amino-acid residues. The primary structure is 70% homologous to thermolysin, a thermostable neutral proteinase and 45% homologous to Bacillus subtilis neutral proteinase. The zinc-binding site and the hydrophobic pocket of the active site are highly similar in all three proteinases. B. cereus neutral proteinase which is 20 degrees C less thermostable (60 degrees C) than thermolysin (80 degrees C) shows only minor differences in calcium binding sites and salt bridges compared to thermolysin (known from its X-ray diffraction analysis), whereas B. subtilis neutral proteinase (50 degrees C) differs considerably. Therefore it was assumed that the difference in thermostability between B. cereus neutral proteinase and thermolysin is not caused by different metal binding properties, or differences in the active site, but by changes within the rest of the molecule. Calculation of secondary structure potentials according to Chou & Fasman, hydrophobicity and bulkiness of the different structural elements and preferred cold----hot amino-acid residue exchanges indicated, that the thermostability of thermolysin compared to B. cereus neutral proteinase is caused by small effects contributed by numerous amino-acid exchanges distributed over the whole molecule, resulting in increased hydrophobicity of beta-pleated sheet and higher bulkiness of alpha-helical regions.
|
273. |
Madgwick PJ,
Waley SG,
( 1987 ) beta-lactamase I from Bacillus cereus. Structure and site-directed mutagenesis. PMID : 3124817 : DOI : 10.1042/bj2480657 PMC : PMC1148599 Abstract >>
The sequence of the gene for beta-lactamase I from Bacillus cereus 569/H has been redetermined. Oligonucleotide-directed mutagenesis has been carried out, and the effects of the changes on the ampicillin-resistance of Escherichia coli TG1 expressing the mutant genes have been studied. Lysine-73, close to the active-site serine-70 and a highly-conserved residue, has been converted into arginine. This change had a large effect on activity, but did not abolish it. An even larger effect was found in the mutant in which glutamate-166 had been converted into glutamine; this had little or no activity. On the other hand, the conversion of glutamate-168 into aspartate gave fully active enzyme. Glutamate-166 is an invariant residue, but glutamate-168 is not. Alanine-123 has been replaced by cysteine, to give active enzyme; this change forms part of the plan to introduce a disulphide bond into the enzyme.
|
274. |
Sutton BJ,
Artymiuk PJ,
Cordero-Borboa AE,
Little C,
Phillips DC,
Waley SG,
( 1987 ) An X-ray-crystallographic study of beta-lactamase II from Bacillus cereus at 0.35 nm resolution. PMID : 3124808 : DOI : 10.1042/bj2480181 PMC : PMC1148516 Abstract >>
Crystals of beta-lactamase II (EC 3.5.2.6., 'penicillinase') from Bacillus cereus were grown with Cd(II) in place of the natural Zn(II) cofactor and stabilized by cross-linking with glutaraldehyde. Their space group is C2, the cell dimensions are a = 5.44 nm, b = 6.38 nm, c = 7.09 nm and beta = 93.6 degrees, and there is one molecule in the asymmetric unit. Diffraction data were collected from cross-linked crystals of the Cd(II)-enzyme, the apoenzyme and six heavy-atom derivatives. The electron-density map calculated at 0.35 nm resolution reveals the essential Cd(II) ion surrounded by three histidine residues and one cysteine residue. The position of a glutamic acid residue, modification of which destroys activity [Little, Emanuel, Gagnon & Waley (1986) Biochem. J. 233, 465-469], suggests the probable location of the active site of the enzyme. Two minor Cd(II) sites not essential for activity were also located. The structure of the apoenzyme at this resolution appears to differ from that of the Cd(II)-enzyme only in the orientation of two of the histidine residues and the cysteine residue that surround the metal ion.
|
275. |
Johansen T,
Holm T,
Guddal PH,
Sletten K,
Haugli FB,
Little C,
( 1988 ) Cloning and sequencing of the gene encoding the phosphatidylcholine-preferring phospholipase C of Bacillus cereus. PMID : 3137122 : DOI : 10.1016/0378-1119(88)90466-0 Abstract >>
A synthetic oligodeoxynucleotide probe was used to clone the gene encoding the phosphatidylcholine-preferring phospholipase C of Bacillus cereus. The sequence of a 2050-bp restriction fragment containing the gene was determined. Analysis of the gene-derived amino acid (aa) sequence showed that this exoenzyme is probably synthesized as a 283-aa precursor with a 24-aa signal peptide and a 14-aa propeptide. The mature, secreted enzyme comprises 245 aa residues. Sonicates of Escherichia coli HB101 carrying the gene on a multicopy plasmid showed phospholipase C activity. This activity was inhibited by Tris, a known inhibitor of the B. cereus enzyme and also by antiserum raised against pure B. cereus phospholipase C. We conclude therefore that the gene is expressed in E. coli. The cloning and sequencing described here complete the first step toward using in vitro mutagenesis for investigations of the structure-function relationships of B. cereus phospholipase C.
|
276. |
Lim HM,
Pène JJ,
Shaw RW,
( 1988 ) Cloning, nucleotide sequence, and expression of the Bacillus cereus 5/B/6 beta-lactamase II structural gene. PMID : 3131315 : DOI : 10.1128/jb.170.6.2873-2878.1988 PMC : PMC211218 Abstract >>
Two forms of heat-stable, zinc-containing beta-lactamase II have been described for strains of Bacillus cereus and have been shown to differ in substrate specificity (R. B. Davies, E. P. Abraham, J. Fleming, and M. R. Pollock, Biochem. J. 145: 409-411, 1975). We report here the nucleotide sequence, inferred amino acid sequence, and expression of beta-lactamase II from B. cereus 5/B/6 and compare our results with those for its homolog characterized in B. cereus 569/H (M. Hussain, C. Anthony, M. J. Madonna, and J. O. Lampen, J. Bacteriol. 164: 223-229, 1985) to document amino acid differences contributing to the specific properties of these enzymes.
