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1. Tao  YP, Hudspeth  DS, Vary  PS,     ( N/A )

Cloning and sequencing of the Bacillus megaterium spoIIA operon.

Biochimie 74 (7��8��)
PMID : 1391049  :   DOI  :   10.1016/0300-9084(92)90142-2    
Abstract >>
The spoIIA operon of Bacillus megaterium has been cloned and the nucleotide sequence determined. The spoIIA sequence contains three open reading frames coding for putative proteins of 116 aa, 147 aa, and 253 aa; the first and the third genes are preceded by a ribosomal binding site. The genes are in the same order as those of B subtilis and B licheniformis. The deduced amino acid sequences of these three open reading frames show 78-92% homology with SpoIIAA, SpoIIAB and SpoIIAC of B subtilis and B licheniformis. Northern hybridization revealed that B megaterium also has two spoIIA transcripts, 1.77 kb and 2.92 kb, attaining maximum expression at t1 and t3, respectively. In addition, homology to a possible penicillin binding protein gene upstream and the first part of a spoVA operon downstream has been identified on the 3.34-kb fragment. The spoIIA and the downstream spoVA promoter regions are highly conserved among these three species. Sequence analysis of the spoVA promoter revealed a region upstream to the -35 that is highly conserved across Bacillus species.
KeywordMeSH Terms
Sigma Factor
Transcription Factors
2. Hudspeth  DS, Vary  PS,     ( 1992 )

spoVG sequence of Bacillus megaterium and Bacillus subtilis.

Biochimica et biophysica acta 1130 (2)
PMID : 1373326  :   DOI  :   10.1016/0167-4781(92)90536-9    
Abstract >>
We have sequenced the stage V sporulation specific gene spoVG in both Bacillus megaterium and Bacillus subtilis. The open reading frames encode polypeptides of 96 and 97 residues, respectively, and have an 88.6% amino acid identity. Both genes have putative rho-independent terminators. No significant amino acid or nucleotide homology of either gene was found when compared with sequences contained in either the Genbank or EMBL data bases.
KeywordMeSH Terms
Genes, Bacterial
3. Leech  HK, Raux  E, McLean  KJ, Munro  AW, Robinson  NJ, Borrelly  GP, Malten  M, Jahn  D, Rigby  SE, Heathcote  P, Warren  MJ,     ( 2003 )

Characterization of the cobaltochelatase CbiXL: evidence for a 4Fe-4S center housed within an MXCXXC motif.

The Journal of biological chemistry 278 (43)
PMID : 12917443  :   DOI  :   10.1074/jbc.M306112200    
Abstract >>
CbiX is a cobaltochelatase required for the biosynthesis of vitamin B12 and is found in Archaea as a short form (CbiXS containing 120-145 amino acids) and in some bacteria as a longer version (CbiXL containing 300-350 amino acids). Purification of either recombinant Bacillus megaterium or Synechocystis CbiXL in Escherichia coli, which is facilitated by the presence of a naturally occurring histidine-rich region of the protein, results in the isolation of a dark brown protein solution. The UV/visible spectrum of the protein is consistent with the presence of a redox group, and the lack of definition within the spectrum is suggestive of a 4Fe-4S center. The presence of an iron-sulfur center was confirmed by EPR analysis of the proteins, which produces a pseudoaxial spectrum with g values at 2.04, 1.94, and 1.90. The EPR spectrum was absent at 70 K, an observation that is diagnostic of a 4Fe-4S center. Redox potentiometry coupled with optical spectroscopy allowed the midpoint potential of the redox center to be determined for the CbiXL from both B. megaterium and Synechocystis. Sequence analysis of CbiXL proteins reveals only two conserved cysteine residues within the CbiXL proteins, which are part of an MXCXXC motif. Mutagenesis of the two cysteines leads to loss of both the EPR spectrum and UV/visible spectral features of the Fe-S center in the protein, clearly indicating that these residues are involved in ligating the cofactor to the apoprotein possibly in a butterfly arrangement. The potential physiological role of the iron-sulfur center is discussed.
KeywordMeSH Terms
Bacterial Proteins
4. 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.

Journal of clinical microbiology 41 (7)
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.
KeywordMeSH Terms
5. Wittchen  KD, Strey  J, Bültmann  A,     ( 1998 )

Molecular characterization of the operon comprising the spoIV gene of Bacillus megaterium DSM319 and generation of a deletion mutant.

The Journal of general and applied microbiology 44 (5)
PMID : 12501411  :  
Abstract >>
According to sequence analysis, the spoIV-locus of Bacillus megaterium DSM 319 is 1,185 bp long; it is the second gene of a sporulation operon, which altogether contains three open reading frames. The ORF preceding spoIV encodes a putative polypeptide with 94 amino acids; the 3rd ORF of the operon has 972 bp corresponding to 324 amino acids. The operon is flanked on both sides by palindromic sequences, probably representing Rho-independent terminators. A primer extension analysis revealed that mRNA synthesis starts immediately downstream of a promoter, which is similar to the consensus sequence of Bacillus subtilis sigma(E) dependent promoters. Both the -35 and the -10 region are within the terminator region of the preceding operon. Gene knockout experiments and reporter gene assays with a newly developed system based on the heterologous Paenibacillus macerans glucanase gene (bgl) confirmed sigma(E)-dependent transcription. Two open reading frames of a further upstream operon were also identified. Northern analysis revealed that transcription of these ORFs comes about in late sporulation phases. The genetic organization of the spoIV comprising operon and adjacent loci clearly resembles that of the B. subtilis yqfa-phoH gene cluster. Thus our findings are of general significance for endospore-forming bacteria.
KeywordMeSH Terms
6. Raux  E, Leech  HK, Beck  R, Schubert  HL, Santander  PJ, Roessner  CA, Scott  AI, Martens  JH, Jahn  D, Thermes  C, Rambach  A, Warren  MJ,     ( 2003 )

Identification and functional analysis of enzymes required for precorrin-2 dehydrogenation and metal ion insertion in the biosynthesis of sirohaem and cobalamin in Bacillus megaterium.

The Biochemical journal 370 (Pt 2)
PMID : 12408752  :   DOI  :   10.1042/BJ20021443     PMC  :   PMC1223173    
Abstract >>
In Bacillus megaterium, the hemAXBCDL genes were isolated and were found to be highly similar to the genes from Bacillus subtilis that are required for the conversion of glutamyl-tRNA into uroporphyrinogen III. Overproduction and purification of HemC (porphobilinogen deaminase) and -D (uroporphyrinogen III synthase) allowed these enzymes to be used for the in vitro synthesis of uroporphyrinogen III from porphobilinogen. A second smaller cluster of three genes (termed sirABC) was also isolated and found to encode the enzymes that catalyse the transformation of uroporphyrinogen III into sirohaem on the basis of their ability to complement a defined Escherichia coli (cysG) mutant. The functions of SirC and -B were investigated by direct enzyme assay, where SirC was found to act as a precorrin-2 dehydrogenase, generating sirohydrochlorin, and SirB was found to act as a ferrochelatase responsible for the final step in sirohaem synthesis. CbiX, a protein found encoded within the main B. megaterium cobalamin biosynthetic operon, shares a high degree of similarity with SirB and acts as the cobaltochelatase associated with cobalamin biosynthesis by inserting cobalt into sirohydrochlorin. CbiX contains an unusual histidine-rich region in the C-terminal portion of the protein, which was not found to be essential in the chelation process. Sequence alignments suggest that SirB and CbiX share a similar active site to the cobaltochelatase, CbiK, from Salmonella enterica.
KeywordMeSH Terms
7. Chiou  CY, Wang  HH, Shaw  GC,     ( 2002 )

Identification and characterization of the non-PTS fru locus of Bacillus megaterium ATCC 14581.

Molecular genetics and genomics : MGG 268 (2)
PMID : 12395198  :   DOI  :   10.1007/s00438-002-0741-y    
Abstract >>
A genetic locus that is adjacent to the gene encoding the small acid-soluble protein SASP C-4 of Bacillus megaterium has been identified. This locus, designated fru, contains a beta-fructosidase gene (fruA), a gene encoding a hydrophobic protein that is closely related to non-PTS sugar permeases of the proton symport type (fruP), and a gene coding for a transcriptional regulator of the LacI/GalR family (fruR). The FruA protein can hydrolyze sucrose and raffinose, but not maltose, isomaltose, trehalose, melibiose or lactose. The transcription initiation site of fruP has been mapped and the fruP promoter identified. Gel mobility shift assays showed that the FruR protein can bind specifically to a DNA fragment containing the fruP promoter region. DNase I footprinting analysis has defined the FruR binding site. Disruption of fruR led to high-level constitutive expression of fruPA, but had no effect on expression from the fruR promoter itself, indicating that FruR acts as a repressor of fruPA expression, but does not autoregulate its own synthesis. Interestingly, expression of fruPA in B. megaterium was not induced by sucrose, raffinose, fructose or inulin, whereas the constitutive expression of fruPA in a fruR mutant was repressed by both glucose and sucrose. Possible physiological implications of these findings are discussed.
KeywordMeSH Terms
Genes, Regulator
8. Yang  S, Huang  YH, Huang  XD, Li  SY, Yuan  ZY,     ( 1999 )

High Expression of Penicillin G Acylase Gene from Bacillus megaterium in Bacillus subtilis.

Sheng wu hua xue yu sheng wu wu li xue bao Acta biochimica et biophysica Sinica 31 (5)
PMID : 12114980  :  
Abstract >>
The penicillin G acylase gene (pga) amplified by PCR from Bacillus megaterium was subcloned into an expressing vector pPZW103 (P43 as promoter). The recombinant plasmid was transferred into Bacillus subtilis DB104. Penicillin G acylase production in the B. subtilis transformant was 3-6 u/ml, higher than that of published recombinant strains. Penicillin G acylase production was induced by phenylacetic acid in B. megaterium, whereas the enzyme was produced constitutively in the B. subtilis transformant carrying B. megaterium pga. The recombinant strain showed high stability in antibiotic-free medium for 10 days. Enzyme in crude broth was purified by Al(2)O(3) chromatography and phenyl-Sepharose CL-4B hydrophobic chromatography and the total yield is 79%. The purified enzyme with specific activity of 52 u/mg can be directly immobilized for use.
KeywordMeSH Terms
9. Haines  DC, Tomchick  DR, Machius  M, Peterson  JA,     ( 2001 )

Pivotal role of water in the mechanism of P450BM-3.

Biochemistry 40 (45)
PMID : 11695892  :   DOI  :   10.1021/bi011197q    
Abstract >>
Cytochrome P450s constitute a superfamily of enzymes that catalyze the oxidation of a vast number of structurally and chemically diverse hydrophobic substrates. Herein, we describe the crystal structure of a complex between the bacterial P450BM-3 and the novel substrate N-palmitoylglycine at a resolution of 1.65 A, which reveals previously unrecognizable features of active site reorganization upon substrate binding. N-palmitoylglycine binds with higher affinity than any other known substrate and reacts with a higher turnover number than palmitic acid but with unaltered regiospecificity along the fatty acid moiety. Substrate binding induces conformational changes in distinct regions of the enzyme including part of the I-helix adjacent to the active site. These changes cause the displacement by about 1 A of the pivotal water molecule that ligands the heme iron, resulting in the low-spin to high-spin conversion of the iron. The water molecule is trapped close to the heme group, which allows it to partition between the iron and the new binding site. This partitioning explains the existence of a high-spin-low-spin equilibrium after substrate binding. The close proximity of the water molecule to the heme iron indicates that it may also participate in the proton-transfer cascade that leads to heterolytic bond scission of oxygen in P450BM-3.
KeywordMeSH Terms
Bacterial Proteins
10. Ost  TW, Munro  AW, Mowat  CG, Taylor  PR, Pesseguiero  A, Fulco  AJ, Cho  AK, Cheesman  MA, Walkinshaw  MD, Chapman  SK,     ( 2001 )

Structural and spectroscopic analysis of the F393H mutant of flavocytochrome P450 BM3.

Biochemistry 40 (45)
PMID : 11695889  :   DOI  :   10.1021/bi010717e    
Abstract >>
In the preceding paper in this issue [Ost, T. W. B., Miles, C. S., Munro, A. W., Murdoch, J., Reid, G. A., and Chapman, S. K. (2001) Biochemistry 40, 13421-13429], we have established that the primary role of the phylogenetically conserved phenylalanine in flavocytochrome P450 BM3 (F393) is to control the thermodynamic properties of the heme iron, so as to optimize electron-transfer both to the iron (from the flavin redox partner) and onto molecular oxygen. In this paper, we report a detailed study of the F393H mutant enzyme, designed to probe the structural, spectroscopic, and metabolic profile of the enzyme in an attempt to identify the factors responsible for causing the changes. The heme domain structure of the F393H mutant has been solved to 2.0 A resolution and demonstrates that the histidine replaces the phenylalanine in almost exactly the same conformation. A solvent water molecule is hydrogen bonded to the histidine, but there appears to be little other gross alteration in the environment of the heme. The F393H mutant displays an identical ferric EPR spectrum to wild-type, implying that the degree of splitting of the iron d orbitals is unaffected by the substitution, however, the overall energy of the d-orbitals have changed relative to each other. Magnetic CD studies show that the near-IR transition, diagnostic of heme ligation state, is red-shifted by 40 nm in F393H relative to wild-type P450 BM3, probably reflecting alteration in the strength of the iron-cysteinate bond. Studies of the catalytic turnover of fatty acid (myristate) confirms NADPH oxidation is tightly coupled to fatty acid oxidation in F393H, with a product profile very similar to wild-type. The results indicate that gross conformational changes do not account for the perturbations in the electronic features of the P450 BM3 heme system and that the structural environment on the proximal side of the P450 heme must be conformationally conserved in order to optimize catalytic function.
KeywordMeSH Terms
Bacterial Proteins
11. Setlow  P, Ozols  J,     ( 1979 )

Covalent structure of protein A. A low molecular weight protein degraded during germination of Bacillus megaterium spores.

The Journal of biological chemistry 254 (23)
PMID : 115874  :  
Abstract >>
The complete covalent structure of Protein A, a protein degraded during bacterial spore germination, has been determined. The intact protein was cleaved with a highly specific spore protease into two peptides, residues 1 to 21 and 22 to 61. The larger peptide was further cleaved into two fragments with either cyanogen bromide or by trypsin cleavage following arginine modification with cyclohexanedione. The peptides derived from cyanogen bromide fragmentation encompassed residues 22 to 53 and 54 to 61 while trypsin hydrolysis yielded overlapping fragments comprising residues 22 to 48 and 49 to 61. Automated sequenator analysis together with carboxypeptidase Y digestion of the intact protein and the peptide fragments provided data from which the following unique amino acid sequence was deduced. NH2-Ala-Asn-Thr-Asn-Lys-Leu-Val-Ala-Pro-Gly10-Ser-Ala-Ala-Ala-Ile-Asp-Gln-Met-Lys-Tyr20-Glu-Ile-Ala-Ser-Glu-Phe-Gly-Val-Asn-Leu30-Gly-Pro-Glu-Ala-Thr-Ala-Arg-Ala-Asn-Gly40-Ser-Val-Gly-Gly-Glu-Ile-Thr-Lys-Arg-Leu50-Val-Gln-Met-Ala-Glu-Gln-Gln-Leu-Gly-Gly60-Lys-COOH.
KeywordMeSH Terms
Staphylococcal Protein A
12. Lee  JS, Wittchen  KD, Stahl  C, Strey  J, Meinhardt  F,     ( 2001 )

Cloning, expression, and carbon catabolite repression of the bamM gene encoding beta-amylase of Bacillus megaterium DSM319.

Applied microbiology and biotechnology 56 (1��2��)
PMID : 11499932  :  
Abstract >>
The bamM gene from Bacillus megaterium DSM319 encoding an extracellular beta-amylase was isolated and completely sequenced. Chromosomal inactivation by deletion mutagenesis resulted in total loss of amylolytic activity, indicative of a single starch-degrading enzyme. Functional characterization of the expressed protein revealed a maltogenic enzyme exhibiting optimal activities at pH 7.5 and 50 degrees C. Amylase expression is subject to catabolite repression by glucose. A putative cis-acting catabolite-responsive element (CRE) was identified; it is located within the bamM coding region, matching the position of the predicted signal peptide processing site. Base substitutions introduced by site-directed mutagenesis within the bamM-CRE--retaining unchanged the amino acid sequence--provoked a remarkable relief from carbon catabolite repression (CCR), thereby proving functionality of the CRE for CCR.
KeywordMeSH Terms
Enzyme Repression
Response Elements
13. McCool  GJ, Cannon  MC,     ( 2001 )

PhaC and PhaR are required for polyhydroxyalkanoic acid synthase activity in Bacillus megaterium.

Journal of bacteriology 183 (14)
PMID : 11418564  :   DOI  :   10.1128/JB.183.14.4235-4243.2001     PMC  :   PMC95313    
Abstract >>
Polyhydroxyalkanoic acids (PHAs) are a class of polyesters stored in inclusion bodies and found in many bacteria and in some archaea. The terminal step in the synthesis of PHA is catalyzed by PHA synthase. Genes encoding this enzyme have been cloned, and the primary sequence of the protein, PhaC, is deduced from the nucleotide sequences of more than 30 organisms. PHA synthases are grouped into three classes based on substrate range, molecular mass, and whether or not there is a requirement for phaE in addition to the phaC gene product. Here we report the results of an analysis of a PHA synthase that does not fit any of the described classes. This novel PHA synthase from Bacillus megaterium required PhaC (PhaC(Bm)) and PhaR (PhaR(Bm)) for activity in vivo and in vitro. PhaC(Bm) showed greatest similarity to the PhaCs of class III in both size and sequence. Unlike those in class III, the 40-kDa PhaE was not required, and furthermore, the 22-kDa PhaR(Bm) had no obvious homology to PhaE. Previously we showed that PhaC(Bm), and here we show that PhaR(Bm), is localized to inclusion bodies in living cells. We show that two forms of PHA synthase exist, an active form in PHA-accumulating cells and an inactive form in nonaccumulating cells. PhaC was constitutively produced in both cell types but was more susceptible to protease degradation in the latter type. Our data show that the role of PhaR is posttranscriptional and that it functions directly or indirectly with PhaC(Bm) to produce an active PHA synthase.
KeywordMeSH Terms
Repressor Proteins
14. Vazquez  GJ, Pettinari  MJ, Méndez  BS,     ( 2001 )

Phosphotransbutyrylase expression in Bacillus megaterium.

Current microbiology 42 (5)
PMID : 11400055  :   DOI  :   10.1007/s002840010227    
Abstract >>
The molecular analysis of a genomic region of B. megaterium revealed the presence of a gene coding for the enzyme phosphotransbutyrylase (Ptb). The enzyme activity was measured throughout the different phases of growth in B. megaterium, and its activity was found to be maximal in the late exponential growth phase. The branched amino acids isoleucine and valine activated Ptb expression. PtbBm was capable of using butyryl-CoA and 2-methyl-propionyl CoA as substrates. ActBm, a final sigma54 regulator from B. megaterium whose gene is situated upstream from the ptb gene, activated its expression.
KeywordMeSH Terms
DNA-Binding Proteins
Gene Expression Regulation, Bacterial
15. Yamamoto  K, Kurisu  G, Kusunoki  M, Tabata  S, Urabe  I, Osaki  S,     ( 2001 )

Crystal structure of glucose dehydrogenase from Bacillus megaterium IWG3 at 1.7 A resolution.

Journal of biochemistry 129 (2)
PMID : 11173533  :   DOI  :   10.1093/oxfordjournals.jbchem.a002858    
Abstract >>
The crystal structure of glucose dehydrogenase (GlcDH) from Bacillus megaterium IWG3 has been determined to an R-factor of 17.9% at 1.7 A resolution. The enzyme consists of four identical subunits, which are similar to those of other short-chain reductases/dehydrogenases (SDRs) in their overall folding and subunit architecture, although cofactor binding sites and subunit interactions differ. Whereas a pair of basic residues is well conserved among NADP(+)-preferring SDRs, only Arg39 was found around the adenine ribose moiety of GlcDH. This suggests that one basic amino acid is enough to determine the coenzyme specificity. The four subunits are interrelated by three mutually perpendicular diad axes (P, Q, and R). While subunit interactions through the P-axis for GlcDH are not so different from those of the other SDRs, those through the Q-axis differ significantly. GlcDH was found to have weaker hydrophobic interactions in the Q-interface. Moreover, GlcDH lacks the salt bridge that stabilizes the subunit interaction in the Q-interface in the other SDRs. Hydrogen bonds between Q-axis related subunits are also less common than in the other SDRs. The GlcDH tetramer dissociates into inactive monomers at pH 9.0, which can be attributed mainly to the weakness of the Q-axis interface.
KeywordMeSH Terms
Models, Molecular
16. Wiedmann  M, Arcuri  EF,     ( 2000 )

Phylogeny and functional conservation of sigma(E) in endospore-forming bacteria.

Microbiology (Reading, England) 146 (Pt 7) (N/A)
PMID : 10878124  :   DOI  :   10.1099/00221287-146-7-1593    
Abstract >>
Conservation of the sporulation processes between Bacillus spp. and Clostridium spp. was investigated through evolutionary and complementation analyses of sigma(E). Alignment of partial predicted sigma(E) amino acid sequences from three Bacillus spp., Paenibacillus polymyxa and five Clostridium spp. revealed that amino acid residues previously reported to be involved in promoter utilization (M124, E119 and N120) and strand opening (C117) are conserved among all these species. Phylogenetic analyses of various sigma factor sequences from endospore-forming bacteria revealed that homologues of sigma(E), sigma(K) and sigma(G) clustered together regardless of genus, suggesting a common origin of sporulation sigma factors. The functional equivalence between Clostridium acetobutylicum sigma(E) and Bacillus subtilis sigma(E) was investigated by complementing a non-polar B. subtilis sigma(E) null mutant with the spoIIG operon from either B. subtilis (spoIIG(Bs)) or C. acetobutylicum (spoIIG(Ca)). Single-copy integration of spoIIG(Bs) into the amyE locus of the sigma(E) null mutant completely restored the wild-type sporulation phenotype, while spoIIG(Ca) only partially restored sporulation. Maximal expression of spoIIG(Ca)-lacZ occurred approximately 12 h later than maximal expression of spoIIG(Bs)-lacZ. Differences in temporal expression patterns for spoIIG(Ca) and spoIIG(Bs) in the B. subtilis background may at least partially explain the observed sporulation complementation phenotypes. This study suggests a common phylogenetic ancestor for sigma(E) in Bacillus spp. and Clostridium spp., although regulation of sigma(E) expression may differ in these two genera.
KeywordMeSH Terms
17. Berg  A, Ingelman-Sundberg  M, Gustafsson  JA,     ( 1979 )

Purification and characterization of cytochrome P-450meg.

The Journal of biological chemistry 254 (12)
PMID : 109432  :  
Abstract >>
N/A
KeywordMeSH Terms
18. Narita  M, Huang  CC,     ( 1999 )

Identification of three merB genes and characterization of a broad-spectrum mercury resistance module encoded by a class II transposon of Bacillus megaterium strain MB1.

Gene 239 (2)
PMID : 10548738  :   DOI  :   10.1016/s0378-1119(99)00388-1    
Abstract >>
The complete structure of a broad-spectrum mercury resistance module was shown by sequencing the Gram-positive bacterial transposon TnMERI1 of Bacillus megaterium MB1. The regions encoding organomercury resistance were identified. Upstream of a previously identified organomercurial lyase merB (merB1) region of TnMERI1, a second merR (merR2) and a second merB gene (merB2) were found. These genes constitute a second operon (mer operon 2) following a promoter/operator (P(merR2)) region. A third organomercurial lyase gene (merB3) was found immediately upstream of the mer operon (mer operon 1) followed by a promoter/operator (P(merB3)) region homologous to that of the mer operon 1 (P(merR1)-merR1-merE-like-merT-merP-merA). The complete genetic structure of the mercury resistance module is organized as P(merB3)-merB3-P(merR1)-merR1-merE-like-merT+ ++ -merP-merA-P(merR2)-merR2 -merB2-merB1. The subcloning analysis of these three merB genes showed distinct substrate specificity as different organomercury lyase genes.
KeywordMeSH Terms
Drug Resistance, Microbial
Lyases
19. Endo  G, Narita  M, Yamagata  T, Itoh  Y,     ( 1999 )

Structure analysis of a class II transposon encoding the mercury resistance of the Gram-positive Bacterium bacillus megaterium MB1, a strain isolated from minamata bay, Japan.

Gene 234 (2)
PMID : 10395910  :   DOI  :   10.1016/s0378-1119(99)00184-5    
Abstract >>
A unique transposon was found in the chromosome of Bacillus megaterium MB1, a Gram-positive bacterium isolated from mercury-polluted sediments of Minamata Bay, Japan. The transposon region of a 14.5kb DNA fragment was amplified by PCR using a single PCR primer designed from the nucleotide sequence of an inverted repeat of class II transposons. The molecular analysis revealed that the PCR-amplified DNA fragment encodes a transposition module similar to that of Tn21. The transposon also encodes a broad-spectrum mercury resistance region having a restriction endonuclease map identical to that of Bacillus cereus RC607, a strain isolated from Boston Harbor, USA. The result of a phylogenetic analysis of the amino acid sequence of putative resolvase of the transposon showed that the transposon is phylogenetically closer to the transposons of Gram-positive bacteria than those of Gram-negative bacteria. Besides the transposition module and mer operon, the transposon encodes a mobile genetic element of bacterial group II introns between the resolvase gene and mer operon. The intron, however, does not intervene in any exon gene. The discovery of this newly found combination of the complex mobile elements may offer a clue to understanding the horizontal dissemination of broad-spectrum mercury resistance among microbes.
KeywordMeSH Terms
Transposon Resolvases
Water Microbiology
20. Wittchen  KD, Meinhardt  F,     ( 1999 )

Regulation of beta-galactosidase expression in Bacillus megaterium DSM319 by a XylS/AraC-type transcriptional activator.

Journal of bacteriology 181 (10)
PMID : 10322036  :   PMC  :   PMC93790    
Abstract >>
The beta-galactosidase-encoding bgaM gene of Bacillus megaterium DSM319 and the divergently orientated bgaR operon were isolated and sequenced. Both traits are subject to catabolite repression. A set of single-gene replacement mutants was generated and used to analyze gene function. BgaR was found to be a XylS/AraC-type positive transcriptional regulator of bgaM; a potential regulator binding site overlaps the bgaM promoter. A mechanism for regulation of beta-galactosidase expression in B. megaterium is proposed.
KeywordMeSH Terms
Gene Expression Regulation, Bacterial
21. Sevrioukova  IF, Poulos  TL, Peterson  JA,     ( 1999 )

Structure of a cytochrome P450-redox partner electron-transfer complex.

