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1. Riccio  ML, Pallecchi  L, Fontana  R, Rossolini  GM,     ( 2001 )

In70 of plasmid pAX22, a bla(VIM-1)-containing integron carrying a new aminoglycoside phosphotransferase gene cassette.

Antimicrobial agents and chemotherapy 45 (4)
PMID : 11257042  :   DOI  :   10.1128/AAC.45.4.1249-1253.2001     PMC  :   PMC90451    
Abstract >>
An Achromobacter xylosoxydans strain showing broad-spectrum resistance to beta-lactams (including carbapenems) and aminoglycosides was isolated at the University Hospital of Verona (Verona, Italy). This strain was found to produce metallo-beta-lactamase activity and to harbor a 30-kb nonconjugative plasmid, named pAX22, carrying a bla(VIM-1) determinant inserted into a class 1 integron. Characterization of this integron, named In70, revealed an original array of four gene cassettes containing, respectively, the bla(VIM-1) gene and three different aminoglycoside resistance determinants, including an aacA4 allele, a new aph-like gene named aphA15, and an aadA1 allele. The aphA15 gene is the first example of an aph-like gene carried on a mobile gene cassette, and its product exhibits close similarity to the APH(3')-IIa aminoglycoside phosphotransferase encoded by Tn5 (36% amino acid identity) and to an APH(3')-IIb enzyme from Pseudomonas aeruginosa (38% amino acid identity). Expression of the cloned aphA15 gene in Escherichia coli reduced the susceptibility to kanamycin and neomycin as well as (slightly) to amikacin, netilmicin, and streptomycin. Characterization of the 5' and 3' conserved segments of In70 and of their flanking regions showed that In70 belongs to the group of class 1 integrons associated with defective transposon derivatives originating from Tn402-like elements. The structure of the 3' conserved segment indicates the closest ancestry with members of the In0-In2 lineage. In70, with its array of cassette-borne resistance genes, can mediate broad-spectrum resistance to most beta-lactams and aminoglycosides.
KeywordMeSH Terms
beta-Lactam Resistance
DNA Transposable Elements
Genes, Bacterial
2. Vedler  E, Kõiv  V, Heinaru  A,     ( 2000 )

Analysis of the 2,4-dichlorophenoxyacetic acid-degradative plasmid pEST4011 of Achromobacter xylosoxidans subsp. denitrificans strain EST4002.

Gene 255 (2)
PMID : 11024288  :   DOI  :   10.1016/s0378-1119(00)00329-2    
Abstract >>
The 2,4-dichlorophenoxyacetic acid (2,4-D)-degradative bacterium Achromobacter xylosoxidans subsp. denitrificans strain EST4002, isolated in Estonia more than 10years ago, was found to contain the 70kb plasmid pEST4011 that is responsible for the bacterium having had obtained a stable 2,4-D(+) phenotype. The tfd-like genes for 2, 4-D degradation of the strain EST4002 were located on a 10.5kb region of pEST4011, but without functional genes coding for chloromuconate cycloisomerase and chlorodienelactone hydrolase. The latter two genes are probably encoded by homologous, tcb-like genes, located elsewhere on pEST4011. We also present evidence of two copies of insertion element IS1071-like sequences on pEST4011. IS1071 is a class II (Tn3 family) insertion element, associated with different catabolic genes and operons and globally distributed in the recent past. We speculate that this insertion element might have had a role in the formation of plasmid pEST4011. The 28kb plasmid pEST4012 is generated by deletion from pEST4011 when cells of A. xylosoxidans EST4002 are grown in the absence of 2,4-D in growth medium. We propose that this is the result of homologous recombination between the two putative copies of IS1071-like sequences on pEST4011.
KeywordMeSH Terms
3. Kõiv  V, Vedler  E,     ( 2000 )

TfdR, the LysR-type transcriptional activator, is responsible for the activation of the tfdCB operon of Pseudomonas putida 2, 4-dichlorophenoxyacetic acid degradative plasmid pEST4011.

