Identification of Amino Acid Synthesis Pathways in Desulfovibrio vulgaris by Isotopic Labeling, Metabolite Analysis, and Genome Sequence Analysis

We used isotopic labeling and metabolite analyses to test the predicted amino acid synthesis pathways in the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough. The data suggest several pathways that were not apparent in the initial genome annotation. First, D. vulgaris synthesizes isoleucine via citramalate synthase (DVU1914). Second, D. vulgaris synthesizes methionine via O-succinyl-homoserine, cystathionine, and homocysteine. DVU0171 is a candidate for cystathionine beta-lyase, but genes for the other steps are not apparent. Third, in vitro assays confirm the presence of Re-citrate-synthase (DVU0398), which is closely related to the recently identified Re-citrate-synthase found in some Clostridia. We also propose that D. vulgaris synthesizes 3-dehydroquinate, which is required for the synthesis of aromatic amino acids, via archaeal-like transaldolase and 3-dehydroquinate cyclase/deaminase (DVU0460,DVU0461).