Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development
The Actinomycetales bacteria Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 bioconvert a diverse range of organic substrates through lipid biosynthesis into large quantities of energy-rich triacylglycerols (TAGs). To describe the genetic basis of the Rhodococcus oleaginous metabolism, we seque...
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| Veröffentlicht in: | PLoS genetics 2011-09, Vol.7 (9), p.e1002219-e1002219 |
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| creator | Holder, Jason W Ulrich, Jil C DeBono, Anthony C Godfrey, Paul A Desjardins, Christopher A Zucker, Jeremy Zeng, Qiandong Leach, Alex L B Ghiviriga, Ion Dancel, Christine Abeel, Thomas Gevers, Dirk Kodira, Chinnappa D Desany, Brian Affourtit, Jason P Birren, Bruce W Sinskey, Anthony J |
| description | The Actinomycetales bacteria Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 bioconvert a diverse range of organic substrates through lipid biosynthesis into large quantities of energy-rich triacylglycerols (TAGs). To describe the genetic basis of the Rhodococcus oleaginous metabolism, we sequenced and performed comparative analysis of the 9.27 Mb R. opacus PD630 genome. Metabolic-reconstruction assigned 2017 enzymatic reactions to the 8632 R. opacus PD630 genes we identified. Of these, 261 genes were implicated in the R. opacus PD630 TAGs cycle by metabolic reconstruction and gene family analysis. Rhodococcus synthesizes uncommon straight-chain odd-carbon fatty acids in high abundance and stores them as TAGs. We have identified these to be pentadecanoic, heptadecanoic, and cis-heptadecenoic acids. To identify bioconversion pathways, we screened R. opacus PD630, R. jostii RHA1, Ralstonia eutropha H16, and C. glutamicum 13032 for growth on 190 compounds. The results of the catabolic screen, phylogenetic analysis of the TAGs cycle enzymes, and metabolic product characterizations were integrated into a working model of prokaryotic oleaginy. |
| doi_str_mv | 10.1371/journal.pgen.1002219 |
| format | Article |
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To describe the genetic basis of the Rhodococcus oleaginous metabolism, we sequenced and performed comparative analysis of the 9.27 Mb R. opacus PD630 genome. Metabolic-reconstruction assigned 2017 enzymatic reactions to the 8632 R. opacus PD630 genes we identified. Of these, 261 genes were implicated in the R. opacus PD630 TAGs cycle by metabolic reconstruction and gene family analysis. Rhodococcus synthesizes uncommon straight-chain odd-carbon fatty acids in high abundance and stores them as TAGs. We have identified these to be pentadecanoic, heptadecanoic, and cis-heptadecenoic acids. To identify bioconversion pathways, we screened R. opacus PD630, R. jostii RHA1, Ralstonia eutropha H16, and C. glutamicum 13032 for growth on 190 compounds. The results of the catabolic screen, phylogenetic analysis of the TAGs cycle enzymes, and metabolic product characterizations were integrated into a working model of prokaryotic oleaginy.</description><identifier>ISSN: 1553-7404</identifier><identifier>ISSN: 1553-7390</identifier><identifier>EISSN: 1553-7404</identifier><identifier>DOI: 10.1371/journal.pgen.1002219</identifier><identifier>PMID: 21931557</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Actinomycetes ; Bacteria ; Biodiesel fuels ; Biofuels ; Biology ; Biomass energy ; Biosynthesis ; Fatty acids ; Fatty Acids - genetics ; Fatty Acids - metabolism ; Genes ; Genetic aspects ; Genome, Bacterial ; Genomes ; Genomics ; Life sciences ; Lipids ; Lipids - biosynthesis ; Metabolic Networks and Pathways - genetics ; Metabolism ; Microbiology ; PCB ; Phylogeny ; Physiological