Gene 245 (1)
PMID : 10713456  :   DOI  :   10.1016/s0378-1119(00)00017-2    
Abstract >>
In Pseudomonas putida EST4021, the tfdCB operon of plasmid pEST4011 encodes enzymes involved in 2,4-dichlorophenoxyacetic acid degradation. We have identified a gene, tfdR, important for the regulation of the tfdCB operon. Sequence analysis of the tfdR gene revealed an open reading frame with amino acid sequence similar to the LysR family of transcriptional activators. The tfdR gene is located upstream and transcribed divergently from the tfdCB operon. Utilizing primer extension analysis, the transcription initiation sites of the gene tfdR and the tfdCB operon were localized 85 (84)bp and 292bp upstream from the coding sequences of these genes, respectively. Multiple sequence analysis revealed that the genes tfdR, tfdC and tfdB of plasmid pEST4011 are most similar to the regulatory gene tfdR and the module 2 genes tfdC(II) and tfdB(II) of pJP4, respectively. The promoter-operator sequences of tfdR and its target tfdCB operon of pEST4011 have regions with highly conserved nucleotides characteristic for the catechol-subgroup LysR-type transcriptional activators. We showed that the pEST4011 tfdR gene product activates the expression of the tfdCB operon and the effector molecule for TfdR is 2,4-dichloro-cis,cis-muconate. Our data indicate that the structure and the mode of regulation of tfd genes are similar, despite the bacteria being isolated from different geographical regions.
KeywordMeSH Terms
4. Heylen  K, Vanparys  B, Gevers  D, Wittebolle  L, Boon  N, De Vos  P,     ( 2007 )

Nitric oxide reductase (norB) gene sequence analysis reveals discrepancies with nitrite reductase (nir) gene phylogeny in cultivated denitrifiers.

Environmental microbiology 9 (4)
PMID : 17359277  :   DOI  :   10.1111/j.1462-2920.2006.01194.x    
Abstract >>
Gene sequence analysis of cnorB and qnorB, both encoding nitric oxide reductases, was performed on pure cultures of denitrifiers, for which previously nir genes were analysed. Only 30% of the 227 denitrifying strains rendered a norB amplicon. The cnorB gene was dominant in Alphaproteobacteria, and dominantly coexisted with the nirK gene, coding for the copper-containing nitrite reductase. Both norB genes were equally present in Betaproteobacteria but no linked distributional pattern of nir and norB genes could be observed. The overall cnorB phylogeny was not congruent with the widely accepted organism phylogeny based on 16S rRNA gene sequence analysis, with strains from different bacterial classes having identical cnorB sequences. Denitrifiers and non-denitrifiers could be distinguished through qnorB gene phylogeny, without further grouping at a higher taxonomic resolution. Comparison of nir and norB phylogeny revealed that genetic linkage of both genes is not widespread among denitrifiers. Thus, independent evolution of the genes for both nitrogen oxide reductases does also occur.
KeywordMeSH Terms
5. Diavatopoulos  DA, Cummings  CA, van der Heide  HG, van Gent  M, Liew  S, Relman  DA, Mooi  FR,     ( 2006 )

Characterization of a highly conserved island in the otherwise divergent Bordetella holmesii and Bordetella pertussis genomes.

Journal of bacteriology 188 (24)
PMID : 17041054  :   DOI  :   10.1128/JB.01081-06     PMC  :   PMC1698220    
Abstract >>
The recently discovered pathogen Bordetella holmesii has been isolated from the airways and blood of diseased humans. Genetic events contributing to the emergence of B. holmesii are not understood, and its phylogenetic position among the bordetellae remains unclear. To address these questions, B. holmesii strains were analyzed by comparative genomic hybridization (CGH) to a Bordetella pertussis microarray and by multilocus sequence typing. Both methods indicated substantial sequence divergence between B. pertussis and B. holmesii. However, CGH identified a putative pathogenicity island of 66 kb that is highly conserved between these species and contains several IS481 elements that may have been laterally transferred from B. pertussis to B. holmesii. This island contains, among other genes, a functional, iron-regulated locus encoding the biosynthesis, export, and uptake of the siderophore alcaligin. The acquisition of this genomic island by B. holmesii may have significantly contributed to its emergence as a human pathogen. Horizontal gene transfer between B. pertussis and B. holmesii may also explain the unusually high sequence identity of their 16S rRNA genes.
KeywordMeSH Terms
6. Heylen  K, Gevers  D, Vanparys  B, Wittebolle  L, Geets  J, Boon  N, De Vos  P,     ( 2006 )

The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers.

Environmental microbiology 8 (11)
PMID : 17014499  :   DOI  :   10.1111/j.1462-2920.2006.01081.x    
Abstract >>
Gene sequence analysis of nirS and nirK, both encoding nitrite reductases, was performed on cultivated denitrifiers to assess their incidence in different bacterial taxa and their taxonomical value. Almost half of the 227 investigated denitrifying strains did not render an nir amplicon with any of five previously described primers. NirK and nirS were found to be prevalent in Alphaproteobacteria and Betaproteobacteria, respectively, nirK was detected in the Firmicutes and Bacteroidetes and nirS and nirK with equal frequency in the Gammaproteobacteria. These observations deviated from the hitherto reported incidence of nir genes in bacterial taxa. NirS gene phylogeny was congruent with the 16S rRNA gene phylogeny on family or genus level, although some strains did group within clusters of other bacterial classes. Phylogenetic nirK gene sequence analysis was incongruent with the 16S rRNA gene phylogeny. NirK sequences were also found to be significantly more similar to nirK sequences from the same habitat than to nirK sequences retrieved from highly related taxa. This study supports the hypothesis that horizontal gene transfer events of denitrification genes have occurred and underlines that denitrification genes should not be linked with organism diversity of denitrifiers in cultivation-independent studies.
KeywordMeSH Terms
7. Vedler  E, Vahter  M, Heinaru  A,     ( 2004 )

The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation.

