Valinomycin biosynthetic gene cluster in Streptomyces: conservation, ecology and evolution
Many Streptomyces strains are known to produce valinomycin (VLM) antibiotic and the VLM biosynthetic gene cluster (vlm) has been characterized in two independent isolates. Here we report the phylogenetic relationships of these strains using both parsimony and likelihood methods, and discuss whether...
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| description | Many Streptomyces strains are known to produce valinomycin (VLM) antibiotic and the VLM biosynthetic gene cluster (vlm) has been characterized in two independent isolates. Here we report the phylogenetic relationships of these strains using both parsimony and likelihood methods, and discuss whether the vlm gene cluster shows evidence of horizontal transmission common in natural product biosynthetic genes. Eight Streptomyces strains from around the world were obtained and sequenced for three regions of the two large nonribosomal peptide synthetase genes (vlm1 and vlm2) involved in VLM biosynthesis. The DNA sequences representing the vlm gene cluster are highly conserved among all eight environmental strains. The geographic distribution pattern of these strains and the strict congruence between the trees of the two vlm genes and the housekeeping genes, 16S rDNA and trpB, suggest vertical transmission of the vlm gene cluster in Streptomyces with no evidence of horizontal gene transfer. We also explored the relationship of the sequence of vlm genes to that of the cereulide biosynthetic genes (ces) found in Bacillus cereus and found them highly divergent from each other at DNA level (genetic distance values >or= 95.6%). It is possible that the vlm gene cluster and the ces gene cluster may share a relatively distant common ancestor but these two gene clusters have since evolved independently. |
| doi_str_mv | 10.1371/journal.pone.0007194 |
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Here we report the phylogenetic relationships of these strains using both parsimony and likelihood methods, and discuss whether the vlm gene cluster shows evidence of horizontal transmission common in natural product biosynthetic genes. Eight Streptomyces strains from around the world were obtained and sequenced for three regions of the two large nonribosomal peptide synthetase genes (vlm1 and vlm2) involved in VLM biosynthesis. The DNA sequences representing the vlm gene cluster are highly conserved among all eight environmental strains. The geographic distribution pattern of these strains and the strict congruence between the trees of the two vlm genes and the housekeeping genes, 16S rDNA and trpB, suggest vertical transmission of the vlm gene cluster in Streptomyces with no evidence of horizontal gene transfer. We also explored the relationship of the sequence of vlm genes to that of the cereulide biosynthetic genes (ces) found in Bacillus cereus and found them highly divergent from each other at DNA level (genetic distance values >or= 95.6%). It is possible that the vlm gene cluster and the ces gene cluster may share a relatively distant common ancestor but these two gene clusters have since evolved independently.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0007194</identifier><identifier>PMID: 19787052</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Anti-Bacterial Agents - chemistry ; Anti-Bacterial Agents - metabolism ; Antibiotics ; Bacillus cereus - metabolism ; Bacteria ; Bayes Theorem ; Bioinformatics ; Biological Evolution ; Biosynthesis ; Cereulide ; Clusters ; Conservation ; Cyanobacteria ; Deoxyribonucleic acid ; Disease transmission ; Dissertations & theses ; DNA ; DNA biosynthesis ; DNA sequencing ; Ecology ; Evolution ; Evolutionary biology ; Evolutionary Biology/Microbial Evolution and Genomics ; Evolutionary conservation ; Gene clusters ; Gene sequencing ; Gene transfer ; Gene Transfer, Horizontal ; Genes ; Genetic distance ; Genetic research ; Geographical distribution ; Ligases ; Likelihood Functions ; Microbiology/Environmental Microbiology ; Microbiology/Microbial Evolution and Genomics ; Microbiology/Microbial Physiology and Metabolism ; Multigene Family ; Natural products ; Nucleotide sequence ; Oryza ; Peptide Synthases - metabolism ; Phylogenetics ; Phylogeny ; Polymerase Chain