Sequence-Based and Functional Analysis for the Discovery of N-Glycan Degrading Glycosidases From the Microbial Metagenome of the Infant Gut.

The role of bacterial glycosyl hydrolases (GHs) in degrading free human milk oligosaccharides is well documented. However, their activity on glycoconjugates is less well known. Here, an in silico analysis of the metagenome of the fecal microbiome of breastfed infants was employed to identify GH2 β-galactosidases, GH20 exo-N-acetylglucosaminidases and GH18 endo-N-acetylglucosaminidases active on N-glycans. A total of nine β-galactosidases were recombinantly expressed and two of them, Gal1b and Gal99, were able to remove galactose from the G2 peptide and asialofetuin. Gal1b, Gal25, Gal37c, Gal99 and Gal296 hydrolyzed lactose and N-acetyllactosamine, indicating specificity for galactose β1,4-linked to glucose or GlcNAc. All of the exo-β-N-acetylglucosaminidases studied here (Exo10a, Exo18, Exo38, Exo39b, Exo360 and Exo399) hydrolyzed the disaccharide N-acetylglucosaminyl-β1,2-mannose, which forms part of the N-glycan structures. Exo10a, Exo38 and Exo360 hydrolyzed N-acetylglucosamine (GlcNAc) from the G2 peptide pretreated with Gal1b. Notably, Exo360 hydrolyzed GlcNAc at both the α1,3 and α1,6 branches of the G2 peptide core mannose simultaneously, whereas Exo10a showed a preference for GlcNAc at one branch. Exo38 and Exo360 also release GlcNAc from asialofetuin once galactose has been removed. The whole structures of N-glycans were liberated from glycoproteins by the action of the endo-N-acetylglucosaminidases Endo38 and Endo358. These enzymes hydrolyze the N,N'-diacetylchitobiose core of N-linked glycans of the high-mannose and non-sialylated complex types, respectively. Overall, these results provide insight into the range of glycosyl hydrolases present in the infant gut microbiota that act on glycoconjugates, which may play a role in the establishment and composition of the newborn microbiota.