Journal of bacteriology 186 (21)
PMID : 15489427  :   DOI  :   10.1128/JB.186.21.7161-7174.2004     PMC  :   PMC523222    
Abstract >>
The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium Achromobacter xylosoxidans subsp. denitrificans strain EST4002 contains plasmid pEST4011. This plasmid ensures its host a stable 2,4-D(+) phenotype. We determined the complete 76,958-bp nucleotide sequence of pEST4011. This plasmid is a deletion and duplication derivative of pD2M4, the 95-kb highly unstable laboratory ancestor of pEST4011, and was self-generated during different laboratory manipulations performed to increase the stability of the 2,4-D(+) phenotype of the original strain, strain D2M4(pD2M4). The 47,935-bp catabolic region of pEST4011 forms a transposon-like structure with identical copies of the hybrid insertion element IS1071::IS1471 at the two ends. The catabolic regions of pEST4011 and pJP4, the best-studied 2,4-D-degradative plasmid, both contain homologous, tfd-like genes for complete 2,4-D degradation, but they have little sequence similarity other than that. The backbone genes of pEST4011 are most similar to the corresponding genes of broad-host-range self-transmissible IncP1 plasmids. The backbones of the other three IncP1 catabolic plasmids that have been sequenced (the 2,4-D-degradative plasmid pJP4, the haloacetate-catabolic plasmid pUO1, and the atrazine-catabolic plasmid pADP-1) are nearly identical to the backbone of R751, the archetype plasmid of the IncP1 beta subgroup. We show that despite the overall similarity in plasmid organization, the pEST4011 backbone is sufficiently different (51 to 86% amino acid sequence identity between individual backbone genes) from the backbones of members of the three IncP1 subgroups (the alpha, beta, and gamma subgroups) that it belongs to a new IncP1subgroup, the delta subgroup. This conclusion was also supported by a phylogenetic analysis of the trfA2, korA, and traG gene products of different IncP1 plasmids.
KeywordMeSH Terms
DNA Transposable Elements
Sequence Analysis, DNA
8. Hill  JE, Penny  SL, Crowell  KG, Goh  SH, Hemmingsen  SM,     ( 2004 )

cpnDB: a chaperonin sequence database.

Genome research 14 (8)
PMID : 15289485  :   DOI  :   10.1101/gr.2649204     PMC  :   PMC509277    
Abstract >>
Type I chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes. Sequences of cpn60 genes, encoding 60-kDa chaperonin protein subunits (CPN60, also known as GroEL or HSP60), are useful for phylogenetic studies and as targets for detection and identification of organisms. Conveniently, a 549-567-bp segment of the cpn60 coding region can be amplified with universal PCR primers. Here, we introduce cpnDB, a curated collection of cpn60 sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic, and microbial ecology studies. The growing database currently contains approximately 2000 records covering over 240 genera of bacteria, eukaryotes, and archaea. The database also contains over 60 sequences for the archaeal Type II chaperonin (thermosome, a homolog of eukaryotic cytoplasmic chaperonin) from 19 archaeal genera. As the largest curated collection of sequences available for a protein-encoding gene, cpnDB provides a resource for researchers interested in exploiting the power of cpn60 as a diagnostic or as a target for phylogenetic or microbial ecology studies, as well as those interested in broader subjects such as lateral gene transfer and codon usage. We built cpnDB from open source tools and it is available at http://cpndb.cbr.nrc.ca.
KeywordMeSH Terms
9. Yun  H, Lim  S, Cho  BK, Kim  BG,     ( 2004 )

omega-Amino acid:pyruvate transaminase from Alcaligenes denitrificans Y2k-2: a new catalyst for kinetic resolution of beta-amino acids and amines.