Proceedings of the National Academy of Sciences of the United States of America 96 (5)
PMID : 10051560  :   DOI  :   10.1073/pnas.96.5.1863     PMC  :   PMC26702    
Abstract >>
The crystal structure of the complex between the heme- and FMN-binding domains of bacterial cytochrome P450BM-3, a prototype for the complex between eukaryotic microsomal P450s and P450 reductase, has been determined at 2.03 A resolution. The flavodoxin-like flavin domain is positioned at the proximal face of the heme domain with the FMN 4.0 and 18.4 A from the peptide that precedes the heme-binding loop and the heme iron, respectively. The heme-binding peptide represents the most efficient and coupled through-bond electron pathway to the heme iron. Substantial differences between the FMN-binding domains of P450BM-3 and microsomal P450 reductase, observed around the flavin-binding sites, are responsible for different redox properties of the FMN, which, in turn, control electron flow to the P450.
KeywordMeSH Terms
Bacterial Proteins
Protein Structure, Secondary
22. Huang  WC, Westlake  AC, Maréchal  JD, Joyce  MG, Moody  PC, Roberts  GC,     ( 2007 )

Filling a hole in cytochrome P450 BM3 improves substrate binding and catalytic efficiency.

Journal of molecular biology 373 (3)
PMID : 17868686  :   DOI  :   10.1016/j.jmb.2007.08.015    
Abstract >>
Cytochrome P450BM3 (CYP102A1) from Bacillus megaterium, a fatty acid hydroxylase, is a member of a very large superfamily of monooxygenase enzymes. The available crystal structures of the enzyme show non-productive binding of substrates with their omega-end distant from the iron in a hydrophobic pocket at one side of the active site. We have constructed and characterised mutants in which this pocket is filled by large hydrophobic side-chains replacing alanine at position 82. The mutants having phenylalanine or tryptophan at this position have very much (approximately 800-fold) greater affinity for substrate, with a greater conversion of the haem iron to the high-spin state, and similarly increased catalytic efficiency. The enzyme as isolated contains bound palmitate, reflecting this much higher affinity. We have determined the crystal structure of the haem domain of the Ala82Phe mutant with bound palmitate; this shows that the substrate is binding differently from the wild-type enzyme but still distant from the haem iron. Detailed analysis of the structure indicates that the tighter binding in the mutant reflects a shift in the conformational equilibrium of the substrate-free enzyme towards the conformation seen in the substrate complex rather than differences in the enzyme-substrate interactions. On this basis, we outline a sequence of events for the initial stages of the catalytic cycle. The Ala82Phe and Ala82Trp mutants are also very much more effective catalysts of indole hydroxylation than the wild-type enzyme, suggesting that they will be valuable starting points for the design of mutants to catalyse synthetically useful hydroxylation reactions.
KeywordMeSH Terms
23. Kuper  J, Wong  TS, Roccatano  D, Wilmanns  M, Schwaneberg  U,     ( 2007 )

Understanding a mechanism of organic cosolvent inactivation in heme monooxygenase P450 BM-3.

Journal of the American Chemical Society 129 (18)
PMID : 17429965  :   DOI  :   10.1021/ja067036x    
Abstract >>
N/A
KeywordMeSH Terms
Cytochrome P-450 Enzyme Inhibitors
24. Schumacher  MA, Seidel  G, Hillen  W, Brennan  RG,     ( 2007 )

Structural mechanism for the fine-tuning of CcpA function by the small molecule effectors glucose 6-phosphate and fructose 1,6-bisphosphate.

Journal of molecular biology 368 (4)
PMID : 17376479  :   DOI  :   10.1016/j.jmb.2007.02.054     DOI  :   10.1016/j.jmb.2007.02.054    
Abstract >>
In Gram-positive bacteria, carbon catabolite regulation (CCR) is mediated by the carbon catabolite control protein A (CcpA), a member of the LacI-GalR family of transcription regulators. Unlike other LacI-GalR proteins, CcpA is activated to bind DNA by binding the phosphoproteins HPr-Ser46-P or Crh-Ser46-P. However, fine regulation of CCR is accomplished by the small molecule effectors, glucose 6-phosphate (G6P) and fructose 1,6-bisphosphate (FBP), which somehow enhance CcpA-(HPr-Ser46-P) binding to DNA. Unlike the CcpA-(HPr-Ser46-P) complex, DNA binding by CcpA-(Crh-Ser46-P) is not stimulated by G6P or FBP. To understand the fine-tuning mechanism of these effectors, we solved the structures of the CcpA core, DeltaCcpA, which lacks the N-terminal DNA-binding domain, in complex with HPr-Ser46-P and G6P or FBP. G6P and FBP bind in a deep cleft, between the N and C subdomains of CcpA. Neither interacts with HPr-Ser46-P. This suggests that one role of the adjunct corepressors is to buttress the DNA-binding conformation effected by the binding of HPr-Ser46-P to the CcpA dimer N subdomains. However, the structures reveal that an unexpected function of adjunct corepressor binding is to bolster cross interactions between HPr-Ser46-P residue Arg17 and residues Asp69 and Asp99 of the other CcpA subunit. These cross contacts, which are weak or not present in the CcpA-(Crh-Ser46-P) complex, stimulate the CcpA-(HPr-Ser46-P)-DNA interaction specifically. Thus, stabilization of the closed conformation and bolstering of cross contacts between CcpA and its other corepressor, HPr-Ser46-P, provide a molecular explanation for how adjunct corepressors G6P and FBP enhance the interaction between CcpA-(HPr-Ser46-P) and cognate DNA.
KeywordMeSH Terms
Models, Molecular
Models, Molecular
25. Christie  G, Lowe  CR,     ( 2007 )

Role of chromosomal and plasmid-borne receptor homologues in the response of Bacillus megaterium QM B1551 spores to germinants.

Journal of bacteriology 189 (12)
PMID : 17434971  :   DOI  :   10.1128/JB.00110-07     PMC  :   PMC1913376    
Abstract >>
Spores of Bacillus megaterium QM B1551 germinate in response to a number of trigger compounds, including glucose, proline, leucine, and inorganic salts. An approximate 6-kb region of the 165-kb plasmid was found to harbor a tricistronic receptor operon, gerU, and a monocistronic receptor component, gerVB. The gerU operon was observed to complement the germination response in plasmidless strain PV361 to glucose and leucine, with KBr acting as a cogerminant. Proline recognition is conferred by the monocistronic gerVB gene, the presence of which also improves the germination response to other single-trigger compounds. A chimeric receptor, GerU*, demonstrates interchangeability between receptor components and provides evidence that it is the B protein of the receptor that determines germinant specificity. Introduction of the gerU/gerVB gene cluster to B. megaterium KM extends the range of germinants recognized by this strain to include glucose, proline, and KBr in addition to alanine and leucine. A chromosomally encoded receptor, GerA, the B component of which is predicted to be truncated, was found to be functionally redundant. Similarly, the plasmid-borne antiporter gene, grmA, identified previously as being essential for germination in QM B1551, did not complement the germination defect in the plasmidless variant PV361. Wild-type spores carrying an insertion-deletion mutation in this cistron germinated normally; thus, the role of GrmA in spore germination needs to be reevaluated in this species.
KeywordMeSH Terms
Genes, Bacterial
26. Boddupalli  SS, Pramanik  BC, Slaughter  CA, Estabrook  RW, Peterson  JA,     ( 1992 )

Fatty acid monooxygenation by P450BM-3: product identification and proposed mechanisms for the sequential hydroxylation reactions.

Archives of biochemistry and biophysics 292 (1)
PMID : 1727637  :   DOI  :   10.1016/0003-9861(92)90045-x    
Abstract >>
The soluble P450 isolated from Bacillus megaterium (the product of the CYP 102 gene) (P450BM-3) is a catalytically self-sufficient fatty acid hydroxylase which converts lauric, myristic, and palmitic acids to omega-1, omega-2, and omega-3 hydroxy analogs. The percentage distribution of the regioisomers depends on the substrate chain length. Lauric and myristic acids were preferentially metabolized to their omega-1 hydroxy counterparts while no hydroxylation occurred when capric acid was used as the substrate. Palmitic acid, when present at concentrations greater than the concentration of oxygen in the reaction medium (greater than 250 microM), was hydroxylated to its omega-1, omega-2, and omega-3 hydroxy analogs, with the percentage distribution of the regioisomers being 21:44:35, respectively. No omega hydroxylation of any of the fatty acids was detected. When the concentration of palmitic acid was less than the concentration of oxygen in the reaction mixture, it was noted that a number of additional products were formed. Under these conditions, unlike lauric and myristic acids, it was observed that palmitic acid was first converted to its monohydroxy isomers which were subsequently metabolized to a mixture of 14-ketohexadecanoic, 15-ketohexadecanoic, 13-hydroxy-14-ketohexadecanoic, 14-hydroxy-15-ketohexadecanoic, and 13,14-dihydroxyhexadecanoic acids with a relative distribution of 8:2:40:30:20, respectively. Thus, P450BM-3 is able not only to monohydroxylate a variety of fatty acids but also to further metabolize some of these primary metabolites to secondary and tertiary products. The present paper characterizes the products formed during the sequential hydroxylation of palmitic acid and proposes reaction pathways to explain these results.
KeywordMeSH Terms
Bacterial Proteins
27. Rygus  T, Scheler  A, Allmansberger  R, Hillen  W,     ( 1991 )

Molecular cloning, structure, promoters and regulatory elements for transcription of the Bacillus megaterium encoded regulon for xylose utilization.

Archives of microbiology 155 (1��6��)
PMID : 1719948  :   DOI  :   10.1007/bf00245346    
Abstract >>
The xylA and xylB genes of Bacillus subtilis BR151 encoding xylose isomerase and xylulokinase, respectively, were disrupted by gene replacement rendering the constructed mutant strain unable to grow on xylose as the sole carbon source. The Bacillus megaterium encoded xyl genes were cloned by complementation of this strain to xylose utilization. The nucleotide sequence of about 4 kbp of the insertion indicates the presence of the xylA and xylB genes on the complementing plasmid. Furthermore, a regulatory gene, xylR, is located upstream of xylA and has opposite polarity to it. The intergenic region between the divergently oriented reading frames of xylR and xylA contains palindromic sequences of 24 bp spaced by five central bp and 29 bp spaced by 11 bp, respectively, and two promoters with opposite orientation as determined by primer extension analysis. They overlap with one nucleotide of their--35 consensus boxes. Transcriptional fusions of lacZ to xylA, xylB and xylR were constructed and revealed that xylA and xylB are repressed in the absence and can be 200-fold induced in the presence of xylose. The increased level of xylAB mRNA in induced and its absence in repressed cells confirms that this regulation occurs on the level of transcription. Deletion of the xylR gene encoding the Xyl repressor results in constitutive expression of xylAB. The transcription of xylR is autoregulated and can be induced 9-fold by xylose. The mechanism of this regulation is not clear. While the apparent xyl operator palindrome is upstream of the xylR promoter, the potential recognition of another palindrome downstream of this promoter by Xyl repressor is discussed.
KeywordMeSH Terms
Aldose-Ketose Isomerases
Gene Expression Regulation, Bacterial
Phosphotransferases (Alcohol Group Acceptor)
Promoter Regions, Genetic
Transcription, Genetic
28. Girvan  HM, Seward  HE, Toogood  HS, Cheesman  MR, Leys  D, Munro  AW,     ( 2007 )

Structural and spectroscopic characterization of P450 BM3 mutants with unprecedented P450 heme iron ligand sets. New heme ligation states influence conformational equilibria in P450 BM3.

The Journal of biological chemistry 282 (1)
PMID : 17077084  :   DOI  :   10.1074/jbc.M607949200    
Abstract >>
Two novel P450 heme iron ligand sets were generated by directed mutagenesis of the flavocytochrome P450 BM3 heme domain. The A264H and A264K variants produce Cys-Fe-His and Cys-Fe-Lys axial ligand sets, which were validated structurally and characterized by spectroscopic analysis. EPR and magnetic circular dichroism (MCD) provided fingerprints defining these P450 ligand sets. Near IR MCD spectra identified ferric low spin charge-transfer bands diagnostic of the novel ligands. For the A264K mutant, this is the first report of a Cys-Fe-Lys near-IR MCD band. Crystal structure determination showed that substrate-free A264H and A264K proteins crystallize in distinct conformations, as observed previously in substrate-free and fatty acid-bound wild-type P450 forms, respectively. This, in turn, likely reflects the positioning of the I alpha helix section of the protein that is required for optimal configuration of the ligands to the heme iron. One of the monomers in the asymmetric unit of the A264H crystals was in a novel conformation with a more open substrate access route to the active site. The same species was isolated for the wildtype heme domain and represents a novel conformational state of BM3 (termed SF2). The "locking" of these distinct conformations is evident from the fact that the endogenous ligands cannot be displaced by substrate or exogenous ligands. The consequent reduction of heme domain conformational heterogeneity will be important in attempts to determine atomic structure of the full-length, multidomain flavocytochrome, and thus to understand in atomic detail interactions between its heme and reductase domains.
KeywordMeSH Terms
29. Wang  W, Sun  J, Hollmann  R, Zeng  AP, Deckwer  WD,     ( 2006 )

Proteomic characterization of transient expression and secretion of a stress-related metalloprotease in high cell density culture of Bacillus megaterium.

Journal of biotechnology 126 (3)
PMID : 16820240  :   DOI  :   10.1016/j.jbiotec.2006.05.005    
Abstract >>
Intracellular and extracellular proteome analysis was carried out by combined two-dimensional gel electrophoresis and mass spectrometric analysis (2DE/MS) for high cell density fed-batch culture of recombinant Bacillus megaterium strains. In the early feeding phase with a constant growth rate of 0.12h(-1) under glucose limitation, high expression and secretion of a metalloprotease (referred as Bmg1465) was detected. The transient appearance of this metalloprotease was found both as cell-associated and as secreted into the culture medium. Searching homologous proteins for functional assignment led to an unambiguous identification of Bmg1465 as a zinc-binding metalloprotease of the type immune inhibitor A (InhA). Metalloproteases of this type are currently considered as typical virulence factors associated with pathogenic Bacillus species. The result raises questions concerning the intrinsic function(s) of Bmg1465 in B. megaterium, which has the GRAS status, with respect to its stress response in high cell density culture.
KeywordMeSH Terms
30. Takaku  H, Kimoto  A, Kodaira  S, Nashimoto  M, Takagi  M,     ( 2006 )

Isolation of a Gram-positive poly(3-hydroxybutyrate) (PHB)-degrading bacterium from compost, and cloning and characterization of a gene encoding PHB depolymerase of Bacillus megaterium N-18-25-9.

FEMS microbiology letters 264 (2)
PMID : 17064368  :   DOI  :   10.1111/j.1574-6968.2006.00448.x    
Abstract >>
A Gram-positive poly(3-hydroxybutyrate) (PHB)-degrading bacterial strain was isolated from compost. This organism, identified as Bacillus megaterium N-18-25-9, produced a clearing zone on opaque NB-PHB agar, indicating the presence of extracellular PHB depolymerase. A PHB depolymerase gene, PhaZ(Bm), of B. megaterium N-18-25-9 was cloned and sequenced, and the recombinant gene product was purified from Escherichia coli. The N-terminal half region of PhaZ(Bm) shared significant homologies with a catalytic domain of other PHB depolymerases. Although the C-terminal half region of PhaZ(Bm) showed no significant similarity with those of other PHB depolymerases, that region was necessary for the PHB depolymerase activity. Therefore, this enzyme's domain structure is unique among extracellular PHB depolymerase domain structures. The addition of PHB to the medium led to a sixfold increase in PhaZ(Bm) mRNA, while the presence of glucose repressed PhaZ(Bm) expression. The maximum activity was observed at pH 9.0 at 65 degrees C.
KeywordMeSH Terms
Soil Microbiology
31. Xu  Z, Jing  K, Liu  Y, Cen  P,     ( 2007 )

High-level expression of recombinant glucose dehydrogenase and its application in NADPH regeneration.

Journal of industrial microbiology & biotechnology 34 (1)
PMID : 16941118  :   DOI  :   10.1007/s10295-006-0168-2    
Abstract >>
Two glucose dehydrogenase (E.C. 1.1.1.47) genes, gdh223 and gdh151, were cloned from Bacillus megaterium AS1.223 and AS1.151, and were inserted into pQE30 to construct the expression vectors, pQE30-gdh223 and pQE30-gdh151, respectively. The transformant Escherichia coli M15 with pQE30-gdh223 gave a much higher glucose dehydrogenase activity than that with the plasmid pQE30-gdh151. Thus it was used to optimize the expression of glucose dehydrogenase. An proximately tenfold increase in GDH activity was achieved by the optimization of culture and induction conditions, and the highest productivity of glucose dehydrogenase (58.7 U/ml) was attained. The recombinant glucose dehydrogenase produced by E. coli M15 (pQE30-gdh223) was then used to regenerate NADPH. NADPH was efficiently regenerated in vivo and in vitro when 0.1 M glucose was supplemented concomitantly in the reaction system. Finally, this coenzyme-regenerating system was coupled with a NADPH-dependent bioreduction for efficient synthesis of ethyl (R)-4-chloro-3-hydroxybutanoate from ethyl 4-chloro-3-oxobutanoate.
KeywordMeSH Terms
32. Kajiwara  Y, Santander  PJ, Roessner  CA, Pérez  LM, Scott  AI,     ( 2006 )

Genetically engineered synthesis and structural characterization of cobalt-precorrin 5A and -5B, two new intermediates on the anaerobic pathway to vitamin B12: definition of the roles of the CbiF and CbiG enzymes.

Journal of the American Chemical Society 128 (30)
PMID : 16866557  :   DOI  :   10.1021/ja062940a    
Abstract >>
Two new cobalt corrinoid intermediates, cobalt-precorrin 5A and cobalt-precorrin 5B, have been synthesized with the aid of overexpressed enzymes of the vitamin B(12) pathway of Salmonella entericaserovar typhimurium. These compounds were made in several regioselectively (13)C-labeled forms, and their structures have been established by multidimensional NMR spectroscopy. The addition of CbiF to the enzymes known to synthesize cobalt-precorrin 4 resulted in the formation of cobalt-precorrin 5A, and the inclusion of CbiG with CbiF produced cobalt-precorrin 5B, which has allowed us to define the role of these enzymes in the anaerobic biosynthetic pathway. CbiF is the C-11 methylase, and CbiG, an enzyme which shows homology with CobE of the aerobic pathway, is the gene product responsible for the opening of the ring A delta-lactone and extrusion of the "C(2)" unit. The discovery of these long-sought intermediates paves the way for defining the final stages of the anaerobic pathway. It is of considerable evolutionary interest that nature uses two distinct pathways to vitamin B(12), both conserved over several billion years and featuring completely different mechanisms for ring-contraction of the porphyrinoid to the corrinoid ring system. Thus the aerobic pathway utilizes molecular oxygen to trigger the events at C-20 leading to contraction and expulsion of the "C(2)" unit as acetic acid from a metal-free intermediate, whereas the anaerobic route features internal delivery of oxygen from a carboxylic acid terminus to C-20 followed by extrusion of the "C(2)" unit as acetaldehyde, using cobalt complexes as substrates.
KeywordMeSH Terms
Genetic Engineering
33. Budde  M, Morr  M, Schmid  RD, Urlacher  VB,     ( 2006 )

Selective hydroxylation of highly branched fatty acids and their derivatives by CYP102A1 from Bacillus megaterium.

Chembiochem : a European journal of chemical biology 7 (5)
PMID : 16566047  :   DOI  :   10.1002/cbic.200500444    
Abstract >>
Highly branched fatty acids, the main components of the preen-gland waxes of the domestic goose and the Muscovy duck, and their derivatives are promising chiral precursors for the synthesis of macrolide antibiotics. The key step in the utilisation of these compounds is their regioselective hydroxylation, which cannot be achieved in a classical chemical approach. Three P450 monooxygenases, CYP102A1, CYP102A2 and CYP102A3, demonstrating high turnover numbers in the hydroxylation of iso and anteiso fatty acids (>400 min(-1)), were tested for their activity towards these substrates. CYP102A1 from Bacillus megaterium and its A74G F87V L188Q triple mutant hydroxylate a variety of these substrates with high activity and regioselectivity. In all cases, the triple mutant showed much higher activities than the wild-type enzyme. The binding constants, determined for wild-type CYP102A1 and the triple mutant with tetramethylnonanol as substrate, were >200 microM and approximately 23 microM, respectively. Data derived from binding analysis support the differences in activity found for the wild-type CYP102A1 and the triple mutant. Surprisingly, CYP102A2 and CYP102A3 from Bacillus subtilis did not show any activity. Substrate binding spectra, recorded to investigate substrate accessibility to the enzyme's active sites, revealed that the substrates either could not access the active site of the Bacillus subtilis monooxygenases, or did not come into proximity with the heme.
KeywordMeSH Terms
34. Clark  JP, Miles  CS, Mowat  CG, Walkinshaw  MD, Reid  GA, Daff  SN, Chapman  SK,     ( 2006 )

The role of Thr268 and Phe393 in cytochrome P450 BM3.

Journal of inorganic biochemistry 100 (5��6��)
PMID : 16403573  :   DOI  :   10.1016/j.jinorgbio.2005.11.020    
Abstract >>
In flavocytochrome P450 BM3 there are several active site residues that are highly conserved throughout the P450 superfamily. Of these, a phenylalanine (Phe393) has been shown to modulate heme reduction potential through interactions with the implicitly conserved heme-ligand cysteine. In addition, a distal threonine (Thr268) has been implicated in a variety of roles including proton donation, oxygen activation and substrate recognition. Substrate binding in P450 BM3 causes a shift in the spin state from low- to high-spin. This change in spin-state is accompanied by a positive shift in the reduction potential (DeltaE(m) [WT+arachidonate (120 microM)]=+138 mV). Substitution of Thr268 by an alanine or asparagine residue causes a significant decrease in the ability of the enzyme to generate the high-spin complex via substrate binding and consequently leads to a decrease in the substrate-induced potential shift (DeltaE(m) [T268A+arachidonate (120 microM)]=+73 mV, DeltaE(m) [T268N+arachidonate (120 microM)]=+9 mV). Rate constants for the first electron transfer and for oxy-ferrous decay were measured by pre-steady-state stopped-flow kinetics and found to be almost entirely dependant on the heme reduction potential. More positive reduction potentials lead to enhanced rate constants for heme reduction and more stable oxy-ferrous species. In addition, substitutions of the threonine lead to an increase in the production of hydrogen peroxide in preference to hydroxylated product. These results suggest an important role for this active site threonine in substrate recognition and in maintaining an efficiently functioning enzyme. However, the dependence of the rate constants for oxy-ferrous decay on reduction potential raises some questions as to the importance of Thr268 in iron-oxo stabilisation.
KeywordMeSH Terms
35. Nagao  T, Mitamura  T, Wang  XH, Negoro  S, Yomo  T, Urabe  I, Okada  H,     ( 1992 )

Cloning, nucleotide sequences, and enzymatic properties of glucose dehydrogenase isozymes from Bacillus megaterium IAM1030.

Journal of bacteriology 174 (15)
PMID : 1629157  :   DOI  :   10.1128/jb.174.15.5013-5020.1992     PMC  :   PMC206315    
Abstract >>
Bacillus megaterium is known to have several genes that code for isozymes of glucose dehydrogenase. Two of them, gdhI and gdhII, were cloned from B. megaterium IAM1030 in our previous work (T. Mitamura, R. V. Evora, T. Nakai, Y. Makino, S. Negoro, I. Urabe, and H. Okada, J. Ferment. Bioeng. 70:363-369, 1990). In the present study, two new genes, gdhIII and gdhIV, were isolated from the same strain and their nucleotide sequences were identified. Each gene has an open reading frame of 783 bp available to encode a peptide of 261 amino acids. Thus, a total of four glucose dehydrogenase genes have been cloned from B. megaterium IAM1030. In addition, this strain does not seem to have other glucose dehydrogenase genes that can be distinguished from the four cloned genes so far examined by Southern hybridization analysis. The two newly cloned genes were expressed in Escherichia coli cells, and the products, GlcDH-III and GlcDH-IV, were purified and characterized and compared with the other isozymes, GlcDH-I and GlcDH-II, encoded by gdhI and gdhII, respectively. These isozymes showed different mobilities in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (GlcDH-I greater than GlcDH-III = GlcDH-IV greater than GlcDH-II), although they have the same number of amino acid residues. Double-immunodiffusion tests showed that GlcDH-I is immunologically different from the other isozymes and that GlcDH-III and GlcDH-IV are identical to one another but a little different from GlcDH-II. These glucose dehydrogenases were stabilized in the presence of 2 M NaCl. The effect of NaCl was especially large for GlcDH-III, which is most unstable enzyme. Kinetic studies showed that these isozymes are divided into two groups with respect to coenzyme specificity, although they can utilize both NAD and NADP: GlcDH-III and GlcDH-IV prefer NAD, and GlcDH-I and GlcDH-II prefer NADP. The phylogenic relationship of these glucose dehydrogenase genes is also discussed.
KeywordMeSH Terms
Cloning, Molecular
36. Narasaki  R, Kuribayashi  H, Shimizu  K, Imamura  D, Sato  T, Hasumi  K,     ( 2005 )

Bacillolysin MA, a novel bacterial metalloproteinase that produces angiostatin-like fragments from plasminogen and activates protease zymogens in the coagulation and fibrinolysis systems.

The Journal of biological chemistry 280 (14)
PMID : 15677446  :   DOI  :   10.1074/jbc.M500241200    
Abstract >>
We isolated a novel protease that converts plasminogen to angiostatin-like fragments (BL-angiostatins) from a culture of Bacillus megaterium A9542 through a single-step chromatography on CM-cellulose. The protease, designated bacillolysin MA (BL-MA), belongs to a family of neutral metalloproteinases based on the nucleotide sequence of its gene. At an enzyme:substrate ratio of 1:540, BL-MA cleaved human plasminogen mainly at Ser441-Val442 to form BL-angiostatin and miniplasminogen with a K(m) of 3.0 +/- 0.8 microM and a k(cat) of 0.70 +/- 0.09 s(-1). The resulting BL-angiostatins inhibited the proliferation, migration, and tube formation of vascular endothelial cells at concentrations of 1-10 microg/ml. Although BL-MA failed to activate plasminogen, it increased urokinase-catalyzed activation of plasminogen caused by production of miniplasminogen, which is highly susceptible to activation. In addition, BL-MA was active in converting prourokinase, prothrombin, coagulation factor X, and protein C to their active forms. BL-MA enhanced both the clotting of human plasma and clot dissolution in the presence of prourokinase. Thus, BL-MA affects blood coagulation and fibrinolysis systems and can be used to produce angiostatin-like plasminogen fragments and active serine proteases of human plasma.
KeywordMeSH Terms
37. Lammers  M, Nahrstedt  H, Meinhardt  F,     ( 2004 )

The Bacillus megaterium comE locus encodes a functional DNA uptake protein.

