TY - JOUR
T1 - A metabolic pathway for bile acid dehydroxylation by the gut microbiome
AU - Funabashi, Masanori
AU - Grove, Tyler L.
AU - Wang, Min
AU - Varma, Yug
AU - McFadden, Molly E.
AU - Brown, Laura C.
AU - Guo, Chunjun
AU - Higginbottom, Steven
AU - Almo, Steven C.
AU - Fischbach, Michael A.
N1 - Funding Information:
Acknowledgements We thank C. T. Walsh, D. Dodd, C. O’Loughlin and members of the Fischbach and Almo laboratories for helpful comments on the manuscript. This work was supported by National Institutes of Health (NIH) grants DP1 DK113598 (to M.A.F.), R01 DK110174 (to M.A.F.), P01 HL147823 (to M.A.F.), P01 GM118303-01 (to S.C.A.), U54 GM093342 (to S.C.A.), U54 GM094662 (to S.C.A.) and DP2 HD101401-01 (to C.G.); the Chan–Zuckerberg Biohub (to M.A.F.); a Howard Hughes Medical Institute (HHMI)–Simons Faculty Scholars Award (to M.A.F.); an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Foundation (to M.A.F.); and the Price Family Foundation (to S.C.A.).
PY - 2020/6/25
Y1 - 2020/6/25
N2 - The gut microbiota synthesize hundreds of molecules, many of which influence host physiology. Among the most abundant metabolites are the secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA), which accumulate at concentrations of around 500 μM and are known to block the growth of Clostridium difficile1, promote hepatocellular carcinoma2 and modulate host metabolism via the G-protein-coupled receptor TGR5 (ref. 3). More broadly, DCA, LCA and their derivatives are major components of the recirculating pool of bile acids4; the size and composition of this pool are a target of therapies for primary biliary cholangitis and nonalcoholic steatohepatitis. Nonetheless, despite the clear impact of DCA and LCA on host physiology, an incomplete knowledge of their biosynthetic genes and a lack of genetic tools to enable modification of their native microbial producers limit our ability to modulate secondary bile acid levels in the host. Here we complete the pathway to DCA and LCA by assigning and characterizing enzymes for each of the steps in its reductive arm, revealing a strategy in which the A–B rings of the steroid core are transiently converted into an electron acceptor for two reductive steps carried out by Fe–S flavoenzymes. Using anaerobic in vitro reconstitution, we establish that a set of six enzymes is necessary and sufficient for the eight-step conversion of cholic acid to DCA. We then engineer the pathway into Clostridium sporogenes, conferring production of DCA and LCA on a nonproducing commensal and demonstrating that a microbiome-derived pathway can be expressed and controlled heterologously. These data establish a complete pathway to two central components of the bile acid pool.
AB - The gut microbiota synthesize hundreds of molecules, many of which influence host physiology. Among the most abundant metabolites are the secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA), which accumulate at concentrations of around 500 μM and are known to block the growth of Clostridium difficile1, promote hepatocellular carcinoma2 and modulate host metabolism via the G-protein-coupled receptor TGR5 (ref. 3). More broadly, DCA, LCA and their derivatives are major components of the recirculating pool of bile acids4; the size and composition of this pool are a target of therapies for primary biliary cholangitis and nonalcoholic steatohepatitis. Nonetheless, despite the clear impact of DCA and LCA on host physiology, an incomplete knowledge of their biosynthetic genes and a lack of genetic tools to enable modification of their native microbial producers limit our ability to modulate secondary bile acid levels in the host. Here we complete the pathway to DCA and LCA by assigning and characterizing enzymes for each of the steps in its reductive arm, revealing a strategy in which the A–B rings of the steroid core are transiently converted into an electron acceptor for two reductive steps carried out by Fe–S flavoenzymes. Using anaerobic in vitro reconstitution, we establish that a set of six enzymes is necessary and sufficient for the eight-step conversion of cholic acid to DCA. We then engineer the pathway into Clostridium sporogenes, conferring production of DCA and LCA on a nonproducing commensal and demonstrating that a microbiome-derived pathway can be expressed and controlled heterologously. These data establish a complete pathway to two central components of the bile acid pool.
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U2 - 10.1038/s41586-020-2396-4
DO - 10.1038/s41586-020-2396-4
M3 - Article
C2 - 32555455
AN - SCOPUS:85086711568
VL - 582
SP - 566
EP - 570
JO - Nature
JF - Nature
SN - 0028-0836
IS - 7813
ER -