Applied and environmental microbiology 70 (4)
PMID : 15066855  :   DOI  :   10.1128/aem.70.4.2529-2534.2004     PMC  :   PMC383019    
Abstract >>
Alcaligenes denitrificans Y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed omega-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic beta-amino acid, and the corresponding structural gene (aptA) was cloned. The gene was functionally expressed in Escherichia coli BL21 by using an isopropyl-beta-D-thiogalactopyranoside (IPTG)-inducible pET expression system (9.6 U/mg), and the recombinant AptA was purified to show a specific activity of 77.2 U/mg for L-beta-amino-n-butyric acid (L-beta-ABA). The enzyme converts various beta-amino acids and amines to the corresponding beta-keto acids and ketones by using pyruvate as an amine acceptor. The apparent K(m) and V(max) for L-beta-ABA were 56 mM and 500 U/mg, respectively, in the presence of 10 mM pyruvate. In the presence of 10 mM L-beta-ABA, the apparent K(m) and V(max) for pyruvate were 11 mM and 370 U/mg, respectively. The enzyme exhibits high stereoselectivity (E > 80) in the kinetic resolution of 50 mM D,L-beta-ABA, producing optically pure D-beta-ABA (99% enantiomeric excess) with 53% conversion.
KeywordMeSH Terms
10. Hoitink  CW, Woudt  LP, Turenhout  JC, van de Kamp  M, Canters  GW,     ( 1990 )

Isolation and sequencing of the Alcaligenes denitrificans azurin-encoding gene: comparison with the genes encoding blue copper proteins from Pseudomonas aeruginosa and Alcaligenes faecalis.

Gene 90 (1)
PMID : 2116366  :   DOI  :   10.1016/0378-1119(90)90434-s    
Abstract >>
The gene (azu) encoding azurin from Alcaligenes denitrificans has been cloned and sequenced. The gene codes for a pre-protein with a 19-aa signal peptide. Comparison with the sequences coding for the blue copper proteins from Pseudomonas aeruginosa and Alcaligenes faecalis reveals the presence of ntrA and fnr boxes in front of all three genes, instead of a regular [-10, -35]-promoter. In P. aeruginosa, the azu gene is terminated by a bidirectional terminator and flanked by open reading frames on the opposite strand.
KeywordMeSH Terms
Genes, Bacterial
11. Ruldeekulthamrong  P, Maeda  S, Kato  S, Shinji  N, Sittipraneed  S, Packdibamrung  K, Misono  H,     ( 2008 )

Molecular characterization of lysine 6-dehydrogenase from Achromobacter denitrificans.

BMB reports 41 (11)
PMID : 19017491  :   DOI  :   10.5483/bmbrep.2008.41.11.790    
Abstract >>
An inducible lysine 6-dehydrogenase (Lys 6-DH), which catalyzes the oxidative deamination of the 6-amino group of L-lysine in the presence of NAD(+), was purified to homogeneity from Achromobacter denitrificans, yielding a homodimeric protein of 80 kDa. The enzyme was specific for the substrate L-lysine and NAD(+) served as a cofactor. The dimeric enzyme associated into a hexamer in the presence of 10 mM L-lysine. The K(m) values for L-lysine and NAD(+) were 5.0 and 0.09 mM, respectively. The lys 6-dh gene was cloned and overexpressed in E. coli. The open reading frame was 1,107 nucleotides long and encoded a peptide containing 368 amino acids with 39,355 Da. The recombinant enzyme was purified to homogeneity and characterized. Enzyme activities and kinetic properties of the recombinant enzyme were almost the same as those of the endogenous enzyme obtained from A. denitrificans. Crystals of the enzyme were obtained using the hanging drop method.
KeywordMeSH Terms
12. Ingvorsen  K, Højer-Pedersen  B, Godtfredsen  SE,     ( 1991 )

Novel cyanide-hydrolyzing enzyme from Alcaligenes xylosoxidans subsp. denitrificans.

Applied and environmental microbiology 57 (6)
PMID : 1872607  :   PMC  :   PMC183468    
Abstract >>
A cyanide-metabolizing bacterium, strain DF3, isolated from soil was identified as Alcaligenes xylosoxidans subsp. denitrificans. Whole cells and cell extracts of strain DF3 catalyzed hydrolysis of cyanide to formate and ammonia (HCN + 2H2O----HCOOH + NH3) without forming formamide as a free intermediate. The cyanide-hydrolyzing activity was inducibly produced in cells during growth in cyanide-containing media. Cyanate (OCN-) and a wide range of aliphatic and aromatic nitriles were not hydrolyzed by intact cells of A. xylosoxidans subsp. denitrificans DF3. Strain DF3 hydrolyzed cyanide with great efficacy. Thus, by using resting induced cells at a concentration of 11.3 mg (dry weight) per ml, the cyanide concentration could be reduced from 0.97 M (approximately 25,220 ppm) to less than 77 nM (approximately 0.002 ppm) in 55 h. Enzyme purification established that cyanide hydrolysis by A. xylosoxidans subsp. denitrificans DF3 was due to a single intracellular enzyme. The soluble enzyme was purified approximately 160-fold, and the first 25 NH2-terminal amino acids were determined by automated Edman degradation. The molecular mass of the active enzyme (purity, greater than 97% as determined by amino acid sequencing) was estimated to be greater than 300,000 Da. The cyanide-hydrolyzing enzyme of A. xylosoxidans subsp. denitrificans DF3 was tentatively named cyanidase to distinguish it from known nitrilases (EC which act on organic nitriles.
KeywordMeSH Terms
Waste Disposal, Fluid
13. Gomila  M, Prince-Manzano  C, Svensson-Stadler  L, Busquets  A, Erhard  M, Martínez  DL, Lalucat  J, Moore  ER,     ( 2014 )

Genotypic and phenotypic applications for the differentiation and species-level identification of achromobacter for clinical diagnoses.