|
277. |
Sun DX,
Setlow P,
( 1987 ) Cloning and nucleotide sequencing of genes for a second type of small, acid-soluble spore proteins of Bacillus cereus, Bacillus stearothermophilus, and "Thermoactinomyces thalpophilus". PMID : 3036769 : DOI : 10.1128/jb.169.7.3088-3093.1987 PMC : PMC212353 Abstract >>
The nucleotide sequences of the single genes coding for the B-type small, acid-soluble spore proteins (SASP) of Bacillus cereus, B. stearothermophilus, and "Thermoactinomyces thalpophilus" were determined, and the amino acid sequences of all B-type SASP were compared. While this type of SASP showed significant sequence conservation around the two spore protease cleavage sites, alignment of these sequences required the introduction of gaps, and even then only 19 of the residues were conserved exactly in all five proteins. However, all five B-type SASP did contain a large (27 to 35-residue), rather well-conserved amino acid sequence repeat, and four of the five proteins had well-conserved regions of 14 to 17 amino acids which appeared three times.
|
278. |
Michalska K,
Quan Nhan D,
Willett JLE,
Stols LM,
Eschenfeldt WH,
Jones AM,
Nguyen JY,
Koskiniemi S,
Low DA,
Goulding CW,
Joachimiak A,
Hayes CS,
( 2018 ) Functional plasticity of antibacterial EndoU toxins. PMID : 29923643 : DOI : 10.1111/mmi.14007 PMC : PMC6173971 Abstract >>
Bacteria use several different secretion systems to deliver toxic EndoU ribonucleases into neighboring cells. Here, we present the first structure of a prokaryotic EndoU toxin in complex with its cognate immunity protein. The contact-dependent growth inhibition toxin CdiA-CTSTECO31 from Escherichia coli STEC_O31 adopts the eukaryotic EndoU fold and shares greatest structural homology with the nuclease domain of coronavirus Nsp15. The toxin contains a canonical His-His-Lys catalytic triad in the same arrangement as eukaryotic EndoU domains, but lacks the uridylate-specific ribonuclease activity that characterizes the superfamily. Comparative sequence analysis indicates that bacterial EndoU domains segregate into at least three major clades based on structural variations in the N-terminal subdomain. Representative EndoU nucleases from clades I and II degrade tRNA molecules with little specificity. In contrast, CdiA-CTSTECO31 and other clade III toxins are specific anticodon nucleases that cleave tRNAGlu between nucleotides C37 and m2 A38. These findings suggest that the EndoU fold is a versatile scaffold for the evolution of novel substrate specificities. Such functional plasticity may account for the widespread use of EndoU effectors by diverse inter-bacterial toxin delivery systems.
|
279. |
Giastas P,
Andreou A,
Papakyriakou A,
Koutsioulis D,
Balomenou S,
Tzartos SJ,
Bouriotis V,
Eliopoulos EE,
( 2018 ) Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase Bc1974 and Its Complexes with Zinc Metalloenzyme Inhibitors. PMID : 29257674 : DOI : 10.1021/acs.biochem.7b00919 Abstract >>
The cell wall peptidoglycan is recognized as a primary target of the innate immune system, and usually its disintegration results in bacterial lysis. Bacillus cereus, a close relative of the highly virulent Bacillus anthracis, contains 10 polysaccharide deacetylases. Among these, the peptidoglycan N-acetylglucosamine deacetylase Bc1974 is the highest homologue to the Bacillus anthracis Ba1977 that is required for full virulence and is involved in resistance to the host's lysozyme. These metalloenzymes belong to the carbohydrate esterase family 4 (CE4) and are attractive targets for the development of new anti-infective agents. Herein we report the first X-ray crystal structures of the NodB domain of Bc1974, the conserved catalytic core of CE4s, in the unliganded form and in complex with four known metalloenzyme inhibitors and two amino acid hydroxamates that target the active site metal. These structures revealed the presence of two conformational states of a catalytic loop known as motif-4 (MT4), which were not observed previously for peptidoglycan deacetylases, but were recently shown in the structure of a Vibrio clolerae chitin deacetylase. By employing molecular docking of a substrate model, we describe a catalytic mechanism that probably involves initial binding of the substrate in a receptive, more open state of MT4 and optimal catalytic activity in the closed state of MT4, consistent with the previous observations. The ligand-bound structures presented here, in addition to the five Bc1974 inhibitors identified, provide a valuable basis for the design of antibacterial agents that target the peptidoglycan deacetylase Ba1977.
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280. |
Il Kim M,
Lee C,
Park J,
Jeon BY,
Hong M,
( 2018 ) Crystal structure of Bacillus cereus flagellin and structure-guided fusion-protein designs. PMID : 29643437 : DOI : 10.1038/s41598-018-24254-w PMC : PMC5895748 Abstract >>
Flagellin is a major component of the flagellar filament. Flagellin also functions as a specific ligand that stimulates innate immunity through direct interaction with Toll-like receptor 5 (TLR5) in the host. Because flagellin activates the immune response, it has been of interest to develop as a vaccine adjuvant in subunit vaccines or antigen fusion vaccines. Despite the widespread application of flagellin fusion in preventing infectious diseases, flagellin-antigen fusion designs have never been biophysically and structurally characterized. Moreover, flagellin from Salmonella species has been used extensively despite containing hypervariable regions not required for TLR5 that can cause an unexpected immune response. In this study, flagellin from Bacillus cereus (BcFlg) was identified as the smallest flagellin molecule containing only the conserved TLR5-activating D0 and D1 domains. The crystal structure of BcFlg was determined to provide a scheme for fusion designs. Through homology-based modeling and comparative structural analyses, diverse fusion strategies were proposed. Moreover, cellular and biophysical analysis of an array of fusion constructs indicated that insertion fusion at BcFlg residues 178-180 does not interfere with the protein stability or TLR5-stimulating capacity of flagellin, suggesting its usefulness in the development and optimization of flagellin fusion vaccines.
