S138: 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 sequenced and performed comparative analysis of the 9.27 Mb R. opacus PD630 genome. Metabolic-reconstruction of 8632 genes in the R. opacus PD630 genome assigned 2017 enzymatic reactions to the genes we identified.

R. opacus PD630 has a large 9.27 Mb genome that contains many homologous genes dedicated to lipid metabolism. 261 genes were implicated in the R. opacus PD630 TAGs cycle by metabolic reconstruction and gene family analysis. To provide pathway insight and describe a major fraction of the TAGs stored in Rhodococcus, we purified and characterized uncommon straight-chain odd-carbon fatty acids. 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 chemical 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 Rhodococcus oleaginous physiology. Our synthesis of genome sequence and phenotypic information supports a model for the genetic basis for prokaryotic oleaginy and provides key insights for the engineering of next-generation biofuels with genes that are conserved in both prokaryotic and eukaryotic kingdoms.