scholarly journals A Gene Cluster Involved in Degradation of Substituted Salicylates via ortho Cleavage in Pseudomonas sp. Strain MT1 Encodes Enzymes Specifically Adapted for Transformation of 4-Methylcatechol and 3-Methylmuconate

2006 ◽  
Vol 189 (5) ◽  
pp. 1664-1674 ◽  
Author(s):  
Beatriz Cámara ◽  
Piotr Bielecki ◽  
Filip Kaminski ◽  
Vitor Martins dos Santos ◽  
Iris Plumeier ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Gene Clusters ◽  
Gene Arrangement ◽  
Kinetic Properties ◽  
Pseudomonas Sp ◽  
Genes Encoding ◽  
Catechol 1,2 Dioxygenase ◽  
Muconate Cycloisomerase ◽  
Sequence Similarities ◽  
Substrate Spectrum

ABSTRACT Pseudomonas sp. strain MT1 has recently been reported to degrade 4- and 5-chlorosalicylate by a pathway assumed to consist of a patchwork of reactions comprising enzymes of the 3-oxoadipate pathway. Genes encoding the initial steps in the degradation of salicylate and substituted derivatives were now localized and sequenced. One of the gene clusters characterized (sal) showed a novel gene arrangement, with salA, encoding a salicylate 1-hydroxylase, being clustered with salCD genes, encoding muconate cycloisomerase and catechol 1,2-dioxygenase, respectively, and was expressed during growth on salicylate and chlorosalicylate. A second gene cluster (cat), exhibiting the typical catRBCA arrangement of genes of the catechol branch of the 3-oxoadipate pathway in Pseudomonas strains, was expressed during growth on salicylate. Despite their high sequence similarities with isoenzymes encoded by the cat gene cluster, the catechol 1,2-dioxygenase and muconate cycloisomerase encoded by the sal cluster showed unusual kinetic properties. Enzymes were adapted for turnover of 4-chlorocatechol and 3-chloromuconate; however, 4-methylcatechol and 3-methylmuconate were identified as the preferred substrates. Investigation of the substrate spectrum identified 4- and 5-methylsalicylate as growth substrates, which were effectively converted by enzymes of the sal cluster into 4-methylmuconolactone, followed by isomerization to 3-methylmuconolactone. The function of the sal gene cluster is therefore to channel both chlorosubstituted and methylsubstituted salicylates into a catechol ortho cleavage pathway, followed by dismantling of the formed substituted muconolactones through specific pathways.

scholarly journals Characterization of a Gene Cluster Involved in 4-Chlorocatechol Degradation by Pseudomonas reinekei MT1

2009 ◽  
Vol 191 (15) ◽  
pp. 4905-4915 ◽  
Author(s):  
Beatriz Cámara ◽  
Patricia Nikodem ◽  
Piotr Bielecki ◽  
Roberto Bobadilla ◽  
Howard Junca ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Regulatory Gene ◽  
Genomic Region ◽  
Genes Encoding ◽  
Catechol 1,2 Dioxygenase ◽  
Dienelactone Hydrolase ◽  
Intradiol Cleavage ◽  
Maleylacetate Reductase ◽  
Muconate Cycloisomerase

ABSTRACT Pseudomonas reinekei MT1 has previously been reported to degrade 4- and 5-chlorosalicylate by a pathway with 4-chlorocatechol, 3-chloromuconate, 4-chloromuconolactone, and maleylacetate as intermediates, and a gene cluster channeling various salicylates into an intradiol cleavage route has been reported. We now report that during growth on 5-chlorosalicylate, besides a novel (chloro)catechol 1,2-dioxygenase, C12OccaA, a novel (chloro)muconate cycloisomerase, MCIccaB, which showed features not yet reported, was induced. This cycloisomerase, which was practically inactive with muconate, evolved for the turnover of 3-substituted muconates and transforms 3-chloromuconate into equal amounts of cis-dienelactone and protoanemonin, suggesting that it is a functional intermediate between chloromuconate cycloisomerases and muconate cycloisomerases. The corresponding genes, ccaA (C12OccaA) and ccaB (MCIccaB), were located in a 5.1-kb genomic region clustered with genes encoding trans-dienelactone hydrolase (ccaC) and maleylacetate reductase (ccaD) and a putative regulatory gene, ccaR, homologous to regulators of the IclR-type family. Thus, this region includes genes sufficient to enable MT1 to transform 4-chlorocatechol to 3-oxoadipate. Phylogenetic analysis showed that C12OccaA and MCIccaB are only distantly related to previously described catechol 1,2-dioxygenases and muconate cycloisomerases. Kinetic analysis indicated that MCIccaB and the previously identified C12OsalD, rather than C12OccaA, are crucial for 5-chlorosalicylate degradation. Thus, MT1 uses enzymes encoded by a completely novel gene cluster for degradation of chlorosalicylates, which, together with a gene cluster encoding enzymes for channeling salicylates into the ortho-cleavage pathway, form an effective pathway for 4- and 5-chlorosalicylate mineralization.