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281. |
Hong HJ,
Kim TH,
Song WS,
Ko HJ,
Lee GS,
Kang SG,
Kim PH,
Yoon SI,
( 2018 ) Crystal structure of FlgL and its implications for flagellar assembly. PMID : 30250171 : DOI : 10.1038/s41598-018-32460-9 PMC : PMC6155364 Abstract >>
Bacteria move toward attractants and away from repellants by rotating their flagellum. The bacterial flagellum assembles through the ordered organization of more than 30 different proteins. Among the diverse flagellar proteins, FlgL forms the junction between the hook and the filament in the flagellum together with FlgK and provides a structural base where flagellin, a filament-forming protein, is inserted for the initiation of filament elongation. However, the functional and structural information available for FlgL is highly limited. To provide structural insights into the cross-linkage between the FlgL junction and the flagellin filament, we determined the crystal structures of FlgL from gram-positive Bacillus cereus (bcFlgL) and gram-negative Xanthomonas campestris (xcFlgL). bcFlgL contains one domain (D1), whereas xcFlgL adopts a two-domain structure that consists of the D1 and D2 domains. The constant D1 domain of FlgL adopts a rod structure that is generated by four longitudinal segments. This four-segment structure is recapitulated in filament and junction proteins but not in hook and rod proteins, allowing us to propose a junction-filament assembly mechanism based on a quasi-homotypic interaction. The D2 domain of xcFlgL resembles that of another junction protein, FlgK, suggesting the structural and functional relatedness of FlgL and FlgK.
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282. |
Higuchi Y,
Matsufuji H,
Tanuma M,
Arakawa T,
Mori K,
Yamada C,
Shofia R,
Matsunaga E,
Tashiro K,
Fushinobu S,
Takegawa K,
( 2018 ) Identification and characterization of a novel �]-D-galactosidase that releases pyruvylated galactose. PMID : 30104607 : DOI : 10.1038/s41598-018-30508-4 PMC : PMC6090015 Abstract >>
Pyruvyl modification of oligosaccharides is widely seen in both prokaryotes and eukaryotes. Although the biosynthetic mechanisms of pyruvylation have been investigated, enzymes that metabolize and degrade pyruvylated oligosaccharides are not well known. Here, we searched for a pyruvylated galactose (PvGal)-releasing enzyme by screening soil samples. We identified a Bacillus strain, as confirmed by the 16S ribosomal RNA gene analysis, that exhibited PvGal-ase activity toward p-nitrophenyl-�]-D-pyruvylated galactopyranose (pNP-�]-D-PvGal). Draft genome sequencing of this strain, named HMA207, identified three candidate genes encoding potential PvGal-ases, among which only the recombinant protein encoded by ORF1119 exhibited PvGal-ase activity. Although ORF1119 protein displayed broad substrate specificity for pNP sugars, pNP-�]-D-PvGal was the most favorable substrate. The optimum pH for the ORF1119 PvGal-ase was determined as 7.5. A BLAST search suggested that ORF1119 homologs exist widely in bacteria. Among two homologs tested, BglC from Clostridium but not BglH from Bacillus showed PvGal-ase activity. Crystal structural analysis together with point mutation analysis revealed crucial amino acids for PvGal-ase activity. Moreover, ORF1119 protein catalyzed the hydrolysis of PvGal from galactomannan of Schizosaccharomyces pombe, suggesting that natural polysaccharides might be substrates of the PvGal-ase. This novel PvGal-catalyzing enzyme might be useful for glycoengineering projects to produce new oligosaccharide structures.
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283. |
Wang W,
Mézes PS,
Yang YQ,
Blacher RW,
Lampen JO,
( 1985 ) Cloning and sequencing of the beta-lactamase I gene of Bacillus cereus 5/B and its expression in Bacillus subtilis. PMID : 2991192 : PMC : PMC219148 Abstract >>
The beta-lactamases of Bacillus cereus have attracted interest because they are secreted efficiently, because multiple enzymes are frequently present, and because their regulation has unusual features. beta-Lactamase I of strain 5/B is produced constitutively at a high level, and the exoenzyme appears to be several thousand daltons larger than the corresponding product of strain 569/H. We have cloned the gene for 5/B beta-lactamase I in Escherichia coli and B. subtilis and have sequenced the structural portion and the regulatory regions. The 5/B enzyme is produced at a low level in E. coli RR1(pRWY200) and remains cellbound. In B. subtilis it is formed in large amounts, and over 90% of it is released into the medium. There is a large degree of homology between the promoter and leader peptide regions of the 5/B and 569/H genes; both utilize UUG as the translation initiation codon (P. S. F. M?zes, R. W. Blacher, and J. O. Lampen, (J. Biol. Chem. 260:1218-1223, 1985). Although there are significant differences in the peptide segment where processing would be expected to occur, the NH2 terminus of the major 5/B product from B. subtilis BD170(pRWY215) is His-44, which is the same as the NH2 terminus of the major 569/H product from B. subtilis BD170(pRWM5).
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284. |
Caballero J,
Peralta C,
Molla A,
Del Valle EE,
Caballero P,
Berry C,
Felipe V,
Yaryura P,
Palma L,
( 2018 ) Draft Genome Sequence of Bacillus cereus CITVM-11.1, a Strain Exhibiting Interesting Antifungal Activities. PMID : 29694975 : DOI : 10.1159/000487597 Abstract >>
Bacillus cereus is a gram-positive, spore-forming bacterium possessing an important and historical record as a human-pathogenic bacterium. However, several strains of this species exhibit interesting potential to be used as plant growth-promoting rhizobacteria. Here, we report the draft genome sequence of B. cereus strain CITVM-11.1, which consists of 37 contig sequences, accounting for 5,746,486 bp (with a GC content of 34.8%) and 5,752 predicted protein-coding sequences. Several of them could potentially be involved in plant-bacterium interactions and may contribute to the strong antagonistic activity shown by this strain against the charcoal root rot fungus, Macrophomina phaseolina. This genomic sequence also showed a number of genes that may confer this strain resistance against several polluting heavy metals and for the bioconversion of mycotoxins.
