Biology subjects

Doden, H. L.

Publications and source records attributed to Doden, H. L..

3 recordsLinked to original sources

bioRxiv2020

Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine

Bile salt synthesis, secretion into the intestinal lumen, and resorption in the ileum occurs in all vertebrate classes. In mammals, bile salt composition is determined by host and microbial enzymes, affecting signaling through the bile salt-binding transcription factor Farnesoid X receptor (Fxr). However, these processes in other vertebrate classes remain poorly understood. We show that key components of hepatic bile salt synthesis and ileal transport pathways are conserved and under control of Fxr in zebrafish. Zebrafish bile salts consist primarily of a C27 bile alcohol and a C24 bile acid which undergo multiple microbial modifications including bile acid deconjugation that augments Fxr activity. Using single-cell RNA sequencing, we provide a cellular atlas of the zebrafish intestinal epithelium and uncover roles for Fxr in transcriptional and differentiation programs in ileal and other cell types. These results establish zebrafish as a non-mammalian vertebrate model for studying bile salt metabolism and Fxr signaling.

physiology↗

bioRxiv2020

Identification and characterization of a gene encoding NADP(H)-dependent bile acid 12β-hydroxysteroid dehydrogenase from Clostridium paraputrificum ATCC 25780

Bile acids are detergent molecules that solubilize dietary lipids and lipid-soluble vitamins. Humans synthesize bile acids with -orientation hydroxyl groups which can be biotransformed by gut microbiota to toxic, hydrophobic bile acids, such as deoxycholic acid (DCA). Gut microbiota can also convert hydroxyl groups from the -orientation through an oxo-intermediate to the {beta}-orientation, resulting in more hydrophilic, less toxic bile acids. This interconversion is catalyzed by regio-(C-3 vs. C-7) and stereospecific ( vs. {beta}) hydroxysteroid dehydrogenases (HSDHs). So far, genes encoding the urso-(7-HSDH & 7{beta}-HSDH) and iso-(3-HSDH & 3{beta}-HSDH) bile acid pathways have been described. Recently, multiple human gut clostridia were reported to encode 12-HSDH, which interconverts DCA and 12-oxolithocholic acid (12-oxoLCA). 12{beta}-HSDH completes the epi-bile acid pathway by converting 12-oxoLCA to the 12{beta}-bile acid denoted epiDCA; however, gene(s) encoding this enzyme have yet to be identified. We confirmed 12{beta}-HSDH activity in cultures of Clostridium paraputrificum ATCC 25780. From six candidate C. paraputrificum ATCC 25780 oxidoreductase genes, we discovered the first gene (DR024_RS09610) encoding bile acid 12{beta}-HSDH. Phylogenetic analysis revealed unforeseen diversity for 12{beta}-HSDH, leading to validation of two additional bile acid 12{beta}-HSDHs through a synthetic biology approach. By comparison to a previous phylogenetic analysis of 12-HSDH, we identified the first potential C-12 epimerizing strains: Collinsella tanakaei YIT 12063 and Collinsella stercoris DSM 13279. A Hidden Markov Model search against human gut metagenomes located putative 12{beta}-HSDH genes in about 30% of subjects within the cohorts analyzed, indicating this gene is relevant in the human gut microbiome.

microbiology↗

bioRxiv2020

Bacteria on steroids: the enzymatic mechanism of an NADH-dependent dehydrogenase that regulates the conversion of cortisol to androgen in the gut microbiome

Microorganisms extensively modify host steroids, but whether these reactions merely eliminate hormones or create signals with new biological identities is largely unknown. Gut bacteria have been known for more than four decades to reduce cortisol to 20-dihydrocortisol, yet the physiological consequence of this transformation remained unresolved. Here we show that microbial cortisol reduction creates a distinct host signalling molecule. A 2.0-[A] structure of the bacterial enzyme DesC, together with molecular dynamics, biochemical perturbation and hybrid quantum mechanics/molecular mechanics simulations, defines substrate recognition and an ordered hydride-transfer and proton-relay mechanism. In gnotobiotic mice, isogenic bacteria expressing active DesC--but not a catalytically inactive S47A variant produced 20-dihydrocortisol in the intestine and circulation and reprogrammed colonic transcription. In primary intestinal epithelial cells, 20-dihydrocortisol, but not cortisol, activated ERK-dependent inflammatory and growth-associated programmes. These responses required nuclear receptor subfamily 4 group A member 3 (NR4A3), whose purified ligand-binding domain bound 20-dihydrocortisol but showed no detectable binding to cortisol. A Chicago colonoscopy cohort linked chronic cortisol exposure, faecal desC, the microbial metabolite and colorectal phenotypes. Thus, bacterial metabolism can change receptor selectivity and biological activity rather than simply terminate host hormone action, expanding the endocrine chemistry of the host.

microbiology↗