scholarly journals DNA sequence of a gene cluster coding for subunits of the F0 membrane sector of ATP synthase in Rhodospirillum rubrum. Support for modular evolution of the F1 and F0 sectors

1988 ◽  
Vol 254 (1) ◽  
pp. 109-122 ◽  
Author(s):  
G Falk ◽  
J E Walker
Keyword(s):  
Gene Cluster ◽  
Atp Synthase ◽  
Rhodospirillum Rubrum ◽  
Gene Arrangement ◽  
Amino Acid Residues ◽  
Stem Loop ◽  
Transcription Terminator ◽  
E Coli ◽  
Modular Evolution ◽  
Genes Encoding

A region was cloned from the genome of the purple non-sulphur photobacterium Rhodospirillum rubrum that contains genes coding for the membrane protein subunits of the F0 sector of ATP synthase. The clone was identified by hybridization with a synthetic oligonucleotide designed on the basis of the known protein sequence of the dicyclohexylcarbodi-imide-reactive proteolipid, or subunit c. The complete nucleotide sequence of 4240 bp of this region was determined. It is separate from an operon described previously that encodes the five subunits of the extrinsic membrane sector of the enzyme, F1-ATPase. It contains a cluster of structural genes encoding homologues of all three membrane subunits a, b and c of the Escherichia coli ATP synthase. The order of the genes in Rsp. rubrum is a-c-b'-b where b and b' are homologues. A similar gene arrangement for F0 subunits has been found in two cyanobacteria, Synechococcus 6301 and Synechococcus 6716. This suggests that the ATP synthase complexes of all these photosynthetic bacteria contain nine different polypeptides rather than eight found in the E. coli enzyme; the chloroplast ATP synthase complex is probably similar to the photosynthetic bacterial enzymes in this respect. The Rsp. rubrum b subunit is modified after translation. As shown by N-terminal sequencing of the protein, the first seven amino acid residues are removed before or during assembly of the ATP synthase complex. The subunit-a gene is preceded by a gene coding for a small hydrophobic protein, as has been observed previously in the atp operons in E. coli, bacterium PS3 and cyanobacteria. A number of features suggest that the Rsp. rubrum cluster of F0 genes is an operon. On its 5′ side are found sequences resembling the -10 (Pribnow) and -35 boxes of E. coli promoters, and the gene cluster is followed by a sequence potentially able to form a stable stem-loop structure, suggesting that it acts as a rho-independent transcription terminator. These features and the small intergenic non-coding sequences suggest that the genes are cotranscribed, and so the name atp2 is proposed for this second operon coding for ATP synthase subunits in Rsp. rubrum. The finding that genes for the F0 and F1 sectors of the enzyme are in separate clusters supports the view that these represent evolutionary modules.

scholarly journals Novel Structural Elements within the NonproteolyticClostridium botulinumType F Toxin Gene Cluster

2010 ◽  
Vol 77 (5) ◽  
pp. 1904-1906 ◽  
Author(s):  
N. Dover ◽  
J. R. Barash ◽  
K. K. Hill ◽  
J. C. Detter ◽  
S. S. Arnon
Keyword(s):  
Gene Cluster ◽  
Clostridium Botulinum ◽  
Gene Clusters ◽  
Gene Arrangement ◽  
Toxin Gene ◽  
Structural Elements ◽  
Novel Gene ◽  
First Time

ABSTRACTWe sequenced for the first time the complete neurotoxin gene cluster of a nonproteolyticClostridium botulinumtype F. The neurotoxin gene cluster contained a novel gene arrangement that, compared to otherC. botulinumneurotoxin gene clusters, lacked the regulatorybotRgene and contained an intergeniciselement between itsorfX2andorfX3genes.

scholarly journals A Physical Map of the Syringomycin and Syringopeptin Gene Clusters Localized to an Approximately 145-kb DNA Region of Pseudomonas syringae pv. syringae Strain B301D

