A Bacteroidetes locus dedicated to fungal 1,6-β-glucan degradation: Unique substrate conformation drives specificity of the key endo-1,6-β-glucanase

Abstract

Glycans are major nutrients available to the human gut microbiota. The Bacteroides are generalist glycan degraders, and this function is mediated largely by polysaccharide utilization loci (PULs). The genomes of several Bacteroides species contain a PUL, PUL1,6-β-glucan, that was predicted to target mixed linked plant 1,3;1,4-β-glucans. To test this hypothesis we characterized the proteins encoded by this locus in Bacteroides thetaiotaomicron, a member of the human gut microbiota. We show here that PUL1,6-β-glucan does not orchestrate the degradation of a plant polysaccharide but targets a fungal cell wall glycan, 1,6-β-glucan, which is a growth substrate for the bacterium. The locus is up-regulated by 1,6-β-glucan and encodes two enzymes, a surface endo-1,6-β-glucanase, BT3312, and a periplasmic β-glucosidase that targets primarily 1,6-β-glucans. The non-catalytic proteins encoded by PUL1,6-β-glucan target 1,6-β-glucans and comprise a surface glycan-binding protein and a SusD homologue that delivers glycans to the outer membrane transporter. We identified the central role of the endo-1,6-β-glucanase in 1,6-β-glucan depolymerization by deleting bt3312, which prevented the growth of B. thetaiotaomicron on 1,6-β-glucan. The crystal structure of BT3312 in complex with β-glucosyl-1,6-deoxynojirimycin revealed a TIM barrel catalytic domain that contains a deep substrate-binding cleft tailored to accommodate the hook-like structure adopted by 1,6-β-glucan. Specificity is driven by the complementarity of the enzyme active site cleft and the conformation of the substrate. We also noted that PUL1,6-β-glucan is syntenic to many PULs from other Bacteroidetes, suggesting that utilization of yeast and fungal cell wall 1,6-β-glucans is a widespread adaptation within the human microbiota.

Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides

“…The present study underscores that dietary specificity of related gut commensal strains is gleaned most precisely by systems-based approaches involving genomic, biochemical, and structural biological dissection of PULs (14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27), which otherwise could not have been predicted based on sequencing data alone. Whereas the GH complement of PULs has been shown to drive specificity in the levan/fructan system (14), to our knowledge the present study describes the first case in which the interplay of GHs and SGBPs, underpinned by HTCS specificity, collectively dictate glycan utilization among species.…”

Complex dietary polysaccharide modulates gut immune function and microbiota, and promotes protection from autoimmune diabetes

“…Colonic microbial communities can ferment non‐digestible dietary polysaccharides and use them as energy sources for their growth . Therefore, these polysaccharides are being considered as prebiotics with the ability to promote the growth of specific beneficial microbial communities.…”

“…Colonic microbial communities can ferment nondigestible dietary polysaccharides and use them as energy sources for their growth. [40][41][42] Therefore, these polysaccharides are being considered as prebiotics with the ability to promote the growth of specific beneficial microbial communities. We observed that prolonged oral treatment using low-dose YBG causes changes in the gut microbial composition by reducing the abundance of Firmicutes and increasing the abundance of the Bacteroidetes and Verrucomicrobia phyla, which include many polysaccharide-fermenting bacteria.…”

Complex dietary-polysaccharide modulates gut immune function and microbiota, and promotes protection from autoimmune diabetes

“…Colonic microbial communities can ferment non-digestible dietary polysaccharides and use them as energy sources for their growth [41][42][43] . Therefore, these polysaccharides are being considered as prebiotics with the ability to promote growth of specific beneficial microbial communities.…”