Reaction ; RNA polymerase ; RNA, Ribosomal, 16S - metabolism ; rRNA 16S ; Sequence Analysis, DNA ; Streptomyces ; Streptomyces - genetics ; Streptomyces - metabolism ; Valinomycin ; Valinomycin - chemistry ; Valinomycin - metabolism</subject><ispartof>PloS one, 2009-09, Vol.4 (9), p.e7194-e7194</ispartof><rights>COPYRIGHT 2009 Public Library of Science</rights><rights>2009 Matter et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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Here we report the phylogenetic relationships of these strains using both parsimony and likelihood methods, and discuss whether the vlm gene cluster shows evidence of horizontal transmission common in natural product biosynthetic genes. Eight Streptomyces strains from around the world were obtained and sequenced for three regions of the two large nonribosomal peptide synthetase genes (vlm1 and vlm2) involved in VLM biosynthesis. The DNA sequences representing the vlm gene cluster are highly conserved among all eight environmental strains. The geographic distribution pattern of these strains and the strict congruence between the trees of the two vlm genes and the housekeeping genes, 16S rDNA and trpB, suggest vertical transmission of the vlm gene cluster in Streptomyces with no evidence of horizontal gene transfer. We also explored the relationship of the sequence of vlm genes to that of the cereulide biosynthetic genes (ces) found in Bacillus cereus and found them highly divergent from each other at DNA level (genetic distance values >or= 95.6%). It is possible that the vlm gene cluster and the ces gene cluster may share a relatively distant common ancestor but these two gene clusters have since evolved independently.</description><subject>Anti-Bacterial Agents - chemistry</subject><subject>Anti-Bacterial Agents - metabolism</subject><subject>Antibiotics</subject><subject>Bacillus cereus - metabolism</subject><subject>Bacteria</subject><subject>Bayes Theorem</subject><subject>Bioinformatics</subject><subject>Biological Evolution</subject><subject>Biosynthesis</subject><subject>Cereulide</subject><subject>Clusters</subject><subject>Conservation</subject><subject>Cyanobacteria</subject><subject>Deoxyribonucleic acid</subject><subject>Disease transmission</subject><subject>Dissertations & theses</subject><subject>DNA</subject><subject>DNA biosynthesis</subject><subject>DNA sequencing</subject><subject>Ecology</subject><subject>Evolution</subject><subject>Evolutionary biology</subject><subject>Evolutionary Biology/Microbial Evolution and Genomics</subject><subject>Evolutionary conservation</subject><subject>Gene clusters</subject><subject>Gene sequencing</subject><subject>Gene transfer</subject><subject>Gene Transfer, Horizontal</subject><subject>Genes</subject><subject>Genetic distance</subject><subject>Genetic research</subject><subject>Geographical distribution</subject><subject>Ligases</subject><subject>Likelihood Functions</subject><subject>Microbiology/Environmental Microbiology</subject><subject>Microbiology/Microbial Evolution and Genomics</subject><subject>Microbiology/Microbial Physiology and Metabolism</subject><subject>Multigene Family</subject><subject>Natural products</subject><subject>Nucleotide sequence</subject><subject>Oryza</subject><subject>Peptide Synthases - metabolism</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Polymerase Chain Reaction</subject><subject>RNA polymerase</subject><subject>RNA, Ribosomal, 16S - metabolism</subject><subject>rRNA 16S</subject><subject>Sequence Analysis, DNA</subject><subject>Streptomyces</subject><subject>Streptomyces - genetics</subject><subject>Streptomyces - metabolism</subject><subject>Valinomycin</subject><subject>Valinomycin - chemistry</subject><subject>Valinomycin - metabolism</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNkl2LEzEUhgdR3HX1H4gOCIpga75mMvFCWBY_CgsLru6FNyGTOZlmmSY1yRT7703tqK14IblIOHnOe3JO3qJ4jNEcU45f3_oxODXM197BHCHEsWB3ilMsKJnVBNG7B-eT4kGMtwhVtKnr-8UJFrzhqCKnxdcbNVjnV1ttXdlaH7cuLSFZXfbgoNTDGBOEMl9epwDrtCMhvim1dxHCRiXr3asStB98vy2V60rY-GHchR8W94waIjya9rPiy_t3ny8-zi6vPiwuzi9nuhI0zWrMFFItCFFxwxslgBjIzRhTKWUUM6ZVmggjGBDcdlCxTkFNGoJITSvD6FnxdK-7HnyU01iixEQQQhitmkws9kTn1a1cB7tSYSu9svJnwIdeqpB7HkBqw3jXIM6FblgDXICqG9MI1ooKNxXOWm-namO7gk6DS0ENR6LHN84uZe83knBWU4yywItJIPhvI8QkVzZqGAblwI9RcspQXVFRZ_LZX-S_m5vvqV7l91tnfC6r8-pgZfM3gbE5fs44aSqO8C7h5VFCZhJ8T70aY5SL60__z17dHLPPD9glqCEt4-SFeAyyPaiDjzGA-T09jOTO27_6lDtvy8nbOe3J4eT_JE1mpj8ABhP20Q</recordid><startdate>20090929</startdate><enddate>20090929</enddate><creator>Matter, Andrea