2001 ◽  
Vol 14 (12) ◽  
pp. 1426-1435 ◽  
Author(s):  
Brenda K. Scholz-Schroeder ◽  
Jonathan D. Soule ◽  
Shi-En Lu ◽  
Ingeborg Grgurina ◽  
Dennis C. Gross
Keyword(s):  
Gene Cluster ◽  
Pseudomonas Syringae ◽  
Physical Map ◽  
Regulatory Element ◽  
Gene Clusters ◽  
Gene Encoding ◽  
Peptide Synthetases ◽  
Peptide Synthetase ◽  
Genes Encoding ◽  
Size Estimates

Genetic and phenotypic mapping of an approximately 145-kb DraI fragment of Pseudomonas syringae pv. syringae strain B301D determined that the syringomycin (syr) and syringopeptin (syp) gene clusters are localized to this fragment. The syr and syp gene clusters encompass approximately 55 kb and approximately 80 kb, respectively. Both phytotoxins are synthesized by a thiotemplate mechanism of biosynthesis, requiring large multienzymatic proteins called peptide synthetases. Genes encoding peptide synthetases were identified within the syr and syp gene clusters, accounting for 90% of the DraI fragment. In addition, genes encoding regulatory and secretion proteins were localized to the DraI fragment. In particular, the salA gene, encoding a regulatory element responsible for syringomycin production and lesion formation in P. syringae pv. syringae strain B728a, was localized to the syr gene cluster. A putative ATP-binding cassette (ABC) transporter homolog was determined to be physically located in the syp gene cluster, but phenotypically affects production of both phytotoxins. Preliminary size estimates of the syr and syp gene clusters indicate that they represent two of the largest nonribosomal peptide synthetase gene clusters. Together, the syr and syp gene clusters encompass approximately 135 kb of DNA and may represent a genomic island in P. syringae pv. syringae that contributes to virulence in plant hosts.

scholarly journals Distribution of Suicin Gene Clusters in Streptococcus suis Serotype 2 Belonging to Sequence Types 25 and 28

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Taryn B. T. Athey ◽  
Katy Vaillancourt ◽  
Michel Frenette ◽  
Nahuel Fittipaldi ◽  
Marcelo Gottschalk ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Streptococcus Suis ◽  
Gene Clusters ◽  
Sequence Type ◽  
Purification And Characterization ◽  
Heterogeneous Distribution ◽  
Genes Encoding ◽  
Sequence Types ◽  
Suis Serotype

Recently, we reported the purification and characterization of three distinct lantibiotics (named suicin 90-1330, suicin 3908, and suicin 65) produced by Streptococcus suis. In this study, we investigated the distribution of the three suicin lantibiotic gene clusters among serotype 2 S. suis strains belonging to sequence type (ST) 25 and ST28, the two dominant STs identified in North America. The genomes of 102 strains were interrogated for the presence of suicin gene clusters encoding suicins 90-1330, 3908, and 65. The gene cluster encoding suicin 65 was the most prevalent and mainly found among ST25 strains. In contrast, none of the genes related to suicin 90-1330 production were identified in 51 ST25 strains nor in 35/51 ST28 strains. However, the complete suicin 90-1330 gene cluster was found in ten ST28 strains, although some genes in the cluster were truncated in three of these isolates. The vast majority (101/102) of S. suis strains did not possess any of the genes encoding suicin 3908. In conclusion, this study indicates heterogeneous distribution of suicin genes in S. suis.

scholarly journals Molecular analysis ofShigella boydiiO1 O-antigen gene cluster and its PCR typing

2005 ◽  
Vol 51 (5) ◽  
pp. 387-392 ◽  
Author(s):  
Jiang Tao ◽  
Lei Wang ◽  
Dan Liu ◽  
Yue Li ◽  
David A Bastin ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Gene Clusters ◽  
Pcr Assay ◽  
Pcr Screening ◽  
E Coli ◽  
Antigen Gene ◽  
O Antigen ◽  
Genes Encoding ◽  
Type Strains ◽  
Overnight Culture

Shigella is an important human pathogen and is closely related to Escherichia coli. O-antigen is the most variable part of the lipopolysaccharide on the cell surface of Gram-negative bacteria and plays an important role in pathogenicity. The O-antigen gene cluster of S. boydii O1 was sequenced. The putative genes encoding enzymes for rhamnose synthesis, transferases, O-unit flippase, and O-unit polymerase were identified on the basis of homology. The O-antigen gene clusters of S. boydii O1 and E. coli O149, which share the same O-antigen form, were found to have the same genes and organization by adjacent gene PCR assay. Two genes specific for S. boydii O1 and E. coli O149 were identified by PCR screening against E. coli- and Shigella-type strains of the 186 known O-antigen forms and 39 E. coli clinical isolates. A PCR sensitivity of 103to 104CFU/mL overnight culture of S. boydii O1 and E. coli O149 was obtained. S. boydii O1 and E. coli O149 were differentiated by PCR using lacZ- and cadA-based primers.Key words: O-antigen gene cluster, S. boydii O1, E. coli O149, molecular typing.