PloS one 9 (12)
PMID : 25474264  :   DOI  :   10.1371/journal.pone.0114356     PMC  :   PMC4256396    
Abstract >>
The Achromobacter is a genus in the family Alcaligenaceae, comprising fifteen species isolated from different sources, including clinical samples. The ability to detect and correctly identify Achromobacter species, particularly A. xylosoxidans, and differentiate them from other phenotypically similar and genotypically related Gram-negative, aerobic, non-fermenting species is important for patients with cystic fibrosis (CF), as well as for nosocomial and other opportunistic infections. Traditional phenotypic profile-based analyses have been demonstrated to be inadequate for reliable identifications of isolates of Achromobacter species and genotypic-based assays, relying upon comparative 16S rRNA gene sequence analyses are not able to insure definitive identifications of Achromobacter species, due to the inherently conserved nature of the gene. The uses of alternative methodologies to enable high-resolution differentiation between the species in the genus are needed. A comparative multi-locus sequence analysis (MLSA) of four selected 'house-keeping' genes (atpD, gyrB, recA, and rpoB) assessed the individual gene sequences for their potential in developing a reliable, rapid and cost-effective diagnostic protocol for Achromobacter species identifications. The analysis of the type strains of the species of the genus and 46 strains of Achromobacter species showed congruence between the cluster analyses derived from the individual genes. The MLSA gene sequences exhibited different levels of resolution in delineating the validly published Achromobacter species and elucidated strains that represent new genotypes and probable new species of the genus. Our results also suggested that the recently described A. spritinus is a later heterotypic synonym of A. marplatensis. Strains were analyzed, using whole-cell Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF MS), as an alternative phenotypic profile-based method with the potential to support the identifications determined by the genotypic DNA sequence-based MLSA. The MALDI-TOF MS data showed good accordance in strain groupings and identifications by the MLSA data.
KeywordMeSH Terms
14. Di Pilato  V, Pollini  S, Rossolini  GM,     ( 2014 )

Characterization of plasmid pAX22, encoding VIM-1 metallo-�]-lactamase, reveals a new putative mechanism of In70 integron mobilization.

The Journal of antimicrobial chemotherapy 69 (1)
PMID : 23928025  :   DOI  :   10.1093/jac/dkt311    
Abstract >>
VIM-type enzymes are among the most widespread acquired metallo-�]-lactamases among Gram-negative pathogens. Integron In70 is a class 1 integron that has emerged as a successful genetic support for blaVIM-1 (one of the most prevalent blaVIM allelic variants) in Gram-negative non-fermenters, and is usually chromosome borne. The objective of this study was to characterize plasmid pAX22 from Achromobacter xylosoxidans AX22, which represents the only In70-harbouring plasmid known so far, to gather insights into the mechanisms of evolution and dissemination of In70-like elements. The complete sequence of pAX22 was obtained by pyrosequencing and assembled with Roche Newbler software. The draft sequence, completed using a PCR-based strategy, was annotated via the BASys tool and compared with known sequences using BLAST algorithms. The backbone of pAX22 showed significant similarity with that of pNOR-2000, a blaVIM-2-harbouring plasmid from Pseudomonas aeruginosa, and with the TnCP23 transposon. The three elements differed from each other mainly by the class 1 integron cassette arrays and by some integron-associated structures. In pAX22, In70 was associated with a novel putative transposon, Tn7017, composed of a defective Tn402-like transposon carrying In70 and the ISPa17 insertion sequence. Plasmid pAX22 belongs to a lineage of plasmids circulating among Gram-negative non-fermenters. In70 was probably acquired by pAX22 by transposition of Tn7017, revealing a novel putative mechanism of In70 mobilization. Our results highlight the potential role that ISPa17 could have in mobilizing defective Tn402-like transposons carrying class 1 integrons.
KeywordMeSH Terms
Gram negative
insertion sequence
15. Ridderberg  W, Wang  M,     ( 2012 )

Multilocus sequence analysis of isolates of Achromobacter from patients with cystic fibrosis reveals infecting species other than Achromobacter xylosoxidans.

