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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| Format: | Article |
| Language: | en_US |
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Public Library of Science
2012
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| Online Access: | http://hdl.handle.net/1721.1/69085 https://orcid.org/0000-0002-1015-1270 |
| _version_ | 1811093427538886656 |
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| author | Ghiviriga, Ion Dancel, Christine Kodira, Chinnappa D. Desany, Brian Affourtit, Jason P. Abeel, Thomas Gevers, Dirk Birren, Bruce W. Godfrey, Paul Desjardins, Christopher A. Holder, Jason W. DeBono, Tony Ulrich, Jil Zucker, Jeremy Zeng, Qiandong Leach, Alex L. B. Sinskey, Anthony J |
| author2 | Harvard University--MIT Division of Health Sciences and Technology |
| author_facet | Harvard University--MIT Division of Health Sciences and Technology Ghiviriga, Ion Dancel, Christine Kodira, Chinnappa D. Desany, Brian Affourtit, Jason P. Abeel, Thomas Gevers, Dirk Birren, Bruce W. Godfrey, Paul Desjardins, Christopher A. Holder, Jason W. DeBono, Tony Ulrich, Jil Zucker, Jeremy Zeng, Qiandong Leach, Alex L. B. Sinskey, Anthony J |
| author_sort | Ghiviriga, Ion |
| collection | MIT |
| 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. |
| first_indexed | 2024-09-23T15:44:33Z |
| format | Article |
| id | mit-1721.1/69085 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T15:44:33Z |
| publishDate | 2012 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | mit-1721.1/690852022-10-02T03:49:14Z Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development Ghiviriga, Ion Dancel, Christine Kodira, Chinnappa D. Desany, Brian Affourtit, Jason P. Abeel, Thomas Gevers, Dirk Birren, Bruce W. Godfrey, Paul Desjardins, Christopher A. Holder, Jason W. DeBono, Tony Ulrich, Jil Zucker, Jeremy Zeng, Qiandong Leach, Alex L. B. Sinskey, Anthony J Harvard University--MIT Division of Health Sciences and Technology Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Engineering Systems Division Sinskey, Anthony J. Holder, Jason W. DeBono, Tony Ulrich, Jil Zucker, Jeremy Zeng, Qiandong Leach, Alex L. B. Sinskey, Anthony J. 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. Cambridge-MIT Institute Massachusetts Institute of Technology. (Seed Grant program) Shell Oil Company National Institute of Allergy and Infectious Diseases (U.S.) United States. National Institutes of Health National Institutes of Health. Department of Health and Human Services (Contract No. HHSN272200900006C) 2012-02-10T19:03:16Z 2012-02-10T19:03:16Z 2011-09 2011-03 Article http://purl.org/eprint/type/JournalArticle 1553-7390 1553-7404 http://hdl.handle.net/1721.1/69085 Holder, Jason W. et al. “Comparative and Functional Genomics of Rhodococcus Opacus PD630 for Biofuels Development.” Ed. Paul M. Richardson. PLoS Genetics 7.9 (2011): e1002219. Web. 10 Feb. 2012. https://orcid.org/0000-0002-1015-1270 en_US http://dx.doi.org/10.1371/journal.pgen.1002219 PLoS Genetics Creative Commons Attribution http://creativecommons.org/licenses/by/2.5/ application/pdf Public Library of Science PLoS |
| spellingShingle | Ghiviriga, Ion Dancel, Christine Kodira, Chinnappa D. Desany, Brian Affourtit, Jason P. Abeel, Thomas Gevers, Dirk Birren, Bruce W. Godfrey, Paul Desjardins, Christopher A. Holder, Jason W. DeBono, Tony Ulrich, Jil Zucker, Jeremy Zeng, Qiandong Leach, Alex L. B. Sinskey, Anthony J Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development |
| title | Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development |
| title_full | Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development |
| title_fullStr | Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development |
| title_full_unstemmed | Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development |
| title_short | Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development |
| title_sort | comparative and functional genomics of rhodococcus opacus pd630 for biofuels development |
| url | http://hdl.handle.net/1721.1/69085 https://orcid.org/0000-0002-1015-1270 |
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