Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration

Abstract

Anaerobic respiration encompasses a major class of microbial energy metabolisms that employ reductases to respire different non-oxygen electron acceptors. Respiratory reductases play important roles in multiple geochemical cycles but their significance in other contexts remains unclear. Here we identify three taxonomically distinct families of gut bacteria that encode exceptionally large arsenals of tens to hundreds of respiratory-like reductases per genome. By screening representative species from each family, we discover 22 metabolites used as respiratory electron acceptors in a species-specific manner. Identified respiratory reactions transform multiple classes of dietary-and host-derived fecal metabolites, including bioactive molecules like resveratrol and the immunometabolite itaconate. Reductase substrate-profiling identifies enzyme-substrate pairs and paints a striking picture of reductase evolution, including evidence that reductases with specificities for related cinnamate substrates but distinct mechanisms independently emerged at least four separate times. These studies define an exceptionally versatile form of respiration that directly links microbial central metabolism to the gut metabolome.

The dietary ellagitannin metabolite urolithin A is produced by a molybdenum-dependent dehydroxylase encoded by prevalent human gutEnteroclosterspp

“…These molybdoenzymes, which belong to the DMSO reductase superfamily 56 , dehydroxylate substrates like catechol lignan (Cldh), dopamine (Dadh), DOPAC (Dodh), hydrocaffeic acid (Hcdh), and caffeic acid (Cadh), which can promote growth by using these substrates as alternative electron acceptors 14 . A recent survey of reductases in gut bacteria established that most respiratory reductases contain N-terminal signal sequences and are translocated across the cytoplasmic membrane, while non-respiratory reductases, which lack signal sequences, remain in the cytoplasm 57 . The UcdCFO enzyme complex we found in Enterocloster spp.…”

“…differs from catechol dehydroxylases in Eggerthellaceae in important ways as it does not require a catechol structural motif for activity, belongs to the xanthine oxidase superfamily, and is composed of 3 subunits that each lack signal sequences. Based on the absence of signal sequences and the cytoplasmic localization of xanthine dehydrogenases, the ucd operon likely encodes for a non-respiratory reductase serving a different role than previously characterized catechol dehydroxylases 57 .…”

“…The UcdCFO enzyme complex differs from catechol dehydroxylases in Eggerthellaceae in important ways as it 1) does not require a catechol structural motif for activity, 2) belongs to the xanthine oxidase superfamily (MCD cofactor), and 3) is composed of 3 subunits (UcdCFO) that each lack signal sequences. A recent survey of reductases in gut bacteria established that most respiratory reductases contain N-terminal signal sequences and are translocated across the cytoplasmic membrane, while non-respiratory reductases, which lack signal sequences, remain in the cytoplasm 51 . Based on the absence of signal sequences and the cytoplasmic localization of xanthine dehydrogenases, the ucd operon encodes for a non-respiratory reductase (see 51 Supplementary Table 2).…”

“…A recent survey of reductases in gut bacteria established that most respiratory reductases contain N-terminal signal sequences and are translocated across the cytoplasmic membrane, while non-respiratory reductases, which lack signal sequences, remain in the cytoplasm 51 . Based on the absence of signal sequences and the cytoplasmic localization of xanthine dehydrogenases, the ucd operon encodes for a non-respiratory reductase (see 51 Supplementary Table 2).…”

Acrylate reductase of an anaerobic electron transport chain of the marine bacteriumShewanella woodyi

“…The most typical organic terminal acceptor is fumarate, but the variability of catalytic amino acid residues in homologues of fumarate reductase in various bacteria suggests the existence of other 2-enoate reductase activities [1]. Enzymes with different substrate specificities, such as cytochrome c:methacrylate reductase, cytochrome c:urocanate reductase, NADH:(hydroxy)cinnamate reductase, and NADH:acrylate reductase [1][2][3][4][5][6], have been indeed identified among fumarate reductase homologues.…”