Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation.

Louise E Tailford,John Walshaw,Emmanuelle H Crost,Gwenaelle Le Gall,Willem M De Vos,Garry L Taylor,Nathalie Juge,C David Owen,Jemma Hardy-Goddard

doi:10.1038/ncomms8624

Abstract

The gastrointestinal mucus layer is colonized by a dense community of microbes catabolizing dietary and host carbohydrates during their expansion in the gut. Alterations in mucosal carbohydrate availability impact on the composition of microbial species. Ruminococcus gnavus is a commensal anaerobe present in the gastrointestinal tract of >90% of humans and overrepresented in inflammatory bowel diseases (IBD). Using a combination of genomics, enzymology and crystallography, we show that the mucin-degrader R. gnavus ATCC 29149 strain produces an intramolecular trans-sialidase (IT-sialidase) that cleaves off terminal α2-3-linked sialic acid from glycoproteins, releasing 2,7-anhydro-Neu5Ac instead of sialic acid. Evidence of IT-sialidases in human metagenomes indicates that this enzyme occurs in healthy subjects but is more prevalent in IBD metagenomes. Our results uncover a previously unrecognized enzymatic activity in the gut microbiota, which may contribute to the adaptation of intestinal bacteria to the mucosal environment in health and disease.

Highlights

The gastrointestinal mucus layer is colonized by a dense community of microbes catabolizing dietary and host carbohydrates during their expansion in the gut
The canonical cluster nanA/K/E, first described for Escherichia coli[14] involves genes encoding the enzymes N-acetylneuraminate lyase (NanA), kinase (NanK) and N-acteylmannosamine (ManAc) epimerase (NanE), converting sialic acid (Neu5Ac) into N-acetylglucosamine-6-P (GlcNAc-6-P), whereas the genes encoding NagA (GlcNAc-6-P deacetylase) and NagB converting GlcNAc-6-P into fructose-6-P, which is a substrate in the glycolytic pathway, vary in their locations among the different genomes that encode the Nan cluster[15]
An alternative pathway for sialic acid metabolism has later been discovered in Bacteroides fragilis, relying on the action of an aldolase (NanL), a novel ManNAc-6-P epimerase and a hexokinase (RokA), converting Neu5Ac into GlcNAc-6-P, an intermediate in the common pathway for aminosugar utilization[16]

Summary

Introduction

The gastrointestinal mucus layer is colonized by a dense community of microbes catabolizing dietary and host carbohydrates during their expansion in the gut. The sialidase and Nan cluster is absent from the genome of R. gnavus E1, which is unable to grow on mucin as a sole carbon source[21] Taken together, these data indicate that sialic acid metabolism is key to the ability of R. gnavus strains to utilize mucin as a nutrient source, which is in agreement with earlier studies on mucin degradation in the human colon ecosystem[22,23,24]. We functionally and structurally characterize R. gnavus ATCC 29149 sialidase (RgNanH), demonstrating that the enzyme is an intramolecular trans-sialidase (IT-sialidase) producing 2,7-anhydro-Neu5Ac selectively from a2-3-linked sialic acid substrates, the first one reported in a gut commensal microbe suggesting an unprecedented mechanism underpinning adaptation of gut bacteria to the sialylated-rich mucosal environment

Methods

Results

Conclusion