Journal of basic microbiology 44 (6)
PMID : 15558816  :   DOI  :   10.1002/jobm.200410450    
Abstract >>
From Bacillus megaterium, a genomic region was isolated and structurally characterized which strongly resembles the Bacillus subtilis competence locus comE encoding proteins involved in DNA uptake. Functionality of the B. megaterium comEA gene was proven by complementing a DNA-receptor mutant of B. subtilis. This finding provides first evidence for a latent ability of B. megaterium to develop natural competence, although such physiological state has not as yet been identified in this organism.
KeywordMeSH Terms
38. Shaw  GC, Fulco  AJ,     ( 1992 )

Barbiturate-mediated regulation of expression of the cytochrome P450BM-3 gene of Bacillus megaterium by Bm3R1 protein.

The Journal of biological chemistry 267 (8)
PMID : 1544926  :  
Abstract >>
In a previous publication (Wen, L.-P., Ruettinger, R. T., and Fulco, A.J. (1989) J. Biol. Chem. 264, 10996-11003), we reported that about 1 kilobase of 5' flanking sequence was required for barbiturate-inducible expression of the cytochrome P450BM-3 gene in Bacillus megaterium. We have now found, by analysis of various deletion and frameshift derivatives of this region, that an open reading frame immediately upstream of the B. megaterium cytochrome P450BM-3 structural gene encodes a protein, designated Bm3R1, which negatively controls the expression of the P450BM-3 gene at the transcriptional level. A helix-turn-helix DNA binding motif was found near the N-terminal portion of Bm3R1 protein. The 5' terminus of the bm3R1 transcript generated in vivo was determined by nuclease S1 mapping and primer extension analysis to be 44 base pairs upstream of the translation initiation sequence GTG of bm3R1. A putative promoter sequence with a high degree of similarity to the -35 and -10 consensus sequence recognized by the Bacillus subtilis sigma-43 factor was located at an appropriate distance from the transcription start site. A B. megaterium mutant which highly constitutively produced P450BM-3 protein was isolated and complementation of this cytochrome P450BM-3-constitutive mutant by a DNA fragment containing the wild-type bm3R1 gene indicated that the mutation in this locus was trans-dominant. Sequence analysis of the bm3R1 gene and its upstream region from this mutant, after amplification by the polymerase chain reaction, identified a single base change that resulted in a glycine to glutamate substitution in the beta-turn region of the DNA binding motif. By placing the bm3R1 gene under the control of a tac promoter and changing the translation initiation sequence from GTG to ATG, we succeeded in overproducing the Bm3R1 protein in Escherichia coli. A 20-bp perfect palindromic putative operator site, located between the presumed promoter sequences and the bm3R1 structural gene, was defined both by in vivo titration of Bm3R1 repressor and by gel mobility shift assays using the cell-free extracts containing the overproduced wild-type or mutant Bm3R1 protein. The barbiturate effect in mediating the induction of cytochrome P450BM-3 appears to be indirect but probably involves, in part, the release of inhibition by Bm3R1 repressor protein by interfering with its binding to the palindromic putative operator sequence and perhaps to other sites on the regulatory region of the gene encoding cytochrome P450BM-3.
KeywordMeSH Terms
Genes, Bacterial
Repressor Proteins
Transcription Factors
Genes, Bacterial
Repressor Proteins
Transcription Factors
39. Shaw  GC, Fulco  AJ,     ( 1992 )

Barbiturate-mediated regulation of expression of the cytochrome P450BM-3 gene of Bacillus megaterium by Bm3R1 protein.

The Journal of biological chemistry 267 (8)
PMID : 1544926  :  
Abstract >>
In a previous publication (Wen, L.-P., Ruettinger, R. T., and Fulco, A.J. (1989) J. Biol. Chem. 264, 10996-11003), we reported that about 1 kilobase of 5' flanking sequence was required for barbiturate-inducible expression of the cytochrome P450BM-3 gene in Bacillus megaterium. We have now found, by analysis of various deletion and frameshift derivatives of this region, that an open reading frame immediately upstream of the B. megaterium cytochrome P450BM-3 structural gene encodes a protein, designated Bm3R1, which negatively controls the expression of the P450BM-3 gene at the transcriptional level. A helix-turn-helix DNA binding motif was found near the N-terminal portion of Bm3R1 protein. The 5' terminus of the bm3R1 transcript generated in vivo was determined by nuclease S1 mapping and primer extension analysis to be 44 base pairs upstream of the translation initiation sequence GTG of bm3R1. A putative promoter sequence with a high degree of similarity to the -35 and -10 consensus sequence recognized by the Bacillus subtilis sigma-43 factor was located at an appropriate distance from the transcription start site. A B. megaterium mutant which highly constitutively produced P450BM-3 protein was isolated and complementation of this cytochrome P450BM-3-constitutive mutant by a DNA fragment containing the wild-type bm3R1 gene indicated that the mutation in this locus was trans-dominant. Sequence analysis of the bm3R1 gene and its upstream region from this mutant, after amplification by the polymerase chain reaction, identified a single base change that resulted in a glycine to glutamate substitution in the beta-turn region of the DNA binding motif. By placing the bm3R1 gene under the control of a tac promoter and changing the translation initiation sequence from GTG to ATG, we succeeded in overproducing the Bm3R1 protein in Escherichia coli. A 20-bp perfect palindromic putative operator site, located between the presumed promoter sequences and the bm3R1 structural gene, was defined both by in vivo titration of Bm3R1 repressor and by gel mobility shift assays using the cell-free extracts containing the overproduced wild-type or mutant Bm3R1 protein. The barbiturate effect in mediating the induction of cytochrome P450BM-3 appears to be indirect but probably involves, in part, the release of inhibition by Bm3R1 repressor protein by interfering with its binding to the palindromic putative operator sequence and perhaps to other sites on the regulatory region of the gene encoding cytochrome P450BM-3.
KeywordMeSH Terms
Genes, Bacterial
Repressor Proteins
Transcription Factors
Genes, Bacterial
Repressor Proteins
Transcription Factors
40. Schumacher  MA, Allen  GS, Diel  M, Seidel  G, Hillen  W, Brennan  RG,     ( 2004 )

Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P.

Cell 118 (6)
PMID : 15369672  :   DOI  :   10.1016/j.cell.2004.08.027     DOI  :   10.1016/j.cell.2004.08.027    
Abstract >>
Carbon catabolite repression (CCR) is one of the most fundamental environmental-sensing mechanisms in bacteria and imparts competitive advantage by establishing priorities in carbon metabolism. In gram-positive bacteria, the master transcription regulator of CCR is CcpA. CcpA is a LacI-GalR family member that employs, as an allosteric corepressor, the phosphoprotein HPr-Ser46-P, which is formed in glucose-replete conditions. Here we report structures of the Bacillus megaterium apoCcpA and a CcpA-(HPr-Ser46-P)-DNA complex. These structures reveal that HPr-Ser46-P mediates a novel two-component allosteric DNA binding activation mechanism that involves both rotation of the CcpA subdomains and relocation of pivot-point residue Thr61, which leads to juxtaposition of the DNA binding regions permitting "hinge" helix formation in the presence of cognate DNA. The structure of the CcpA-(HPr-Ser46-P)-cre complex also reveals the elegant mechanism by which CcpA family-specific interactions with HPr-Ser46-P residues Ser46-P and His15 partition the high-energy CCR and low-energy PTS pathways, the latter requiring HPr-His15-P.
KeywordMeSH Terms
41. Li  H, Poulos  TL,     ( 1995 )

Modeling protein-substrate interactions in the heme domain of cytochrome P450(BM-3).

Acta crystallographica. Section D, Biological crystallography 51 (Pt 1)
PMID : 15299332  :   DOI  :   10.1107/S0907444994009194    
Abstract >>
The crystal structure of heme domain of the fatty acid monooxygenase, cytochrome P450(BM-3), consisting of residues 1-455 has been independently solved to R = 0.18 at 2.0 A. The crystal form used, space group P2(1) with two molecules per asymmetric unit, is isomorphous with that form with residues 1-471 first described by Boddupalli et al. [Boddupalli, Hasemann, Ravinchandran, Lu, Goldsmith, Deisenhofer & Peterson (1992). Proc. Natl Acad. Sci. USA, 89, 5567-5571] and used by Ravichandran, Boddupalli, Hasemann, Peterson & Deisenhofer [(1993). Science, 261, 731-736] to determine the crystal structure. The substrate-access channel consists of a large, hydrophobic cleft that appears to be the most likely route taken by fatty acid substrates. Attempts to soak crystals in mother liquor containing a variety of fatty acid substrates yielded featureless difference Fouriers even though fatty acid substrates are known to bind with dissociation constants in the micro M range. Modeling substrate-enzyme interactions reveals few contacts between the enzyme and substrate. More detailed modeling was carried out by subjecting both molecules in the asymmetric unit to extensive energy minimization. These studies reveal that the heme-domain active-site cleft can undergo a large conformational change that closes the access channel thereby providing enhanced protein-substrate interactions. These conformational changes are prevented from occurring by intermolecular contacts in the crystal lattice which lock the protein in the 'open' conformation.
KeywordMeSH Terms
42. Lisurek  M, Kang  MJ, Hartmann  RW, Bernhardt  R,     ( 2004 )

Identification of monohydroxy progesterones produced by CYP106A2 using comparative HPLC and electrospray ionisation collision-induced dissociation mass spectrometry.

Biochemical and biophysical research communications 319 (2)
PMID : 15178459  :   DOI  :   10.1016/j.bbrc.2004.05.037    
Abstract >>
Two previously uncharacterised products, produced by recombinant CYP106A2 of Bacillus megaterium ATCC 13368 using progesterone as substrate, were identified. For this purpose a combination of comparative HPLC and electrospray ionisation collision induced dissociation mass spectrometry (ESI CID MS) was established and applied for rapid identification of the steroids, which were identified as 11alpha-hydroxyprogesterone and 9alpha-hydroxyprogesterone. The pharmaceutical relevance of these steroids is discussed. Furthermore, the hydroxylation activity was quantified for all monohydroxylation products (15beta-hydroxyprogesterone, 6beta-hydroxyprogesterone, 11alpha-hydroxyprogesterone, and 9alpha-hydroxyprogesterone). The V(max) values for 15beta-hydroxyprogesterone, 6beta-hydroxyprogesterone, 11alpha-hydroxyprogesterone, and 9alpha-hydroxyprogesterone were determined as 337.3+/-43.7, 22.3+/-0.9, 17.5+/-0.9, and 6.5+/-0.3nmol product/min/nmol CYP106A2, respectively.
KeywordMeSH Terms
43. Nahrstedt  H, Meinhardt  F,     ( 2004 )

Structural and functional characterization of the Bacillus megaterium uvrBA locus and generation of UV-sensitive mutants.

Applied microbiology and biotechnology 65 (2)
PMID : 14872291  :   DOI  :   10.1007/s00253-004-1572-z    
Abstract >>
The Bacillus megaterium genes uvrB and uvrA, encoding two subunits of the (A)BC excinuclease, which is responsible for nucleotide excision repair, were isolated and functionally characterized. RNA analyses revealed co-transcription of both genes probably forming a bicistronic operon. Expression of uvrB and uvrA was inducible by the DNA-damaging agent mitomycin C. This finding agrees with the presence of a potential DinR box within the uvrBA promoter. Single inactivation of uvrB or uvrA as well as the parallel knockout of both genes resulted in mutants highly sensitive to UV irradiation. Thus, this locus represents an attractive target for generating biologically safe containment strains of B. megaterium.
KeywordMeSH Terms
Ultraviolet Rays
44. Joyce  MG, Girvan  HM, Munro  AW, Leys  D,     ( 2004 )

A single mutation in cytochrome P450 BM3 induces the conformational rearrangement seen upon substrate binding in the wild-type enzyme.

The Journal of biological chemistry 279 (22)
PMID : 15020590  :   DOI  :   10.1074/jbc.M401717200    
Abstract >>
The multidomain fatty-acid hydroxylase flavocytochrome P450 BM3 has been studied as a paradigm model for eukaryotic microsomal P450 enzymes because of its homology to eukaryotic family 4 P450 enzymes and its use of a eukaryotic-like diflavin reductase redox partner. High-resolution crystal structures have led to the proposal that substrate-induced conformational changes lead to removal of water as the sixth ligand to the heme iron. Concomitant changes in the heme iron spin state and heme iron reduction potential help to trigger electron transfer from the reductase and to initiate catalysis. Surprisingly, the crystal structure of the substrate-free A264E heme domain mutant reveals the enzyme to be in the conformation observed for substrate-bound wild-type P450, but with the iron in the low-spin state. This provides strong evidence that the spin-state shift observed upon substrate binding in wild-type P450 BM3 not only is caused indirectly by structural changes in the protein, but is a direct consequence of the presence of the substrate itself, similar to what has been observed for P450cam. The crystal structure of the palmitoleate-bound A264E mutant reveals that substrate binding promotes heme ligation by Glu(264), with little other difference from the palmitoleate-bound wild-type structure observable. Despite having a protein-derived sixth heme ligand in the substrate-bound form, the A264E mutant is catalytically active, providing further indication for structural rearrangement of the active site upon reduction of the heme iron, including displacement of the glutamate ligand to allow binding of dioxygen.
KeywordMeSH Terms
Bacterial Proteins
Cytochrome P-450 Enzyme System
Mixed Function Oxygenases
45. Gueneau de Novoa  P, Williams  KP,     ( 2004 )

The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts.

Nucleic acids research 32 (Database issue)
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.
KeywordMeSH Terms
Databases, Nucleic Acid
Evolution, Molecular
Internet
46. Ost  TW, Clark  J, Mowat  CG, Miles  CS, Walkinshaw  MD, Reid  GA, Chapman  SK, Daff  S,     ( 2003 )

Oxygen activation and electron transfer in flavocytochrome P450 BM3.

Journal of the American Chemical Society 125 (49)
PMID : 14653735  :   DOI  :   10.1021/ja035731o    
Abstract >>
In flavocytochrome P450 BM3, there is a conserved phenylalanine residue at position 393 (Phe393), close to Cys400, the thiolate ligand to the heme. Substitution of Phe393 by Ala, His, Tyr, and Trp has allowed us to modulate the reduction potential of the heme, while retaining the structural integrity of the enzyme's active site. Substrate binding triggers electron transfer in P450 BM3 by inducing a shift from a low- to high-spin ferric heme and a 140 mV increase in the heme reduction potential. Kinetic analysis of the mutants indicated that the spin-state shift alone accelerates the rate of heme reduction (the rate determining step for overall catalysis) by 200-fold and that the concomitant shift in reduction potential is only responsible for a modest 2-fold rate enhancement. The second step in the P450 catalytic cycle involves binding of dioxygen to the ferrous heme. The stabilities of the oxy-ferrous complexes in the mutant enzymes were also analyzed using stopped-flow kinetics. These were found to be surprisingly stable, decaying to superoxide and ferric heme at rates of 0.01-0.5 s(-)(1). The stability of the oxy-ferrous complexes was greater for mutants with higher reduction potentials, which had lower catalytic turnover rates but faster heme reduction rates. The catalytic rate-determining step of these enzymes can no longer be the initial heme reduction event but is likely to be either reduction of the stabilized oxy-ferrous complex, i.e., the second flavin to heme electron transfer or a subsequent protonation event. Modulating the reduction potential of P450 BM3 appears to tune the two steps in opposite directions; the potential of the wild-type enzyme appears to be optimized to maximize the overall rate of turnover. The dependence of the visible absorption spectrum of the oxy-ferrous complex on the heme reduction potential is also discussed.
KeywordMeSH Terms
47. Nahrstedt  H, Wittchen  K, Rachman  MA, Meinhardt  F,     ( 2004 )

Identification and functional characterization of a type I signal peptidase gene of Bacillus megaterium DSM319.

Applied microbiology and biotechnology 64 (2)
PMID : 14593507  :   DOI  :   10.1007/s00253-003-1469-2    
Abstract >>
The sipM gene of Bacillus megaterium encoding a type I signal peptidase (SPase) was isolated and structurally characterized. RNA analysis revealed a transcript size in accordance with a bicistronic operon comprising sipM and an adjacent open reading frame. Inactivation of sipM by targeted gene disruption could not be achieved, indicating its essential role for cell viability since there might be no other type I SPase of major importance present in B. megaterium. Plasmid-assisted amplification of the gene resulted in an increase in activity of the heterologous glucanase used as an extracellular reporter, suggesting a potential bottleneck for protein secretion within this species.
KeywordMeSH Terms
48. Haines  DC, Hegde  A, Chen  B, Zhao  W, Bondlela  M, Humphreys  JM, Mullin  DA, Tomchick  DR, Machius  M, Peterson  JA,     ( 2011 )

A single active-site mutation of P450BM-3 dramatically enhances substrate binding and rate of product formation.

Biochemistry 50 (39)
PMID : 21875028  :   DOI  :   10.1021/bi201099j     PMC  :   PMC3235725    
Abstract >>
Identifying key structural features of cytochromes P450 is critical in understanding the catalytic mechanism of these important drug-metabolizing enzymes. Cytochrome P450BM-3 (BM-3), a structural and mechanistic P450 model, catalyzes the regio- and stereoselective hydroxylation of fatty acids. Recent work has demonstrated the importance of water in the mechanism of BM-3, and site-specific mutagenesis has helped to elucidate mechanisms of substrate recognition, binding, and product formation. One of the amino acids identified as playing a key role in the active site of BM-3 is alanine 328, which is located in the loop between the K helix and �] 1-4. In the A328V BM-3 mutant, substrate affinity increases 5-10-fold and the turnover number increases 2-8-fold compared to wild-type enzyme. Unlike wild-type enzyme, this mutant is purified from E. coli with endogenous substrate bound due to the higher binding affinity. Close examination of the crystal structures of the substrate-bound native and A328V mutant BMPs indicates that the positioning of the substrate is essentially identical in the two forms of the enzyme, with the two valine methyl groups occupying voids present in the active site of the wild-type substrate-bound structure.
KeywordMeSH Terms
49. Whitehouse  CJ, Yang  W, Yorke  JA, Rowlatt  BC, Strong  AJ, Blanford  CF, Bell  SG, Bartlam  M, Wong  LL, Rao  Z,     ( 2010 )

Structural basis for the properties of two single-site proline mutants of CYP102A1 (P450BM3).

Chembiochem : a European journal of chemical biology 11 (18)
PMID : 21110374  :   DOI  :   10.1002/cbic.201000421    
Abstract >>
The crystal structures of the haem domains of Ala330Pro and Ile401Pro, two single-site proline variants of CYP102A1 (P450(BM3)) from Bacillus megaterium, have been solved. In the A330P structure, the active site is constricted by the relocation of the Pro329 side chain into the substrate access channel, providing a basis for the distinctive C-H bond oxidation profiles given by the variant and the enhanced activity with small molecules. I401P, which is exceptionally active towards non-natural substrates, displays a number of structural similarities to substrate-bound forms of the wild-type enzyme, notably an off-axial water ligand, a drop in the proximal loop, and the positioning of two I-helix residues, Gly265 and His266, the reorientation of which prevents the formation of several intrahelical hydrogen bonds. Second-generation I401P variants gave high in vitro oxidation rates with non-natural substrates as varied as fluorene and propane, towards which the wild-type enzyme is essentially inactive. The substrate-free I401P haem domain had a reduction potential slightly more oxidising than the palmitate-bound wild-type haem domain, and a first electron transfer rate that was about 10 % faster. The electronic properties of A330P were, by contrast, similar to those of the substrate-free wild-type enzyme.
KeywordMeSH Terms
50. Ener  ME, Lee  YT, Winkler  JR, Gray  HB, Cheruzel  L,     ( 2010 )

Photooxidation of cytochrome P450-BM3.

Proceedings of the National Academy of Sciences of the United States of America 107 (44)
PMID : 20947800  :   DOI  :   10.1073/pnas.1012381107     PMC  :   PMC2973866    
Abstract >>
High-valent iron-oxo species are thought to be intermediates in the catalytic cycles of oxygenases and peroxidases. An attractive route to these iron-oxo intermediates involves laser flash-quench oxidation of ferric hemes, as demonstrated by our work on the ferryl (compound II) and ferryl porphyrin radical cation (compound I) intermediates of horseradish peroxidase. Extension of this work to include cytochrome P450-BM3 (CYP102A1) has required covalent attachment of a Ru(II) photosensitizer to a nonnative cysteine near the heme (RuIIK97C-FeIIIP450), in order to promote electron transfer from the Fe(III) porphyrin to photogenerated Ru(III). The conjugate was structurally characterized by X-ray crystallography (2.4 ? resolution; Ru-Fe distance, 24 ?). Flash-quench oxidation of the ferric-aquo heme produces an Fe(IV)-hydroxide species (compound II) within 2 ms. Difference spectra for three singly oxidized P450-BM3 intermediates were obtained from kinetics modeling of the transient absorption data in combination with generalized singular value decomposition analysis and multiexponential fitting.
KeywordMeSH Terms
Models, Chemical
Photochemical Processes
51. Sendovski  M, Kanteev  M, Ben-Yosef  VS, Adir  N, Fishman  A,     ( 2011 )

First structures of an active bacterial tyrosinase reveal copper plasticity.

Journal of molecular biology 405 (1)
PMID : 21040728  :   DOI  :   10.1016/j.jmb.2010.10.048    
Abstract >>
Tyrosinase is a member of the type 3 copper enzyme family that is involved in the production of melanin in a wide range of organisms. The crystal structures of a tyrosinase from Bacillus megaterium were determined at a resolution of 2.0-2.3 ?. The enzyme crystallized as a dimer in the asymmetric unit and was shown to be active in crystal. The overall monomeric structure is similar to that of the monomer of the previously determined tyrosinase from Streptomyces castaneoglobisporus, but it does not contain an accessory Cu-binding "caddie" protein. Two Cu(II) ions, serving as the major cofactors within the active site, are coordinated by six conserved histidine residues. However, determination of structures under different conditions shows varying occupancies and positions of the copper ions. This apparent mobility in copper binding modes indicates that there is a pathway by which copper is accumulated or lost by the enzyme. Additionally, we suggest that residues R209 and V218, situated in a second shell of residues surrounding the active site, play a role in substrate binding orientation based on their flexibility and position. The determination of a structure with the inhibitor kojic acid, the first tyrosinase structure with a bound ligand, revealed additional residues involved in the positioning of substrates in the active site. Comparison of wild-type structures with the structure of the site-specific variant R209H, which possesses a higher monophenolase/diphenolase activity ratio, lends further support to a previously suggested mechanism by which monophenolic substrates dock mainly to CuA.
KeywordMeSH Terms
52. Zou  C, Li  Z, Yu  D,     ( 2010 )

Bacillus megaterium strain XTBG34 promotes plant growth by producing 2-pentylfuran.

Journal of microbiology (Seoul, Korea) 48 (4)
PMID : 20799087  :   DOI  :   10.1007/s12275-010-0068-z    
Abstract >>
Several chemical changes in soil are associated with plant growth-promoting rhizobacteria. An endosporeforming bacterium, strain XTBG34, was isolated from a Xishuangbanna Tropical Botanical Garden soil sample and identified as Bacillus megaterium. The strain's volatiles had remarkable plant growth promotion activity in Arabidopsis thaliana plants; after 15 days treatment, the fresh weight of plants inoculated with XTBG34 was almost 2-fold compared with those inoculated with DH5alpha. Head space volatile compounds produced by XTBG34, trapped with headspace solid phase microextraction and identified by gas chromatography-mass spectrometry, included aldehydes, alkanes, ketones and aroma components. Of the 11 compounds assayed for plant growth promotion activity in divided Petri plates, only 2-pentylfuran increased plant growth. We have therefore identified a new plant growth promotion volatile of B. megaterium XTBG34, which deserves further study in the mechanisms of interaction between plant growth-promoting rhizobacteria and plants.
KeywordMeSH Terms
Soil Microbiology
53. Ghollasi  M, Khajeh  K, Naderi-Manesh  H, Ghasemi  A,     ( 2010 )

Engineering of a Bacillus alpha-amylase with improved thermostability and calcium independency.

Applied biochemistry and biotechnology 162 (2)
PMID : 20177823  :   DOI  :   10.1007/s12010-009-8879-2    
Abstract >>
Successful industrial use of amylases requires that they are sufficiently stable and active at application conditions, e.g., at high temperature in starch-liquefaction process. In the present study, site-directed mutagenesis was used to enhance the thermal stability and calcium independency of a mesophilic alpha-amylase from Bacillus megaterium WHO. Mutations (A53S and H58I) were designed at the calcium-binding site based on the sequence alignment. Kinetic and thermostability parameters of the mutants were analyzed and compared with that of the wild type. In the presence of calcium, the affinity of the enzymes (wild type and mutants) toward starch was increased. In comparison to the wild type, calcium ion had more effect on the catalytic efficiency, k (cat)/K (m), and half-life (at 60 degrees C) of A53S mutant. In A53S, the dependence of half-life on calcium concentration showed that the enhanced calcium binding is likely to be responsible for the increased stability. In contrast, calcium-independent mutant (H58I) possessed high thermostability. In addition, thermodynamic parameters of amylolytic reaction exhibited an increase in the activation energy and the entropy of the system. Kinetics of irreversible thermal inactivation suggests that the activation energy increased by 1.4-fold in the most stable variant.
KeywordMeSH Terms
54. Girvan  HM, Levy  CW, Williams  P, Fisher  K, Cheesman  MR, Rigby  SE, Leys  D, Munro  AW,     ( 2010 )

Glutamate-haem ester bond formation is disfavoured in flavocytochrome P450 BM3: characterization of glutamate substitution mutants at the haem site of P450 BM3.