Journal of clinical microbiology 50 (8)
PMID : 22675125  :   DOI  :   10.1128/JCM.00728-12     PMC  :   PMC3421494    
Abstract >>
A multilocus sequence analysis (MLSA) scheme was developed for characterization of strains and species from the genus Achromobacter, which are increasingly recovered from patients with cystic fibrosis (CF). Five conserved housekeeping genes were selected for the MLSA, which was applied to a diverse collection of 77 strains originating from Europe, Asia, and South America and including type strains of the seven recognized Achromobacter species, six environmental strains, eight non-CF clinical strains, and 56 CF clinical strains. The discriminatory power of MLSA, based on 2,098 nucleotides (nt), was much superior to a 16S rRNA gene comparison based on 1,309 nt. Congruence was observed between single-gene trees and a concatenated gene tree. MLSA differentiated all seven current Achromobacter species and also demonstrated the presence of at least four novel potential species within the genus. CF isolates were predominantly Achromobacter xylosoxidans (64%), an undescribed Achromobacter species (18%), and Achromobacter ruhlandii (7%). A clone of Achromobacter, which has spread among patients from Danish CF centers in Aarhus and Copenhagen, was identified as Achromobacter ruhlandii. MLSA facilitates the specific identification of isolates of Achromobacter necessary for describing their role in clinical infections.
KeywordMeSH Terms
Multilocus Sequence Typing
16.     ( 1996 )

Sequence analysis of the 2,4-dichlorophenol hydroxylase gene tfdB and 3,5-dichlorocatechol 1,2-dioxygenase gene tfdC of 2,4-dichlorophenoxyacetic acid degrading plasmid pEST4011.

Gene 174 (2)
PMID : 8890750  :   DOI  :   10.1016/0378-1119(96)00043-1    
Abstract >>
Chlorocatechol 1,2-dioxygenase (CC12O) and 1,2-dichlorophenol hydroxylase (DCPH) encoding genes tfdC and tfdB are located on a 4.2-kb DNA fragment cloned from the 2,4-dichlorophenoxyacetic acid (2,4D) degrading plasmid pEST4011. The nucleotide sequences of tfdC and tfdB were determined. The DCPH is coded by a 1758-bp gene and CC12O is coded by a 762-bp gene. The deduced M(r) of these proteins are 64.09 kDa and 28.2 kDa, respectively. Expression analysis of tfdB and tfdC in Escherichia coli suggested that these genes form one operon, tfdCB.
KeywordMeSH Terms
17.     ( 1993 )

X-ray analysis and spectroscopic characterization of M121Q azurin. A copper site model for stellacyanin.

Journal of molecular biology 229 (4)
PMID : 8383207  :   DOI  :   10.1006/jmbi.1993.1101    
Abstract >>
The dependence of the properties of the azurin blue copper site on the nature of the axial ligand at position 121 was tested by site-directed mutagenesis. This residue was substituted for a glutamine, the purported fourth copper ligand in the related protein stellacyanin. M121Q azurin was isolated and purified from Escherichia coli and characterized by spectroscopic methods. The mutant copper site has the ultra-violet-vis and electron paramagnetic resonance (EPR) characteristics of a type I site, but the spectroscopic details differ significantly from wild-type (wt) azurin. The X and S-band EPR spectra of M121Q azurin can be well stimulated with the parameters for stellacyanin, indicating that the copper sites of both proteins in the oxidized state are similar. The midpoint potential of M121Q is 263 mV, 25 mV lower than for wt azurin. The reactivity of the mutant was probed by measuring the electron self exchange rate by nuclear magnetic resonance spectroscopy. The rate was 8 x 10(3) mol-1 s-1, almost two orders of magnitude lower than the value for wt azurin (5 x 10(5) mol-1 s-1). Detailed structural information on the M121Q Cu(II)-site was obtained by X-ray analysis of M121Q azurin crystals at 1.9 A resolution. The histidine and cysteine copper ligand distances and angles in the equatorial plane around the copper are very similar to the wt protein. Gln121 is co-ordinated in a monodentate fashion via its side-chain oxygen atom at a distance of 2.26 A. The distance between copper and the carbonyl group of Gly45 is increased from 3.13 A (wt) to 3.37 A resulting in a distorted tetrahedral N2SO copper co-ordination. The possible significance of these results for the structure of the copper site of stellacyanin, the only small blue copper protein lacking a methionine ligand, is discussed. Conformational changes with respect to the wt azurin are seen in some of the connecting loops between secondary structure elements, in the mutation site and in the beta-strand 2a. The side-chains involved in the hydrophobic patch surrounding His117 are subject to large changes in their conformations. In contrast to wt azurin, the copper site in M121Q azurin undergoes significant structural changes on reduction.(ABSTRACT TRUNCATED AT 400 WORDS)
KeywordMeSH Terms
18.     ( 1996 )

Paramagnetic cobalt and nickel derivatives of Alcaligenes denitrificans azurin and its M121Q mutant. A 1H NMR study.

