BaiJ and BaiB are key enzymes in the chenodeoxycholic acid 7α-dehydroxylation pathway in the gut microbe Clostridium scindens ATCC 35704

References

• Hamilton JP, Xie G, Raufman JP, Hogan S, Griffin TL, Packard CA, Chatfield DA, Hagey LR, Steinbach JH, Hofmann AF. Human cecal bile acids: concentration and spectrum. Am J Physiol-Gastrointest Liver Physiol. 2007;293(1):G256–23. doi:10.1152/ajpgi.00027.2007.
   PubMed Web of Science ®Google Scholar
• Ridlon JM, Kang D-J, Hylemon PB. Bile salt biotransformations by human intestinal bacteria. J Lipid Res. 2006;47(2):241–259. doi:10.1194/jlr.R500013-JLR200.
   PubMed Web of Science ®Google Scholar
• Hofmann AF. The enterohepatic circulation of bile acids in mammals: form and functions. Front Biosci. 2009;Volume(14):2584. doi:10.2741/3399.
   Google Scholar
• Wahlström A, Sayin SI, Marschall H-U, Bäckhed F. Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism. Cell Metab. 2016;24(1):41–50. doi:10.1016/j.cmet.2016.05.005.
   PubMed Web of Science ®Google Scholar
• Lin S, Wang S, Wang P, Tang C, Wang Z, Chen L, Luo G, Chen H, Liu Y, Feng B. et al. Bile acids and their receptors in regulation of gut health and diseases. Prog Lipid Res. 2023;89:101210. doi:10.1016/j.plipres.2022.101210.
   PubMed Web of Science ®Google Scholar
• Mallonee DH, White WB, Hylemon PB. Cloning and sequencing of a bile acid-inducible operon from eubacterium sp. strain VPI 12708. J Bacteriol. 1990;172(12):7011–7019. doi:10.1128/jb.172.12.7011-7019.1990.
   PubMed Web of Science ®Google Scholar
• Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H. et al. The ‘in vivo lifestyle’ of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice. Gut Microbes. 2020;11(3):381–404. doi:10.1080/19490976.2019.1618173.
   PubMed Web of Science ®Google Scholar
• Ridlon JM, Harris SC, Bhowmik S, Kang D-J, Hylemon PB. Consequences of bile salt biotransformations by intestinal bacteria. Gut Microbes. 2016;7(1):22–39. doi:10.1080/19490976.2015.1127483.
   PubMed Web of Science ®Google Scholar
• Funabashi M, Grove TL, Wang M, Varma Y, McFadden ME, Brown LC, Guo C, Higginbottom S, Almo SC, Fischbach MA. A metabolic pathway for bile acid dehydroxylation by the gut microbiome. Nature. 2020;582(7813):566–570. doi:10.1038/s41586-020-2396-4.
   PubMed Web of Science ®Google Scholar
• Mallonee DH, Hylemon PB. Sequencing and expression of a gene encoding a bile acid transporter from Eubacterium sp. strain VPI 12708. J Bacteriol. 1996;178(24):7053–7058. doi:10.1128/jb.178.24.7053-7058.1996.
   PubMed Web of Science ®Google Scholar
• Mallonee DH, Adams JL, Hylemon PB. The bile acid-inducible baiB gene from Eubacterium sp. strain VPI 12708 encodes a bile acid-coenzyme A ligase. J Bacteriol. 1992;174(7):2065–2071. doi:10.1128/jb.174.7.2065-2071.1992.
   PubMed Web of Science ®Google Scholar
• Bhowmik S, Jones DH, Chiu H-P, Park I-H, Chiu H-J, Axelrod HL, Farr CL, Tien HJ, Agarwalla S, Lesley SA. Structural and functional characterization of BaiA, an enzyme involved in secondary bile acid synthesis in human gut microbe. Proteins Struct Funct Bioinforma. 2014;82(2):216–229. doi:10.1002/prot.24353.
   PubMed Web of Science ®Google Scholar
• Kang DJ, Ridlon, JM, Moore, DR, Barnes, S, Hylemon, PB. Clostridium scindens baiCD and baiH genes encode stereo-specific 7α/7β-hydroxy-3-oxo-Δ4-cholenoic acid oxidoreductases☆. Biochim Biophys Acta BBA - Mol Cell Biol Lipids. 2008;1781(1–2):16–25. doi:10.1016/j.bbalip.2007.10.008.