The Biochemical journal 427 (3)
PMID : 20180779  :   DOI  :   10.1042/BJ20091603    
Abstract >>
Bacillus megaterium flavocytochrome P450 BM3 (CYP102A1) is a biotechnologically important cytochrome P450/P450 reductase fusion enzyme. Mutants I401E, F261E and L86E were engineered near the haem 5-methyl group, to explore the ability of the glutamate carboxylates to form ester linkages with the methyl group, as observed for eukaryotic CYP4 relatives. Although no covalent linkage was detected, mutants displayed marked alterations in substrate/inhibitor affinity, with L86E and I401E mutants having lower Kd values for arachidonic acid and dodecanoic (lauric) acid than WT (wild-type) BM3. All mutations induced positive shifts in haem Fe(III)/Fe(II) potential, with substrate-free I401E (-219 mV) being >170 mV more positive than WT BM3. The elevated potential stimulated FMN-to-haem electron transfer ~2-fold (to 473 s-1) in I401E, and resulted in stabilization of Fe(II)O2 complexes in the I401E and L86E P450s. EPR demonstrated some iron co-ordination by glutamate carboxylate in L86E and F261E mutants, indicating structural plasticity in the haem domains. The Fe(II)O2 complex is EPR-silent, probably resulting from antiferromagnetic coupling between Fe(III) and bound superoxide in a ferric superoxo species. Structural analysis of mutant haem domains revealed modest rearrangements, including altered haem propionate interactions that may underlie the thermodynamic perturbations observed. The mutant flavocytochromes demonstrated WT-like hydroxylation of dodecanoic acid, but regioselectivity was skewed towards omega-3 hydroxydodecanoate formation in F261E and towards omega-1 hydroxydodecanoate production in I401E. Our data point strongly to a likelihood that glutamate-haem linkages are disfavoured in this most catalytically efficient P450, possibly due to the absence of a methylene radical species during catalysis.
KeywordMeSH Terms
55. Chen  HJ, Pan  SC, Shaw  GC,     ( 2009 )

Identification and characterization of a novel intracellular poly(3-hydroxybutyrate) depolymerase from Bacillus megaterium.

Applied and environmental microbiology 75 (16)
PMID : 19561190  :   DOI  :   10.1128/AEM.00621-09     PMC  :   PMC2725475    
Abstract >>
A gene that codes for a novel intracellular poly(3-hydroxybutyrate) (PHB) depolymerase, designated PhaZ1, has been identified in the genome of Bacillus megaterium. A native PHB (nPHB) granule-binding assay showed that purified soluble PhaZ1 had strong affinity for nPHB granules. Turbidimetric analyses revealed that PhaZ1 could rapidly degrade nPHB granules in vitro without the need for protease pretreatment of the granules to remove surface proteins. Notably, almost all the final hydrolytic products produced from the in vitro degradation of nPHB granules by PhaZ1 were 3-hydroxybutyric acid (3HB) monomers. Unexpectedly, PhaZ1 could also hydrolyze denatured semicrystalline PHB, with the generation of 3HB monomers. The disruption of the phaZ1 gene significantly affected intracellular PHB mobilization during the PHB-degrading stage in B. megaterium, as demonstrated by transmission electron microscopy and the measurement of the PHB content. These results indicate that PhaZ1 is functional in intracellular PHB mobilization in vivo. Some of these features, which are in striking contrast with those of other known nPHB granule-degrading PhaZs, may provide an advantage for B. megaterium PhaZ1 in fermentative production of the biotechnologically valuable chiral compound (R)-3HB.
KeywordMeSH Terms
Carboxylic Ester Hydrolases
Gene Expression Regulation, Bacterial
56. Whitehouse  CJ, Bell  SG, Yang  W, Yorke  JA, Blanford  CF, Strong  AJ, Morse  EJ, Bartlam  M, Rao  Z, Wong  LL,     ( 2009 )

A highly active single-mutation variant of P450BM3 (CYP102A1).

Chembiochem : a European journal of chemical biology 10 (10)
PMID : 19492389  :   DOI  :   10.1002/cbic.200900279    
Abstract >>
The power of proline: Bold amino acid substitutions in sensitive protein regions are frequently unproductive, while more subtle mutations can be sufficient to bring about dramatic changes. But introducing proline at the residue next to the sulfur ligand in P450(BM3) (CYP102A1) has the unexpected and desirable effect of enhancing the activity of this fatty acid hydroxylase with a broad range of non-natural substrates, as illustrated by the figure.
KeywordMeSH Terms
57. Setlow  B, Peng  L, Loshon  CA, Li  YQ, Christie  G, Setlow  P,     ( 2009 )

Characterization of the germination of Bacillus megaterium spores lacking enzymes that degrade the spore cortex.

Journal of applied microbiology 107 (1)
PMID : 19302310  :   DOI  :   10.1111/j.1365-2672.2009.04210.x    
Abstract >>
To determine roles of cortex lytic enzymes (CLEs) in Bacillus megaterium spore germination. Genes for B. megaterium CLEs CwlJ and SleB were inactivated and effects of loss of one or both on germination were assessed. Loss of CwlJ or SleB did not prevent completion of germination with agents that activate the spore's germinant receptors, but loss of CwlJ slowed the release of dipicolinic acid (DPA). Loss of both CLEs also did not prevent release of DPA and glutamate during germination with KBr. However, cwlJ sleB spores had decreased viability, and could not complete germination. Loss of CwlJ eliminated spore germination with Ca2+ chelated to DPA (Ca-DPA), but loss of CwlJ and SleB did not affect DPA release in dodecylamine germination. CwlJ and SleB play redundant roles in cortex degradation during B. megaterium spore germination, and CwlJ accelerates DPA release and is essential for Ca-DPA germination. The roles of these CLEs are similar in germination of B. megaterium and Bacillus subtilis spores. These results indicate that redundant roles of CwlJ and SleB in cortex degradation during germination are similar in spores of Bacillus species; consequently, inhibition of these enzymes will prevent germination of Bacillus spores.
KeywordMeSH Terms
58. Shuster  V, Fishman  A,     ( 2009 )

Isolation, cloning and characterization of a tyrosinase with improved activity in organic solvents from Bacillus megaterium.

Journal of molecular microbiology and biotechnology 17 (4)
PMID : 19672047  :   DOI  :   10.1159/000233506    
Abstract >>
A tyrosinase-expressing bacterium was isolated from soil, and extracellular enzymatic activity was induced by the presence of tyrosine and CuSO(4). Amplification of the 16S rDNA genes revealed a high similarity with Bacillus megaterium. The enzyme was over-expressed in Escherichia coli BL21 and purified using an affinity column. The tyrosinase was composed of 297 amino acids and was determined to be a monomer with a relative molecular mass of 31 kDa according to gel filtration. The K(m) values for 3,4-dihydroxy-L-phenylalanine (L-DOPA) and L-tyrosine were 0.35 and 0.075 mM, respectively, and the K(cat)/K(m) values were 28.9 x 10(3) and 32.9 x 10(3) (s(-1) x M(-1)). The maximum activity for both monophenolase and diphenolase was observed at 50 degrees C and pH 7.0. Enzymatic activity was enhanced in the presence of 10-50% water-miscible organic solvents, which included ethanol, methanol, 2-propanol and dimethyl sulfoxide (DMSO). The activity in 30% DMSO was 170% of the activity in water and the enantioselectivity towards L-DOPA decreased by 40%. The residual activity following an incubation period of 17 h in 0-70% methanol was constant. This newly isolated and characterized tyrosinase may have potential applications in organic synthesis due to its high activity and stability at typically denaturing conditions.
KeywordMeSH Terms
59. Batisson  I, Crouzet  O, Besse-Hoggan  P, Sancelme  M, Mangot  JF, Mallet  C, Bohatier  J,     ( 2009 )

Isolation and characterization of mesotrione-degrading Bacillus sp. from soil.

Environmental pollution (Barking, Essex : 1987) 157 (4)
PMID : 19121884  :   DOI  :   10.1016/j.envpol.2008.12.009    
Abstract >>
Dissipation kinetics of mesotrione, a new triketone herbicide, sprayed on soil from Limagne (Puy-de-D?me, France) showed that the soil microflora were able to biotransform it. Bacteria from this soil were cultured in mineral salt solution supplemented with mesotrione as sole source of carbon for the isolation of mesotrione-degrading bacteria. The bacterial community structure of the enrichment cultures was analyzed by temporal temperature gradient gel electrophoresis (TTGE). The TTGE fingerprints revealed that mesotrione had an impact on bacterial community structure only at its highest concentrations and showed mesotrione-sensitive and mesotrione-adapted strains. Two adapted strains, identified as Bacillus sp. and Arthrobacter sp., were isolated by colony hybridization methods. Biodegradation assays showed that only the Bacillus sp. strain was able to completely and rapidly biotransform mesotrione. Among several metabolites formed, 2-amino-4-methylsulfonylbenzoic acid (AMBA) accumulated in the medium. Although sulcotrione has a chemical structure closely resembling that of mesotrione, the isolates were unable to degrade it.
KeywordMeSH Terms
Soil Microbiology
60. Robin  C, Blanche  F, Cauchois  L, Cameron  B, Couder  M, Crouzet  J,     ( 1991 )

Primary structure, expression in Escherichia coli, and properties of S-adenosyl-L-methionine:uroporphyrinogen III methyltransferase from Bacillus megaterium.

Journal of bacteriology 173 (15)
PMID : 1906874  :   DOI  :   10.1128/jb.173.15.4893-4896.1991     PMC  :   PMC208169    
Abstract >>
A Bacillus megaterium DNA fragment encoding S-adenosyl-L-methionine:uroporphyrinogen III methyltransferase (SUMT) activity was subcloned and sequenced. The encoded polypeptide showed more than 43.5% strict homology to Pseudomonas denitrificans SUMT (F. Blanche, L. Debussche, D. Thibaut, J. Crouzet, and B. Cameron, J. Bacteriol. 171:4222-4231, 1989). The B. megaterium polypeptide was overexpressed in Escherichia coli, partially purified, and shown to exhibit, like P. denitrificans SUMT, substrate inhibition at uroporphyrinogen III concentrations above 0.5 microM, suggesting a common regulation for aerobic cobalamin-producing organisms.
KeywordMeSH Terms
Plasmids
61. Fasan  R, Meharenna  YT, Snow  CD, Poulos  TL, Arnold  FH,     ( 2008 )

Evolutionary history of a specialized p450 propane monooxygenase.

Journal of molecular biology 383 (5)
PMID : 18619466  :   DOI  :   10.1016/j.jmb.2008.06.060     PMC  :   PMC2637765    
Abstract >>
The evolutionary pressures that shaped the specificity and catalytic efficiency of enzymes can only be speculated. While directed evolution experiments show that new functions can be acquired under positive selection with few mutations, the role of negative selection in eliminating undesired activities and achieving high specificity remains unclear. Here we examine intermediates along the 'lineage' from a naturally occurring C12-C20 fatty acid hydroxylase (P450BM3) to a laboratory-evolved P450 propane monooxygenase (P450PMO) having 20 heme domain substitutions compared to P450BM3. Biochemical, crystallographic, and computational analyses show that a minimal perturbation of the P450BM3 fold and substrate-binding pocket accompanies a significant broadening of enzyme substrate range and the emergence of propane activity. In contrast, refinement of the enzyme catalytic efficiency for propane oxidation (approximately 9000-fold increase in kcat/Km) involves profound reshaping and partitioning of the substrate access pathway. Remodeling of the substrate-recognition mechanisms ultimately results in remarkable narrowing of the substrate profile around propane and enables the acquisition of a basal iodomethane dehalogenase activity as yet unknown in natural alkane monooxygenases. A highly destabilizing L188P substitution in a region of the enzyme that undergoes a large conformational change during catalysis plays an important role in adaptation to the gaseous alkane. This work demonstrates that positive selection alone is sufficient to completely respecialize the cytochrome P450 for function on a nonnative substrate.
KeywordMeSH Terms
Evolution, Molecular
62. Schubert  HL, Rose  RS, Leech  HK, Brindley  AA, Hill  CP, Rigby  SE, Warren  MJ,     ( 2008 )

Structure and function of SirC from Bacillus megaterium: a metal-binding precorrin-2 dehydrogenase.

The Biochemical journal 415 (2)
PMID : 18588505  :   DOI  :   10.1042/BJ20080785     PMC  :   PMC2857972    
Abstract >>
In Bacillus megaterium, the synthesis of vitamin B(12) (cobalamin) and sirohaem diverges at sirohydrochlorin along the branched modified tetrapyrrole biosynthetic pathway. This key intermediate is made by the action of SirC, a precorrin-2 dehydrogenase that requires NAD(+) as a cofactor. The structure of SirC has now been solved by X-ray crystallography to 2.8 A (1 A = 0.1 nm) resolution. The protein is shown to consist of three domains and has a similar topology to the multifunctional sirohaem synthases Met8p and the N-terminal region of CysG, both of which catalyse not only the dehydrogenation of precorrin-2 but also the ferrochelation of sirohydrochlorin to give sirohaem. Guided by the structure, in the present study a number of active-site residues within SirC were investigated by site-directed mutagenesis. No active-site general base was identified, although surprisingly some of the resulting protein variants were found to have significantly enhanced catalytic activity. Unexpectedly, SirC was found to bind metal ions such as cobalt and copper, and to bind them in an identical fashion with that observed in Met8p. It is suggested that SirC may have evolved from a Met8p-like protein by loss of its chelatase activity. It is proposed that the ability of SirC to act as a single monofunctional enzyme, in conjunction with an independent chelatase, may provide greater control over the intermediate at this branchpoint in the synthesis of sirohaem and cobalamin.
KeywordMeSH Terms
63. Lisurek  M, Simgen  B, Antes  I, Bernhardt  R,     ( 2008 )

Theoretical and experimental evaluation of a CYP106A2 low homology model and production of mutants with changed activity and selectivity of hydroxylation.

Chembiochem : a European journal of chemical biology 9 (9)
PMID : 18481342  :   DOI  :   10.1002/cbic.200700670    
Abstract >>
Steroids are important pharmaceutically active compounds. In contrast to the liver drug-metabolising cytochrome P450s, which metabolise a variety of substrates, steroid hydroxylases generally display a rather narrow substrate specificity. It is therefore a challenging goal to change their regio- and stereoselectivity. CYP106A2 is one of only a few bacterial steroid hydroxylases and hydroxylates 3-oxo-Delta4-steroids mainly in 15beta-position. In order to gain insights into the structure and function of this enzyme, whose crystal structure is unknown, a homology model has been created. The substrate progesterone was then docked into the active site to predict which residues might affect substrate binding. The model was substantiated by using a combination of theoretical and experimental investigations. First, numerous computational structure evaluation tools assessed the plausibility of its protein geometry and its quality. Second, the model explains many key properties of common cytochrome P450s. Third, two sets of mutants have been heterologously expressed, and the influence of the mutations on the catalytic activity towards deoxycorticosterone and progesterone has been studied experimentally: the first set comprises six mutations located in the structurally variable regions of this enzyme that are very difficult to predict by cytochrome P450 modelling (K27R, I86T, E90V, I71T, D185G and I215T). For these positions, no participation in the active-site formation was predicted, or could be experimentally demonstrated. The second set comprises five mutants in substrate recognition site 6 (S394I, A395L, T396R, G397P and Q398S). For these residues, participation in active-site formation and an influence on substrate binding was predicted by docking. These mutants are based on an alignment with human CYP11B1, and in fact most of these mutants altered the active-site structure and the hydroxylation activity of CYP106A2 dramatically.
KeywordMeSH Terms
Models, Molecular
Mutation
Sequence Homology, Amino Acid
64. Bao  F, Gong  L, Shao  W,     ( 2008 )

Cloning, sequencing and analysis of dnaK -dnaJ gene cluster of Bacillus megaterium.

Journal of basic microbiology 48 (6)
PMID : 18785662  :   DOI  :   10.1002/jobm.200800116    
Abstract >>
The DNA fragment of heat shock genes (hrcA-grpE-dnaK-dnaJ) containing complete hrcA-grpE-dnaK operon and the transcription unit of dnaJ was cloned, sequensed and analyzed from Bacillus megaterium RF5. The sequence of hrcA, grpE and dnaJ were first time reported, and their coding products exibit 60%, 63% and 81% of identities to the homologs of B. subtilis. A sigmaA-type promoter of Gram-positive bacteria (PA1) and a terminator were located upstream of the hrcA and downstream of dnaK, and a Controlling inverted repeat of chaperone expression element (CIRCE) was identified between PA1 and hrcA. Another sigmaA-type promoter (PA2) and a terminator were found upstream and downstream of dnaJ, indicating B. megaterium has a transcription unit containing a single gene dnaJ. The structure of dnaJ transcription unit is more similar to that of Listeria monocytogenes than other species of Bacillus. A partial protein-based phylogenetic tree, derived from Gram-positive bacteria using HrcA sequence, indicated a closer phylogenetic relationship between B. megaterium and Geobacillus species than other two Bacillus species.
KeywordMeSH Terms
65. Girvan  HM, Toogood  HS, Littleford  RE, Seward  HE, Smith  WE, Ekanem  IS, Leys  D, Cheesman  MR, Munro  AW,     ( 2009 )

Novel haem co-ordination variants of flavocytochrome P450BM3.

The Biochemical journal 417 (1)
PMID : 18721129  :   DOI  :   10.1042/BJ20081133    
Abstract >>
Bacillus megaterium flavocytochrome P450 BM3 is a catalytically self-sufficient fatty acid hydroxylase formed by fusion of soluble NADPH-cytochrome P450 reductase and P450 domains. Selected mutations at residue 264 in the haem (P450) domain of the enzyme lead to novel amino acid sixth (distal) co-ordination ligands to the haem iron. The catalytic, spectroscopic and thermodynamic properties of the A264M, A264Q and A264C variants were determined in both the intact flavocytochromes and haem domains of P450 BM3. Crystal structures of the mutant haem domains demonstrate axial ligation of P450 haem iron by methionine and glutamine ligands trans to the cysteine thiolate, creating novel haem iron ligand sets in the A264M/Q variants. In contrast, the crystal structure of the A264C variant reveals no direct interaction between the introduced cysteine side chain and the haem, although EPR data indicate Cys(264) interactions with haem iron in solution. The A264M haem potential is elevated by comparison with wild-type haem domain, and substrate binding to the A264Q haem domain results in a approximately 360 mV increase in potential. All mutant haem domains occupy the conformation adopted by the substrate-bound form of wild-type BM3, despite the absence of added substrate. The A264M mutant (which has higher dodecanoate affinity than wild-type BM3) co-purifies with a structurally resolved lipid. These data demonstrate that a single mutation at Ala(264) is enough to perturb the conformational equilibrium between substrate-free and substrate-bound P450 BM3, and provide firm structural and spectroscopic data for novel haem iron ligand sets unprecedented in nature.
KeywordMeSH Terms
Mutation
66. Kiss  A, Balikó  G, Csorba  A, Chuluunbaatar  T, Medzihradszky  KF, Alföldi  L,     ( 2008 )

Cloning and characterization of the DNA region responsible for Megacin A-216 production in Bacillus megaterium 216.

Journal of bacteriology 190 (19)
PMID : 18689470  :   DOI  :   10.1128/JB.00557-08     PMC  :   PMC2565993    
Abstract >>
Upon induction, Bacillus megaterium 216 produces the bacteriocin megacin A-216, which leads to lysis of the producer cell and kills B. megaterium and a few other bacterial species. The DNA region responsible for megacinogeny was cloned in B. megaterium. The nucleotide sequence of a 5,494-bp-long subfragment was determined, and the function of the genes on this fragment was studied by generating deletions and analyzing their effects on MegA phenotypes. An open reading frame (ORF) encoding a 293-amino-acid protein was identified as the gene (megA) coding for megacin A-216. BLAST searches detected sequence similarity between megacin A-216 and proteins with phospholipase A2 activity. Purified biologically active megacin A-216 preparations contained three proteins. Mass spectrometry analysis showed that the largest protein is the full-length translation product of the megA gene, whereas the two shorter proteins are fragments of the long protein created by cleavage between Gln-185 and Val-186. The molecular masses of the three polypeptides are 32,855, 21,018, and 11,855 Da, respectively. Comparison of different megacin preparations suggests that the intact chain as well as the two combined fragments can form biologically active megacin. An ORF located next to the megA gene and encoding a 91-amino-acid protein was shown to be responsible for the relative immunity displayed by the producer strain against megacin A-216. Besides the megA gene, at least two other genes, including a gene encoding a 188-amino-acid protein sharing high sequence similarity with RNA polymerase sigma factors, were shown to be required for induction of megacin A-216 expression.
KeywordMeSH Terms
67. Haines  DC, Chen  B, Tomchick  DR, Bondlela  M, Hegde  A, Machius  M, Peterson  JA,     ( 2008 )

Crystal structure of inhibitor-bound P450BM-3 reveals open conformation of substrate access channel.

Biochemistry 47 (12)
PMID : 18298086  :   DOI  :   10.1021/bi7023964    
Abstract >>
P450BM-3 is an extensively studied P450 cytochrome that is naturally fused to a cytochrome P450 reductase domain. Crystal structures of the heme domain of this enzyme have previously generated many insights into features of P450 structure, substrate binding specificity, and conformational changes that occur on substrate binding. Although many P450s are inhibited by imidazole, this compound does not effectively inhibit P450BM-3. Omega-imidazolyl fatty acids have previously been found to be weak inhibitors of the enzyme and show some unusual cooperativity with the substrate lauric acid. We set out to improve the properties of these inhibitors by attaching the omega-imidazolyl fatty acid to the nitrogen of an amino acid group, a tactic that we used previously to increase the potency of substrates. The resulting inhibitors were significantly more potent than their parent compounds lacking the amino acid group. A crystal structure of one of the new inhibitors bound to the heme domain of P450BM-3 reveals that the mode of interaction of the amino acid group with the enzyme is different from that previously observed for acyl amino acid substrates. Further, required movements of residues in the active site to accommodate the imidazole group provide an explanation for the low affinity of imidazole itself. Finally, the previously observed cooperativity with lauric acid is explained by a surprisingly open substrate-access channel lined with hydrophobic residues that could potentially accommodate lauric acid in addition to the inhibitor itself.
KeywordMeSH Terms
Cytochrome P-450 Enzyme Inhibitors
68. Bao  Y, Higgins  L, Zhang  P, Chan  SH, Laget  S, Sweeney  S, Lunnen  K, Xu  SY,     ( 2008 )

Expression and purification of BmrI restriction endonuclease and its N-terminal cleavage domain variants.

Protein expression and purification 58 (1)
PMID : 18164625  :   DOI  :   10.1016/j.pep.2007.11.002     PMC  :   PMC2275207    
Abstract >>
BmrI (ACTGGG N5/N4) is one of the few metal-independent restriction endonucleases (REases) found in bacteria. The BmrI restriction-modification system was cloned by the methylase selection method, inverse PCR, and PCR. BmrI REase shows significant amino acid sequence identity to BfiI and a putative endonuclease MspBNCORF3798 from the sequenced Mesorhizobium sp. BNC1 genome. The EDTA-resistant BmrI REase was successfully over-expressed in a pre-modified E. coli strain from pET21a or pBAC-expIQ vectors. The recombinant BmrI REase shows strong promiscuous activity (star activity) in NEB buffers 1, 4, and an EDTA buffer. Star activity was diminished in buffers with 100-150 mM NaCl and 10 mM MgCl(2). His-tagged BmrI192, the N-terminal cleavage domain of BmrI, was expressed in E. coli and purified from inclusion bodies. The refolded BmrI192 protein possesses non-specific endonuclease activity. BmrI192 variants with a single Ser to Cys substitution (S76C or S90C) and BmrI200 (T200C) with a single Cys at the C-terminal end were also constructed and purified. BmrI200 digests both single-strand (ss) and double-strand (ds) DNA and the nuclease activity on ss DNA is at least 5-fold higher than that on ds DNA. The Cys-containing BmrI192 and BmrI200 nuclease variants may be useful for coupling to other DNA binding elements such as synthetic zinc fingers, thio-containing locked nucleic acids (LNA) or peptide nucleic acids (PNA).
KeywordMeSH Terms
Deoxyribonucleases, Type II Site-Specific
69. Hegde  A, Haines  DC, Bondlela  M, Chen  B, Schaffer  N, Tomchick  DR, Machius  M, Nguyen  H, Chowdhary  PK, Stewart  L, Lopez  C, Peterson  JA,     ( 2007 )

Interactions of substrates at the surface of P450s can greatly enhance substrate potency.

Biochemistry 46 (49)
PMID : 18004886  :   DOI  :   10.1021/bi701667m    
Abstract >>
Cytochrome P450s are a superfamily of heme containing enzymes that use molecular oxygen and electrons from reduced nicotinamide cofactors to monooxygenate organic substrates. The fatty acid hydroxylase P450BM-3 has been particularly widely studied due to its stability, high activity, similarity to mammalian P450s, and presence of a cytochrome P450 reductase domain that allows the enzyme to directly receive electrons from NADPH without a requirement for additional redox proteins. We previously characterized the substrate N-palmitoylglycine, which found extensive use in studies of P450BM-3 due to its high affinity, high turnover number, and increased solubility as compared to fatty acid substrates. Here, we report that even higher affinity substrates can be designed by acylation of other amino acids, resulting in P450BM-3 substrates with dissociation constants below 100 nM. N-Palmitoyl-l-leucine and N-palmitoyl-l-methionine were found to have the highest affinity, with dissociation constants of less than 8 nM and turnover numbers similar to palmitic acid and N-palmitoylglycine. The interactions of the amino acid side chains with a hydrophobic pocket near R47, as revealed by our crystal structure determination of N-palmitoyl-l-methionine bound to the heme domain of P450BM-3, appears to be responsible for increasing the affinity of substrates. The side chain of R47, previously shown to be important in interactions with negatively charged substrates, does not interact strongly with N-palmitoyl-l-methionine and is found positioned at the enzyme-solvent interface. These are the tightest binding substrates for P450BM-3 reported to date, and the affinity likely approaches the maximum attainable affinity for the binding of substrates of this size to P450BM-3.
KeywordMeSH Terms
70. Chowdhary  PK, Keshavan  N, Nguyen  HQ, Peterson  JA, González  JE, Haines  DC,     ( 2007 )

Bacillus megaterium CYP102A1 oxidation of acyl homoserine lactones and acyl homoserines.

Biochemistry 46 (50)
PMID : 18020460  :   DOI  :   10.1021/bi701945j    
Abstract >>
Quorum sensing, the ability of bacteria to sense their own population density through the synthesis and detection of small molecule signals, has received a great deal of attention in recent years. Acyl homoserine lactones (AHLs) are a major class of quorum sensing signaling molecules. In nature, some bacteria that do not synthesize AHLs themselves have developed the ability to degrade these compounds by cleaving the amide bond or the lactone ring. By inactivating this signal used by competing bacteria, the degrading microbe is believed to gain a competitive advantage. In this work we report that CYP102A1, a widely studied cytochrome P450 from Bacillus megaterium, is capable of very efficient oxidation of AHLs and their lactonolysis products acyl homoserines. The previously known substrates for this enzyme, fatty acids, can also be formed in nature by hydrolysis of the amide of AHLs, so CYP102A1 is capable of inactivating the active parent compound and the products of both known pathways for AHL inactivation observed in nature. AHL oxidation primarily takes place at the omega-1, omega-2, and omega-3 carbons of the acyl chain, similar to this enzyme's well-known activity on fatty acids. Acyl homoserines and their lactones are better substrates for CYP102A1 than fatty acids. Bioassay of the quorum sensing activity of oxidation products reveals that the subterminally hydroxylated AHLs exhibit quorum sensing activity, but are 18-fold less active than the parent compound. In vivo, B. megaterium inactivates AHLs by a CYP102A1 dependent mechanism that must involve additional components that further sequester or metabolize the products, eliminating their quorum sensing activity. Cytochrome P450 oxidation of AHLs represents an important new mechanism of quorum quenching.
KeywordMeSH Terms
71. 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.