Biochemistry 35 (6)
PMID : 8639662  :   DOI  :   10.1021/bi951748a    
Abstract >>
Using cobalt or nickel to replace copper in native azurin allows one to fingerprint the metal coordination site of the protein. The metal sites of wild type Alcaligenes denitrificans azurin and its M121Q mutant are clearly distinguishable through the paramagnetic 1H NMR spectra of the Ni(II) and Co(II) derivatives. In the wild type azurin, Gly45 coordinates to nickel or cobalt, while Met121 appears as a weak metal ligand. On the contrary, in the M121Q azurin mutant, the metal exhibits a clear preference for the Gln121, which coordinates through the side chain carbonyl oxygen, and Gly45 is not a ligand. Changes in the isotropic shifts and relaxation properties of signals from the Cys112, His46, and His117 metal ligands suggest a movement of the metal ion out of the equatorial plane, indicating that the metal site is tetrahedral. These effects are less pronounced in the Ni(II) M121Q azurin than in the Co(II) metalloderivative. The similarity between the NMR spectra of the Co(II) derivatives of stellacyanin and the M121Q azurin is in agreement with a very similar metal site in both proteins and supports the existence of a coordinated Gln in stellacyanin.
KeywordMeSH Terms
19. Norris  GE, Anderson  BF, Baker  EN,     ( 1983 )

Structure of azurin from Alcaligenes denitrificans at 2.5 A resolution.

Journal of molecular biology 165 (3)
PMID : 6842609  :   DOI  :   10.1016/s0022-2836(83)80216-2    
Abstract >>
The structure of the blue copper protein, azurin, from Alcaligenes denitrificans has been determined from an electron density map at a nominal resolution of 3.0 A. Four isomorphous heavy-atom derivatives, prepared with KAu(CN)2, uranyl acetate, Hg(NH3)2Cl2 and KAu(CN)2 + uranyl acetate (a double derivative) were used to calculate phases by the method of isomorphous replacement. The overall figure of merit was 0.61. The two molecules in the asymmetric unit are related by an approximate 2-fold axis. Independent interpretations of the density were made for the two molecules, and the structures have since been partially refined. After 12 refinement cycles, using the Hendrickson-Konnert restrained least-squares program, the R factor is 0.318 for data to 2.5 A resolution and there are no major conformational differences between the two molecules. Refinement is continuing. Eight extended strands of the polypeptide chain form a beta-barrel structure whose topology is the same as that of plastocyanin and the alternative folding proposed for Pseudomonas aeruginosa azurin. As in the latter two proteins, the copper atom forms three short bonds, with His-46 N delta 1, His117 N delta 1 and Cys112 S gamma, and one longer bond, with Met121 S delta, these four ligands forming a very distorted tetrahedron. A possible additional interaction, between copper and the carbonyl oxygen of Gly45, cannot be discounted at the present stage of the analysis. A surface hydrophobic patch, around the edge of the imidazole ring of His117 appears the most likely electron transfer locus. The sequences of azurin and plastocyanin have been aligned and the homology between the two proteins is discussed.
KeywordMeSH Terms
Bacterial Proteins
20. Baker  EN,     ( 1988 )

Structure of azurin from Alcaligenes denitrificans refinement at 1.8 A resolution and comparison of the two crystallographically independent molecules.

Journal of molecular biology 203 (4)
PMID : 3210236  :   DOI  :   10.1016/0022-2836(88)90129-5    
Abstract >>
The structure of the blue copper protein azurin, from Alcaligenes denitrificans, has been refined crystallographically by restrained least-squares methods. The final crystallographic R value for 21,980 observed reflections to 1.8 A (1 A = 0.1 nm) resolution is 0.157. The asymmetric unit of the crystal contains two independent azurin molecules, the model for which comprises 1973 protein atoms, together with three SO2-4 ions, and 281 water molecules. Comparison of the two molecules shows very high correspondence. For 125 out of 129 residues (excluding only the chain termini, residues 1 to 2 and 128 to 129) the root-mean-square (r.m.s.) deviation in main-chain atom positions is 0.27 A. For other structural parameters r.m.s. deviations are also low; torsion angles 6.5 degrees, hydrogen bond lengths 0.12 A, bonds to copper 0.04 A and bond angles at the copper 3.9 degrees. The only significant differences are at the chain termini and in several loops. Some of these can be attributed to crystal packing effects, others to genuine structural microheterogeneity. Refinement has confirmed that the copper co-ordination is best described as distorted trigonal planar, with strong in-plane bonds to His46 N delta 1, His117 N delta 1 and Cys112 S gamma, and much weaker axial interactions with Met121 S delta and Gly45 C = O. Two N-H...S hydrogen bonds characterize Cys112 S gamma as a thiolate (S-) sulphur and may influence the visible absorption maximum. Atoms in and around the copper site have very low mobility, whereas the most mobile regions of the molecule are the chain termini and some of the connecting loops between secondary structure elements, especially those at the "southern" end, remote from the copper site. Main-chain to side-chain hydrogen bonds supply important stabilizing interactions at the "northern" end. Surface features include the hydrophobic patch around His117, probably important for electron transfer, the SO2-4 site at His83, and the general absence of ion pairs, despite the presence of many charged amino acid residues. The 281 water molecules include 182 that occur as approximately twofold-related pairs. There are no internal water molecules. The water sites common to both azurin molecules include those in surface pockets and some in intermolecular contact regions. They are characterized by relatively low thermal parameters and numerous protein contacts.
KeywordMeSH Terms
Bacterial Proteins
21. Liston  SD, McMahon  SA, Le Bas  A, Suits  MDL, Naismith  JH, Whitfield  C,     ( 2018 )