   PubMed Web of Science ®Google Scholar
• Bhowmik S, Chiu H-P, Jones DH, Chiu HJ, Miller MD, Xu Q, Farr CL, Ridlon JM, Wells JE, Elsliger MA. et al. Structure and functional characterization of a bile acid 7α dehydratase B ai E in secondary bile acid synthesis. Proteins Struct Funct Bioinforma. 2016;84(3):316–331. doi:10.1002/prot.24971.
   PubMed Web of Science ®Google Scholar
• Ridlon JM, Hylemon PB. Identification and characterization of two bile acid coenzyme a transferases from Clostridium scindens, a bile acid 7α-dehydroxylating intestinal bacterium. J Lipid Res. 2012;53(1):66–76. doi:10.1194/jlr.M020313.
   PubMed Web of Science ®Google Scholar
• Lee JW, Cowley ES, Wolf PG, Doden HL, Murai T, Caicedo KYO, Ly LK, Sun F, Takei H, Nittono H. et al. Formation of secondary allo-bile acids by novel enzymes from gut Firmicutes. Gut Microbes. 2022;14(1):2132903. doi:10.1080/19490976.2022.2132903.
   PubMed Web of Science ®Google Scholar
• Harris SC, Devendran S, Alves JMP, Mythen SM, Hylemon PB, Ridlon JM. Identification of a gene encoding a flavoprotein involved in bile acid metabolism by the human gut bacterium Clostridium scindens ATCC 35704. Biochim Biophys Acta BBA - Mol Cell Biol Lipids. 2018;1863(3):276–283. doi:10.1016/j.bbalip.2017.12.001.
   PubMed Web of Science ®Google Scholar
• Heinken A, Ravcheev DA, Baldini F, Heirendt L, Fleming RMT, Thiele I. Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. Microbiome. 2019;7(1):75. doi:10.1186/s40168-019-0689-3.
   PubMed Web of Science ®Google Scholar
• MORRIS GN, WINTER J, CATO EP, RITCHIE AE, BOKKENHEUSER VD. Clostridium scindens sp. nov., a human intestinal bacterium with desmolytic activity on corticoids. Int J Syst Evol Microbiol. 1985;35(4):478–481. doi:10.1099/00207713-35-4-478.
   Google Scholar
• Marion S, Studer N, Desharnais L, Menin L, Escrig S, Meibom A, Hapfelmeier S, Bernier-Latmani R. In vitro and in vivo characterization of Clostridium scindens bile acid transformations. Gut Microbes. 2019;10(4):481–503. doi:10.1080/19490976.2018.1549420.
   PubMed Web of Science ®Google Scholar
• Vico-Oton E, Volet C, Jacquemin N, Dong Y, Hapfelmeier S, Meibom KL, Bernier-Latmani R. Strain-Dependent Induction Of Primary Bile Acid 7-Dehydroxylation By Cholic Acid. 2022. doi:10.1101/2022.02.15.480494.
   Google Scholar
• Yoshimoto T, Higashi H, Kanatani A, Lin XS, Nagai H, Oyama H, Kurazono K, Tsuru D. Cloning and sequencing of the 7 alpha-hydroxysteroid dehydrogenase gene from Escherichia coli HB101 and characterization of the expressed enzyme. J Bacteriol. 1991;173(7):2173–2179. doi:10.1128/jb.173.7.2173-2179.1991.
   PubMed Web of Science ®Google Scholar
• Devendran S, Shrestha R, Alves JMP, Wolf PG, Ly L, Hernandez AG, Méndez-García C, Inboden A, Wiley J, Paul O. et al. Clostridium scindens ATCC 35704: integration of nutritional requirements, the complete genome sequence, and global transcriptional responses to bile acids. Appl Environ Microbiol. 2019;85(7):e00052–19. doi:10.1128/AEM.00052-19.
   PubMed Web of Science ®Google Scholar
• Mallonee DH, Lijewski MA, Hylemon PB. Expression in Escherichia coli and characterization of a bile acid-inducible 3alpha-hydroxysteroid dehydrogenase from Eubacterium sp. strain VPI 12708. Curr Microbiol. 1995;30(5):259–263. doi:10.1007/BF00295498.
   PubMed Web of Science ®Google Scholar
• Ridlon JM, Kang D-J, Hylemon PB. Isolation and characterization of a bile acid inducible 7α-dehydroxylating operon in Clostridium hylemonae TN271. Anaerobe. 2010;16(2):137–146. doi:10.1016/j.anaerobe.2009.05.004.