Journal of food protection 70 (10)
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.
KeywordMeSH Terms
Bacterial Typing Techniques
Food-Processing Industry
Phylogeny
72. Bridwell-Rabb  J, Zhong  A, Sun  HG, Drennan  CL, Liu  HW,     ( 2017 )

A B12-dependent radical SAM enzyme involved in oxetanocin A biosynthesis.

Nature 544 (7650)
PMID : 28346939  :   DOI  :   10.1038/nature21689     PMC  :   PMC5398914    
Abstract >>
Oxetanocin A (OXT-A) is a potent antitumour, antiviral and antibacterial compound. Biosynthesis of OXT-A has been linked to a plasmid-borne Bacillus megaterium gene cluster that contains four genes: oxsA, oxsB, oxrA and oxrB. Here we show that both the oxsA and oxsB genes are required for the production of OXT-A. Biochemical analysis of the encoded proteins, a cobalamin (Cbl)-dependent S-adenosylmethionine (AdoMet) radical enzyme, OxsB, and an HD-domain phosphohydrolase, OxsA, reveals that OXT-A is derived from a 2'-deoxyadenosine phosphate in an OxsB-catalysed ring contraction reaction initiated by hydrogen atom abstraction from C2'. Hence, OxsB represents the first biochemically characterized non-methylating Cbl-dependent AdoMet radical enzyme. X-ray analysis of OxsB reveals the fold of a Cbl-dependent AdoMet radical enzyme, a family of enzymes with an estimated 7,000 members. Overall, this work provides a framework for understanding the interplay of AdoMet and Cbl cofactors and expands the catalytic repertoire of Cbl-dependent AdoMet radical enzymes.
KeywordMeSH Terms
Biocatalysis
73. Bridwell-Rabb  J, Kang  G, Zhong  A, Liu  HW, Drennan  CL,     ( 2016 )

An HD domain phosphohydrolase active site tailored for oxetanocin-A biosynthesis.

Proceedings of the National Academy of Sciences of the United States of America 113 (48)
PMID : 27849620  :   DOI  :   10.1073/pnas.1613610113     PMC  :   PMC5137760    
Abstract >>
HD domain phosphohydrolase enzymes are characterized by a conserved set of histidine and aspartate residues that coordinate an active site metallocenter. Despite the important roles these enzymes play in nucleotide metabolism and signal transduction, few have been both biochemically and structurally characterized. Here, we present X-ray crystal structures and biochemical characterization of the Bacillus megaterium HD domain phosphohydrolase OxsA, involved in the biosynthesis of the antitumor, antiviral, and antibacterial compound oxetanocin-A. These studies reveal a previously uncharacterized reaction for this family; OxsA catalyzes the conversion of a triphosphorylated compound into a nucleoside, releasing one molecule of inorganic phosphate at a time. Remarkably, this functionality is a result of the OxsA active site, which based on structural and kinetic analyses has been tailored to bind the small, four-membered ring of oxetanocin-A over larger substrates. Furthermore, our OxsA structures show an active site that switches from a dinuclear to a mononuclear metal center as phosphates are eliminated from substrate.
KeywordMeSH Terms
X-ray crystallography
metalloenzymes
natural products
nucleosides
phosphohydrolase
Protein Conformation
74. Deri  B, Kanteev  M, Goldfeder  M, Lecina  D, Guallar  V, Adir  N, Fishman  A,     ( 2016 )

The unravelling of the complex pattern of tyrosinase inhibition.

Scientific reports 6 (N/A)
PMID : 27725765  :   DOI  :   10.1038/srep34993     PMC  :   PMC5057104    
Abstract >>
Tyrosinases are responsible for melanin formation in all life domains. Tyrosinase inhibitors are used for the prevention of severe skin diseases, in skin-whitening creams and to avoid fruit browning, however continued use of many such inhibitors is considered unsafe. In this study we provide conclusive evidence of the inhibition mechanism of two well studied tyrosinase inhibitors, KA (kojic acid) and HQ (hydroquinone), which are extensively used in hyperpigmentation treatment. KA is reported in the literature with contradicting inhibition mechanisms, while HQ is described as both a tyrosinase inhibitor and a substrate. By visualization of KA and HQ in the active site of TyrBm crystals, together with molecular modeling, binding constant analysis and kinetic experiments, we have elucidated their mechanisms of inhibition, which was ambiguous for both inhibitors. We confirm that while KA acts as a mixed inhibitor, HQ can act both as a TyrBm substrate and as an inhibitor.
KeywordMeSH Terms
75. van Oosterwijk  N, Willies  S, Hekelaar  J, Terwisscha van Scheltinga  AC, Turner  NJ, Dijkstra  BW,     ( 2016 )

Structural Basis of the Substrate Range and Enantioselectivity of Two (S)-Selective �s-Transaminases.

Biochemistry 55 (31)
PMID : 27428867  :   DOI  :   10.1021/acs.biochem.6b00370    
Abstract >>
�s-Transaminases are enzymes that can introduce an amino group in industrially interesting compounds. We determined crystal structures of two (S)-selective �s-transaminases, one from Arthrobacter sp. (Ars-�sTA) and one from Bacillus megaterium (BM-�sTA), which have 95% identical sequences but somewhat different activity profiles. Substrate profiling measurements using a range of (R)- and (S)-substrates showed that both enzymes have a preference for substrates with large, flat cyclic side groups, for which the activity of BM-�sTA is generally somewhat higher. BM-�sTA has a preference for (S)-3,3-dimethyl-2-butylamine significantly stronger than that of Ars-�sTA, as well as a weaker enantiopreference for 1-cyclopropylethylamine. The crystal structures showed that, as expected for (S)-selective transaminases, both enzymes have the typical transaminase type I fold and have spacious active sites to accommodate largish substrates. A structure of BM-�sTA with bound (R)-�\-methylbenzylamine explains the enzymes' preference for (S)-substrates. Site-directed mutagenesis experiments revealed that the presence of a tyrosine, instead of a cysteine, at position 60 increases the relative activities on several small substrates. A structure of Ars-�sTA with bound l-Ala revealed that the Arg442 side chain has been repositioned to bind the l-Ala carboxylate. Compared to the arginine switch residue in other transaminases, Arg442 is shifted by six residues in the amino acid sequence, which appears to be a consequence of extra loops near the active site that narrow the entrance to the active site.
KeywordMeSH Terms
76. Matsui  K, Yoshinami  S, Narita  M, Chien  MF, Phung  le T, Silver  S, Endo  G,     ( 2016 )

Mercury resistance transposons in Bacilli strains from different geographical regions.

FEMS microbiology letters 363 (5)
PMID : 26802071  :   DOI  :   10.1093/femsle/fnw013    
Abstract >>
A total of 65 spore-forming mercury-resistant bacteria were isolated from natural environments worldwide in order to understand the acquisition of additional genes by and dissemination of mercury resistance transposons across related Bacilli genera by horizontal gene movement. PCR amplification using a single primer complementary to the inverted repeat sequence of TnMERI1-like transposons showed that 12 of 65 isolates had a transposon-like structure. There were four types of amplified fragments: Tn5084, Tn5085, Tn(d)MER3 (a newly identified deleted transposon-like fragment) and Tn6294 (a newly identified transposon). Tn(d)MER3 is a 3.5-kb sequence that carries a merRETPA operon with no merB or transposase genes. It is related to the mer operon of Bacillus licheniformis strain FA6-12 from Russia. DNA homology analysis shows that Tn6294 is an 8.5-kb sequence that is possibly derived from Tn(d)MER3 by integration of a TnMERI1-type transposase and resolvase genes and in addition the merR2 and merB1 genes. Bacteria harboring Tn6294 exhibited broad-spectrum mercury resistance to organomercurial compounds, although Tn6294 had only merB1 and did not have the merB2 and merB3 sequences for organomercurial lyases found in Tn5084 of B. cereus strain RC607. Strains with Tn6294 encode mercuric reductase (MerA) of less than 600 amino acids in length with a single N-terminal mercury-binding domain, whereas MerA encoded by strains MB1 and RC607 has two tandem domains. Thus, Tn(d)MER3 and Tn6294 are shorter prototypes for TnMERI1-like transposons. Identification of Tn6294 in Bacillus sp. from Taiwan and in Paenibacillus sp. from Antarctica indicates the wide horizontal dissemination of TnMERI1-like transposons across bacterial species and geographical barriers.
KeywordMeSH Terms
Bacilli
broad-spectrum mercury resistance
horizontal gene transfer
mer operon
worldwide gene dissemination
77. Carles  L, Besse-Hoggan  P, Joly  M, Vigouroux  A, Moréra  S, Batisson  I,     ( 2016 )

Functional and structural characterization of two Bacillus megaterium nitroreductases biotransforming the herbicide mesotrione.

The Biochemical journal 473 (10)
PMID : 27005432  :   DOI  :   10.1042/BJ20151366    
Abstract >>
Mesotrione is a selective herbicide belonging to the triketone family, commonly used on maize cultures since 2003. A mesotrione-transforming Bacillus megaterium Mes11 strain isolated from an agricultural soil was used as a model to identify the key enzymes initiating the biotransformation of this herbicide. Two enzymes (called NfrA1 and NfrA2/YcnD) were identified, and functionally and structurally characterized. Both belong to the NfsA FRP family of the nitro-FMN reductase superfamily (type I oxygen-insensitive nitroreductase) and show optimal pH and temperature of 6-6.5 and 23-25�XC, respectively. Both undergo a Ping Pong Bi Bi mechanism, with NADPH and NADPH/NADH as cofactors for NfrA1 and NfrA2/YcnD, respectively. It is interesting that both can also reduce various nitro compounds including pesticides, antibiotics, one prodrug and 4-methylsulfonyl-2-nitrobenzoic acid, one of the mesotrione metabolites retrieved from the environment. The present study constitutes the first identification of mesotrione-transforming enzymes. These enzymes (or their corresponding genes) could be used as biomarkers to predict the capacity of ecosystems to transform mesotrione and assess their contamination by both the parent molecule and/or the metabolites.
KeywordMeSH Terms
Bacillus megaterium
biotransformation
mesotrione herbicide
nitroreductase enzyme
78. Wahba  HM, Lecoq  L, Stevenson  M, Mansour  A, Cappadocia  L, Lafrance-Vanasse  J, Wilkinson  KJ, Sygusch  J, Wilcox  DE, Omichinski  JG,     ( 2016 )

Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity.

Biochemistry 55 (7)
PMID : 26820485  :   DOI  :   10.1021/acs.biochem.5b01298    
Abstract >>
In bacterial resistance to mercury, the organomercurial lyase (MerB) plays a key role in the detoxification pathway through its ability to cleave Hg-carbon bonds. Two cysteines (C96 and C159; Escherichia coli MerB numbering) and an aspartic acid (D99) have been identified as the key catalytic residues, and these three residues are conserved in all but four known MerB variants, where the aspartic acid is replaced with a serine. To understand the role of the active site serine, we characterized the structure and metal binding properties of an E. coli MerB mutant with a serine substituted for D99 (MerB D99S) as well as one of the native MerB variants containing a serine residue in the active site (Bacillus megaterium MerB2). Surprisingly, the MerB D99S protein copurified with a bound metal that was determined to be Cu(II) from UV-vis absorption, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and electron paramagnetic resonance studies. X-ray structural studies revealed that the Cu(II) is bound to the active site cysteine residues of MerB D99S, but that it is displaced following the addition of either an organomercurial substrate or an ionic mercury product. In contrast, the B. megaterium MerB2 protein does not copurify with copper, but the structure of the B. megaterium MerB2-Hg complex is highly similar to the structure of the MerB D99S-Hg complexes. These results demonstrate that the active site aspartic acid is crucial for both the enzymatic activity and metal binding specificity of MerB proteins and suggest a possible functional relationship between MerB and its only known structural homologue, the copper-binding protein NosL.
KeywordMeSH Terms
Models, Molecular
79. Ruettinger  RT, Wen  LP, Fulco  AJ,     ( 1989 )

Coding nucleotide, 5' regulatory, and deduced amino acid sequences of P-450BM-3, a single peptide cytochrome P-450:NADPH-P-450 reductase from Bacillus megaterium.

The Journal of biological chemistry 264 (19)
PMID : 2544578  :  
Abstract >>
Cytochrome P-450BM-3 (P-450BM-3) from Bacillus megaterium incorporates both a P-450 and an NADPH:P-450 reductase in proteolytically separable domains of a single, 119-kDa polypeptide and functions as a fatty acid monooxygenase independently of any other protein. A 5-kilobase DNA fragment which contains the gene encoding P-450BM-3 was sequenced. A single continuous open reading frame starting at nucleotide 1541 of the 5-kilobase fragment correctly predicted the previously determined NH2-terminal protein sequences of the trypsin-generated P-450 and reductase domains and, in toto, predicted a mature polypeptide of 1,048-amino acid residues with Mr = 117,641. The trypsin site was found at arginine residue 471. The P-450 domain is most similar (about 25%) to the fatty acid omega-hydroxylases of P-450 family IV, while the reductase domain exhibits some 33% sequence similarity with the NADPH:P-450 reductases of mammalian liver. Both the P-450 and reductase domains of P-450BM-3 define new gene families but contain highly conserved segments which display as much as 50% sequence similarity with P-450s and reductases of eukaryotic origin. The mRNA for P-450BM-3 was found by S1 mapping to be 3,339 +/- 10 nucleotides in length. In the accompanying paper, two regions in the 1.5 kilobases 5' to the P-450BM-3 coding region have been implicated in the regulation of P-450BM-3 gene expression.
KeywordMeSH Terms
Bacterial Proteins
Bacterial Proteins
80. Ruettinger  RT, Wen  LP, Fulco  AJ,     ( 1989 )

Coding nucleotide, 5' regulatory, and deduced amino acid sequences of P-450BM-3, a single peptide cytochrome P-450:NADPH-P-450 reductase from Bacillus megaterium.

The Journal of biological chemistry 264 (19)
PMID : 2544578  :  
Abstract >>
Cytochrome P-450BM-3 (P-450BM-3) from Bacillus megaterium incorporates both a P-450 and an NADPH:P-450 reductase in proteolytically separable domains of a single, 119-kDa polypeptide and functions as a fatty acid monooxygenase independently of any other protein. A 5-kilobase DNA fragment which contains the gene encoding P-450BM-3 was sequenced. A single continuous open reading frame starting at nucleotide 1541 of the 5-kilobase fragment correctly predicted the previously determined NH2-terminal protein sequences of the trypsin-generated P-450 and reductase domains and, in toto, predicted a mature polypeptide of 1,048-amino acid residues with Mr = 117,641. The trypsin site was found at arginine residue 471. The P-450 domain is most similar (about 25%) to the fatty acid omega-hydroxylases of P-450 family IV, while the reductase domain exhibits some 33% sequence similarity with the NADPH:P-450 reductases of mammalian liver. Both the P-450 and reductase domains of P-450BM-3 define new gene families but contain highly conserved segments which display as much as 50% sequence similarity with P-450s and reductases of eukaryotic origin. The mRNA for P-450BM-3 was found by S1 mapping to be 3,339 +/- 10 nucleotides in length. In the accompanying paper, two regions in the 1.5 kilobases 5' to the P-450BM-3 coding region have been implicated in the regulation of P-450BM-3 gene expression.
KeywordMeSH Terms
Bacterial Proteins
Bacterial Proteins
81. Chang  CC, Lin  LY, Zou  XW, Huang  CC, Chan  NL,     ( 2015 )

Structural basis of the mercury(II)-mediated conformational switching of the dual-function transcriptional regulator MerR.

Nucleic acids research 43 (15)
PMID : 26150423  :   DOI  :   10.1093/nar/gkv681     PMC  :   PMC4551924    
Abstract >>
The mer operon confers bacterial resistance to inorganic mercury (Hg(2+)) and organomercurials by encoding proteins involved in sensing, transport and detoxification of these cytotoxic agents. Expression of the mer operon is under tight control by the dual-function transcriptional regulator MerR. The metal-free, apo MerR binds to the mer operator/promoter region as a repressor to block transcription initiation, but is converted into an activator upon Hg(2+)-binding. To understand how MerR interacts with Hg(2+) and how Hg(2+)-binding modulates MerR function, we report here the crystal structures of apo and Hg(2+)-bound MerR from Bacillus megaterium, corresponding respectively to the repressor and activator conformation of MerR. To our knowledge, the apo-MerR structure represents the first visualization of a MerR family member in its intact and inducer-free form. And the Hg(2+)-MerR structure offers the first view of a triligated Hg(2+)-thiolate center in a metalloprotein, confirming that MerR binds Hg(2+) via trigonal planar coordination geometry. Structural comparison revealed the conformational transition of MerR is coupled to the assembly/disassembly of a buried Hg(2+) binding site, thereby providing a structural basis for the Hg(2+)-mediated functional switching of MerR. The pronounced Hg(2+)-induced repositioning of the MerR DNA-binding domains suggests a plausible mechanism for the transcriptional regulation of the mer operon.
KeywordMeSH Terms
82. Goldfeder  M, Kanteev  M, Isaschar-Ovdat  S, Adir  N, Fishman  A,     ( 2014 )

Determination of tyrosinase substrate-binding modes reveals mechanistic differences between type-3 copper proteins.

Nature communications 5 (N/A)
PMID : 25074014  :   DOI  :   10.1038/ncomms5505    
Abstract >>
Tyrosinase is responsible for the two initial enzymatic steps in the conversion of tyrosine to melanin. Many tyrosinase mutations are the leading cause of albinism in humans, and it is a prominent biotechnology and pharmaceutical industry target. Here we present crystal structures that show that both monophenol hydroxylation and diphenol oxidation occur at the same site. It is suggested that concurrent presence of a phenylalanine above the active site and a restricting thioether bond on the histidine coordinating CuA prevent hydroxylation of monophenols by catechol oxidases. Furthermore, a conserved water molecule activated by E195 and N205 is proposed to mediate deprotonation of the monophenol at the active site. Overall, the structures reveal precise steps in the enzymatic catalytic cycle as well as differences between tyrosinases and other type-3 copper enzymes.
KeywordMeSH Terms
Models, Molecular
83. Kong  XD, Yuan  S, Li  L, Chen  S, Xu  JH, Zhou  J,     ( 2014 )

Engineering of an epoxide hydrolase for efficient bioresolution of bulky pharmaco substrates.

Proceedings of the National Academy of Sciences of the United States of America 111 (44)
PMID : 25331869  :   DOI  :   10.1073/pnas.1404915111     PMC  :   PMC4226085    
Abstract >>
Optically pure epoxides are essential chiral precursors for the production of (S)-propranolol, (S)-alprenolol, and other �]-adrenergic receptor blocking drugs. Although the enzymatic production of these bulky epoxides has proven difficult, here we report a method to effectively improve the activity of BmEH, an epoxide hydrolase from Bacillus megaterium ECU1001 toward �\-naphthyl glycidyl ether, the precursor of (S)-propranolol, by eliminating the steric hindrance near the potential product-release site. Using X-ray crystallography, mass spectrum, and molecular dynamics calculations, we have identified an active tunnel for substrate access and product release of this enzyme. The crystal structures revealed that there is an independent product-release site in BmEH that was not included in other reported epoxide hydrolase structures. By alanine scanning, two mutants, F128A and M145A, targeted to expand the potential product-release site displayed 42 and 25 times higher activities toward �\-naphthyl glycidyl ether than the wild-type enzyme, respectively. These results show great promise for structure-based rational design in improving the catalytic efficiency of industrial enzymes for bulky substrates.
KeywordMeSH Terms
X-ray crystallography
bulky substrate
epoxide hydrolase
product release
protein engineering
84. Brusilow  WS, Scarpetta  MA, Hawthorne  CA, Clark  WP,     ( 1989 )

Organization and sequence of the genes coding for the proton-translocating ATPase of Bacillus megaterium.

The Journal of biological chemistry 264 (3)
PMID : 2521483  :  
Abstract >>
We have cloned and sequenced the genes for the subunits of the proton-translocating ATP synthase of Bacillus megaterium QM B1551. The arrangement of the genes is identical to the arrangement of the same genes (the unc operon) in Escherichia coli. The genes for the Fo subunits immediately precede the genes for the F1 subunits and are themselves preceded by an open reading frame which codes for a protein similar to the E. coli i protein. In contrast to the E. coli ATPase genes, the transcript for these ATPase genes does not include this open reading frame.
KeywordMeSH Terms
85. 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.

Genome announcements 3 (2)
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.
KeywordMeSH Terms
86. Azim  N, Deery  E, Warren  MJ, Wolfenden  BA, Erskine  P, Cooper  JB, Coker  A, Wood  SP, Akhtar  M,     ( 2014 )

Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution.

Acta crystallographica. Section D, Biological crystallography 70 (Pt 3)
PMID : 24598743  :   DOI  :   10.1107/S139900471303294X     PMC  :   PMC3949521    
Abstract >>
The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging �\-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form.
KeywordMeSH Terms
dipyrromethane cofactor
porphobilinogen deaminase
tetrapyrrole biosynthesis
87. He  JS, Ruettinger  RT, Liu  HM, Fulco  AJ,     ( 1989 )

Molecular cloning, coding nucleotides and the deduced amino acid sequence of P-450BM-1 from Bacillus megaterium.

Biochimica et biophysica acta 1009 (3)
PMID : 2597681  :   DOI  :   10.1016/0167-4781(89)90120-6    
Abstract >>
The gene encoding barbiturate-inducible cytochrome P-450BM-1 from Bacillus megaterium ATCC 14581 has been cloned and sequenced. An open reading frame in the 1.9 kb of cloned DNA correctly predicted the NH2-terminal sequence of P-450BM-1 previously determined by protein sequencing, and, in toto, predicted a polypeptide of 410 amino acid residues with an Mr of 47,439. The sequence is most, but less than 27%, similar to that of P-450CAM from Pseudomonas putida, so that P-450BM-1 clearly belongs to a new P-450-gene family, distinct especially from that of the P-450 domain of P-450BM-3, a barbiturate-inducible single polypeptide cytochrome P-450:NADPH-P-450 reductase from the same strain of B. megaterium (Ruettinger, R.T., Wen, L.-P. and Fulco, A.J. (1989) J. Biol. Chem. 264, 10987-10995).
KeywordMeSH Terms
Cloning, Molecular
88. Makino  Y, Negoro  S, Urabe  I, Okada  H,     ( 1989 )

Stability-increasing mutants of glucose dehydrogenase from Bacillus megaterium IWG3.

The Journal of biological chemistry 264 (11)
PMID : 2495285  :  
Abstract >>
A glucose dehydrogenase gene was isolated from Bacillus megaterium IWG3, and its nucleotide sequence was identified. The amino acid sequence of the enzyme deduced from the nucleotide sequence is very similar to the protein sequence of the enzyme from B. megaterium M1286 reported by Jany et al. (Jany, K.-D., Ulmer, W., Froschle, M., and Pfleiderer, G. (1984) FEBS Lett. 165, 6-10). The isolated gene was mutagenized with hydrazine, formic acid, or sodium nitrite, and 12 clones (H35, H39, F18, F20, F191, F192, N1, N13, N14, N28, N71, and N72) containing mutant genes for thermostable glucose dehydrogenase were obtained. The nucleotide sequences of the 12 genes show that they include 8 kinds of mutants having the following amino acid substitutions: H35 and H39, Glu-96 to Gly; F18 and F191, Glu-96 to Ala; F20, Gln-252 to Leu; F192, Gln-252 to Leu and Ala-258 to Gly; N1, Glu-96 to Lys and Val-183 to Ile; N13 and N14, Glu-96 to Lys, Val-112 to Ala, Glu-133 to Lys, and Tyr-217 to His; N28, Glu-96 to Lys, Asp-108 to Asn, Pro-194 to Gln, and Glu-210 to Lys; and N71 and N72, Tyr-253 to Cys. These mutant enzymes have higher stability at 60 degrees C than the wild-type enzyme. The results of this study indicate that the tetrameric structure of glucose dehydrogenase is stabilized by several kinds of mutation, and at least one of the following amino acid substitutions stabilizes the enzyme: Glu-96 to Gly, Glu-96 to Ala, Gln-252 to Leu, and Tyr-253 to Cys.
KeywordMeSH Terms
89. Metz  RJ, Allen  LN, Cao  TM, Zeman  NW,     ( 1988 )

Nucleotide sequence of an amylase gene from Bacillus megaterium.

Nucleic acids research 16 (11)
PMID : 2455281  :   DOI  :   10.1093/nar/16.11.5203     PMC  :   PMC336738    
Abstract >>
N/A
KeywordMeSH Terms
Genes, Bacterial
90. Hackett  RH, Setlow  B, Setlow  P,     ( 1986 )

Cloning and nucleotide sequence of the Bacillus megaterium gene coding for small, acid-soluble spore protein B.

Journal of bacteriology 168 (2)
PMID : 2430935  :   DOI  :   10.1128/jb.168.2.1023-1025.1986     PMC  :   PMC213588    
Abstract >>
The Bacillus megaterium gene coding for small, acid-soluble spore protein (SASP) B was cloned and its nucleotide sequence was determined. The amino acid sequence predicted from the DNA sequence was identical to that determined previously for SASP B, with the exception of the amino-terminal methionine predicted from the gene sequence which is presumably removed posttranslationally and an asparagine residue predicted at position 21 which was originally identified as an aspartate residue. The mRNA encoded by the SASP B gene is synthesized for only a discrete period midway in sporulation, in parallel with mRNAs coding for other SASPs. The small size of the SASP B mRNA (365 nucleotides) indicated that the mRNA is monocistronic. The SASP B gene itself hybridized strongly to only one band in Southern blots of restriction enzyme digests of B. megaterium DNA, suggesting that the SASP B gene is not a member of a highly conserved multigene family, as is the case for other SASP genes.
KeywordMeSH Terms
Cloning, Molecular
Sigma Factor
Transcription Factors
91. Kanteev  M, Goldfeder  M, Chojnacki  M, Adir  N, Fishman  A,     ( 2013 )

The mechanism of copper uptake by tyrosinase from Bacillus megaterium.

Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry 18 (8)
PMID : 24061559  :   DOI  :   10.1007/s00775-013-1034-0    
Abstract >>
Tyrosinase belongs to the type 3 copper enzyme family, containing a dinuclear copper center, CuA and CuB. It is mainly responsible for melanin production in a wide range of organisms. Although copper ions are essential for the activity of tyrosinase, the mechanism of copper uptake is still unclear. We have recently determined the crystal structure of tyrosinase from Bacillus megaterium (TyrBm) and revealed that this enzyme has tighter binding of CuA in comparison with CuB. Investigating copper accumulation in TyrBm, we found that the presence of copper has a more significant effect on the diphenolase activity. By decreasing the concentration of copper, we increased the diphenolase to monophenolase activity ratio twofold. Using a rational design approach, we identified five variants having an impact on copper uptake. We have found that a major role of the highly conserved Asn205 residue is to stabilize the orientation of the His204 imidazole ring in the binding site, thereby promoting the correct coordination of CuB. Further investigation of these variants revealed that Phe197, Met61, and Met184, which are located at the entrance to the binding site, not only play a role in copper uptake, but are also important for enhancing the diphenolase activity. We propose a mechanism of copper accumulation by the enzyme as well as an approach to changing the selectivity of TyrBm towards L-dopa production.
KeywordMeSH Terms
92. Goldfeder  M, Egozy  M, Shuster Ben-Yosef  V, Adir  N, Fishman  A,     ( 2013 )

Changes in tyrosinase specificity by ionic liquids and sodium dodecyl sulfate.

Applied microbiology and biotechnology 97 (5)
PMID : 22539021  :   DOI  :   10.1007/s00253-012-4050-z    
Abstract >>
Tyrosinase is a member of the type 3 copper enzyme family involved in the production of melanin in a wide range of organisms. The ability of tyrosinases to convert monophenols into diphenols has stimulated studies regarding the production of substituted catechols, important intermediates for the synthesis of pharmaceuticals, agrochemicals, polymerization inhibitors, and antioxidants. Despite its enormous potential, the use of tyrosinases for catechol synthesis has been limited due to the low monophenolase/diphenolase activity ratio. In the presence of two water miscible ionic liquids, [BMIM][BF(4)] and ethylammonium nitrate, the selectivity of a tyrosinase from Bacillus megaterium (TyrBm) was altered, and the ratio of monophenolase/diphenolase activity increased by up to 5-fold. Furthermore, the addition of sodium dodecyl sulphate (SDS) at levels of 2-50 mM increased the activity of TyrBm by 2-fold towards the natural substrates L-tyrosine and L-Dopa and 15- to 20-fold towards the non-native phenol and catechol. The R209H tyrosinase variant we previously identified as having a preferential ratio of monophenolase/diphenolase activity was shown to have a 45-fold increase in activity towards phenol in the presence of SDS. We propose that the effect of SDS on the ability of tyrosinase to convert non-natural substrates is due to the interaction of surfactant molecules with residues located at the entrance to the active site, as visualized by the newly determined crystal structure of TyrBm in the presence of SDS. The effect of SDS on R209 may enable less polar substrates such as phenol and catechol, to penetrate more efficiently into the enzyme catalytic pocket.
KeywordMeSH Terms
93. Moore  SJ, Lawrence  AD, Biedendieck  R, Deery  E, Frank  S, Howard  MJ, Rigby  SE, Warren  MJ,     ( 2013 )

Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12).

Proceedings of the National Academy of Sciences of the United States of America 110 (37)
PMID : 23922391  :   DOI  :   10.1073/pnas.1308098110     PMC  :   PMC3773766    
Abstract >>
It has been known for the past 20 years that two pathways exist in nature for the de novo biosynthesis of the coenzyme form of vitamin B12, adenosylcobalamin, representing aerobic and anaerobic routes. In contrast to the aerobic pathway, the anaerobic route has remained enigmatic because many of its intermediates have proven technically challenging to isolate, because of their inherent instability. However, by studying the anaerobic cobalamin biosynthetic pathway in Bacillus megaterium and using homologously overproduced enzymes, it has been possible to isolate all of the intermediates between uroporphyrinogen III and cobyrinic acid. Consequently, it has been possible to detail the activities of purified cobinamide biosynthesis (Cbi) proteins CbiF, CbiG, CbiD, CbiJ, CbiET, and CbiC, as well as show the direct in vitro conversion of 5-aminolevulinic acid into cobyrinic acid using a mixture of 14 purified enzymes. This approach has resulted in the isolation of the long sought intermediates, cobalt-precorrin-6A and -6B and cobalt-precorrin-8. EPR, in particular, has proven an effective technique in following these transformations with the cobalt(II) paramagnetic electron in the dyz orbital, rather than the typical dz2. This result has allowed us to speculate that the metal ion plays an unexpected role in assisting the interconversion of pathway intermediates. By determining a function for all of the pathway enzymes, we complete the tool set for cobalamin biosynthesis and pave the way for not only enhancing cobalamin production, but also design of cobalamin derivatives through their combinatorial use and modification.
KeywordMeSH Terms
NMR
cobalt
metabolism
precorrin
tetrapyrrole
94.     ( 1997 )

Regulation of expression, genetic organization and substrate specificity of xylose uptake in Bacillus megaterium.

Molecular microbiology 23 (5)
PMID : 9076741  :   DOI  :   10.1046/j.1365-2958.1997.2881654.x    
Abstract >>
Xylose uptake in Bacillus megaterium depends on expression of a putative H+/xylose symporter encoded by xylT, the last gene in the xyl operon. Insertional inactivation of xylT leads to an apparent uptake deficiency determined with whole cells and severely slower growth on xylose as sole carbon source. Expression of xylT is xylose inducible and subject to carbon catabolite repression mediated by CcpA and cre. Northern analysis of the xyl mRNA reveals that a potential stem-loop structure located in the non-translated region between xylA and xylB presumably acts as a transcriptional terminator, as it leads to different amounts of the respective mRNA sections: the 5'-xylA portion is very abundant, while the 3'-xylBT portion constitutes only a fraction of it. XylT has an apparent Michaelis constant (KM) of approx. 100 microM and is competitively inhibited by glucose with an inhibitor constant KI of 16 mM.
KeywordMeSH Terms
Aldose-Ketose Isomerases
Bacterial Proteins
Dioxygenases
Gene Expression Regulation, Bacterial
Gene Expression Regulation, Enzymologic
95.     ( 1996 )

Cloning and sequencing of the spore germination gene of Bacillus megaterium ATCC 12872: similarities to the NaH-antiporter gene of Enterococcus hirae.

Microbiology and immunology 40 (2)
PMID : 8867604  :   DOI  :   10.1111/j.1348-0421.1996.tb03323.x    
Abstract >>
The germination mutant TM-31 of Bacillus megaterium ATCC 12872, was isolated by transposon Tn917 insertional mutagenesis. Glucose, L-proline, L-leucine and KNO3 germinated TM-31 poorly. The DNA in the region of the Tn917 insertion was cloned, and its nucleotide sequence determined. One major open reading frame was present on the cloned DNA. The hydrophobic protein encoded is presumably membrane-associated. A homology search revealed that the gene encoded in the region of the Tn917 insertion is homologous to napA of Enterococcus hirae. napA codes for the NaH-antiporter. It is hypothesized that transport of cations must play an important role in spore germination in B. megaterium ATCC 12872.
KeywordMeSH Terms
96.     ( 1997 )

The structure of the cytochrome p450BM-3 haem domain complexed with the fatty acid substrate, palmitoleic acid.

Nature structural biology 4 (2)
PMID : 9033595  :  
Abstract >>
The substrate-bound structures of two cytochrome P450s, P450cam and P450eryF, are known. While these structures reveal important features that control substrate specificity, the problem of how conformational changes allow for substrate entry and product release remains unsolved. The structure of the haem domain of the bacterial fatty acid hydroxylase, P450BM-3, previously was solved in the substrate-free form. Unlike the substrate-bound P450cam and P450eryF structures, the substrate access channel is open in substrate-free P450BM-3. Here we present the X-ray structure of P450BM-3 at 2.7 A bound with a fatty acid substrate, palmitoleic acid. A comparison of the substrate-bound and -free forms reveals major conformational differences and provides the first detailed picture of substrate-induced conformational changes in a P450.
KeywordMeSH Terms
Bacterial Proteins
Protein Conformation
Protein Structure, Secondary
97.     ( 1996 )

Structure and function of the Bacillus SpoIIE protein and its localization to sites of sporulation septum assembly.

Molecular microbiology 19 (5)
PMID : 8830262  :   DOI  :   10.1046/j.1365-2958.1996.433963.x    
Abstract >>
Functioning of the spoIIE locus of Bacillus subtilis is required for formation of a normal polar septum during sporulation and for activation of the transcription factor sigma F, which directs early forespore-specific gene expression. We have determined the DNA sequence of the wild type and several mutant alleles of the spoIIE gene of B. subtilis and sequenced a substantial portion of its presumptive homologue in Bacillus megaterium. We show that the spoIIE locus encodes a single large protein with a predicted molecular mass of 92 kDa. Each of five point-mutation alleles, which have traditionally defined the locus, and two transposon-generated mutations were shown to fall within the coding sequence for the 92 kDa gene product or within sequences expected to be required for its expression. The amino-terminal portion of the predicted SpoIIE gene product, comprising approximately 40% of the protein, is extremely hydrophobic and is expected to contain up to 12 membrane-spanning segments. The remainder of the protein contains no hydrophobic segments long enough to span a lipid bilayer and is therefore presumed to comprise one or more globular, aqueous-phase exposed domains. An in-frame fusion joining the 3' end of the B. megaterium spoIIE coding sequence to the 5' end of gfp, a gene encoding the green fluorescent protein (GFP) of Aquorea victoria, resulted in a strong, sporulation-specific fluorescent signal localized to the sites of sporulation septum assembly. We speculate that SpoIIE plays a role in assembling the sporulation septum, perhaps determining the special properties of the structure that permit intercompartment signalling during development.
KeywordMeSH Terms
Sigma Factor
Transcription Factors
98.     ( 1993 )

Cloning and nucleotide sequence of a plasmid-carried gene coding for a minor small, acid-soluble protein from Bacillus megaterium spores.

Journal of bacteriology 175 (19)
PMID : 8407806  :   DOI  :   10.1128/jb.175.19.6337-6340.1993     PMC  :   PMC206731    
Abstract >>
The gene (termed sspG) coding for a small, acid-soluble protein (SASP) from spores of Bacillus megaterium QMB1551, termed SASP-G, has been cloned, and its nucleotide sequence has been determined. SASP-G is a 42-residue protein containing 2 tryptophan and 11 lysine residues, including a hexalysine sequence, and is not homologous to any previously described SASP. The sspG gene appears to be an additional member of the sigma G regulon. No gene homologous to sspG is present in B. cereus T or B. subtilis 168. The reason for the absence of sspG from other Bacillus species appears to be that in B. megaterium, sspG is present only on a 111-kb plasmid; this plasmid is not present in B. cereus T or B. subtilis 168. The sspG gene is the first forespore-expressed gene found to be on a plasmid.
KeywordMeSH Terms
Genes, Bacterial
Sigma Factor
Transcription Factors
99.     ( 1993 )

Inhibition by barbiturates of the binding of Bm3R1 repressor to its operator site on the barbiturate-inducible cytochrome P450BM-3 gene of Bacillus megaterium.

The Journal of biological chemistry 268 (4)
PMID : 8428974  :  
Abstract >>
In our previous publication (Shaw, G.-C., and Fulco, A. J. (1992) J. Biol. Chem. 267, 5515-5526), we reported that Bm3R1, a protein encoded in an open reading frame just upstream from the cytochrome P450BM-3 gene, is a repressor critically involved in the barbiturate-inducible expression of this gene in Bacillus megaterium. We now describe the purification of the Bm3R1 protein from an overproducing Escherichia coli strain harboring a bm3R1 gene-carrying plasmid and report the effect of barbiturate inducers on the interaction of Bm3R1 with a fragment of B. megaterium DNA containing the bicistronic operator and promoter sequences. Gel filtration analysis revealed that, under our experimental conditions, most of the Bm3R1 protein exists in highly aggregated forms. Gel mobility shift assays showed that Bm3R1 protein bound specifically to a segment of DNA containing the promoter-operator region of the bm3R1 gene while DNase I footprinting experiments established that Bm3R1 protected a region of DNA that covers and flanks the palindromic operator sequence. The interaction between Bm3R1 repressor and its operator, in vitro, was strongly inhibited by the addition of 2 mM pentobarbital or 2 mM methohexital (strong in vivo inducers of P450BM-3) but not by the same concentration of phenobarbital (a relatively weak inducer) or by mephobarbital (a non-inducer). A detailed comparison of pentobarbital and methohexital at concentrations lower than 2 mM indicated that methohexital was 5-10 times more effective as an inhibitor of Bm3R1 binding in vitro, as compared with its 7-fold greater inducer potency in vivo. The observation that the in vitro inhibition effects of barbiturates on the interaction of Bm3R1 repressor and its operator correlate strongly with their in vivo potency as inducers of cytochrome P450BM-3 suggests a mechanism for the induction process. It seems plausible that the barbiturate inducers might bear a conformational resemblance to and mimic the mode of action of an as yet unidentified endogenous inducer(s) in B. megaterium that functions by releasing the binding of Bm3R1 repressor from its operator site.
KeywordMeSH Terms
Gene Expression Regulation, Bacterial
Genes, Bacterial
Operator Regions, Genetic
Transcription Factors
100.     ( 1994 )

Sequences of ccpA and two downstream Bacillus megaterium genes with homology to the motAB operon from Bacillus subtilis.

Gene 143 (1)
PMID : 8200532  :   DOI  :   10.1016/0378-1119(94)90621-1    
Abstract >>
A regulatory gene with 69% nucleotide sequence identity to the Bacillus subtilis ccpA was cloned from Bacillus megaterium by complementation of a mutant relieved of catabolite repression. Sequencing of the gene and its adjacent regions revealed two additional open reading frames (ORFs) downstream from ccpA. These three genes are presumably in one operon. ORF1 and ORF2 show homology to two genes downstream from ccpA in B. subtilis, as well as to the B. subtilis motA and motB genes, respectively.
KeywordMeSH Terms
Genes, Regulator
101.     ( 1993 )

[Isolation and characteristics of Bacillus megaterium metalloproteinase].

Biokhimiia (Moscow, Russia) 58 (6)
PMID : 8364112  :  
Abstract >>
Stepwise application of affinity chromatography on bacitracin-silochrome, gel filtration on Acrylex P-10, rechromatography on bacitracin-Sepharose 4B and gel filtration on Sephadex G-15, a homogeneous metalloproteinase (M(r) = 35,000 Da) has been isolated from the cultural filtrate of B. megaterium strain 599. The amino acid composition and N-terminal sequence (20 amino acids) of the enzyme have been determined. The proteinase is not inhibited by diisopropyl-fluorophosphate, is inhibited by o-phenanthroline, EDTA, and Zn2+, and is activated by Co2+. The enzyme has a peak activity at 60-65 degrees C. The maximum of the enzymatic activity after hydrolysis of synthetic substrates is at pH 6.5-7.0. The enzyme is stable at pH 7.0-9.0 and retains its stability at 45-60 C for several hours. In acid media the enzyme undergoes irreversible inactivation. The dependence of kcat/Km on pH points to the involvement of an ionogenic group with pKa 7.5 in the catalytic act, most probably of the imidazole group of histidine. The metalloproteinase hydrolyzes synthetic peptide substrates at the bonds formed by the amino groups of hydrophobic amino acids-Phe, Leu, Ile and Val.
KeywordMeSH Terms
102.     ( 1993 )

Cloning sequencing and expression of the gene for cytochrome P450meg, the steroid-15 beta-monooxygenase from Bacillus megaterium ATCC 13368.

Molecular & general genetics : MGG 241 (1��2��)
PMID : 8232201  :   DOI  :   10.1007/bf00280214    
Abstract >>
A 4.3 kb EcoRI fragment carrying the gene for cytochrome P450meg, the steroid-15 beta-monooxygenase from Bacillus megaterium ATCC 13368, was cloned and completely sequenced. The gene codes for a protein of 410 amino acids and was expressed in Escherichia coli and B. subtilis. Protein extracts from the recombinant E. coli strains were able to hydroxylate corticosteroids in the 15 beta position when supplemented with an extract from a P450- mutant of B. megaterium ATCC 13368 as a source of megaredoxin and megaredoxin reductase. In contrast, 15 beta-hydroxylation was obtained in vitro and in vivo without the addition of external electron transfer proteins, when cytochrome P450meg was produced in B. subtilis 168. Protein extracts from nonrecombinant B. subtilis 168 could also support the in vitro hydroxylation by cytochrome P450meg produced in E. coli.
KeywordMeSH Terms
Aryl Hydrocarbon Hydroxylases
103.     ( 1993 )

Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450's.

Science (New York, N.Y.) 261 (5122)
PMID : 8342039  :   DOI  :   10.1126/science.8342039    
Abstract >>
Cytochrome P450BM-3, a bacterial fatty acid monoxygenase, resembles the eukaryotic microsomal P450's and their flavoprotein reductase in primary structure and function. The three-dimensional structure of the hemoprotein domain of P450BM-3 was determined by x-ray diffraction and refined to an R factor of 16.9 percent at 2.0 angstrom resolution. The structure consists of an alph and a beta domain. The active site heme is accessible through a long hydrophobic channel formed primarily by the beta domain and the B' and F helices of the alpha domain. The two molecules in the asymmetric unit differ in conformation around the substrate binding pocket. Substantial differences between P450BM-3 and P450cam, the only other P450 structure available, are observed around the substrate binding pocket and the regions important for redox partner binding. A general mechanism for proton transfer in P450's is also proposed.
KeywordMeSH Terms
Bacterial Proteins
104.     ( 1993 )

Molecular cloning and nucleotide sequence of the gene encoding a calcium-dependent exoproteinase from Bacillus megaterium ATCC 14581.

Journal of general microbiology 139 (1)
PMID : 8450307  :   DOI  :   10.1099/00221287-139-1-39    
Abstract >>
The gene nprM encoding the calcium-dependent extracellular proteinase from Bacillus megaterium ATCC 14581 was cloned in the vector pBR322 and expressed in Escherichia coli HB101. The DNA sequence of the cloned 3.7 kb fragment revealed only one open reading frame consisting of 1686 bp with a coding capacity of 562 amino acid residues. A predicted Shine-Dalgarno (SD) sequence was observed 9 bp upstream from the presumptive translation start site (ATG). A possible promoter sequence (TAGACG for the -35 region and TATAAT for the -10 region) was found about 69 bp upstream of the ATG start site. The deduced amino acid sequence exhibited a 24 amino acid residue signal peptide and an additional polypeptide 'pro' sequence of 221 amino acids preceding the putative mature protein of 317 amino acid residues. Amino acid sequence comparison revealed 84.5% homology between the mature protein and that of a thermolabile neutral protease from B. cereus. It also shares 73% homology with the thermostable neutral proteases of B. thermoproteolyticus and B. stearothermophilus. The zinc-binding sites and the catalytic residues are completely conserved in all four proteases. NprM has a temperature optimum of 58 degrees C, a pH optimum of between 6.4 and 7.2, and is stimulated by calcium ions and inhibited by EDTA. These results indicate that the enzyme is a neutral (metallo-) protease.
KeywordMeSH Terms
Bacterial Proteins
105. 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.

Molecular microbiology 14 (3)
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.
KeywordMeSH Terms
106. Martín  L, Prieto  MA, Cortés  E, García  JL,     ( 1995 )

Cloning and sequencing of the pac gene encoding the penicillin G acylase of Bacillus megaterium ATCC 14945.

FEMS microbiology letters 125 (2��3��)
PMID : 7875576  :   DOI  :   10.1016/0378-1097(94)00510-x    
Abstract >>
The pac gene encoding the penicillin G acylase (PGA) of Bacillus megaterium ATCC 14945 has been cloned in Escherichia coli HB101 (proA, leuB) using a selective minimal medium containing phenylacetyl-L-leucine instead of L-leucine. The nucleotide sequence of this gene has been determined and contains an open reading frame of 2406 nucleotides. The deduced amino acid sequence shows significant similarity with other beta-lactam acylases. Although the PGA of B. megaterium is extracellular, the enzyme produced in E. coli appears to have a cytoplasmic localization.
KeywordMeSH Terms
Genes, Bacterial
107. Eweda  W, Lunau  S, Fortnagel  P,     ( 1994 )

Cloning and sequencing of a B. subtilis sigmaF dependent gene from B. megaterium.

Microbiological research 149 (4)
PMID : 7842232  :   DOI  :   10.1016/S0944-5013(11)80080-7    
Abstract >>
A promoter-monocistronic structural gene complex from genomic DNA of Bacillus megaterium has been isolated and sequenced. The activity of the promoter during sporulation was measured in B. subtilis using a fusion with the xylE gene of Pseudomonas putida which codes for a catechol-2,3-dioxygenase. From the time of activation in sporulating cells and the activity in a set of defined B. subtilis sporulation mutants we conclude that the promoter requires an active sigmaF-factor of RNA-polymerase. Since this sigma-factor is active only in forespores and not in the mothercell compartment it is likely that we have identified a forespore specific gene of B. megaterium. Its function is still unknown.
KeywordMeSH Terms
Dioxygenases
Genes, Bacterial
108. Fliss  ER, Setlow  P,     ( 1984 )

Complete nucleotide sequence and start sites for transcription and translation of the Bacillus megaterium protein C gene.

Journal of bacteriology 158 (3)
PMID : 6327639  :   PMC  :   PMC215513    
Abstract >>
The nucleotide sequence of the Bacillus megaterium protein C gene, encompassing the coding region and 341 base pairs of flanking regions, has been determined. The gene codes for a 72-residue protein whose predicted amino acid sequence is identical to that previously determined for protein C with the exception of an amino-terminal methionine predicted from the gene sequence, but not found in the mature protein. The translational initiation codon is preceded by an 11-base pair sequence highly complementary to the 3' terminus of B. megaterium 16S rRNA. Protection against S1 nuclease digestion by hybridization of a protein C gene fragment to RNA containing high levels of protein C mRNA localized the transcription initiation site 108 base pairs upstream from the translation start site. Upstream from the transcription initiation site there are no obvious homologies with conserved regions of promoters for previously described B. subtilis vegetative or sporulation genes.
KeywordMeSH Terms
Genes
Genes, Bacterial
Protein Biosynthesis
Transcription, Genetic
109. Fliss  ER, Setlow  P,     ( 1985 )

Genes for Bacillus megaterium small, acid-soluble spore proteins: nucleotide sequence of two genes and their expression during sporulation.

Gene 35 (1��2��)
PMID : 3928443  :   DOI  :   10.1016/0378-1119(85)90167-2    
Abstract >>
The complete nucleotide (nt) sequence of two Bacillus megaterium genes coding for small, acid-soluble spore proteins (SASP), termed C-1 and C-2, has been determined. The nt sequences of the genes are greater than 98% identical in the coding regions, greater than 90% identical in approx. 180 bp and approx. 50 bp of upstream and downstream flanking sequences, respectively, and exhibit features conserved in related B. megaterium SASP genes. Northern blot analyses showed that the SASP-C-1 and/or C-2 genes are transcribed during sporulation in parallel with the related SASP-C and C-3 genes. The promoter regions of the SASP-C-1 and C-2 genes were localized, based on the sizes of their mRNAs and the positions of transcription termination sequences. The SASP-C-1 and C-2 genes' promoter regions exhibit significant homology with those for the SASP-C and C-3 genes.
KeywordMeSH Terms
Genes, Bacterial
Sigma Factor
Transcription Factors
110. Setlow  P, Ozols  J,     ( 1980 )

The complete covalent structure of protein B. The third major protein degraded during germination of Bacillus megaterium spores.

The Journal of biological chemistry 255 (21)
PMID : 6776116  :  
Abstract >>
The complete covalent structure of Protein B, the third major protein degraded during germination of Bacillus megaterium spores, has been determined. The intact protein was cleaved with the specific B. megaterium spore protease into three peptides, residues 1 to 31 (B-III), 32 to 66 (B-I), and 67 to 96 (B-II). Cleavage of the intact protein with trypsin allowed isolation of the peptide encompassing residues 61 to 77 (T-11) as well as the COOH-terminal peptide, residues 94 to 96 (T-4). Cleavage of Peptide B-I with trypsin or chymotrypsin allowed isolation of peptides encompassing residues 53 to 60 (B-I-T-2) and residues 52 to 66 (B-I-C-4), respectively. Subtractive Edman degradation of Peptide T-4, automated sequenator analysis of Peptides B-I, B-II, T-11, B-I-T-2, and B-I-C-4, previously published partial sequence data on the intact B-protein and carboxypeptidase V digestion of the intact protein provided the data from which the following unique sequence was deduced: NH2-Ala-Lys-Gln-Thr-Asn-Lys-Thr-Ala-Ser-Gly-Thr-Ser-Thr-Gln-His-15 Val-Lys-Gln-Gln-Asp-Ala-Gln-Ala-Ser-Lys-Asn-Asn-Phe-Gly-Thr-30 Glu-Phe-Gly-Ser-Glu-Thr-Asn-Val-Gln-Glu-Val-Lys-Gln-Gln-Asn-45 Ala-Gln-Ala-Ala-Asn-Lys-Ser-Gln-Asn-Ala-Gln-Ala-Ser-Lys-60 Asn-Asn-Phe-Gly-Thr-Glu-Phe-Ala-Ser-Glu-Thr-Ser-Ala-Gln-Glu-75 Val-Arg-Gln-Gln-Asn-Ala-Gln-Ala-Gln-Lys-Lys-Asn-Gln-Asn-90 Ser-Gly-Lys-Tyr-Gln-Gly-COOH. The primary sequence of the B-protein contains a large internal duplication (residues 17 to 50 and 52 to 85), and shows significant sequence homology with the A- and C-proteins, the other major proteins degraded during B. megaterium spore germination.
KeywordMeSH Terms
Bacterial Proteins
Sigma Factor
Transcription Factors
111. Setlow  P, Ozols  J,     ( 1980 )

Covalent structure of protein C. A second major low molecular weight protein degraded during germination of Bacillus megaterium spores.

