Formation of secondary allo-bile acids by novel enzymes from gut Firmicutes

Abstract

The gut microbiome of vertebrates is capable of numerous biotransformations of bile acids, which are responsible for intestinal lipid digestion and function as key nutrient-signaling molecules. The human liver produces bile acids from cholesterol predominantly in the A/B- cis orientation in which the sterol rings are “kinked”, as well as small quantities of A/B- trans oriented “flat” stereoisomers known as “primary allo-bile acids”. While the complex multi-step bile acid 7α-dehydroxylation pathway has been well-studied for conversion of “kinked” primary bile acids such as cholic acid (CA) and chenodeoxycholic acid (CDCA) to deoxycholic acid (DCA) and lithocholic acid (LCA), respectively, the enzymatic basis for the formation of “flat” stereoisomers allo-deoxycholic acid (allo-DCA) and allo-lithocholic acid (allo-LCA) by Firmicutes has remained unsolved for three decades. Here, we present a novel mechanism by which Firmicutes generate the ”flat” bile acids allo-DCA and allo-LCA. The BaiA1 was shown to catalyze the final reduction from 3-oxo-allo-DCA to allo-DCA and 3-oxo-allo-LCA to allo-LCA. Phylogenetic and metagenomic analyses of human stool samples indicate that BaiP and BaiJ are encoded only in Firmicutes and differ from membrane-associated bile acid 5α-reductases recently reported in Bacteroidetes that indirectly generate allo-LCA from 3-oxo-Δ 4 -LCA. We further map the distribution of baiP and baiJ among Firmicutes in human metagenomes, demonstrating an increased abundance of the two genes in colorectal cancer (CRC) patients relative to healthy individuals.

Strain-dependent induction of primary bile acid 7-dehydroxylation by cholic acid

“…The current CA 7-DH-ion pathway would suggest that this gene is not involved in that process in strain VPI 12708 [24], which is consistent with the low level of expression observed here (Figure 7B). Conversely, its high level of upregulation in strain ATCC 35704 matches previously published data [21,33] and suggests that baiJ may play a role in the 7-DH-ion of CA or other BAs in that strain as it does with CDCA [21,43]. Finally, E. muris SJ24, the murine isolate, barely registered any bai gene expression response to CA or any other BA tested.…”

“…From genome analysis, E. muris SJ24 has fragments of baiJKL as pseudogenes. The exact role of these genes has yet to be de ned although there is novel evidence of the role of BaiJ [43].…”

Novel approaches in IBD therapy: targeting the gut microbiota-bile acid axis

“…Recent studies revealed the involvement of two types of bacterial steroid dehydrogenases, namely 5α-reductase (3-oxo-5α-steroid 4-dehydrogenase, 5AR) and 5β-reductase (3-oxo-5β-steroid 4-dehydrogenase, 5BR), in the production of homologous (5α and 5β) BAs. 62 The levels of isolithocholic acid (isoLCA), 3-oxolithocholic acid (3-oxoLCA), allolithocholic acid (alloLCA), 3-oxoallolithocholic acid (3-oxoalloLCA), and isoalloLCA were also found to be significantly higher in the centenarian group (average age, 107 years old) due to the unique gut microbiota in centenarians. 25 Analysis of centenarians’ gut microbiota revealed the presence of many strains with strong 3α-HSDH, 3β-HSDH, 5AR, and/or 5BR activity.…”

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

“…A baiJKL operon is found in some organisms, where baiK encodes a bile acid CoA transferase and BaiJ is a flavoprotein that was shown to be involved in the formation of allo-bile acids. 15 , 16 Indeed, a homologue of BaiJ (named BaiP by authors) found in other organisms, was likewise shown to be a bile acid 5α-reductase leading to allo-bile acid production. 16 BaiN is a flavoprotein that may play a role in the reductive part of the 7α-dehydroxylation pathway and the baiN gene is consistently found next to baiO which encodes a NAD(FAD)-utilizing dehydrogenase for which a role in bile acid metabolism has yet to be shown.…”