N-glycan Utilization by Bifidobacterium Gut Symbionts Involves a Specialist β-Mannosidase

Bifidobacteria represent one of the first colonizers of human gut microbiota, providing to this ecosystem better health and nutrition. To maintain a mutualistic relationship, they have enzymes to degrade and use complex carbohydrates non-digestible by their hosts. To succeed in the densely populated gut environment, they evolved molecular strategies that remain poorly understood. Herein, we report a novel mechanism found in probiotic Bifidobacteria for the depolymerization of the ubiquitous 2-acetamido-2-deoxy-4-O-(β-d-mannopyranosyl)-d-glucopyranose (Man-β-1,4-GlcNAc), a disaccharide that composes the universal core of eukaryotic N-glycans. In contrast to Bacteroidetes, these Bifidobacteria have a specialist and strain-specific β-mannosidase that contains three distinctive structural elements conferring high selectivity for Man-β-1,4-GlcNAc: a lid that undergoes conformational changes upon substrate binding, a tryptophan residue swapped between the two dimeric subunits to accommodate the GlcNAc moiety, and a Rossmann fold subdomain strategically located near to the active site pocket. These key structural elements for Man-β-1,4-GlcNAc specificity are highly conserved in Bifidobacterium species adapted to the gut of a wide range of social animals, including bee, pig, rabbit, and human. Together, our findings uncover an unprecedented molecular strategy employed by Bifidobacteria to selectively uptake carbohydrates from N-glycans in social hosts. [Display omitted] •Bifidobacteria have a specialist β-mannosidase involved in N-glycan degradation.•The specialist β-mannosidase selectively recognizes and cleaves Man-β-1,4-GlcNAc.•Dimerization and the presence of an auxiliary domain contribute to substrate specificity.•A tryptophan swapping between the dimer subunits is crucial for substrate recognition.•A flexible C-terminal lid binds to the GlcNAc moiety and enhances enzyme activity.•This study demonstrates a novel molecular strategy used by Bifidobacteria strains.