A linear megaplasmid, p1CP, carrying the genes for chlorocatechol catabolism of Rhodococcus opacus 1CP

Microbiology ◽  
2004 ◽  
Vol 150 (9) ◽  
pp. 3075-3087 ◽  
Author(s):  
Christina König ◽  
Dirk Eulberg ◽  
Janosch Gröning ◽  
Silvia Lakner ◽  
Volker Seibert ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Gel Electrophoresis ◽  
Restriction Analysis ◽  
Carbon Sources ◽  
Gene Clusters ◽  
Rhodococcus Opacus ◽  
Terminal Inverted Repeat ◽  
Sequence Comparisons ◽  
S1 Nuclease ◽  
Genes Encoding

The Gram-positive actinobacterium Rhodococcus opacus 1CP is able to utilize several (chloro)aromatic compounds as sole carbon sources, and gene clusters for various catabolic enzymes and pathways have previously been identified. Pulsed-field gel electrophoresis indicates the occurrence of a 740 kb megaplasmid, designated p1CP. Linear topology and the presence of covalently bound proteins were shown by the unchanged electrophoretic mobility after S1 nuclease treatment and by the immobility of the native plasmid during non-denaturing agarose gel electrophoresis, respectively. Sequence comparisons of both termini revealed a perfect 13 bp terminal inverted repeat (TIR) as part of an imperfect 583/587 bp TIR, as well as two copies of the highly conserved centre (GCTXCGC) of a palindromic motif. An initial restriction analysis of p1CP was performed. By means of PCR and hybridization techniques, p1CP was screened for several genes encoding enzymes of (chloro)aromatic degradation. A single maleylacetate reductase gene macA, the clc gene cluster for 4-chloro-/3,5-dichlorocatechol degradation, and the clc2 gene cluster for 3-chlorocatechol degradation were found on p1CP whereas the cat and pca gene clusters for the catechol and the protocatechuate pathways, respectively, were not. Prolonged cultivation of the wild-type strain 1CP under non-selective conditions led to the isolation of the clc- and clc2-deficient mutants 1CP.01 and 1CP.02 harbouring the shortened plasmid variants p1CP.01 (500 kb) and p1CP.02 (400 kb).

scholarly journals New Bacterial Pathway for 4- and 5-Chlorosalicylate Degradation via 4-Chlorocatechol and Maleylacetate in Pseudomonas sp. Strain MT1

2003 ◽  
Vol 185 (23) ◽  
pp. 6790-6800 ◽  
Author(s):  
Patricia Nikodem ◽  
Volker Hecht ◽  
Michael Schlömann ◽  
Dietmar H. Pieper
Keyword(s):  
Kinetic Data ◽  
Pseudomonas Sp ◽  
Dead End ◽  
Catechol 1,2 Dioxygenase ◽  
Dienelactone Hydrolase ◽  
Maleylacetate Reductase ◽  
Muconate Cycloisomerase

ABSTRACT Pseudomonas sp. strain MT1 is capable of degrading 4- and 5-chlorosalicylates via 4-chlorocatechol, 3-chloromuconate, and maleylacetate by a novel pathway. 3-Chloromuconate is transformed by muconate cycloisomerase of MT1 into protoanemonin, a dominant reaction product, as previously shown for other muconate cycloisomerases. However, kinetic data indicate that the muconate cycloisomerase of MT1 is specialized for 3-chloromuconate conversion and is not able to form cis-dienelactone. Protoanemonin is obviously a dead-end product of the pathway. A trans-dienelactone hydrolase (trans-DLH) was induced during growth on chlorosalicylates. Even though the purified enzyme did not act on either 3-chloromuconate or protoanemonin, the presence of muconate cylcoisomerase and trans-DLH together resulted in considerably lower protoanemonin concentrations but larger amounts of maleylacetate formed from 3-chloromuconate than the presence of muconate cycloisomerase alone resulted in. As trans-DLH also acts on 4-fluoromuconolactone, forming maleylacetate, we suggest that this enzyme acts on 4-chloromuconolactone as an intermediate in the muconate cycloisomerase-catalyzed transformation of 3-chloromuconate, thus preventing protoanemonin formation and favoring maleylacetate formation. The maleylacetate formed in this way is reduced by maleylacetate reductase. Chlorosalicylate degradation in MT1 thus occurs by a new pathway consisting of a patchwork of reactions catalyzed by enzymes from the 3-oxoadipate pathway (catechol 1,2-dioxygenase, muconate cycloisomerase) and the chlorocatechol pathway (maleylacetate reductase) and a trans-DLH.

