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

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.

Differential Epitope Mapping by STD NMR Spectroscopy To Reveal the Nature of Protein–Ligand Contacts

“…The DEEP‐STD NMR results are in excellent agreement with the published crystal structure of the complex between 2,7‐anhydro‐sialic acid and Rg NanH‐GH33 (Figure 2 c),9 where the ligand sits between aliphatic (I258, I338, and V502) and opposite aromatic (Y667 and W698) patches. The ligand protons CH 3 and H3a point towards the aliphatic residues, while H8, H9, and H9′ are projected towards the aromatic side chains.…”

“…As a proof of principle, we studied two biologically relevant protein–ligand complexes for which high‐resolution X‐ray structures are available: 1) 2,7‐anhydro‐Neu5Ac with Rg NanH‐GH33, the catalytic domain (belonging to glycoside family GH33) of the intramolecular trans‐sialidase from human the gut symbiont Ruminococcus gnavus, 9 and 2) 3‐nitrophenyl‐α‐ d ‐galactopyranoside (3NPG) with Cholera toxin subunit B (CTB) 10. Understanding the binding of 2,7‐anhydro‐Neu5Ac by sialidases is important to unveil mechanisms of gut microbiota adaptation 9, 11.…”

“…Cyan surfaces highlight ligand contacts with aliphatic side chains; magenta surfaces show contacts with aromatic side chains. c) Crystal structure of the complex (PDB ID: 4X4A) 9. Protons were added using Schrodinger software 14.…”

Escherichia coli O157:H7 Strain EDL933 Harbors Multiple Functional Prophage-Associated Genes Necessary for the Utilization of 5- N -Acetyl-9- O -Acetyl Neuraminic Acid as a Growth Substrate

“…In the mucin, they play a role in protection of the core protein against microbes. Nevertheless, there are some anaerobes which can remove the sialic acids from the glycoprotein by sialidases (40)(41)(42). Mostly, sialidases are specialized to cleave only a few bonds of sialic acids to the glycoprotein or to have narrow substrate specificity.…”

Metagenomic analysis of taxonomic and functional changes in gut microbiota of patients with alcoholic dependence syndrome

“…Ряд исследований показал повышение доли этих двух видов при воспалительных заболеваниях кишечника, в том числе были прояснены некоторые механизмы их участия в этом. Так, у R. gnavus был выявлен ген фермента транс-сиалидазы, обеспечивающей адаптацию бактерии к существованию в слизистой [23,24]. С другой стороны, у пациентов была значимо понижена доля видов Akkermansia muciniphila, Coprococcus eutactus, Faecalibacterium prausnitzii и Clostridium sp.…”