aspects ; Polychlorinated biphenyls ; Production processes ; Rhodococcus - genetics ; Rhodococcus - metabolism ; Triglycerides ; Triglycerides - biosynthesis ; Triglycerides - genetics</subject><ispartof>PLoS genetics, 2011-09, Vol.7 (9), p.e1002219-e1002219</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>Holder et al. 2011</rights><rights>2011 Holder et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Holder JW, Ulrich JC, DeBono AC, Godfrey PA, Desjardins CA, et al. (2011) Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development. PLoS Genet 7(9): e1002219. doi:10.1371/journal.pgen.1002219</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c763t-d55c2e5e0b58b768a2b0079b3eae3920d8d6ff66cd964e2407630747f365600e3</citedby><cites>FETCH-LOGICAL-c763t-d55c2e5e0b58b768a2b0079b3eae3920d8d6ff66cd964e2407630747f365600e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169528/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169528/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,2103,2929,23871,27929,27930,53796,53798</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21931557$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Richardson, Paul M.</contributor><creatorcontrib>Holder, Jason W</creatorcontrib><creatorcontrib>Ulrich, Jil C</creatorcontrib><creatorcontrib>DeBono, Anthony C</creatorcontrib><creatorcontrib>Godfrey, Paul A</creatorcontrib><creatorcontrib>Desjardins, Christopher A</creatorcontrib><creatorcontrib>Zucker, Jeremy</creatorcontrib><creatorcontrib>Zeng, Qiandong</creatorcontrib><creatorcontrib>Leach, Alex L B</creatorcontrib><creatorcontrib>Ghiviriga, Ion</creatorcontrib><creatorcontrib>Dancel, Christine</creatorcontrib><creatorcontrib>Abeel, Thomas</creatorcontrib><creatorcontrib>Gevers, Dirk</creatorcontrib><creatorcontrib>Kodira, Chinnappa D</creatorcontrib><creatorcontrib>Desany, Brian</creatorcontrib><creatorcontrib>Affourtit, Jason P</creatorcontrib><creatorcontrib>Birren, Bruce W</creatorcontrib><creatorcontrib>Sinskey, Anthony J</creatorcontrib><title>Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development</title><title>PLoS genetics</title><addtitle>PLoS Genet</addtitle><description>The Actinomycetales bacteria Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 bioconvert a diverse range of organic substrates through lipid biosynthesis into large quantities of energy-rich triacylglycerols (TAGs). To describe the genetic basis of the Rhodococcus oleaginous metabolism, we sequenced and performed comparative analysis of the 9.27 Mb R. opacus PD630 genome. Metabolic-reconstruction assigned 2017 enzymatic reactions to the 8632 R. opacus PD630 genes we identified. Of these, 261 genes were implicated in the R. opacus PD630 TAGs cycle by metabolic reconstruction and gene family analysis. Rhodococcus synthesizes uncommon straight-chain odd-carbon fatty acids in high abundance and stores them as TAGs. We have identified these to be pentadecanoic, heptadecanoic, and cis-heptadecenoic acids. To identify bioconversion pathways, we screened R. opacus PD630, R. jostii RHA1, Ralstonia eutropha H16, and C. glutamicum 13032 for growth on 190 compounds. The results of the catabolic screen, phylogenetic analysis of the TAGs cycle enzymes, and metabolic product characterizations were integrated into a working model of prokaryotic oleaginy.