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Draft genome sequence of Rhodomicrobium udaipurense JA643T with special reference to hopanoid biosynthesis.

Tushar L, Sasikala Ch, Ramana ChV - DNA Res. (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India.

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Schematic representation of hopanoid biosynthetic pathway in Rhodomicrobium udaipurense JA643T based on genes identified, GC–MS analysis and previous reports.3,4,15–26,30 This figure appears in colour in the online version of DNA Research.
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DSU026F3: Schematic representation of hopanoid biosynthetic pathway in Rhodomicrobium udaipurense JA643T based on genes identified, GC–MS analysis and previous reports.3,4,15–26,30 This figure appears in colour in the online version of DNA Research.

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.


Draft genome sequence of Rhodomicrobium udaipurense JA643T with special reference to hopanoid biosynthesis.

Tushar L, Sasikala Ch, Ramana ChV - DNA Res. (2014)

Schematic representation of hopanoid biosynthetic pathway in Rhodomicrobium udaipurense JA643T based on genes identified, GC–MS analysis and previous reports.3,4,15–26,30 This figure appears in colour in the online version of DNA Research.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263297&req=5

DSU026F3: Schematic representation of hopanoid biosynthetic pathway in Rhodomicrobium udaipurense JA643T based on genes identified, GC–MS analysis and previous reports.3,4,15–26,30 This figure appears in colour in the online version of DNA Research.
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.

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India.

Show MeSH
Related in: MedlinePlus