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285. |
Hussain M,
Pastor FI,
Lampen JO,
( 1987 ) Cloning and sequencing of the blaZ gene encoding beta-lactamase III, a lipoprotein of Bacillus cereus 569/H. PMID : 3027036 : DOI : 10.1128/jb.169.2.579-586.1987 PMC : PMC211817 Abstract >>
It has not been clear whether the membrane-bound beta-lactamase III of Bacillus cereus 569 is a separate enzyme or a modified form of the secreted beta-lactamase I. The membrane enzyme is an acyl-glyceride thioether-linked lipoprotein (J. B. K. Nielsen and J. O. Lampen, Biochemistry 22:4652-4656, 1983) and thus is probably a separate entity. We cloned the beta-lactamase III gene (blaZ) on a 4.9-kilobase-pair ClaI fragment from mutant strain 569/H (constitutive for high-level production of beta-lactamases I, II, and III), and the nucleotide sequence was determined. The structural gene was flanked by typical promoter, transcription termination, and translation initiation sequences. Expression of the cloned gene in Escherichia coli was low in exponential-phase cultures and increased only as the cultures reached the stationary phase. The deduced amino acid sequence indicates a pre-beta-lactamase III of 316 amino acid residues (35,021 daltons), with a 29-residue signal peptide and a mature lipoprotein form of approximately 32,500 daltons. The 12 NH2-terminal residues of a 21-kilodalton tryptic peptide from the B. cereus membrane enzyme were in agreement with the sequence deduced from the cloned gene. The amino acid sequence was highly homologous to the class A beta-lactamases, especially that of Bacillus licheniformis 749. beta-Lactamase III is a distinct class A enzyme and the product of a separate gene (blaZ).
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286. |
Gudim I,
Hammerstad M,
Lofstad M,
Hersleth HP,
( 2018 ) The Characterization of Different Flavodoxin Reductase-Flavodoxin (FNR-Fld) Interactions Reveals an Efficient FNR-Fld Redox Pair and Identifies a Novel FNR Subclass. PMID : 30142264 : DOI : 10.1021/acs.biochem.8b00674 DOI : 10.1021/acs.biochem.8b00674 Abstract >>
Flavodoxins (Flds) are small, bacterial proteins that transfer electrons to various redox enzymes. Flavodoxins are reduced by ferredoxin/flavodoxin NADP+ oxidoreductases (FNRs), but little is known of the FNR-Fld interaction. Here, we compare the interactions of two flavodoxins (Fld1-2), one flavodoxin-like protein (NrdI), and three different thioredoxin reductase (TrxR)-like FNRs (FNR1-3), all from Bacillus cereus. Steady-state kinetics shows that the FNR2-Fld2 electron transfer pair is particularly efficient, and redox potential measurements also indicate that this is the most favorable electron donor/acceptor pair. Furthermore, crystal structures of FNR1 and FNR2 show that the proteins have crystallized in different conformations, a closed and an open conformation, respectively. We suggest that a large-scale conformational rearrangement takes place during the FNR catalytic cycle to allow for the binding and reduction of the Fld and, subsequently, the re-reduction of the FNR by NADPH. Finally, inspection of the residues surrounding the FAD cofactor in the FNR active site shows that a key isoalloxazine ring-stacking residue is different in FNR1 and FNR2, which could explain the large difference in catalytic efficiency between the two FNRs. To date, all of the characterized TrxR-like FNRs have a residue with aromatic character stacking against the FAD isoalloxazine ring, and this has been thought to be a conserved feature of this class of FNRs. FNR1, however, has a valine in this position. Bioinformatic analysis shows that the TrxR-like FNRs can actually be divided into two groups, one group where the FAD-stacking residue has aromatic character and another group where it is valine.
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287. |
Balomenou S,
Koutsioulis D,
Tomatsidou A,
Tzanodaskalaki M,
Petratos K,
Bouriotis V,
( 2018 ) Polysaccharide deacetylases serve as new targets for the design of inhibitors against Bacillus anthracis and Bacillus cereus. PMID : 29983281 : DOI : 10.1016/j.bmc.2018.06.045 Abstract >>
Peptidoglycan N-acetylglucosamine (GlcNAc) deacetylases (PGNGdacs) from bacterial pathogens are validated targets for the development of novel antimicrobial agents. In this study we examined the in vitro inhibition of hydroxamate ligand N-hydroxy-4-(naphthalene-1-yl)benzamide (NHNB), a selective inhibitor of histone deacetylases-8 (HDAC8), against two PGNGdacs namely BC1974 and BC1960 from B. cereus, highly homologous to BA1977 and BA1961 of B. anthracis, respectively. Kinetic analysis showed that this compound functions as a competitive inhibitor of both enzymes with apparent Ki's of 8.7 �gM (for BC1974) and 66 �gM (for BC1960), providing thus the most potent CE4 inhibitor reported to date. NHNB was tested in antibacterial assays and showed bactericidal activity against both examined pathogens acting as a multi-target drug. This compound can serve as lead for the development of inhibitors targeting the conserved active sites of the multiple polysaccharide deacetylases (PDAs) of both pathogens.
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288. |
Gudim I,
Lofstad M,
van Beek W,
Hersleth HP,
( 2018 ) High-resolution crystal structures reveal a mixture of conformers of the Gly61-Asp62 peptide bond in an oxidized flavodoxin from Bacillus cereus. PMID : 29722453 : DOI : 10.1002/pro.3436 PMC : PMC6153408 Abstract >>
Flavodoxins (Flds) are small proteins that shuttle electrons in a range of reactions in microorganisms. Flds contain a redox-active cofactor, a flavin mononucleotide (FMN), and it is well established that when Flds are reduced by one electron, a peptide bond close to the FMN isoalloxazine ring flips to form a new hydrogen bond with the FMN N5H, stabilizing the one-electron reduced state. Here, we present high-resolution crystal structures of Flavodoxin 1 from Bacillus cereus in both the oxidized (ox) and one-electron reduced (semiquinone, sq) state. We observe a mixture of conformers in the oxidized state; a 50:50 distribution between the established oxidized conformation where the peptide bond is pointing away from the flavin, and a conformation where the peptide bond is pointing toward the flavin, approximating the conformation in the semiquinone state. We use single-crystal spectroscopy to demonstrate that the mixture of conformers is not caused by radiation damage to the crystal. This is the first time that such a mixture of conformers is reported in a wild-type Fld. We therefore carried out a survey of published Fld structures, which show that several proteins have a pronounced conformational flexibility of this peptide bond. The degree of flexibility seems to be modulated by the presence, or absence, of stabilizing interactions between the peptide bond carbonyl and its surrounding amino acids. We hypothesize that the degree of conformational flexibility will affect the Fld ox/sq redox potential.
