Complex pectin metabolism by gut bacteria reveals novel catalytic functions

Abstract

Carbohydrate polymers drive microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here we show that the gut bacterium Bacteroides thetaiotaomicron utilizes the most structurally complex glycan known; the plant pectic polysaccharide rhamnogalacturonan-II, cleaving all but one of its 21 distinct glycosidic linkages. We show that rhamnogalacturonan-II side-chain and backbone deconstruction are coordinated, to overcome steric constraints, and that degradation reveals previously undiscovered enzyme families and novel catalytic activities. The degradome informs revision of the current structural model of RG-II and highlights how individual gut bacteria orchestrate manifold enzymes to metabolize the most challenging glycans in the human diet.

Molecular Mechanism by which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides

“…Recently, comprehensive functional analysis has revealed the detailed molecular mechanisms by which individual PULs enable human gut Bacteroidetes to utilize predominant plant polysaccharides, including the matrix glycans, xyloglucan (Hemsworth et al, 2016; Larsbrink et al, 2014; Tauzin et al, 2016), xylan (Rogowski et al, 2015), β-mannan (Bågenholm et al, 2017), and rhamnogalacturonan II (Ndeh et al, 2017). Mixed-linkage β(1,3)/β(1,4)-glucans (MLGs, Fig.…”

Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence–Function Space and Genome Context to Discover Novel Functions

“…In unpublished work, the specificities of three ABC SBPs for d -apiose, a branched chain pentose found in plant cell walls, and the iterative use of SSNs and GNNs have been used to discover five catabolic pathways for d -apiose, a branched aldose, two of which are found in species in the human gut microbiome (humans ingest plant cell walls; species of Bacteroides can degrade the rhamnogalacturonan-II component that contains d -apiose to release d -apiose that can be catabolized 99 ). Two pathways include novel RuBisCO-like proteins (RLPs) from the RuBisCO superfamily, one catalyzes a β-ketoacid decarboxylation and the second catalyzes a “transcarboxylation” in which the substrate is decarboxylated (β-ketoacid decarboxylation), with the sequestered CO 2 used to carboxylate the enediolate intermediate on the adjacent carbon, and the resulting isomeric β-ketoacid undergoes hydrolysis as in the canonical RuBisCO reaction.…”

Unusual active site location and catalytic apparatus in a glycoside hydrolase family

“…In-line nucleophilic attack at C1 of rhamnose would involve steric clash with the axial O2 hydroxyl, analogous to the challenges in mannose chemistry (9). Distortion of the pyranoside ring, to place O2 pseudoequatorial, will be needed to minimize these clashes, as has been observed previously for an α-L-rhamnosidase from GH78 (10) and GH106 (11). Furthermore, understanding how microbes remove the rhamnose residues that modify the AGP side chains has significant implications in the food and biorefining industries, and in understanding the ecology of the HGM.…”