   PubMed Web of Science ®Google Scholar
• Tadano T, Kanoh M, Kondoh H, Matsumoto M, Mimura K, Kanoh Y, Sakamoto K, Kamano T. Kinetic analysis of bile acids in the feces of colorectal cancer patients by gas chromatography-mass spectrometry (GC-MS). Rinsho Byori. 2007;55:417–427.
   PubMedGoogle Scholar
• Tadano T, Kanoh M, Matsumoto M, Sakamoto K, Kamano T. Studies of serum and feces bile acids determination by gas chromatography-mass spectrometry. Rinsho Byori. 2006;54:103–110.
   PubMedGoogle Scholar
• Sato Y, Atarashi K, Plichta DR, Arai Y, Sasajima S, Kearney SM, Suda W, Takeshita K, Sasaki T, Okamoto S. et al. Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians. Nature. 2021;599(7885):458–464. doi:10.1038/s41586-021-03832-5.
   PubMed Web of Science ®Google Scholar
• Shiffka SJ, Kane MA, Swaan PW. Planar bile acids in health and disease. Biochim Biophys Acta BBA - Biomembr. 2017;1859(11):2269–2276. doi:10.1016/j.bbamem.2017.08.019.
   PubMed Web of Science ®Google Scholar
• Marion S, Desharnais L, Studer N, Dong Y, Notter MD, Poudel S, Menin L, Janowczyk A, Hettich RL, Hapfelmeier S. et al. Biogeography of microbial bile acid transformations along the murine gut. J Lipid Res. 2020;61(11):1450–1463. doi:10.1194/jlr.RA120001021.
   PubMed Web of Science ®Google Scholar
• Hylemon P, Melone P, Franklund C, Lund E, Björkhem I. Mechanism of intestinal 7 alpha-dehydroxylation of cholic acid: evidence that allo-deoxycholic acid is an inducible side-product. J Lipid Res. 1991;32(1):89–96. doi:10.1016/S0022-2275(20)42247-3.
   PubMed Web of Science ®Google Scholar
• Jin W-B, Li T-T, Huo D, Qu S, Li XV, Arifuzzaman M, Lima SF, Shi H-Q, Wang A, Putzel GG. et al. Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome. Cell. 2022;185(3):547–562.e22. doi:10.1016/j.cell.2021.12.035.
   PubMed Web of Science ®Google Scholar
• Bai Y, Zhao T, Gao M, Zou Y, Lei X. A novel gene alignment in Dorea sp. AM58-8 produces 7-dehydroxy-3β bile acids from primary bile acids. Biochem. 2022;61(24):2870–2878. doi:10.1021/acs.biochem.2c00264.
   PubMed Web of Science ®Google Scholar
• Song I, Gotoh Y, Ogura Y, Hayashi T, Fukiya S, Yokota A. Comparative genomic and physiological analysis against Clostridium scindens reveals Eubacterium sp. c-25 as an atypical deoxycholic acid producer of the human gut microbiota. Microorgan. 2021;9(11):2254. doi:10.3390/microorganisms9112254.
   PubMed Web of Science ®Google Scholar
• Choi K-H, Gaynor JB, White KG, Lopez C, Bosio CM, Karkhoff-Schweizer RR, Schweizer HP. A Tn7-based broad-range bacterial cloning and expression system. Nat Methods. 2005;2(6):443–448. doi:10.1038/nmeth765.
   PubMed Web of Science ®Google Scholar
• Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP, Kumar N, Bresciani A, Martínez I, Just S, Ziegler C. et al. The mouse intestinal bacterial collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol. 2016;1(10):1–15. doi:10.1038/nmicrobiol.2016.131.
   Web of Science ®Google Scholar
• Sabri S, Steen JA, Bongers M, Nielsen LK, Vickers CE. Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci. Microb Cell Fact. 2013;12(1):60. doi:10.1186/1475-2859-12-60.
   PubMedGoogle Scholar
• Jensen SI, Lennen RM, Herrgård MJ, Nielsen AT. Seven gene deletions in seven days: fast generation of Escherichia coli strains tolerant to acetate and osmotic stress. Sci Rep. 2015;5(1):17874. doi:10.1038/srep17874.
   PubMedGoogle Scholar