scholarly journals vanD and vanG-Like Gene Clusters in a Ruminococcus Species Isolated from Human Bowel Flora

2007 ◽  
Vol 51 (11) ◽  
pp. 4111-4117 ◽  
Author(s):  
M.-C. Domingo ◽  
A. Huletsky ◽  
R. Giroux ◽  
F. J. Picard ◽  
M. G. Bergeron
Keyword(s):  
Gene Cluster ◽  
Anaerobic Bacterium ◽  
Anaerobic Bacteria ◽  
Gene Clusters ◽  
Surveillance Program ◽  
Rrna Gene ◽  
Genes Encoding ◽  
Bacterium Strain ◽  
Vancomycin Resistant ◽  
First Time

ABSTRACT A vancomycin-resistant, anaerobic, gram-positive coccus containing the vanD and vanG-like genes (strain CCRI-16110) was isolated from a human fecal specimen during a hospital surveillance program to detect carriers of vancomycin-resistant enterococci. Comparison of the 16S rRNA gene sequence of strain CCRI-16110 with databases revealed a potentially novel Ruminococcus species that was most similar (<94% identity) to Clostridium and Ruminococcus species. Strain CCRI-16110 was highly resistant to vancomycin and teicoplanin (MICs of >256 μg/ml). The complete DNA sequence of the vanD cluster was most similar (98.2% identity) to that of Enterococcus faecium BM4339, containing the vanD1 allele. An intD gene with 99% identity with that of this E. faecium strain was found to be associated with the vanD gene cluster of this novel anaerobic bacterium. Strain CCRI-16110 also harbors genes encoding putative VanSG, VanG, and VanTG proteins displaying 56, 73.6, and 55% amino acid sequence identity, respectively, compared to the corresponding proteins encoded by the vanG1 and vanG2 operons of Enterococcus faecalis BM4518 and N03-0233. This study reports for the first time an anaerobic bacterium containing the vanD gene cluster. This strain also harbors a partial vanG-like gene cluster. The presence of vanD- and vanG-containing anaerobic bacteria in the human bowel flora suggests that these bacteria may serve as a reservoir for the vanD and vanG vancomycin resistance genes.

scholarly journals Cloning and Characterization of the Pyrrolomycin Biosynthetic Gene Clusters from Actinosporangium vitaminophilum ATCC 31673 and Streptomyces sp. Strain UC 11065

2006 ◽  
Vol 51 (3) ◽  
pp. 946-957 ◽  
Author(s):  
Xiujun Zhang ◽  
Ronald J. Parry
Keyword(s):  
Sequence Analysis ◽  
Gene Cluster ◽  
Genetic Locus ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Open Reading Frames ◽  
Biosynthetic Gene ◽  
Genes Encoding ◽  
Cloned Gene

ABSTRACT The pyrrolomycins are a family of polyketide antibiotics, some of which contain a nitro group. To gain insight into the nitration mechanism associated with the formation of these antibiotics, the pyrrolomycin biosynthetic gene cluster from Actinosporangium vitaminophilum was cloned. Sequencing of ca. 56 kb of A. vitaminophilum DNA revealed 35 open reading frames (ORFs). Sequence analysis revealed a clear relationship between some of these ORFs and the biosynthetic gene cluster for pyoluteorin, a structurally related antibiotic. Since a gene transfer system could not be devised for A. vitaminophilum, additional proof for the identity of the cloned gene cluster was sought by cloning the pyrrolomycin gene cluster from Streptomyces sp. strain UC 11065, a transformable pyrrolomycin producer. Sequencing of ca. 26 kb of UC 11065 DNA revealed the presence of 17 ORFs, 15 of which exhibit strong similarity to ORFs in the A. vitaminophilum cluster as well as a nearly identical organization. Single-crossover disruption of two genes in the UC 11065 cluster abolished pyrrolomycin production in both cases. These results confirm that the genetic locus cloned from UC 11065 is essential for pyrrolomycin production, and they also confirm that the highly similar locus in A. vitaminophilum encodes pyrrolomycin biosynthetic genes. Sequence analysis revealed that both clusters contain genes encoding the two components of an assimilatory nitrate reductase. This finding suggests that nitrite is required for the formation of the nitrated pyrrolomycins. However, sequence analysis did not provide additional insights into the nitration process, suggesting the operation of a novel nitration mechanism.

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