The Journal of biological chemistry 255 (18)
PMID : 6773941  :  
Abstract >>
The complete covalent structure of protein C, a protein degraded during germination of Bacillus megaterium spores, has been determined. The intact protein was cleaved with a highly specific spore protease into two peptides, residues 1 to 30 and 31 to 71. The intact protein was also cleaved by cyanogen bromide into two peptides, residues 1 to 27 and 28 to 71. Cleavage of the larger cyanogen bromide peptide with trypsin allowed isolation of the COOH-terminal peptide, residues 59 to 71. Automated sequenator analysis of the intact protein and peptide fragments, together with previously published partial sequence data on this protein and carboxypeptidase A digestion of the intact protein provided data from which the following unique sequence was deduced: (formula: see text). The primary sequence of the C protein shows an extremely high degree of homology with that of the A protein--another protein degraded during germination of B. megaterium spores.
KeywordMeSH Terms
Sigma Factor
Transcription Factors
112. Berg  A, Rafter  JJ,     ( 1981 )

Studies on the substrate specificity and inducibility of cytochrome P-450meg.

The Biochemical journal 196 (3)
PMID : 6797409  :   DOI  :   10.1042/bj1960781     PMC  :   PMC1163098    
Abstract >>
The cytochrome P-450-dependent steroid 15 beta-hydroxylase system in Bacillus megaterium A.T.C.C. 13368 was investigated with regard to its appearance in the cell with respect to the growth curve of the organism, with regard to its inducibility by a number of agents (among them some of the classical inducers of the mammalian liver microsomal cytochrome P-450 system) and with regard to its capacity to convert non-steroidal substances into oxygenated compounds. The enzyme was found to reach a maximum concentration in the cell during the stationary phase of the growth curve. Of all the agents tested as inducers, none showed any capacity to induce cytochrome P-450meg. Finally, of the substances tested as substrates only aniline (p-hydroxylation) was metabolized by the microbial enzyme system. This conversion might be related to the general oxygenase activity of haemoproteins. It is concluded that the substrate specificity of the B. megaterium hydroxylase system is narrow.
KeywordMeSH Terms
113. Yeom  H, Sligar  SG, Li  H, Poulos  TL, Fulco  AJ,     ( 1995 )

The role of Thr268 in oxygen activation of cytochrome P450BM-3.

Biochemistry 34 (45)
PMID : 7578081  :   DOI  :   10.1021/bi00045a014    
Abstract >>
Cytochrome P450BM-3, a catalytically self-sufficient monooxygenase from Bacillus megaterium, catalyzes the omega-n (n = 1-3) hydroxylation of fatty acids in the presence of O2 and NADPH. Like most other P450s, cytochrome P450BM-3 contains a threonine residue (Thr268) in the distal I helix thought to be important for O2 binding and activation. Thr268 has been converted to alanine and the enzymatic properties and heme domain crystal structure determined. Using sodium laurate as the substrate, the mutant exhibited slower rates of O2 and NADPH consumption. In addition, electron transfer is uncoupled from substrate hydroxylation as evidenced by the greater production of water and peroxide in the mutant compared to the wild-type enzyme. The crystal structure of the mutant reveals that the only changes in structure are confined to the site of mutation. These data indicate an important role for Thr268 in O2 binding and activation in the metabolism of sodium laurate by cytochrome P450BM-3.
KeywordMeSH Terms
Bacterial Proteins
114. Ulmer  W, Fröschle  M, Jany  KD,     ( 1983 )

Evidence for an essential histidine residue in glucose dehydrogenase from Bacillus megaterium and sequence analysis of the peptides labeled with bromoacetyl pyridine.

European journal of biochemistry 136 (1)
PMID : 6413208  :   DOI  :   10.1111/j.1432-1033.1983.tb07724.x    
Abstract >>
Bromoacetylpyridine acts as an active-site-directed inhibitor on glucose dehydrogenase from Bacillus megaterium. The inactivation is irreversible with a Ki of 7.7 mM. The coenzyme NAD but not the substrate glucose protects the enzyme from the inactivation. It is proposed that bromoacetylpyridine modifies a residue at or nearby the active site. The inactivation is correlated with the modification of a single histidine residue. Modification of the enzyme with 3-(2-bromo[carbonyl-14C]acetyl)-pyridine and partial acid hydrolysis of the protein yielded one labeled fragment. From the arginine restricted tryptic cleavage of this fragment four radioactively labeled peptides were purified. Comparison of the specific radioactivity leads to the conclusion that the active site histidine residue must be located in the 58-residue fragment AH2-TA3. Sequence analysis showed that only one residue is modified in this fragment and the sequence around the labeled histidine residue is -Met-Ser-Ser-Val-His-Glu-Trp-Lys-Ile-Pro-Trp-Pro-. The minor labeled arginine fragments, comprising 86, 20 and 13 residues, were also sequenced. Only lysine residues are modified in these peptides. The modification of the individual residues does not exceed 10%.
KeywordMeSH Terms
Histidine
115. Jany  KD, Ulmer  W, Fröschle  M, Pfleiderer  G,     ( 1984 )

Complete amino acid sequence of glucose dehydrogenase from Bacillus megaterium.

FEBS letters 165 (1)
PMID : 6420184  :   DOI  :   10.1016/0014-5793(84)80003-4    
Abstract >>
The amino acid sequence of glucose dehydrogenase from Bacillus megaterium has been determined. The enzyme consists of 4 identical subunits, each containing 262 amino acid residues. Its structure was established using manual Edman degradation procedures after modification of the enzyme in the native form with reagents specific to the amino acids histidine, tyrosine, tryptophan and lysine in order to identify residues involved in catalysis or located in the subunit binding area.
KeywordMeSH Terms
Carbohydrate Dehydrogenases
Glucose Dehydrogenases
116. Fliss  ER, Setlow  P,     ( 1984 )

Bacillus megaterium spore protein C-3: nucleotide sequence of its gene and the amino acid sequence at its spore protease cleavage site.

Gene 30 (1��3��)
PMID : 6439604  :   DOI  :   10.1016/0378-1119(84)90117-3    
Abstract >>
The nucleotide sequence of the Bacillus megaterium gene coding for spore-specific protein C-3 has been determined. The gene codes for 65 amino acids and the coding sequence is preceded by an efficient ribosome-binding site. The predicted protein C-3 sequence agrees with both the amino acid composition and the amino terminal sequence of protein C-3, and shows homology (approx. 65% of all residues are identical) with the sequences of the analogous proteins A and C of B. megaterium. Protein C-3 is cleaved by the sequence-specific B. megaterium spore protease, and the amino acid sequence at the new amino-terminus generated is identical to that predicted from the gene sequence, and homologous to the spore protease cleavage sites in the A and C proteins. The protein C-3 gene also shares a number of features with the previously sequenced protein C gene in both upstream and downstream flanking sequence.
KeywordMeSH Terms
Genes, Bacterial
Sigma Factor
Transcription Factors
117. Fröschle  M, Ulmer  W, Jany  KD,     ( 1984 )

Tyrosine modification of glucose dehydrogenase from Bacillus megaterium. Effect of tetranitromethane on the enzyme in the tetrameric and monomeric state.

European journal of biochemistry 142 (3)
PMID : 6432532  :   DOI  :   10.1111/j.1432-1033.1984.tb08318.x    
Abstract >>
The active tetrameric glucose dehydrogenase from Bacillus megaterium is rapidly inactivated upon reaction with tetranitromethane. The inactivation is correlated with the nitration of a single tyrosine residue/subunit. The nitration does not influence the dissociation-reassociation process of the enzyme. The inactivation is prevented by the presence of NAD, AMP, ATP. The sequence around the nitrated tyrosine residue was determined and the residue was identified as Tyr-254 in the covalent structure of the enzyme. After dissociation of the enzyme into its monomers two tyrosine residues become susceptible to nitration. The nitrated subunits are unable to reassociate to the tetramer. Isolation and sequence analysis of the peptides containing nitrotyrosine indicated that two different tyrosine residues are predominantly modified. One residue is Tyr-254 which is essential for the catalytic activity and the other one is Tyr-160 which seems to be located in the subunit binding area.
KeywordMeSH Terms
Carbohydrate Dehydrogenases
Glucose Dehydrogenases
Methane
Tetranitromethane
118. He  JS, Liang  Q, Fulco  AJ,     ( 1995 )

The molecular cloning and characterization of BM1P1 and BM1P2 proteins, putative positive transcription factors involved in barbiturate-mediated induction of the genes encoding cytochrome P450BM-1 of Bacillus megaterium.

The Journal of biological chemistry 270 (31)
PMID : 7629192  :   DOI  :   10.1074/jbc.270.31.18615     DOI  :   10.1074/jbc.270.31.18615    
Abstract >>
Analysis of a 1.3-kilobase segment of 5'-flanking DNA from the barbiturate-inducible P450BM-1 gene (CYP106) of Bacillus megaterium revealed two open reading frames. One, BM1P1, encodes 98 amino acids and is located 267 base pairs upstream from the sequence encoding cytochrome P450BM-1 but in the opposite orientation. The second, BM1P2 (88 amino acids), is 892 base pairs upstream from the P450BM-1 coding sequence and in the same coding strand. The expression of BM1P1 and BM1P2 was strongly stimulated in cells grown in the presence of pentobarbital, and the BM1P1 gene product exerted positive control on expression of P450BM-1. When a 177-base pair fragment encompassing the overlapping promoter regions of the P450BM-1 and BM1P1 genes was used as a probe in DNA binding assays, the BM1P1 and BM1P2 gene products and Bm3R1 (the repressor protein regulating the barbiturate-mediated expression of P450BM-3) could bind individually, but the addition of BM1P1 or BM1P2 to a binding mixture containing Bm3R1 completely prevented the appearance of a Bm3R1 binding band. When a 208-base pair fragment containing a Barbie box sequence and located upstream of the 177-base pair fragment was used as a probe, only a Bm3R1 binding band was detected. Although neither BM1P1 and BM1P2 appeared to bind to this 208-base pair fragment, their presence strongly inhibited the binding of Bm3R1 to the same probe. The evidence suggests that BM1P1 and BM1P2 may, in part, act as positive regulatory proteins involved in the expression of the P450BM-1 gene by interfering with the binding of the repressor protein, Bm3R1, to the regulatory regions of P450BM-1.
KeywordMeSH Terms
Gene Expression Regulation, Bacterial
Repressor Proteins
Gene Expression Regulation, Bacterial
Repressor Proteins
119. Setlow  P, Gerard  C, Ozols  J,     ( 1980 )

The amino acid sequence specificity of a protease from spores of Bacillus megaterium.

The Journal of biological chemistry 255 (8)
PMID : 6767722  :  
Abstract >>
Previous work has shown that the degradation of 20% of total protein which occurs early in germination of Bacillus megaterium spores is initiated by an endoprotease. This enzyme is found only in the spore and is active only on the spore proteins degraded during germination. Action of the spore protease in vitro on the three major proteins (Proteins A, B, and C) which are degraded in vivo during germination results in cleavage of one (A and C protein) or two (B protein) peptide bonds. The sequences surrounding the cleavage sites are -Tyr-Glu- Ile-Ala-Ser-Glu-Phe- in the A protein, -Phe-Glu- Ile-Ala-Ser-Glu-Phe- in the C protein, and -Thr-Glu- Phe-Gly-Ser-Glu-Thr-, and -Thr-Glu- Phe-Ala-Ser-Glu-Thr- in the B protein, with cleavage taking place at the glutamyl bond noted by the arrow. The similarity of these four sequences suggests the possibility that the specificity of the spore protease may be due to its requirement for a specific pentapeptide sequence of the type -R-Glu-(Phe or Ile)-(Gly or Ala)-Ser-Glu-R- for recognition and cleavage. However, it is also possible that it is the conformation of the A, B, and C proteins which determines their site of cleavage by the spore protease.
KeywordMeSH Terms
Peptide Hydrolases
120. He  JS, Liang  Q, Fulco  AJ,     ( 1995 )

The molecular cloning and characterization of BM1P1 and BM1P2 proteins, putative positive transcription factors involved in barbiturate-mediated induction of the genes encoding cytochrome P450BM-1 of Bacillus megaterium.

The Journal of biological chemistry 270 (31)
PMID : 7629192  :   DOI  :   10.1074/jbc.270.31.18615     DOI  :   10.1074/jbc.270.31.18615    
Abstract >>
Analysis of a 1.3-kilobase segment of 5'-flanking DNA from the barbiturate-inducible P450BM-1 gene (CYP106) of Bacillus megaterium revealed two open reading frames. One, BM1P1, encodes 98 amino acids and is located 267 base pairs upstream from the sequence encoding cytochrome P450BM-1 but in the opposite orientation. The second, BM1P2 (88 amino acids), is 892 base pairs upstream from the P450BM-1 coding sequence and in the same coding strand. The expression of BM1P1 and BM1P2 was strongly stimulated in cells grown in the presence of pentobarbital, and the BM1P1 gene product exerted positive control on expression of P450BM-1. When a 177-base pair fragment encompassing the overlapping promoter regions of the P450BM-1 and BM1P1 genes was used as a probe in DNA binding assays, the BM1P1 and BM1P2 gene products and Bm3R1 (the repressor protein regulating the barbiturate-mediated expression of P450BM-3) could bind individually, but the addition of BM1P1 or BM1P2 to a binding mixture containing Bm3R1 completely prevented the appearance of a Bm3R1 binding band. When a 208-base pair fragment containing a Barbie box sequence and located upstream of the 177-base pair fragment was used as a probe, only a Bm3R1 binding band was detected. Although neither BM1P1 and BM1P2 appeared to bind to this 208-base pair fragment, their presence strongly inhibited the binding of Bm3R1 to the same probe. The evidence suggests that BM1P1 and BM1P2 may, in part, act as positive regulatory proteins involved in the expression of the P450BM-1 gene by interfering with the binding of the repressor protein, Bm3R1, to the regulatory regions of P450BM-1.
KeywordMeSH Terms
Gene Expression Regulation, Bacterial
Repressor Proteins
Gene Expression Regulation, Bacterial
Repressor Proteins
121. Stangl  D, Wiederkehr  F, Suter  F, Zuber  H,     ( 1987 )

Structure and function of L-lactate dehydrogenases from thermophilic and mesophilic bacteria, V. The complete amino-acid sequence of the mesophilic L-lactate dehydrogenase from Bacillus megaterium.

Biological chemistry Hoppe-Seyler 368 (9)
PMID : 3118900  :  
Abstract >>
The complete amino-acid sequence of L-lactate-dehydrogenase from the mesophilic Bacillus megaterium was determined. 92% of the 318 amino acids were established by sequence analysis of the N-terminus, of four CNBr fragments and of one fragment obtained by cleavage with BNPS-skatole. The primary structure was completed by sequencing overlapping fragments obtained by further cleavage of suitable CNBr fragments and BNPS fragments with either trypsin, endoproteinase Lys-C, o-iodosobenzoic acid or hydroxylamine. The C-terminal amino acids were determined by degradation with carboxypeptidase A. The sequence homology between lactate dehydrogenases from B. megaterium and those from other Bacilli is 59-61% and 35-37% to those from higher organisms. The high sequence homology among lactate dehydrogenases from Bacilli, adapted to different temperatures, allows comparative studies of the structural basis of protein thermostability.
KeywordMeSH Terms
L-Lactate Dehydrogenase
122. Hanano  A, Shaban  M, Almutlk  D, Almousally  I,     ( 2019 )

The cytochrome P450BM-1 of Bacillus megaterium A14K is induced by 2,3,7,8-Tetrachlorinated dibenzo-p-dioxin: Biophysical, molecular and biochemical determinants.

Chemosphere 216 (N/A)
PMID : 30384294  :   DOI  :   10.1016/j.chemosphere.2018.10.103    
Abstract >>
The current study describes biological changes in Bacillus megaterium A14K cells growing in the presence of 2,3,7,8-Tetrachlorinated dibenzo-p-dioxin (TCDD), the most potent congener of dioxins. The results indicate that the metabolizing of 2,3,7,8-TCDD by BmA14K was accompanied with a novel morphological and biophysical profile typified by the growth of single cells with high levels of biosurfactant production, surface hydrophobicity and cell membrane permeability. Moreover, the TCDD-grown bacteria exhibited a specific fatty acid profile characterized by low ratios of branched/straight chain fatty acids (BCFAs/SCFAs) and saturated/unsaturated fatty acids (SFAs/USFAs) with a specific "signature" due to the presence of branched chain unsaturated fatty acids (BCUFAs). This was synchronized with a significant induction of P450BM-1, an unsaturated fatty acid-metabolizing enzyme in B. megaterium. Subsequently, the profile of oxygenated fatty acids in the TCDD-grown bacteria was typified by the presence of 5,6-epoxy derived from unsaturated C15, C16 and C17 fatty acids, that were absent in control bacteria. A net increase was also detected in both hydroxylated and epoxidized fatty acids, especially those derived from C15:0 and C16:1, respectively, suggesting a specific TCDD-induced "signature" of oxygenated fatty acids in BmA14K. Overall, this study sheds light on the use of B. megaterium A14K as a promising bioindicator/biodegrader of dioxins.
KeywordMeSH Terms
B. megaterium
Oxygenated fatty acids
P450(BM-1)
TCDD
123. Jeffreys  LN, Poddar  H, Golovanova  M, Levy  CW, Girvan  HM, McLean  KJ, Voice  MW, Leys  D, Munro  AW,     ( 2019 )

Novel insights into P450 BM3 interactions with FDA-approved antifungal azole drugs.

Scientific reports 9 (1)
PMID : 30733479  :   DOI  :   10.1038/s41598-018-37330-y     PMC  :   PMC6367340     DOI  :   10.1038/s41598-018-37330-y     PMC  :   PMC6367340    
Abstract >>
Flavocytochrome P450 BM3 is a natural fusion protein constructed of cytochrome P450 and NADPH-cytochrome P450 reductase domains. P450 BM3 binds and oxidizes several mid- to long-chain fatty acids, typically hydroxylating these lipids at the �s-1, �s-2 and �s-3 positions. However, protein engineering has led to variants of this enzyme that are able to bind and oxidize diverse compounds, including steroids, terpenes and various human drugs. The wild-type P450 BM3 enzyme binds inefficiently to many azole antifungal drugs. However, we show that the BM3 A82F/F87V double mutant (DM) variant binds substantially tighter to numerous azole drugs than does the wild-type BM3, and that their binding occurs with more extensive heme spectral shifts indicative of complete binding of several azoles to the BM3 DM heme iron. We report here the first crystal structures of P450 BM3 bound to azole antifungal drugs - with the BM3 DM heme domain bound to the imidazole drugs clotrimazole and tioconazole, and to the triazole drugs fluconazole and voriconazole. This is the first report of any protein structure bound to the azole drug tioconazole, as well as the first example of voriconazole heme iron ligation through a pyrimidine nitrogen from its 5-fluoropyrimidine ring.
KeywordMeSH Terms
124. Fliss  ER, Loshon  CA, Setlow  P,     ( 1986 )

Genes for Bacillus megaterium small, acid-soluble spore proteins: cloning and nucleotide sequence of three additional genes from this multigene family.

Journal of bacteriology 165 (2)
PMID : 3080406  :   DOI  :   10.1128/jb.165.2.467-473.1986     PMC  :   PMC214442    
Abstract >>
Three genes coding for small, acid-soluble spore proteins (SASP) were cloned from Bacillus megaterium, using previously cloned B. megaterium SASP genes (SASP-C and -C-3) as DNA-DNA hybridization probes. One gene (SASP-A) codes for the A protein, a previously identified major SASP. The other two (termed genes for SASP-C-4 and -C-5) are extremely similar in much of their nucleotide sequence to the previously cloned B. megaterium SASP-C-2 gene. The proteins coded for by all these SASP genes had extensive sequence homology with each other and with those coded for by the B. megaterium SASP-C, -C-1, -C-2, and -C-3 genes. Their coding sequences are preceded by strong ribosome-binding sites and are followed by regions of dyad symmetry which presumably are transcription stop sites. The SASP-A, -C-4, and -C-5 genes are expressed in parallel during sporulation, and their transcription start points were localized by the size of the mRNAs produced. The sequences localized 10 and 35 base pairs upstream from the transcription start points show significant homology with the analogous regions of the SASP-C, -C-1, -C-2, and -C-3 genes. The identification of seven closely related SASP genes in B. megaterium indicates that the SASP are the products of a very extensive multigene family.
KeywordMeSH Terms
Genes, Bacterial
Spores, Bacterial
125. Li  Y, Jin  K, Perez-Valdespino  A, Federkiewicz  K, Davis  A, Maciejewski  MW, Setlow  P, Hao  B,     ( 2019 )

Structural and functional analyses of the N-terminal domain of the A subunit of a Bacillus megaterium spore germinant receptor.

Proceedings of the National Academy of Sciences of the United States of America 116 (23)
PMID : 31113879  :   DOI  :   10.1073/pnas.1903675116     PMC  :   PMC6561283    
Abstract >>
Germination of Bacillus spores is induced by the interaction of specific nutrient molecules with germinant receptors (GRs) localized in the spore's inner membrane. GRs typically consist of three subunits referred to as A, B, and C, although functions of individual subunits are not known. Here we present the crystal structure of the N-terminal domain (NTD) of the A subunit of the Bacillus megaterium GerK3 GR, revealing two distinct globular subdomains bisected by a cleft, a fold with strong homology to substrate-binding proteins in bacterial ABC transporters. Molecular docking, chemical shift perturbation measurement, and mutagenesis coupled with spore germination analyses support a proposed model that the interface between the two subdomains in the NTD of GR A subunits serves as the germinant binding site and plays a critical role in spore germination. Our findings provide a conceptual framework for understanding the germinant recruitment mechanism by which GRs trigger spore germination.
KeywordMeSH Terms
Bacillus
spore germinant receptor
spore germination
spores
126. Heilmann  HJ, Mägert  HJ, Gassen  HG,     ( 1988 )

Identification and isolation of glucose dehydrogenase genes of Bacillus megaterium M1286 and their expression in Escherichia coli.

European journal of biochemistry 174 (3)
PMID : 3134196  :   DOI  :   10.1111/j.1432-1033.1988.tb14124.x    
Abstract >>
A gene encoding glucose dehydrogenase of Bacillus megaterium M1286 was isolated from a lambda-EMBL3 phage library. It is transcribed and translated in cells of the heterologous organism Escherichia coli by own control regions. The gene is located on a 1126-bp HindIII fragment. Its nucleotide sequence contains 220 bp in the 5' non-coding region, 783 bp in the coding region and 123 bp in the 3' non-coding region. The amino acid sequence, as deduced from the coding region, consists of 261 amino acids and is different from the known protein sequence of glucose dehydrogenase from B. megaterium M1286. [Jany, K. D., Ulmer, W., Fr?schle, M. & Pfleiderer, G. (1984) FEBS Lett. 165, 6-10]. By using this gene as a hybridization probe a second glucose dehydrogenase gene was isolated, which was also directly expressed in E. coli. Additionally a DNA region with extended sequence homology to the hybridization probe was identified. This work indicates the existence of at least two independent glucose dehydrogenase genes in B. megaterium M1286. Homologies in the primary structures of the two different glucose dehydrogenases of B. megaterium M1286 and of the corresponding Bacillus subtilis enzyme are discussed.
KeywordMeSH Terms
Gene Expression Regulation
127. Sussman  MD, Setlow  P,     ( 1987 )

Nucleotide sequence of a Bacillus megaterium gene homologous to the dnaK gene of Escherichia coli.

Nucleic acids research 15 (9)
PMID : 3035506  :   DOI  :   10.1093/nar/15.9.3923     PMC  :   PMC340797    
Abstract >>
N/A
KeywordMeSH Terms
Genes, Bacterial
128. Waldvogel  S, Weber  H, Zuber  H,     ( 1987 )

Structure and function of L-lactate dehydrogenases from thermophilic and mesophilic bacteria. VII. Nucleotide sequence of the lactate dehydrogenase gene from the mesophilic bacterium Bacillus megaterium. Preparation and properties of a hybrid lactate dehydrogenase comprising moieties of the B. megaterium and B. stearothermophilus enzymes.

Biological chemistry Hoppe-Seyler 368 (10)
PMID : 3122782  :  
Abstract >>
The lactate dehydrogenase (LDH) gene of a mesophilic bacterium, Bacillus megaterium (DSM 090), was cloned in E. coli HB 101 using a pEMBL vector and synthetic oligonucleotide probes. The gene was strongly expressed in the vector used if the orientation of the insert allowed the LDH promoter and the vector's lac promoter to direct transcription in the same direction. The gene and its 5' and 3' flanking regions have been sequenced. Codon usage patterns of LDH genes from mesophilic and thermophilic bacilli were compared and found to be characteristically different. A hybrid gene was constructed from fragments of the LDH genes from B. stearothermophilus (coding for aa 15-100) and B. megaterium (coding for aa 101-331). The hybrid LDH, named S100M, was more thermostable than B. megaterium LDH, less thermostabile than B. stearothermophilus LDH and unlike the two wildtype enzymes, it could not be activated by Fru-P2.
KeywordMeSH Terms
129. Wen  LP, Fulco  AJ,     ( 1987 )

Cloning of the gene encoding a catalytically self-sufficient cytochrome P-450 fatty acid monooxygenase induced by barbiturates in Bacillus megaterium and its functional expression and regulation in heterologous (Escherichia coli) and homologous (Bacillus megaterium) hosts.

The Journal of biological chemistry 262 (14)
PMID : 3106359  :  
Abstract >>
In a previous publication (Narhi, L. O., and Fulco, A. J. (1986) J. Biol. Chem. 261, 7160-7169) we described the characterization of a 119,000-dalton P-450 cytochrome that is strongly induced by barbiturates in Bacillus megaterium. In the presence of NADPH and O2, this single polypeptide can catalyze the hydroxylation of long-chain fatty acids without the aid of any other protein. The gene encoding this unique monooxygenase (cytochrome P-450BM-3) has now been cloned by an immunochemical screening technique. The Escherichia coli clone harboring the recombinant plasmid produces a 119,000-dalton protein that appears to be electrophoretically and immunochemically identical to the B. megaterium enzyme and contains the same N-terminal amino acid sequence. The recombinant DNA product also exhibits the characteristic cytochrome P-450 spectrum and is fully functional as a fatty acid monooxygenase. In E. coli, the synthesis of P-450BM-3 is directed by its own promoter included in the DNA insert and proceeds constitutively at a very high rate but is not stimulated by pentobarbital. However, when the cloned P-450BM-3 gene, either intact or in a truncated form, is introduced back into B. megaterium via an E. coli/Bacillus subtilis shuttle vector, its expression is constitutively repressed but is induced by pentobarbital. This finding demonstrates that the regulatory region of the P-450BM-3 gene that responds to barbiturates is included in the cloned DNA. The evidence also indicates that pentobarbital cannot directly act on the gene to cause induction but presumably interacts with another component such as a repressor molecule that is present in B. megaterium but is absent in the E. coli clone.
KeywordMeSH Terms
Cloning, Molecular
Gene Expression Regulation
Genes
Genes, Bacterial
130. Ozer  A, Uzuner  U, Guler  HI, Ay Sal  F, Belduz  AO, Deniz  I, Canakci  S,     ( 2018 )

Improved pulp bleaching potential of Bacillus subtilis WB800 through overexpression of three lignolytic enzymes from various bacteria.