</description><subject>Actinomycetes</subject><subject>Bacteria</subject><subject>Biodiesel fuels</subject><subject>Biofuels</subject><subject>Biology</subject><subject>Biomass energy</subject><subject>Biosynthesis</subject><subject>Fatty acids</subject><subject>Fatty Acids - genetics</subject><subject>Fatty Acids - metabolism</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genome, Bacterial</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Life sciences</subject><subject>Lipids</subject><subject>Lipids - biosynthesis</subject><subject>Metabolic Networks and Pathways - genetics</subject><subject>Metabolism</subject><subject>Microbiology</subject><subject>PCB</subject><subject>Phylogeny</subject><subject>Physiological aspects</subject><subject>Polychlorinated biphenyls</subject><subject>Production processes</subject><subject>Rhodococcus - genetics</subject><subject>Rhodococcus - metabolism</subject><subject>Triglycerides</subject><subject>Triglycerides - biosynthesis</subject><subject>Triglycerides - genetics</subject><issn>1553-7404</issn><issn>1553-7390</issn><issn>1553-7404</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>DOA</sourceid><recordid>eNqVk1uL1DAUx4so7kW_gWhBUHyYMZcmaV6EZdbLwOLKesG3kKYnMx3SpibtoN_ejDO7TMEHJQ-5_f7_JOfkZNkTjOaYCvx648fQaTfvV9DNMUKEYHkvO8WM0ZkoUHH_aHySncW4QYiyUoqH2UlCadoUp9n3hW97HfTQbCHXXZ3bsTND45Nznox925iYe5vfrH3tjTdmTNNe77pPl5yi3PqQV423I7iY17AF5_sWuuFR9sBqF-HxoT_Pvr57-2XxYXZ1_X65uLiaGcHpMKsZMwQYoIqVleClJhVCQlYUNFBJUF3W3FrOTS15AaRASYVEISzljCME9Dx7tvftnY_qEJSoMMWUFbRgKBHLPVF7vVF9aFodfimvG_VnwYeV0mFojANFZFkgzhA2JIWt5pWwpSmtqQShjGKRvN4cThurFmqTHhq0m5hOd7pmrVZ-qyjmkpEyGbw8GAT_Y4Q4qLaJBpzTHfgxqlLSdDTlOJHP9-RKp5s1nfXJ0OxodUG45KWUkidq_hcqtRpS6nwHtknrE8GriSAxA_wcVnqMUS0_3_wH-_Hf2etvU_bFEbsG7YZ19G7c_bs4BYs9aIKPMYC9izRGalcFtwlXuypQhypIsqfHWboT3X57-htGBwDL</recordid><startdate>20110901</startdate><enddate>20110901</enddate><creator>Holder, Jason W</creator><creator>Ulrich, Jil C</creator><creator>DeBono, Anthony C</creator><creator>Godfrey, Paul A</creator><creator>Desjardins, Christopher A</creator><creator>Zucker, Jeremy</creator><creator>Zeng, Qiandong</creator><creator>Leach, Alex L B</creator><creator>Ghiviriga, Ion</creator><creator>Dancel, Christine</creator><creator>Abeel, Thomas</creator><creator>Gevers, Dirk</creator><creator>Kodira, Chinnappa D</creator><creator>Desany, Brian</creator><creator>Affourtit, Jason P</creator><creator>Birren, Bruce W</creator><creator>Sinskey, Anthony J</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>ISN</scope><scope>ISR</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20110901</creationdate><title>Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development</title><author>Holder, Jason W ; Ulrich, Jil C ; DeBono, Anthony C ; Godfrey, Paul A ; Desjardins, Christopher A ; Zucker, Jeremy ; Zeng, Qiandong ; Leach, Alex L B ; Ghiviriga, Ion ; Dancel, Christine ; Abeel, Thomas ; Gevers, Dirk ; Kodira, Chinnappa D ; Desany, Brian ; Affourtit, Jason P ; Birren, Bruce W ; Sinskey, Anthony J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c763t-d55c2e5e0b58b768a2b0079b3eae3920d8d6ff66cd964e2407630747f365600e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Actinomycetes</topic><topic>Bacteria</topic><topic>Biodiesel fuels</topic><topic>Biofuels</topic><topic>Biology</topic><topic>Biomass energy</topic><topic>Biosynthesis</topic><topic>Fatty acids</topic><topic>Fatty Acids - genetics</topic><topic>Fatty Acids - metabolism</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genome, Bacterial</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Life sciences</topic><topic>Lipids</topic><topic>Lipids - biosynthesis</topic><topic>Metabolic Networks and Pathways - genetics</topic><topic>Metabolism</topic><topic>Microbiology</topic><topic>PCB</topic><topic>Phylogeny</topic><topic>Physiological aspects</topic><topic>Polychlorinated biphenyls</topic><topic>Production processes</topic><topic>Rhodococcus - genetics</topic><topic>Rhodococcus - metabolism</topic><topic>Triglycerides</topic><topic>Triglycerides - biosynthesis</topic><topic>Triglycerides - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Holder, Jason