Periplasmic depolymerase provides insight into ABC transporter-dependent secretion of bacterial capsular polysaccharides.

Proceedings of the National Academy of Sciences of the United States of America 115 (21)
PMID : 29735649  :   DOI  :   10.1073/pnas.1801336115     PMC  :   PMC6003464    
Abstract >>
Capsules are surface layers of hydrated capsular polysaccharides (CPSs) produced by many bacteria. The human pathogen Salmonella enterica serovar Typhi produces "Vi antigen" CPS, which contributes to virulence. In a conserved strategy used by bacteria with diverse CPS structures, translocation of Vi antigen to the cell surface is driven by an ATP-binding cassette (ABC) transporter. These transporters are engaged in heterooligomeric complexes proposed to form an enclosed translocation conduit to the cell surface, allowing the transporter to power the entire process. We identified Vi antigen biosynthesis genetic loci in genera of the Burkholderiales, which are paradoxically distinguished from S. Typhi by encoding VexL, a predicted pectate lyase homolog. Biochemical analyses demonstrated that VexL is an unusual metal-independent endolyase with an acidic pH optimum that is specific for O-acetylated Vi antigen. A 1.22-? crystal structure of the VexL-Vi antigen complex revealed features which distinguish common secreted catabolic pectate lyases from periplasmic VexL, which participates in cell-surface assembly. VexL possesses a right-handed parallel �]-superhelix, of which one face forms an electropositive glycan-binding groove with an extensive hydrogen bonding network that includes Vi antigen acetyl groups and confers substrate specificity. VexL provided a probe to interrogate conserved features of the ABC transporter-dependent export model. When introduced into S Typhi, VexL localized to the periplasm and degraded Vi antigen. In contrast, a cytosolic derivative had no effect unless export was disrupted. These data provide evidence that CPS assembled in ABC transporter-dependent systems is actually exposed to the periplasm during envelope translocation.
KeywordMeSH Terms
Salmonella enterica
bacterial cell surface
capsular polysaccharide
glycan export
22.     ( 2013 )

Cloning, expression and characterization of D-aminoacylase from Achromobacter xylosoxidans subsp. denitrificans ATCC 15173.

Microbiological research 168 (6)
PMID : 23369306  :   DOI  :   10.1016/j.micres.2013.01.002    
Abstract >>
D-Aminoacylase catalyzes the conversion of N-acyl-D-amino acids to d-amino acids and fatty acids. The aim of this study was to identify the D-aminoacylase gene from Achromobacter xylosoxidans subsp. denitrificans ATCC 15173 and investigate the biochemical characterization of the enzyme. A previously uncharacterized D-aminoacylase gene (ADdan) from this organism was cloned and sequenced. The open reading frame (ORF) of ADdan was 1467 bp in size encoding a 488-amino acid polypeptide. ADdan, with a high amino acid similarity to N-acyl-D-aspartate amidohydrolase from Alcaligenes A6, showed relatively low sequence similarities to other characterized D-aminoacylases. The recombinant ADdan protein was expressed in Escherichia coli BL21 (DE3) using pET-28a with a T7 promoter. The enzyme was purified in a single chromatographic step using nickel affinity gel column. The molecular mass of the expressed protein, calculated by SDS-PAGE, was about 52 kDa. The purified ADdan showed optimal activity at pH 8.0 and 50�XC, and was stable at pH 6.0-8.0 and up to 45�XC. Its activity was inhibited by Cu(2+), Fe(2+), Ca(2+), Mn(2+), Ni(2+), Zn(2+) and Hg(2+), whereas Mg(2+) had no significant influence on this recombinant D-aminoacylase. This is the first report on the characterization of D-aminoacylase with activity towards both N-acyl derivatives of neutral D-amino acids and N-acyl-D-aspartate. The characteristics of ADdan could prove to be of interest in industrial production of D-amino acids.
KeywordMeSH Terms
Cloning, Molecular

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