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289. |
Liu S,
Gonen T,
( 2018 ) MicroED structure of the NaK ion channel reveals a Na+ partition process into the selectivity filter. PMID : 30167468 : DOI : 10.1038/s42003-018-0040-8 PMC : PMC6112790 Abstract >>
Sodium (Na+) is a ubiquitous and important inorganic salt mediating many critical biological processes such as neuronal excitation, signaling, and facilitation of various transporters. The hydration states of Na+ are proposed to play critical roles in determining the conductance and the selectivity of Na+ channels, yet they are rarely captured by conventional structural biology means. Here we use the emerging cryo-electron microscopy (cryoEM) method micro-electron diffraction (MicroED) to study the structure of a prototypical tetrameric Na+-conducting channel, NaK, to 2.5 ? resolution from nano-crystals. Two new conformations at the external site of NaK are identified, allowing us to visualize a partially hydrated Na+ ion at the entrance of the channel pore. A process of dilation coupled with Na+ movement is identified leading to valuable insights into the mechanism of ion conduction and gating. This study lays the ground work for future studies using MicroED in membrane protein biophysics.
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290. |
Mullins EA,
Shi R,
Eichman BF,
( 2017 ) Toxicity and repair of DNA adducts produced by the natural product yatakemycin. PMID : 28759018 : DOI : 10.1038/nchembio.2439 PMC : PMC5657529 Abstract >>
Yatakemycin (YTM) is an extraordinarily toxic DNA alkylating agent with potent antimicrobial and antitumor properties and is the most recent addition to the CC-1065 and duocarmycin family of natural products. Though bulky DNA lesions the size of those produced by YTM are normally removed from the genome by the nucleotide-excision repair (NER) pathway, YTM adducts are also a substrate for the bacterial DNA glycosylases AlkD and YtkR2, unexpectedly implicating base-excision repair (BER) in their elimination. The reason for the extreme toxicity of these lesions and the molecular basis for the way they are eliminated by BER have been unclear. Here, we describe the structural and biochemical properties of YTM adducts that are responsible for their toxicity, and define the mechanism by which they are excised by AlkD. These findings delineate an alternative strategy for repair of bulky DNA damage and establish the cellular utility of this pathway relative to that of NER.
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291. |
Bastard K,
Perret A,
Mariage A,
Bessonnet T,
Pinet-Turpault A,
Petit JL,
Darii E,
Bazire P,
Vergne-Vaxelaire C,
Brewee C,
Debard A,
Pellouin V,
Besnard-Gonnet M,
Artiguenave F,
Médigue C,
Vallenet D,
Danchin A,
Zaparucha A,
Weissenbach J,
Salanoubat M,
de Berardinis V,
( 2017 ) Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis. PMID : 28581482 : DOI : 10.1038/nchembio.2397 Abstract >>
Experimental validation of enzyme function is crucial for genome interpretation, but it remains challenging because it cannot be scaled up to accommodate the constant accumulation of genome sequences. We tackled this issue for the MetA and MetX enzyme families, phylogenetically unrelated families of acyl-L-homoserine transferases involved in L-methionine biosynthesis. Members of these families are prone to incorrect annotation because MetX and MetA enzymes are assumed to always use acetyl-CoA and succinyl-CoA, respectively. We determined the enzymatic activities of 100 enzymes from diverse species, and interpreted the results by structural classification of active sites based on protein structure modeling. We predict that >60% of the 10,000 sequences from these families currently present in databases are incorrectly annotated, and suggest that acetyl-CoA was originally the sole substrate of these isofunctional enzymes, which evolved to use exclusively succinyl-CoA in the most recent bacteria. We also uncovered a divergent subgroup of MetX enzymes in fungi that participate only in L-cysteine biosynthesis as O-succinyl-L-serine transferases.
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292. |
( 2013 ) A new family of proteins related to the HEAT-like repeat DNA glycosylases with affinity for branched DNA structures. PMID : 23623903 : DOI : 10.1016/j.jsb.2013.04.007 Abstract >>
The recently discovered HEAT-like repeat (HLR) DNA glycosylase superfamily is widely distributed in all domains of life. The present bioinformatics and phylogenetic analysis shows that HLR DNA glycosylase superfamily members in the genus Bacillus form three subfamilies: AlkC, AlkD and AlkF/AlkG. The crystal structure of AlkF shows structural similarity with the DNA glycosylases AlkC and AlkD, however neither AlkF nor AlkG display any DNA glycosylase activity. Instead, both proteins have affinity to branched DNA structures such as three-way and Holliday junctions. A unique �]-hairpin in the AlkF/AlkG subfamily is most likely inserted into the DNA major groove, and could be a structural determinant regulating DNA substrate affinity. We conclude that AlkF and AlkG represent a new family of HLR proteins with affinity for branched DNA structures.
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293. |
Johansen T,
Haugli FB,
Ikezawa H,
Little C,
( 1988 ) Bacillus cereus strain SE-1: nucleotide sequence of the sphingomyelinase C gene. PMID : 2848222 : DOI : 10.1093/nar/16.21.10370 PMC : PMC338872 Abstract >>
N/A
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294. |
( 2013 ) Discrimination between mesophilic and psychrotolerant strains in the Bacillus cereus group based on the PstI digestion of the pycA gene. PMID : 23475137 : DOI : 10.1007/s00284-013-0339-0 Abstract >>
A simple and rapid assay for the detection of Bacillus weihenstephanensis isolates and other psychrotolerant strains in the Bacillus cereus group was developed. It is based on the presence of a nucleotide substitution at position 795 on the housekeeping pycA gene in all B. weihenstephanensis strains. This mutation creates a PstI recognition site. It is absent in mesophilic strains in the B. cereus group. The pycA gene is amplified by PCR and the amplicons submitted to PstI digestions. In mesophilic strains, a single band of 1,718 bp in length is visualised on an agarose gel. In B. weihenstephanensis strains and in all other psychrotolerant strains from the B. cereus group, the amplicons are cleaved and two bands of 1,175 and 543 bp, respectively, are visualised. This method could be used for the screening of B. cereus collections and for the identification of psychrotolerant and mesophilic isolates from different environments.
