ENZYMOLOGY AND MOLECULAR BIOLOGY OF BILE ACID 7alpha- AND 7beta- DEHYDROXYLATION BY THE INTESTINAL BACTERIA CLOSTRIDIUM SCINDENS AND CLOSTRIDIUM HYLEMONAE (2008)

The collective microbial genomes within our gut(microbiome) represent a powerful metabolic force, leading many authors to call our GI flora an "organ within an organ", and the metagenomic sequencing of our microbiome, "the second human genome project". Bile acids, endogenously produced by the host liver, represent both a strong selective pressure for potential colonizers, aswell as substrates for microbial metabolism. Indeed, microbes have evolved enzymes to deconjugate bile salts, epimerize bile acid hydroxyl groups, and 7alpha-dehydroxylateprimary bile acids. The products of microbial 7alpha-dehydroxylation, secondary bile acids, are suggested by numerous lines of evidence to be involved in promoting colon carcinogenesis. 7alpha-dehydroxylating activity is a multi-step pathway, genes of which have only been identified in a small number of organisms within the genusClostridium. The biochemistry of this pathway has been largely worked out. The third step in the pathway is introduction of a delta-4-double bond; however, the gene product(s) responsible have not been identified. The baiCD and baiH genes were cloned, expressed and shown to have NAD-dependent 3-oxo-delta-4-steroid oxidoreductase activity showing stereospecificity for 7alpha-hydroxy and 7beta-hydroxy bile acid, respectively.In addition, bai genes were isolated from C.hylemonae TN271 by bidirectional genome-walking by PCR. This represents the first report of bai genes from a "low activity" 7alpha-dehydroxylating bacterium. The gene organization and sequence of the baiBCDEFGHI operon was highly conserved between C. hylemonae TN271 and the "high activity" 7alpha-dehydroxylating bacterium C. scindens VPI12708. The baiA gene was located by PCR using degenerate oligonucleotides. Bi-directional genome-walking revealed what appears to be several novel genes involved in bile acid metabolism which were also located in C. scindens VPI 12708. Expression of a 62 kDa flavoprotein and reactionwith [24-14C] 3-oxo-DCA and NADP resulted in a product of greater hydrophilicity than deoxycholic acid. The identity of this product was not determined. A second gene appears to share a common evolutionary origin with the baiF gene. A hypothesis is offered regarding the function of these homologues as Type III CoA transferasesrecognizing 5alpha-bile acids, or 5beta-bile acids (allo-bile acids). A third gene encodes a putative short chain reductase, similar in size and predicted function to the baiA gene, which may be involved in the final reductive step in the pathway. These novel genes also contained a conserved upstream regulatory region with the baioxidative genes. Finally, two genes were identified which may serve as potential drug targets to inhibit bile acid 7alpha-dehydroxylation. The first is an ABC transporter which may be co-transcribed with the other novel bile acid metabolizing genes, and what appears to be a bile acid sensor/regulator similar to the Tryptophan-rich sensory protein (TspO)/mitochondrial peripheral benzodiazepinereceptor (MBR) family of proteins.