Farnesyl diphosphate (FPP) synthase is essential not only for phototrophic bacteria in carotenoid biosynthesis, but also for non-phototrophic bacteria in the biosynthesis of physiologically important compounds. The gene encoding FPP synthase was assessed as a molecular marker to investigate the intermingled relationship between the phototropic and non-phototropic bacteria in the alpha-Proteobacteria based on 16S rRNA analysis. The FPP synthase amino acid sequences from three phototropic bacteria, Rhodobacter sphaeroides ATCC 11167(T), Rhodobacter capsulatus ATCC 11166(T) and Rhodovulum sulfidophilum W4(T), were determined and used in conjunction with sequences of other representative members of the alpha-, gamma- and epsilon-Proteobacteria and the low-G+C Gram-positive bacteria for phylogenetic analyses by the neighbour-joining and maximum-likelihood methods. The overall topology of the FPP synthase gene tree is consistent with that of the 16S rRNA tree, producing a distinct cluster of the three phototropic bacteria. A minor discordance between the two trees was observed in the cluster of the non-phototrophic Bradyrhizobiumjaponicum USDA 110 and Mesorhizobium loti MAFF 303099; the FPP synthase genes of these two rhizobial species are highly homologous as compared with their respective 16S rRNA. The results suggest that the FPP synthase and 16S rRNA genes have the same evolutionary pattern, evolving vertically from each common ancestral gene; the FPP synthase gene, therefore, could possibly be used for further study on the molecular systematics of photosynthetic bacteria.


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