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295. |
Kaplan AR,
Kaus K,
De S,
Olson R,
Alexandrescu AT,
( 2017 ) NMR structure of the Bacillus cereus hemolysin II C-terminal domain reveals a novel fold. PMID : 28607368 : DOI : 10.1038/s41598-017-02917-4 PMC : PMC5468326 Abstract >>
In addition to multiple virulence factors, Bacillus cereus a pathogen that causes food poisoning and life-threatening wound infections, secretes the pore-forming toxin hemolysin II (HlyII). The HlyII toxin has a unique 94 amino acid C-terminal domain (HlyIIC). HlyIIC exhibits splitting of NMR resonances due to cis/trans isomerization of a single proline near the C-terminus. To overcome heterogeneity, we solved the structure of P405M-HlyIIC, a mutant that exclusively stabilizes the trans state. The NMR structure of HlyIIC reveals a novel fold, consisting of two subdomains �\A-�]1-�]2 and �]3-�]4-�\B-�]5, that come together in a barrel-like structure. The barrel core is fastened by three layers of hydrophobic residues. The barrel end opposite the HlyIIC-core has a positively charged surface, that by binding negatively charged moieties on cellular membranes, may play a role in target-cell surface recognition or stabilization of the heptameric pore complex. In the WT domain, dynamic flexibility occurs at the N-terminus and the first �\-helix that connects the HlyIIC domain to the HlyII-core structure. In the destabilizing P405M mutant, increased flexibility is evident throughout the first subdomain, suggesting that the HlyIIC structure may have arisen through gene fusion.
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296. |
( 2013 ) Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide deacetylase from Bacillus cereus. PMID : 23385463 : DOI : 10.1107/S0907444912045829 Abstract >>
The structure of BC0361, a polysaccharide deacetylase from Bacillus cereus, has been determined using an unconventional molecular-replacement procedure. Tens of putative models of the C-terminal domain of the protein were constructed using a multitude of homology-modelling algorithms, and these were tested for the presence of signal in molecular-replacement calculations. Of these, only the model calculated by the SAM-T08 server gave a consistent and convincing solution, but the resulting model was too inaccurate to allow phase determination to proceed to completion. The application of slow-cooling torsion-angle simulated annealing (started from a very high temperature) drastically improved this initial model to the point of allowing phasing through cycles of model building and refinement to be initiated. The structure of the protein is presented with emphasis on the presence of a C(�\)-modified proline at its active site, which was modelled as an �\-hydroxy-L-proline.
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297. |
( 2013 ) Complementary screening, identification and application of a novel class II 5-enopyruvylshikimate-3-phosphate synthase from Bacillus cereus. PMID : 23161452 : DOI : 10.1007/s11274-012-1209-9 Abstract >>
A novel aroA gene encoding 5-enolpyruvylshikimate-3-phosphate synthase from Bacillus cereus was identified and overexpressed by genomic library construction and complementary screening. The enzyme was then purified to homogeneity. We also transformed the aroA (B. cereus) gene into Arabidopsis thaliana by a floral dip method, and demonstrated that transgenic A. thaliana plants exhibited significant glyphosate resistance compared with the wild type. These results strongly suggested that the strategy was highly efficient and advantageous for rapidly cloning aroA genes from microorganisms in natural environments.
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298. |
( 2013 ) Bacillus weihenstephanensis characteristics are present in Bacillus cereus and Bacillus mycoides strains. PMID : 23413955 : DOI : 10.1111/1574-6968.12106 Abstract >>
The Bacillus cereus group comprises seven bacterial species: Bacillus cereus, Bacillus anthracis, Bacillus thuringiensis, Bacillus mycoides, Bacillus pseudomycoides, Bacillus cytotoxicus, and Bacillus weihenstephanensis. Bacillus weihenstephanensis is distinguished based on its capability to grow at 7 �XC but not at 43 �XC, and the presence of specific signature sequences in the 16S rRNA and cspA genes and in several housekeeping genes: glpF, gmK, purH, and tpi. Bacillus weihenstephanensis-specific signature sequences were found in some B. cereus and B. mycoides strains suggesting psychrotolerance. This was confirmed by growth at 7 �XC but not at 43 �XC. The other B. cereus and B. mycoides strains and all B. anthracis, B. thuringiensis, and B. pseudomycoides harbored the mesophilic signature sequences. The strains tested grew at 43 �XC but did not grow at 7 �XC. A maximum-likelihood phylogenetic tree was inferred from comparisons of the concatenated nucleotide sequences. Three groups and one branch were revealed. Group I, II, and III comprised the mesophilic B. cereus, some mesophilic B. mycoides, and all B. anthracis and B. thuringiensis strains; the psychrotolerant B. cereus and B. mycoides, and all B. weihenstephanensis strains; and some mesophilic B. mycoides and all B. pseudomycoides strains, respectively. The branch corresponds to the single B. cytotoxicus strain. Based on psychrotolerance and multilocus sequence analysis, further confirmed by comparisons of amino acid sequences, we show that some B. cereus and B. mycoides strains should be reclassified as B. weihenstephanensis.