Biotechnology and applied biochemistry 65 (4)
PMID : 29286186  :   DOI  :   10.1002/bab.1637    
Abstract >>
A chemical bleaching process of paper pulps gives off excessive amount of chlorinated organic wastes mostly released to environment without exposing complete bioremediaton. Recent alternative and eco-friendly approaches toward pulp bleaching appear more responsive to environmental awareness. Here we report, direct use of a recombinant Bacillus subtilis bacterium for pulp bleaching, endowed with three ligninolytic enzymes from various bacteria. In addition, efficient bleaching performance from glutathione-S-transferase (GST) biocatalyst tested for the first time in pulp bleaching applications was also achieved. Simultaneous and extracellular overproduction of highly active GST, laccase, and lignin peroxidase catalysts were also performed by Bacillus cells. Both enhanced bleaching success and improved delignification rates were identified when enzyme combinations tested on both pine kraft and waste paper pulps, ranging from 69.75% to 79.18% and 60.89% to 74.65%, respectively. Furthermore, when triple enzyme combination applied onto the papers from pine kraft and waste pulps, the best ISO brightness values were identified as 66.45% and 64.67%, respectively. The delignification rates of pulp fibers exposed to various enzymatic bleaching sequences were comparatively examined under SEM. In conclusion, the current study points out that in near future, a more fined-tuned engineering of pulp-colonizing bacteria may become a cost-effective and environmentally friendly alternative to chemical bleaching.
KeywordMeSH Terms
glutathione-S-transferase
laccase
lignin peroxidase
operon cloning
pulp bleaching
glutathione-S-transferase
laccase
lignin peroxidase
operon cloning
pulp bleaching
131. Ferro  S, Deri  B, Germanò  MP, Gitto  R, Ielo  L, Buemi  MR, Certo  G, Vittorio  S, Rapisarda  A, Pazy  Y, Fishman  A, De Luca  L,     ( 2018 )

Targeting Tyrosinase: Development and Structural Insights of Novel Inhibitors Bearing Arylpiperidine and Arylpiperazine Fragments.

Journal of medicinal chemistry 61 (9)
PMID : 29634898  :   DOI  :   10.1021/acs.jmedchem.7b01745    
Abstract >>
The inhibition of tyrosinase (Ty, EC 1.14.18.1) represents an efficient strategy of decreasing melanogenesis and skin hyperpigmentation. A combination of crystallographic and docking studies on two different tyrosinases, that from Bacillus megaterium (TyBm) and that from a mushroom (TyM), has contributed to increasing our knowledge about their structural information and translating that information to the most druggable human Ty (TyH) isozyme. In particular, we designed and synthesized a series of 1-(4-fluorobenzyl)piperazine and 1-(4-fluorobenzyl)piperidine derivatives showing inhibitory activities on TyM at micromolar ranges and more potency than that of the reference compound, kojic acid. The crystal structures of TyBm with inhibitor 3 (IC50 value of 25.11 �gM) and 16 (IC50 value of 5.25 �gM) were solved, confirming the binding poses hypothesized by in silico studies and revealing the main molecular determinants for the binding recognition of the inhibitors.
KeywordMeSH Terms
132. Auiewiriyanukul  W, Saburi  W, Kato  K, Yao  M, Mori  H,     ( 2018 )

Function and structure of GH13_31 �\-glucosidase with high �\-(1��4)-glucosidic linkage specificity and transglucosylation activity.

FEBS letters 592 (13)
PMID : 29870070  :   DOI  :   10.1002/1873-3468.13126    
Abstract >>
�\-Glucosidase hydrolyzes �\-glucosides and transfers �\-glucosyl residues to an acceptor through transglucosylation. In this study, GH13_31 �\-glucosidase BspAG13_31A with high transglucosylation activity is reported in Bacillus sp. AHU2216 and biochemically and structurally characterized. This enzyme is specific to �\-(1��4)-glucosidic linkage as substrates and transglucosylation products. Maltose is the most preferred substrate. Crystal structures of BspAG13_31A wild-type for the substrate-free form and inactive acid/base mutant E256Q in complexes with maltooligosaccharides were solved at 1.6-2.5 ? resolution. BspAG13_31A has a catalytic domain folded by an (�]/�\)8 -barrel. In subsite +1, Ala200 and His203 on �]���\ loop 4 and Asn258 on �]���\ loop 5 are involved in the recognition of maltooligosaccharides. Structural basis for specificity of GH13_31 enzymes to �\-(1��4)-glucosidic linkage is first described.
KeywordMeSH Terms
glycoside hydrolase family 13
transglycosylation
α-glucosidase
133. Agersø  Y, Stuer-Lauridsen  B, Bjerre  K, Jensen  MG, Johansen  E, Bennedsen  M, Brockmann  E, Nielsen  B,     ( 2018 )

Antimicrobial Susceptibility Testing and Tentative Epidemiological Cutoff Values for Five Bacillus Species Relevant for Use as Animal Feed Additives or for Plant Protection.

Applied and environmental microbiology 84 (19)
PMID : 30030233  :   DOI  :   10.1128/AEM.01108-18     PMC  :   PMC6146978    
Abstract >>
Bacillus megaterium (n = 29), Bacillus velezensis (n = 26), Bacillus amyloliquefaciens (n = 6), Bacillus paralicheniformis (n = 28), and Bacillus licheniformis (n = 35) strains from different sources, origins, and time periods were tested for the MICs for nine antimicrobial agents by the CLSI-recommended method (Mueller-Hinton broth, 35�XC, for 18 to 20 h), as well as with a modified CLSI method (Iso-Sensitest [IST] broth, 37�XC [35�XC for B. megaterium], 24 h). This allows a proposal of species-specific epidemiological cutoff values (ECOFFs) for the interpretation of antimicrobial resistance in these species. MICs determined by the modified CLSI method were 2- to 16-fold higher than with the CLSI-recommended method for several antimicrobials. The MIC distributions differed between species for five of the nine antimicrobials. Consequently, use of the modified CLSI method and interpretation of resistance by use of species-specific ECOFFs is recommended. The genome sequences of all strains were determined and used for screening for resistance genes against the ResFinder database and for multilocus sequence typing. A putative chloramphenicol acetyltransferase (cat) gene was found in one B. megaterium strain with an elevated chloramphenicol MIC compared to the other B. megaterium strains. In B. velezensis and B. amyloliquefaciens, a putative tetracycline efflux gene, tet(L), was found in all strains (n = 27) with reduced tetracycline susceptibility but was absent in susceptible strains. All B. paralicheniformis and 23% of B. licheniformis strains had elevated MICs for erythromycin and harbored ermD The presence of these resistance genes follows taxonomy suggesting they may be intrinsic rather than horizontally acquired. Reduced susceptibility to chloramphenicol, streptomycin, and clindamycin could not be explained in all species.IMPORTANCE When commercializing bacterial strains, like Bacillus spp., for feed applications or plant bioprotection, it is required that the strains are free of acquired antimicrobial resistance genes that could potentially spread to pathogenic bacteria, thereby adding to the pool of resistance genes that may cause treatment failures in humans or animals. Conversely, if antimicrobial resistance is intrinsic to a bacterial species, the risk of spreading horizontally to other bacteria is considered very low. Reliable susceptibility test methods and interpretation criteria at the species level are needed to accurately assess antimicrobial resistance levels. In the present study, tentative ECOFFs for five Bacillus species were determined, and the results showed that the variation in MICs followed the respective species. Moreover, putative resistance genes, which were detected by whole-genome sequencing and suggested to be intrinsic rather that acquired, could explain the resistance phenotypes in most cases.
KeywordMeSH Terms
antibiotic
antibiotic resistance
breakpoint
intrinsic resistance
probiotic
134. Guo  J, Erskine  P, Coker  AR, Wood  SP, Cooper  JB,     ( 2017 )

Structural studies of domain movement in active-site mutants of porphobilinogen deaminase from Bacillus megaterium.

Acta crystallographica. Section F, Structural biology communications 73 (Pt 11)
PMID : 29095155  :   DOI  :   10.1107/S2053230X17015436    
Abstract >>
The enzyme porphobilinogen deaminase (PBGD) is one of the key enzymes in tetrapyrrole biosynthesis. It catalyses the formation of a linear tetrapyrrole from four molecules of the substrate porphobilinogen (PBG). It has a dipyrromethane cofactor (DPM) in the active site which is covalently linked to a conserved cysteine residue through a thioether bridge. The substrate molecules are linked to the cofactor in a stepwise head-to-tail manner during the reaction, which is catalysed by a conserved aspartate residue: Asp82 in the B. megaterium enzyme. Three mutations have been made affecting Asp82 (D82A, D82E and D82N) and their crystal structures have been determined at resolutions of 2.7, 1.8 and 1.9 ?, respectively. These structures reveal that whilst the D82E mutant possesses the DPM cofactor, in the D82N and D82A mutants the cofactor is likely to be missing, incompletely assembled or disordered. Comparison of the mutant PBGD structures with that of the wild-type enzyme shows that there are significant domain movements and suggests that the enzyme adopts `open' and `closed' conformations, potentially in response to substrate binding.
KeywordMeSH Terms
Bacillus megaterium
porphobilinogen deaminase
protein crystallography
structural biology
tetrapyrrole biosynthesis
Mutation
135.     ( 2013 )

Characterization of the enzyme CbiH60 involved in anaerobic ring contraction of the cobalamin (vitamin B12) biosynthetic pathway.

The Journal of biological chemistry 288 (1)
PMID : 23155054  :   DOI  :   10.1074/jbc.M112.422535     PMC  :   PMC3537027    
Abstract >>
The anaerobic pathway for the biosynthesis of cobalamin (vitamin B(12)) has remained poorly characterized because of the sensitivity of the pathway intermediates to oxygen and the low activity of enzymes. One of the major bottlenecks in the anaerobic pathway is the ring contraction step, which has not been observed previously with a purified enzyme system. The Gram-positive aerobic bacterium Bacillus megaterium has a complete anaerobic pathway that contains an unusual ring contraction enzyme, CbiH(60), that harbors a C-terminal extension with sequence similarity to the nitrite/sulfite reductase family. To improve solubility, the enzyme was homologously produced in the host B. megaterium DSM319. CbiH(60) was characterized by electron paramagnetic resonance and shown to contain a [4Fe-4S] center. Assays with purified recombinant CbiH(60) demonstrate that the enzyme converts both cobalt-precorrin-3 and cobalt factor III into the ring-contracted product cobalt-precorrin-4 in high yields, with the latter transformation dependent upon DTT and an intact Fe-S center. Furthermore, the ring contraction process was shown not to involve a change in the oxidation state of the central cobalt ion of the macrocycle.
KeywordMeSH Terms
Gene Expression Regulation, Enzymologic
136.     ( 2012 )

phoR sequences as a phylogenetic marker to differentiate the species in the Bacillus subtilis group.

Canadian journal of microbiology 58 (11)
PMID : 23145827  :   DOI  :   10.1139/w2012-106    
Abstract >>
Bacillus subtilis and its closely related species are indistinguishable from one another by morphological characteristics and 16S rDNA sequences. In this study, the partial phoR sequence was tested to determine the phylogenetic relationship of species in the B. subtilis group. Degenerate primers were developed according to the relatively conserved nucleotide sequences of phoR and the linked gene phoP in the B. subtilis group. The primers amplified a 1100 bp phoR fragment from strains representative of 6 species in the B. subtilis group. Based on the sequenced fragments, 26 type strains comprising these 6 species were clearly distinguished. At the intraspecies level, the phoR sequence similarities were 90%-100%, but at the interspecies level, the phoR sequence similarities were 32.8%-75%. Compared with the gyrB sequence, the phoR sequences showed a larger divergence especially at the interspecies levels. Therefore, the phoR sequence may be an efficient alternative marker for phylogenetic and taxonomic analysis of species in the B. subtilis group. Twenty-three Bacillus undomesticated isolates were tested for identification and phylogenetic analysis based on the phoR and gyrB sequences. The 23 isolates could be clearly delineated into 4 distinct groups, 10 as B. subtilis, 3 as B. mojavensis, 2 as B. atrophaeus, and 8 as B. amyloliquefaciens.
KeywordMeSH Terms
Phylogeny
137.     ( 2013 )

Influencing the monophenolase/diphenolase activity ratio in tyrosinase.

Biochimica et biophysica acta 1834 (3)
PMID : 23305929  :   DOI  :   10.1016/j.bbapap.2012.12.021    
Abstract >>
Tyrosinase is a type 3 copper enzyme with great potential for production of commercially valuable diphenols from monophenols. However, the use of tyrosinase is limited by its further oxidation of diphenols to quinones. We recently determined the structure of the Bacillus megaterium tyrosinase revealing a residue, V218, which we proposed to take part in positioning of substrates within the active site. In the structure of catechol oxidase from Ipomoea batatas, the lack of monophenolase activity was attributed to the presence of F261 near CuA. Consequently, we engineered two variants, V218F and V218G. V218F was expected to have a decreased monophenolase activity, due to the bulky residue extending into the active site. Surprisingly, both V218F and V218G exhibited a 9- and 4.4-fold higher monophenolase/diphenolase activity ratio, respectively. X-ray structures of variant V218F display a flexibility of the phenylalanine residue along with an adjacent histidine, which we propose to be the source of the change in activity ratio.
KeywordMeSH Terms
138.     ( 1998 )

Characterization of a theta plasmid replicon with homology to all four large plasmids of Bacillus megaterium QM B1551.

Plasmid 40 (3)
PMID : 9806855  :   DOI  :   10.1006/plas.1998.1359    
Abstract >>
A replicon from one of an array of seven indigenous compatible plasmids of Bacillus megaterium QM B1551 has been cloned and sequenced. The replicon hybridized with all four of the large plasmids (165, 108, 71, and 47 kb) of strain QM B1551. The cloned 2374-bp HindIII fragment was sequenced and contained two upstream palindromes and a large (>419-amino-acid) open reading frame (ORF) truncated at the 3' end. Unlike most plasmid origins, a region of four tandem 12-bp direct repeats was located within the ORF. The direct repeats alone were incompatible with the replicon, suggesting that they are iterons and that the plasmid probably replicates by theta replication. The ORF product was shown to act in trans. A small region with similarity to the B. subtilis chromosomal origin membrane binding region was detected as were possible binding sites for DnaA and IHF proteins. Deletion analysis showed the minimal replicon to be a 1675-bp fragment containing the incomplete ORF plus 536 bp upstream. The predicted ORF protein of >48 kDa was basic and rich in glutamate + glutamine (16%). There was no significant amino acid similarity to any gene, nor were there any obvious motifs present in the ORF. The data suggest that this is a theta replicon with an expressed rep gene required for replication. The replicon contains its iterons within the gene and has no homology to reported replicons. It is the first characterization of a B. megaterium replicon.
KeywordMeSH Terms
139.     ( 1998 )

Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon.

The Biochemical journal 335 (Pt 1) (N/A)
PMID : 9742225  :   DOI  :   10.1042/bj3350159     PMC  :   PMC1219764    
Abstract >>
A 16 kb DNA fragment has been isolated from a Bacillus megaterium genomic library and fully sequenced. The fragment contains 15 open reading frames, 14 of which are thought to constitute a B. megaterium cobalamin biosynthetic (cob) operon. Within the operon, 11 genes display similarity to previously identified Salmonella typhimurium cobalamin biosynthetic genes (cbiH60, -J, -C, -D, -ET, -L, -F, -G, -A, cysGA and btuR), whereas three do not (cbiW, -X and -Y). The genes of the B. megaterium cob operon were compared with the cobalamin biosynthetic genes of Pseudomonas denitrificans, Methanococcus jannaschii and Synechocystis sp. Taking into account the presence of cbiD and cbiG, the absence of a cobF, cobG and cobN, -S and -T, it was concluded that B. megaterium, M. jannaschii and Synechocystis sp., like S. typhimurium, synthesize cobalamin by an anaerobic pathway, in which cobalt is added at an early stage and molecular oxygen is not required.
KeywordMeSH Terms
140.     ( 1998 )

Bacillus subtilis ORF yybQ encodes a manganese-dependent inorganic pyrophosphatase with distinctive properties: the first of a new class of soluble pyrophosphatase?

Microbiology (Reading, England) 144 (Pt 9) (N/A)
PMID : 9782505  :   DOI  :   10.1099/00221287-144-9-2563    
Abstract >>
The N-terminal 15 amino acids of the major protein associated with inorganic pyrophosphatase activity in Bacillus subtilis WB600 are identical to those of B. subtilis ORF yybQ. This ORF was amplified from B. subtilis WB600 DNA by PCR and cloned into an overexpression vector in Escherichia coli. Induction of overexpression produced a soluble protein of 34,000 Da by SDS-PAGE and by matrix-assisted laser desorption and ionization mass spectrometry. The overexpressed protein had a high specific activity for the hydrolysis of magnesium pyrophosphate, and was specifically and reversibly activated by Mn2+ ions. These properties are identical to those of inorganic pyrophosphatase purified from B. subtilis WB600. No significant similarity was found between the derived sequence of the B. subtilis yybQ-encoded protein and published sequences of identified inorganic pyrophosphatases of Eukarya, Bacteria or Archaea domains. However, there is significant similarity to three putative proteins of unknown function from the archaea Methanococcus jannaschii and Archaeoglobus fulgidus, and from Streptococcus gordonii. The genomes of B. subtilis, M. jannaschii and A. fulgidus do not contain sequences similar to those of hitherto known soluble inorganic pyrophosphatases. The present findings, together with a survey of the properties of inorganic pyrophosphatases from 38 different sources, suggest that the B. subtilis yybQ-encoded protein is the first fully characterized member of a new class of inorganic pyrophosphatase.
KeywordMeSH Terms
141.     ( 1998 )

Cloning, expression, and catabolite repression of a gene encoding beta-galactosidase of Bacillus megaterium ATCC 14581.

Journal of bacteriology 180 (17)
PMID : 9721318  :   PMC  :   PMC107490    
Abstract >>
A gene encoding beta-galactosidase, designated mbgA, was isolated from Bacillus megaterium ATCC 14581. Chromosomal beta-galactosidase production could be dramatically induced by lactose but not by isopropyl-beta-D-thiogalactopyranoside (IPTG) and was subject to catabolite repression by glucose. Disruption of mbgA in the B. megaterium chromosome resulted in loss of lactose-inducible beta-galactosidase production. A 27-bp inverted repeat was found to overlap the mbgA promoter sequence. Two partially overlapping catabolite-responsive elements (CREs) were identified within the inverted repeat. Base substitutions within CRE-I and/or CRE-II caused partial relief from catabolite repression. The results suggest that the 27-bp inverted repeat may serve as a target for a catabolite repressor(s).
KeywordMeSH Terms
142.     ( 1999 )

Polyhydroxyalkanoate inclusion body-associated proteins and coding region in Bacillus megaterium.

Journal of bacteriology 181 (2)
PMID : 9882674  :   PMC  :   PMC93414    
Abstract >>
Polyhydroxyalkanoic acids (PHA) are carbon and energy storage polymers that accumulate in inclusion bodies in many bacteria and archaea in response to environmental conditions. This work presents the results of a study of PHA inclusion body-associated proteins and an analysis of their coding region in Bacillus megaterium 11561. A 7, 917-bp fragment of DNA was cloned and shown to carry a 4,104-bp cluster of 5 pha genes, phaP, -Q, -R, -B, and -C. The phaP and -Q genes were shown to be transcribed in one orientation, each from a separate promoter, while immediately upstream, phaR, -B, and -C were divergently transcribed as a tricistronic operon. Transfer of this gene cluster to Escherichia coli and to a PhaC- mutant of Pseudomonas putida gave a Pha+ phenotype in both strains. Translational fusions to the green fluorescent protein localized PhaP and PhaC to the PHA inclusion bodies in living cells. The data presented are consistent with the hypothesis that the extremely hydrophilic protein PhaP is a storage protein and suggests that PHA inclusion bodies are not only a source of carbon, energy, and reducing equivalents but are also a source of amino acids.
KeywordMeSH Terms
Genes, Bacterial
Multigene Family
Operon
143.     ( 1998 )

Trans activation of the Escherichia coli ato structural genes by a regulatory protein from Bacillus megaterium: potential use in polyhydroxyalkanoate production.

Applied microbiology and biotechnology 49 (6)
PMID : 9684307  :  
Abstract >>
A Bacillus megaterium genomic fragment, which encoded an activator homologous to sigma 54 regulators and which was capable of activating Escherichia coli ato genes in trans, was detected in a gene library of B. megaterium screened for beta-ketothiolase activity. The fragment presented only one complete open reading frame (ORF1), which encoded a protein of 398 amino acids. The recombinant plasmid complemented mutations in the Escherichia coli atoC regulatory gene. The constitutive expression of the E. coli ato operon mediated by ORF1 could be useful for the synthesis of polyhydroxyalkanoates with different flexibility properties by recombinant E. coli strains.
KeywordMeSH Terms
Genes, Bacterial
Transcriptional Activation
144.     ( 1998 )

Horizontal spread of mer operons among gram-positive bacteria in natural environments.

Microbiology (Reading, England) 144 (Pt 3) (N/A)
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.
KeywordMeSH Terms
DNA Transposable Elements
145.     ( 1998 )

Cobalamin (vitamin B12) biosynthesis--cloning, expression and crystallisation of the Bacillus megaterium S-adenosyl-L-methionine-dependent cobalt-precorrin-4 transmethylase CbiF.

European journal of biochemistry 254 (2)
PMID : 9660189  :   DOI  :   10.1046/j.1432-1327.1998.2540341.x    
Abstract >>
The Bacillus megaterium cbiF, encoding the cobalt-precorrin-4 S-adenosyl-L-methionine-dependent transmethylase of the anaerobic cobalamin biosynthetic pathway, has been cloned and overexpressed as a His-tagged recombinant protein in Escherichia coli. The protein was purified to homogeneity by a combination of metal chelate chromatography and high-resolution anion-exchange chromatography. The protein migrated with a subunit mass of 31 kDa by SDS/PAGE and with a molecular mass of 62 kDa by analytical gel filtration, suggesting that the native recombinant protein is a homodimer. The His-tagged protein was physiologically active as it was able to complement a Salmonella typhimurium cbiF mutant. However, the protein did not bind S-adenosyl-L-methionine with the same avidity as observed with other corrin biosynthetic transmethylases. A crystallisation screen of the purified protein led to the identification of two discrete crystal forms. One of these forms has been characterised and a full data set collected.
KeywordMeSH Terms
Escherichia coli Proteins
146.     ( 1998 )

Evidence against the Bm1P1 protein as a positive transcription factor for barbiturate-mediated induction of cytochrome P450BM-1 in bacillus megaterium.

The Journal of biological chemistry 273 (14)
PMID : 9525898  :   DOI  :   10.1074/jbc.273.14.7996    
Abstract >>
The Bm1P1 protein was previously proposed to act as a positive transcription factor involved in barbiturate-mediated induction of cytochrome P450BM-1 in Bacillus megaterium. We now report that the bm1P1 gene encodes a protein of 217 amino acids, rather than the 98 amino acids as reported previously. In vitro gel shift assays indicate that the Bm1P1 protein did not interact with probes comprising the regulatory regions of the P450BM-1 gene. Moreover, disruption of the bm1P1 gene did not markedly affect barbiturate induction of P450BM-1 expression. A multicopy plasmid harboring only the P450BM-1 promoter region could increase expression of the chromosome-encoded P450BM-1. The level of expression is comparable with that shown by a multicopy plasmid harboring the P450BM-1 promoter region along with the bm1P1 gene. These results strongly suggest that the Bm1P1 protein is unlikely to act as a positive regulator for barbiturate induction of P450BM-1 expression. Finally, deletion of the Barbie box did not markedly diminish the effect of pentobarbital on expression of a reporter gene transcriptionally fused to the P450BM-1 promoter. This suggests that the Barbie box is unlikely to be a key element in barbiturate-mediated induction of P450BM-1.
KeywordMeSH Terms
Bacterial Proteins
147.     ( 1997 )

Contribution of glucose kinase to glucose repression of xylose utilization in Bacillus megaterium.

Journal of bacteriology 179 (23)
PMID : 9393732  :   DOI  :   10.1128/jb.179.23.7603-7605.1997     PMC  :   PMC179718    
Abstract >>
The glk gene from Bacillus megaterium, which encodes glucose kinase, was isolated and analyzed. Disruption by a transcriptional glk-luxAB fusion indicated that glk is the only glucose kinase gene in that strain but did not affect growth of that mutant on glucose. Determination of luciferase activity under various growth conditions revealed constitutive transcription of glk. Expression of a xylA-lacZ fusion was repressed by glucose in the strain with the glk disruption about twofold less efficiently than in the wild type. The potential contribution of glk expression to glucose repression is discussed.
KeywordMeSH Terms
Gene Expression Regulation, Bacterial
148.     ( 1998 )

Gas vesicle genes identified in Bacillus megaterium and functional expression in Escherichia coli.

Journal of bacteriology 180 (9)
PMID : 9573198  :   PMC  :   PMC107188    
Abstract >>
Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in liquid to access oxygen and/or light. In halobacteria, gas vesicle production is encoded in a 9-kb cluster of 14 genes (4 of known function). In cyanobacteria, the number of genes involved has not been determined. We now report the cloning and sequence analysis of an 8,142-bp cluster of 15 putative gas vesicle genes (gvp) from Bacillus megaterium VT1660 and their functional expression in Escherichia coli. Evidence includes homologies by sequence analysis to known gas vesicle genes, the buoyancy phenotype of E. coli strains that carry this gvp gene cluster, the presence of pressure-sensitive, refractile bodies in phase-contrast microscopy, structural details in phase-contrast microscopy, structural details in direct interference-contrast microscopy, and shape and size revealed by transmission electron microscopy. In B. megaterium, the gvp region carries a cluster of 15 putative genes arranged in one orientation; they are open reading frame 1 and gvpA, -P, -Q, -B, -R, -N, -F, -G, -L, -S, -K, -J, -T, and -U, of which the last 11 genes, in a 5.7-kb gene cluster, are the maximum required for gas vesicle synthesis and function in E. coli. To our knowledge, this is the first example of a functional gas vesicle gene cluster in nonaquatic bacteria and the first example of the interspecies transfer of genes resulting in the synthesis of a functional organelle.
KeywordMeSH Terms
Gases
Genes, Bacterial
Multigene Family

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