Draft genome sequence of Rhodomicrobium udaipurense JA643T with special reference to hopanoid biosynthesis.
Bottom Line: The machinery required for the degradation of aromatic compounds and resistance to solvents as well as all that required for photosynthesis are present in this organism.Also, through extensive functional annotation, 18 genes involved in the biosynthesis of hopanoids are predicted, namely those responsible for the synthesis of diploptene, diplopterol, adenosylhopane, ribosylhopane, aminobacteriohopanetriol, glycosyl group containing hopanoids and unsaturated hopanoids.The hopanoid biosynthetic pathway was then inferred based on the genes identified and through experimental validation of individual hopanoid molecules.
Affiliation: Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India.Show MeSH
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Mentions: hpnI/hpnB genes are associated with hopanoid glycosyltransferase, and glycosylated hopanoids were identified with Geobacter sulfurreducens and Geobacter metallireducens.28,29 Hopanoids with glycosyl moiety is expected in R. udaipurense JA643T since hpnI/hpnB genes were observed in the genome of this organism; however, no glycosyl group containing hopanoids were detected in the GC–MS analysis. hpnC, hpnD and hpnE genes are involved in the modification of squalene. hpnE is a squalene-associated, FAD-dependent desaturase which has oxidoreductase activity. Perzl et al. suggested that it might be involved as an oxidoreductase in hopanoid or terpenoid biosynthesis pathways.21 However, its role in hopanoid biosynthesis is not understood. Gene hpnA encode for NAD-dependent nucleoside diphosphate–sugar epimerase/dehydrates protein, which was not observed in the draft genome of R. udaipurense JA643T. Hopanoid biosynthetic genes between R. udaipurense JA643T and R. vannielii ATCC17100T were compared. Sequence similarity ranges from 95 to 99% between them (Table 2, Supplementary Table S3). The hopanoid biosynthetic pathway was then inferred based on the genes identified, experimental validation of hopanoid molecules and available literature (Fig. 3).3,4,15–30Figure 3.
Affiliation: Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India.