The human gut microbe Bacteroides thetaiotaomicron encodes the founding member of a novel glycosaminoglycan-degrading polysaccharide lyase family PL29

Didier Ndeh,Jose Munoz Munoz,Alan Cartmell,David Bulmer,Corinne Wills,Bernard Henrissat,Joseph Gray

doi:10.1074/jbc.ra118.004510

Abstract

Glycosaminoglycans (GAGs) and GAG-degrading enzymes have wide-ranging applications in the medical and biotechnological industries. The former are also an important nutrient source for select species of the human gut microbiota (HGM), a key player in host-microbial interactions. How GAGs are metabolized by the HGM is therefore of interest and has been extensively investigated in the model human gut microbe Bacteroides thetaiotaomicron. The presence of as-yet uncharacterized GAG-inducible genes in its genome and of related species, however, is testament to our incomplete understanding of this process. Nevertheless, it presents a potential opportunity for the discovery of additional GAG-degrading enzymes. Here, we investigated a gene of unknown function (BT_3328) from the chondroitin sulfate (CS) utilization locus of B. thetaiotaomicron NMR and UV spectroscopic assays revealed that it encodes a novel polysaccharide lyase (PL), hereafter referred to as BtCDH, reflecting its source (B. thetaiotaomicron (Bt)) and its ability to degrade the GAGs CS, dermatan sulfate (DS), and hyaluronic acid (HA). When incubated with HA, BtCDH generated a series of unsaturated HA sugars, including Δ4,5UA-GlcNAc, Δ4,5UA-GlcNAc-GlcA-GlcNac, Δ4,5UA-[GlcNAc-GlcA]2-GlcNac, and Δ4,5UA-[GlcNAc-GlcA]3-GlcNac, as end products and hence was classed as endo-acting. A combination of genetic and biochemical assays revealed that BtCDH localizes to the cell surface of B. thetaiotaomicron where it enables extracellular GAG degradation. BtCDH homologs were also detected in several other HGM species, and we therefore propose that it represents the founding member of a new polysaccharide lyase family (PL29). The current discovery also contributes new insights into CS metabolism by the HGM.

Highlights

Glycosaminoglycans (GAGs) and GAG-degrading enzymes have wide-ranging applications in the medical and biotechnological industries
Top BtCDH lyase homologs were mostly detected in species from the Bacteroides, Alistipes, and Prevotella genera, all highly represented in the human gut microbiota (HGM)
We show that BtCDH exhibits polysaccharide lyase activity toward a variety of GAGs substrates including chondroitin sulfate (CS), dermatan sulfate (DS), and hyaluronic acid (HA)

Summary

Introduction

Glycosaminoglycans (GAGs) and GAG-degrading enzymes have wide-ranging applications in the medical and biotechnological industries The former are an important nutrient source for select species of the human gut microbiota (HGM), a key player in host–microbial interactions. In the model human gut microbe B. thetaiotaomicron, as well as other gut Bacteroidetes, the genes encoding these enzymes are typically located within polysaccharide utilization loci (PULs) (14, 19 –21) These genetic loci are diverse and encode a variety of cell envelope–associated multiprotein systems involved in complex glycan metabolism. In the CS PUL of B. thetaiotaomicron, three of such genes, BT_3328, BT_3329, and BT_3330 (all of unknown function), appear in a distinct operon (BT_3328 –30) conserved in several HGM Bacteroidetes (14, 20, 21) The latter suggests that they might be an important adaptation for CS metabolism in these microbes. Our findings contribute new insights into our knowledge of CS metabolism by the HGM, a key player in host–microbial interactions

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Conclusion