W</creatorcontrib><creatorcontrib>Ulrich, Jil C</creatorcontrib><creatorcontrib>DeBono, Anthony C</creatorcontrib><creatorcontrib>Godfrey, Paul A</creatorcontrib><creatorcontrib>Desjardins, Christopher A</creatorcontrib><creatorcontrib>Zucker, Jeremy</creatorcontrib><creatorcontrib>Zeng, Qiandong</creatorcontrib><creatorcontrib>Leach, Alex L B</creatorcontrib><creatorcontrib>Ghiviriga, Ion</creatorcontrib><creatorcontrib>Dancel, Christine</creatorcontrib><creatorcontrib>Abeel, Thomas</creatorcontrib><creatorcontrib>Gevers, Dirk</creatorcontrib><creatorcontrib>Kodira, Chinnappa D</creatorcontrib><creatorcontrib>Desany, Brian</creatorcontrib><creatorcontrib>Affourtit, Jason P</creatorcontrib><creatorcontrib>Birren, Bruce W</creatorcontrib><creatorcontrib>Sinskey, Anthony J</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Canada</collection><collection>Gale In Context: Science</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Holder, Jason W</au><au>Ulrich, Jil C</au><au>DeBono, Anthony C</au><au>Godfrey, Paul A</au><au>Desjardins, Christopher A</au><au>Zucker, Jeremy</au><au>Zeng, Qiandong</au><au>Leach, Alex L B</au><au>Ghiviriga, Ion</au><au>Dancel, Christine</au><au>Abeel, Thomas</au><au>Gevers, Dirk</au><au>Kodira, Chinnappa D</au><au>Desany, Brian</au><au>Affourtit, Jason P</au><au>Birren, Bruce W</au><au>Sinskey, Anthony J</au><au>Richardson, Paul M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development</atitle><jtitle>PLoS genetics</jtitle><addtitle>PLoS Genet</addtitle><date>2011-09-01</date><risdate>2011</risdate><volume>7</volume><issue>9</issue><spage>e1002219</spage><epage>e1002219</epage><pages>e1002219-e1002219</pages><issn>1553-7404</issn><issn>1553-7390</issn><eissn>1553-7404</eissn><abstract>The Actinomycetales bacteria Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 bioconvert a diverse range of organic substrates through lipid biosynthesis into large quantities of energy-rich triacylglycerols (TAGs). To describe the genetic basis of the Rhodococcus oleaginous metabolism, we sequenced and performed comparative analysis of the 9.27 Mb R. opacus PD630 genome. Metabolic-reconstruction assigned 2017 enzymatic reactions to the 8632 R. opacus PD630 genes we identified. Of these, 261 genes were implicated in the R. opacus PD630 TAGs cycle by metabolic reconstruction and gene family analysis. Rhodococcus synthesizes uncommon straight-chain odd-carbon fatty acids in high abundance and stores them as TAGs. We have identified these to be pentadecanoic, heptadecanoic, and cis-heptadecenoic acids. To identify bioconversion pathways, we screened R. opacus PD630, R. jostii RHA1, Ralstonia eutropha H16, and C. glutamicum 13032 for growth on 190 compounds. The results of the catabolic screen, phylogenetic analysis of the TAGs cycle enzymes, and metabolic product characterizations were integrated into a working model of prokaryotic oleaginy.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>21931557</pmid><doi>10.1371/journal.pgen.1002219</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Actinomycetes Bacteria Biodiesel fuels Biofuels Biology Biomass energy Biosynthesis Fatty acids Fatty Acids - genetics Fatty Acids - metabolism Genes Genetic aspects Genome, Bacterial Genomes Genomics Life sciences Lipids Lipids - biosynthesis Metabolic Networks and Pathways - genetics Metabolism Microbiology PCB Phylogeny Physiological aspects Polychlorinated biphenyls Production processes Rhodococcus - genetics Rhodococcus - metabolism Triglycerides Triglycerides - biosynthesis Triglycerides - genetics |
| title | Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development |
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