A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes

Abstract

A well-balanced human diet includes a significant intake of non-starch polysaccharides, collectively termed “dietary fibre,” from the cell walls of diverse fruits and vegetables.1 Due to a paucity of alimentary enzymes encoded by the human genome,2 our ability to derive energy from dietary fibre depends on saccharification and fermentation of complex carbohydrates by the massive microbial community residing in our distal gut.3,4 The xyloglucans (XyGs), in particular, are a ubiquitous family of highly branched plant cell wall polysaccharides5,6 whose mechanism(s) of degradation in the human gut and consequent importance in nutrition was heretofore unknown.1,7,8 Here, we demonstrate that a single, complex gene locus in Bacteroides ovatus confers xyloglucan catabolism in this common colonic symbiont. Through targeted gene disruption, biochemical analysis of all predicted glycoside hydrolases and carbohydrate-binding proteins, and three-dimensional structural determination of the vanguard endo-xyloglucanase, we reveal the molecular mechanisms through which XyGs are hydrolysed to component monosaccharides for further metabolism. We also observe that orthologous xyloglucan utilization loci (XyGULs) serve as genetic markers of xyloglucan catabolism in Bacteroidetes, that XyGULs are restricted to a limited number of phylogenetically diverse strains, and that XyGULs are ubiquitous in surveyed human metagenomes. Our findings reveal that the metabolism of even highly abundant components of dietary fibre may be mediated by niche species, which has immediate fundamental and practical implications for gut symbiont population ecology in the context of human diet, nutrition and health.9–12

Structure-Function Analysis of a Mixed-linkage β-Glucanase/Xyloglucanase from the Key Ruminal Bacteroidetes Prevotella bryantii B14

“…PbGH5A thus has significant catalytic flexibility, having an ability to tolerate branching xylosylation on ␤-glucan chains. This activity profile clearly distinguishes PbGH5A from the strict endo-xyloglucanases of GH5_4 (16,17) and provides further direct evidence of the polyspecificity of subfamily GH5_4, which also includes a number of characterized carboxymethylcellulases and mixedlinkage endo-glucanases (60 -62).…”

“…Of the GH5 endo-xyloglucanases characterized to date, all cleave the dicot xyloglucan polysaccharide (exemplified by Tamarindus indica xyloglucan) at the unbranched backbone glucosyl unit (Fig. 1) to generate oligosaccharides based on a Glc 4 backbone (16,17,64). This cleavage pattern is also typical for GH7, GH9, GH12, and GH16 members, with known exceptions of certain GH44 and GH74 members (16, 18, 66 -71).…”

“…Among these, GH5 subfamily 4 (GH5_4) constitutes one of the largest, which generally encompasses endo-␤(1,4)-glucanases, including cellulases (EC 3.2.1.4), mixed-linkage endo-␤(1,3)/␤(1,4)-glucanases (EC 3.2.1.73), and highly specific endo-xyloglucanases (EC 3.2.1.151) evolved for the saccharification of plant biomass. GH5_4 endo-xyloglucanases (16,17) are particularly distinguished by their ability to accommodate and harness the numerous extended ␣(1,6)-xylosyl branches in diverse xyloglucans (18). Unfortunately, the current level of functional characterization of GH5_4, which includes the observation that most of the characterized members have not been tested consistently on the same panel of substrates (e.g.…”

Functional and structural characterization of a potent GH74 endo‐xyloglucanase from the soil saprophyte Cellvibrio japonicus unravels the first step of xyloglucan degradation

“…1) [10]. As a result of this structural complexity, complete XyG saccharification requires a consortium of endo-acting and exoacting glycoside hydrolases [11,12].…”

Biochemical and Structural Characterization of a Five-domain GH115 α-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T

“…Both proteins are involved in bacterial pilus biogenesis. More interestingly, domain C ϩ is also structurally similar to the Bacon domain (Bacteriodetes-associated carbohydrate-binding often N-terminal, Pfam 13004) in BoGH5A, a GH5 endoxyloglucanase from B. ovatus (supplemental Table S1) (58). Bacon domains have been identified in several other carbohydrateactive enzymes as well as proteases (2704 sequences deposited in the current Pfam database) (59), suggesting that the C (Figs.…”