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299. |
( 2013 ) Heterologous expression of CYP102A5 variant from Bacillus cereus CYPPB-1: Validation of model for predicting drug metabolism of human P450 probe substrates. PMID : 23287855 : DOI : 10.1007/s00253-012-4654-3 Abstract >>
CYP102A5 variant (ADL27534) from isolated Bacillus cereus CYPPB-1 was heterologously expressed in Escherichia coli Top 10 cells. Comparative sequence analysis of purified CYP102A5 variant with respect to reported CYP102A5 (AAP10153) from Bacillus cereus ATCC 14579 revealed amino acid sequence changes at positions P245S and M318I of heme domain. The binding affinities of 15 selected human P450 probe substrates towards isolated CYP102A5 were analyzed in silico using a homology model together with molecular docking techniques to predict the human drug metabolism. In vitro analysis suggested that the purified CYP102A5 metabolizes typical substrates of human CYP2C9, CYP2D6, CYP2E1, and CYP3A4, such as coumarin, propranolol, aniline, chlorzoxazone, p-nitrophenol, and nifedipine. The calculated K M values for propranolol, chloroxazone, coumarin, aniline, and 4-nitrophenol were calculated to be 0.962 �� 0.041, 1.254 �� 0.057, 2.859 �� 0.083, 2.732 �� 0.106, and 2.528 �� 0.11 mM, respectively. Importantly, taking a ChemScore cutoff value of -31 kJ/mol, substrate binding at active site and in vitro activity as the distinguishing lines between "substrates" and "nonsubstrates" revealed one false-positive and one false-negative results out of the 15 compounds examined. This is the first report on validation of CYP102A family homology model for in silico prediction of human drug metabolism.
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300. |
( 2012 ) Crystal structures of two transcriptional regulators from Bacillus cereus define the conserved structural features of a PadR subfamily. PMID : 23189126 : DOI : 10.1371/journal.pone.0048015 PMC : PMC3506622 Abstract >>
PadR-like transcriptional regulators form a structurally-related family of proteins that control the expression of genes associated with detoxification, virulence and multi-drug resistance in bacteria. Only a few members of this family have been studied by genetic, biochemical and biophysical methods, and their structure/function relationships are still largely undefined. Here, we report the crystal structures of two PadR-like proteins from Bacillus cereus, which we named bcPadR1 and bcPadR2 (products of gene loci BC4206 and BCE3449 in strains ATCC 14579 and ATCC 10987, respectively). BC4206, together with its neighboring gene BC4207, was previously shown to become significantly upregulated in presence of the bacteriocin AS-48. DNA mobility shift assays reveal that bcPadR1 binds to a 250 bp intergenic region containing the putative BC4206-BC4207 promoter sequence, while in-situ expression of bcPadR1 decreases bacteriocin tolerance, together suggesting a role for bcPadR1 as repressor of BC4206-BC4207 transcription. The function of bcPadR2 (48% identical in sequence to bcPadR1) is unknown, but the location of its gene just upstream from genes encoding a putative antibiotic ABC efflux pump, suggests a role in regulating antibiotic resistance. The bcPadR proteins are structurally similar to LmrR, a PadR-like transcription regulator in Lactococcus lactis that controls expression of a multidrug ABC transporter via a mechanism of multidrug binding and induction. Together these proteins define a subfamily of conserved, relatively small PadR proteins characterized by a single C-terminal helix for dimerization. Unlike LmrR, bcPadR1 and bcPadR2 lack a central pore for ligand binding, making it unclear whether the transcriptional regulatory roles of bcPadR1 and bcPadR2 involve direct ligand recognition and induction.
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301. |
( 1990 ) The MerR metalloregulatory protein binds mercuric ion as a tricoordinate, metal-bridged dimer. PMID : 2305262 : DOI : 10.1126/science.2305262 Abstract >>
Bacterial MerR proteins are dimeric DNA-binding proteins that mediate the Hg(II)-dependent induction of mercury resistance operons. Site-directed mutagenesis of the Bacillus sp. RC607 MerR protein reveals that three of four Cys residues per monomer are required for Hg(II) binding at the single high-affinity binding site. Inactive mutant homodimers can exchange subunits to form heterodimers active for Hg(II) binding. Studies of a heterodimer retaining only three of eight cysteine residues per dimer reveal that Cys79 in one subunit and Cys114 and Cys123 in the second subunit are necessary and sufficient for high-affinity Hg(II) binding in an asymmetric, subunit bridging coordination complex.
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302. |
( 1998 ) 1.85 A resolution structure of the zinc (II) beta-lactamase from Bacillus cereus. PMID : 9761898 : DOI : 10.1107/s0907444997010627 Abstract >>
Class B beta-lactamases are wide spectrum enzymes which require bivalent metal ions for activity. The structure of the class B zinc-ion-dependent beta-lactamase from Bacillus cereus (BCII) has been refined at 1.85 A resolution using data collected on cryocooled crystals (100 K). The enzyme from B. cereus has a molecular mass of 24 946 Da and is folded into a beta-sandwich structure with helices on the external faces. The active site is located in a groove running between the two beta-sheets [Carfi et al. (1995). EMBO J. 14, 4914-4921]. The 100 K high-resolution BCII structure shows one fully and one partially occupied zinc sites. The zinc ion in the fully occupied site (the catalytic zinc) is coordinated by three histidines and one water molecule. The second zinc ion is at 3.7 A from the first one and is coordinated by one histidine, one cysteine, one aspartate and one unknown molecule (most likely a carbonate ion). In the B. cereus zinc beta-lactamase the affinity for the second metal-ion is low at the pH of crystallization (Kd = 25 mM, 293 K; [Baldwin et al. (1978). Biochem. J. 175, 441-447] and the dissociation constant of the second zinc ion was thus apparently decreased at the cryogenic temperature. In addition, the structure of the apo enzyme was determined at 2.5 A resolution. The removal of the zinc ion by chelating agents causes small changes in the active-site environment.
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303. |
( 1998 ) Insights into the mechanism of catalysis by the P-C bond-cleaving enzyme phosphonoacetaldehyde hydrolase derived from gene sequence analysis and mutagenesis. PMID : 9649311 : DOI : 10.1021/bi972677d Abstract >>
Phosphonoacetaldehyde hydrolase (phosphonatase) catalyzes the hydrolysis of phosphonoacetaldehyde to acetaldehyde and inorganic phosphate. In this study, the genes encoding phosphonatase in Bacillus cereus and in Salmonella typhimurium were cloned for high-level expression in Escherichia coli. The kinetic properties of the purified, recombinant phosphonatases were determined. The Schiff base mechanism known to operate in the B. cereus enzyme was verified for the S. typhimurium enzyme by phosphonoacetaldehyde-sodium borohydride-induced inactivation and by site-directed mutagenesis of the catalytic lysine 53. The protein sequence inferred from the B. cereus phosphonatase gene was determined, and this sequence was used along with that from the S. typhimurium phosphonatase gene sequence to search the primary sequence databases for possible structural homologues. We found that phosphonatase belongs to a novel family of hydrolases which appear to use a highly conserved active site aspartate residue in covalent catalysis. On the basis of this finding and the known stereochemical course of phosphonatase-catalyzed hydrolysis at phosphorus (retention), we propose a mechanism which involves Schiff base formation with lysine 53 followed by phosphoryl transfer to aspartate (at position 11 in the S. typhimurium enzyme and position 12 in the B. cereusphosphonatase) and last hydrolysis at the imine C(1) and acyl phosphate phosphorus.
