title: Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development.
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.
authors.affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
authors.forename: Jason W
authors.initials: JW
authors.lastname: Holder
authors.forename: Jil C
authors.initials: JC
authors.lastname: Ulrich
authors.forename: Anthony C
authors.initials: AC
authors.lastname: DeBono
authors.forename: Paul A
authors.initials: PA
authors.lastname: Godfrey
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Desjardins
authors.forename: Jeremy
authors.initials: J
authors.lastname: Zucker
authors.forename: Qiandong
authors.initials: Q
authors.lastname: Zeng
authors.forename: Alex L B
authors.initials: AL
authors.lastname: Leach
authors.forename: Ion
authors.initials: I
authors.lastname: Ghiviriga
authors.forename: Christine
authors.initials: C
authors.lastname: Dancel
authors.forename: Thomas
authors.initials: T
authors.lastname: Abeel
authors.forename: Dirk
authors.initials: D
authors.lastname: Gevers
authors.forename: Chinnappa D
authors.initials: CD
authors.lastname: Kodira
authors.forename: Brian
authors.initials: B
authors.lastname: Desany
authors.forename: Jason P
authors.initials: JP
authors.lastname: Affourtit
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Sinskey
mesh_terms: D056804:Biofuels; D005227:Fatty Acids / Q000235:genetics / Q000378:metabolism; D016680:Genome, Bacterial; D023281:Genomics; D008055:Lipids / Q000096:biosynthesis*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D010802:Phylogeny; D012240:Rhodococcus / Q000235:genetics* / Q000378:metabolism; D014280:Triglycerides / Q000096:biosynthesis* / Q000235:genetics
chemical_list: D056804:Biofuels; D005227:Fatty Acids; D008055:Lipids; D014280:Triglycerides