Microbiota‐derived butyrate is an endogenous inhibitor of HIF prolyl‐hydroxylases

Abstract

The diverse population of microbial species present in the human intestines, collectively termed the gut microbiota, is an essential component of human health. Microbial supply of fermentation-derived short-chain fatty acids (SCFAs), particularly butyrate, is a well-established component to gut homeostasis and disease resistance. Reaching millimolar luminal concentrations in the colon, butyrate is sequestered and utilized as the favored energy source for intestinal epithelial cells. Beyond energy provision, butyrate broadly regulates gene expression as a histone deacetylase inhibitor and modulates the intestinal environment via signaling through SCFA-specific G-protein coupled receptors. Additionally, increasing oxygen utilization due to SCFA metabolism has been shown to stabilize hypoxia-inducible factor (HIF), a transcription factor that broadly functions as the master regulator of oxygen homeostasis but also specifically maintains intestinal homeostasis and is essential to intestinal barrier function. Under normoxic conditions, HIF is degraded in a hydroxylation-dependent manner mediated by one of three HIF prolyl-hydroxylases (PHDs). When oxygen is limiting, PHDs are inhibited and HIF is stabilized. Given the low O2 conditions of the intestinal microenvironment, it is of interest whether butyrate could more specifically influence HIF. We show that the microbiota-derived butyrate directly binds and inhibits PHD2 to stabilize HIF. Using cultured epithelia and molecular approaches, we found that butyrate treatment stabilized HIF in vitro independent of oxygen metabolism. Utilizing recombinant PHD protein, we identified butyrate as a unique inhibitor of PHD relative to other SCFAs. We also found that butyrate delivered to the colon of mice stabilizes HIF in a specific manner. Our results suggest that the co-evolution of mammals and commensal bacteria have selected for butyrate to impact a crucial gene regulation pathway that could be extended to beyond the intestinal mucosa. PHDs are a major target for drug development, as HIF regulates numerous genes involved in erythropoiesis, angiogenesis, energy metabolism, ischemia, and inflammation. Small-molecule inhibitors of PHDs have been developed in hopes of treating a variety of diseases not limited to chronic kidney disease and inflammatory bowel diseases. As an endogenous, well-tolerated small-molecule metabolite, butyrate holds far-reaching therapeutic potential as a HIF stabilizing agent.