M</creator><creator>Hoot, Sara B</creator><creator>Anderson, Patrick D</creator><creator>Neves, Susana S</creator><creator>Cheng, Yi-Qiang</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>COVID</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20090929</creationdate><title>Valinomycin biosynthetic gene cluster in Streptomyces: conservation, ecology and evolution</title><author>Matter, Andrea M ; Hoot, Sara B ; Anderson, Patrick D ; Neves, Susana S ; Cheng, Yi-Qiang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c593t-614a0abe9957f78a9e2fe719ff5aafa4ffbac29f94e21bde54dae628202635f43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Anti-Bacterial Agents - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Matter, Andrea M</au><au>Hoot, Sara B</au><au>Anderson, Patrick D</au><au>Neves, Susana S</au><au>Cheng, Yi-Qiang</au><au>Thattai, Mukund</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Valinomycin biosynthetic gene cluster in Streptomyces: conservation, ecology and evolution</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2009-09-29</date><risdate>2009</risdate><volume>4</volume><issue>9</issue><spage>e7194</spage><epage>e7194</epage><pages>e7194-e7194</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Many Streptomyces strains are known to produce valinomycin (VLM) antibiotic and the VLM biosynthetic gene cluster (vlm) has been characterized in two independent isolates. Here we report the phylogenetic relationships of these strains using both parsimony and likelihood methods, and discuss whether the vlm gene cluster shows evidence of horizontal transmission common in natural product biosynthetic genes. Eight Streptomyces strains from around the world were obtained and sequenced for three regions of the two large nonribosomal peptide synthetase genes (vlm1 and vlm2) involved in VLM biosynthesis. The DNA sequences representing the vlm gene cluster are highly conserved among all eight environmental strains. The geographic distribution pattern of these strains and the strict congruence between the trees of the two vlm genes and the housekeeping genes, 16S rDNA and trpB, suggest vertical transmission of the vlm gene cluster in Streptomyces with no evidence of horizontal gene transfer. We also explored the relationship of the sequence of vlm genes to that of the cereulide biosynthetic genes (ces) found in Bacillus cereus and found them highly divergent from each other at DNA level (genetic distance values >or= 95.6%). It is possible that the vlm gene cluster and the ces gene cluster may share a relatively distant common ancestor but these two gene clusters have since evolved independently.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>19787052</pmid><doi>10.1371/journal.pone.0007194</doi><tpages>e7194</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Anti-Bacterial Agents - chemistry Anti-Bacterial Agents - metabolism Antibiotics Bacillus cereus - metabolism Bacteria Bayes Theorem Bioinformatics Biological Evolution Biosynthesis Cereulide Clusters Conservation Cyanobacteria Deoxyribonucleic acid Disease transmission Dissertations & theses DNA DNA biosynthesis DNA sequencing Ecology Evolution Evolutionary biology Evolutionary Biology/Microbial Evolution and Genomics Evolutionary conservation Gene clusters Gene sequencing Gene transfer Gene Transfer, Horizontal Genes Genetic distance Genetic research Geographical distribution Ligases Likelihood Functions Microbiology/Environmental Microbiology Microbiology/Microbial Evolution and Genomics Microbiology/Microbial Physiology and Metabolism Multigene Family Natural products Nucleotide sequence Oryza Peptide Synthases - metabolism Phylogenetics Phylogeny Polymerase Chain Reaction RNA polymerase RNA, Ribosomal, 16S - metabolism rRNA 16S Sequence Analysis, DNA Streptomyces Streptomyces - genetics Streptomyces - metabolism Valinomycin Valinomycin - chemistry Valinomycin - metabolism |
| title | Valinomycin biosynthetic gene cluster in Streptomyces: conservation, ecology and evolution |
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