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304. |
( 1998 ) Role of the gerI operon of Bacillus cereus 569 in the response of spores to germinants. PMID : 9852021 : PMC : PMC107780 Abstract >>
Bacillus cereus 569 (ATCC 10876) germinates in response to inosine or to L-alanine, but the most rapid germination response is elicited by a combination of these germinants. Mutants defective in their germination response to either inosine or to L-alanine were isolated after Tn917-LTV1 mutagenesis and enrichment procedures; one class of mutant could not germinate in response to inosine as a sole germinant but still germinated in response to L-alanine, although at a reduced rate; another mutant germinated normally in response to inosine but was slowed in its germination response to L-alanine. These mutants demonstrated that at least two signal response pathways are involved in the triggering of germination. Stimulation of germination in L-alanine by limiting concentrations of inosine and stimulation of germination in inosine by low concentrations of L-alanine were still detectable in these mutants, suggesting that such stimulation is not dependent on complete functionality of both these germination loci. Two transposon insertions that affected inosine germination were found to be located 2.2 kb apart on the chromosome. This region was cloned and sequenced, revealing an operon of three open reading frames homologous to those in the gerA and related operons of Bacillus subtilis. The individual genes of this gerI operon have been named gerIA, gerIB, and gerIC. The GerIA protein is predicted to possess an unusually long, charged, N-terminal domain containing nine tandem copies of a 13-amino-acid glutamine- and serine-rich sequence.
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305. |
( 1997 ) Detection and speciation of bacteria through PCR using universal major cold-shock protein primer oligomers. PMID : 9439003 : Abstract >>
The detection of bacteria using PCR is a well-established diagnostic technique. However, conventional PCR requires the use of DNA primer oligomers that are specific to the target organism and, as a consequence, a sample can only be tested for the presence of that specific target. A significant advantage would be to probe a sample for the presence of any bacteria, followed by identification. To achieve this it is necessary to identify a DNA sequence common to all bacteria. Here we demonstrate that such a sequence may be that encoding the major cold-shock proteins. Using two universal PCR primer oligomers from conserved regions of these gene homologues, we have amplified a 200 base-pair DNA sequence from more than 30 diverse Gram-positive and Gram-negative bacteria, including representatives from the genera Aeromonas, Bacillus, Citrobacter, Enterobacter, Enterococcus, Escherichia, Klebsiella, Lactobacillus, Lactococcus, Listeria, Pediococcus, Photobacterium, Proteus, Salmonella, Shigella, Staphylococcus, Streptococcus, and Yersinia. Sequence analysis of the amplified products confirmed a high level of DNA homology. Significantly, however, there are sufficient nucleotide variations to allow the unique allocation of each amplified sequence to its parental bacterium.
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306. |
( 1998 ) Horizontal spread of mer operons among gram-positive bacteria in natural environments. PMID : 9534232 : DOI : 10.1099/00221287-144-3-609 Abstract >>
Horizontal dissemination of the genes responsible for resistance to toxic pollutants may play a key role in the adaptation of bacterial populations to environmental contaminants. However, the frequency and extent of gene dissemination in natural environments is not known. A natural horizontal spread of two distinct mercury resistance (mer) operon variants, which occurred amongst diverse Bacillus and related species over wide geographical areas, is reported. One mer variant encodes a mercuric reductase with a single N-terminal domain, whilst the other encodes a reductase with a duplicated N-terminal domain. The strains containing the former mer operon types are sensitive to organomercurials, and are most common in the terrestrial mercury-resistant Bacillus populations studied in this work. The strains containing the latter operon types are resistant to organomercurials, and dominate in a Minamata Bay mercury-resistant Bacillus population, previously described in the literature. At least three distinct transposons (related to a class II vancomycin-resistance transposon, Tn1546, from a clinical Enterococcus strain) and conjugative plasmids are implicated as mediators of the spread of these mer operons.
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307. |
( 1998 ) A cysteine-dependent serine protease associated with the dormant spores of Bacillus cereus: purification of the protein and cloning of the corresponding gene. PMID : 9532782 : DOI : 10.1271/bbb.62.268 Abstract >>
Subtilisin-like serine protease, which is associated with the dormant spores of Bacillus cereus, was solubilized by washing the spores with 2 M KCl and purified to homogeneity by carbobenzoxy-D-phenylalanine-liganded affinity column chromatography and hydrophobic interaction column chromatography. Enzyme activity was completely inhibited by reagents for sulfhydryl groups such as HgCl2 as well as by conventional subtilisin inhibitors, suggesting the enzyme to be cysteine-dependent. The enzyme retained activity in 5 M urea at 4 degrees C for at least 2 months, and the specific activity was 50 times that of subtilisin BPN when measured for a common chromogenic substrate, carbobenzoxy-glycyl-glycyl-L-leucine p-nitroanilide. The gene encoding this protease was cloned in Escherichia coli, and its nucleotide sequence was analyzed. The deduced amino acid sequence suggested that the protease is produced as a precursor comprising three portions; a signal sequence (28 amino acid residues), a prosequence (80 amino acid residues) and a mature enzyme (289 amino acid residues). The mature region of the enzyme had high similarity with a thermitase from Thermoactinomyces vulgaris (72% identity) and a thermostable alkaline protease from Thermoactinomyces sp. E79 (66% identity), which have the N-terminal sequence showing scarcely noticeable similarity with corresponding stretches of subtilisins and mercuric ion-sensitive free cysteine in the equivalent position of the primary structure.
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