Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides

Luís, Ana S.; Briggs, Jonathon A.; Zhang, Xiaoyang; Farnell, Benjamin; Ndeh, Didier; Labourel, Aurore; Baslé, Arnaud; Cartmell, Alan; Terrapon, Nicolas; Stott, Katherine; Lowe, Elisabeth C.; McLean, Richard; Shearer, Kaitlyn; Schückel, Julia; Venditto, I.; Ralet, Marie Christine; Henrissat, Bernard; Martens, Eric C.; Mosimann, S.C.; Abbott, D. Wade; Gilbert, Harry J.

doi:10.1038/s41564-017-0079-1

Cited by 310 publications

(310 citation statements)

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“…4 and Table 3). The conformation of RG oligosaccharides complexed with the enzyme was similar to that of ligands in the crystal structure of the recently reported RG lyase (PDB: 5OLR) [23]. Among these, the O1 of a-L-Rha residues located at the reducing ends of the ligands formed hydrogen bonds with Asp460 positioned at the end of the cleft, indicating that PcRGLX releases a reaction product, DGR, from the reducing end of the substrate.…”

Section: Complex Structuressupporting

confidence: 60%

Crystal structure of exo‐rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26

et al. 2018

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Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX) was recently classified as a member of polysaccharide lyase (PL) family 26 along with hypothetical proteins derived from various organisms. In this study, we determined the crystal structure of PcRGLX as the first structure of a member of this family. Based on the substrate-binding orientation and substrate specificity, PcRGLX is an exo-type PL that cleaves rhamnogalacturonan from the reducing end. Analysis of PcRGLX-complex structures with reaction products indicate that the active site possesses an L-shaped cleft that can accommodate galactosyl side chains, suggesting side-chain-bypassing activity in PcRGLX. Furthermore, we determined the residues critical for catalysis by analyzing the enzyme activities of inactive variants.

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Section: Complex Structuressupporting

confidence: 60%

Crystal structure of exo‐rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26

et al. 2018

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“…All B. theta endoglycanases involved in the first step of polysaccharide breakdown, including SusG, are surface-exposed lipoproteins (29, 32). Because most OMV-enriched lipoproteins contain a LES motif, we investigated a possible association between surface exposure and packing into OMVs.…”

Section: Resultsmentioning

confidence: 99%

“…In the current models for PUL systems, the hydrolytic enzymes and the oligosaccharide importers are present at the outer membrane (20, 32). However, we determined that functional glycosyl hydrolases are mainly packed into OMVs.…”

Section: Discussionmentioning

confidence: 99%

A dual motif mediates outer-membrane translocation and packing of glycosidases intoBacteroidesOuter Membrane Vesicles

Valguarnera

Scott

Feldman³

2018

Preprint

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11Outer membrane vesicles (OMV) are spherical structures derived from the outer 12 membrane (OM) of Gram-negative bacteria. Bacteroides spp. are prominent 13 components of the human gut microbiota, and OMV produced with these species are 14 proposed to play key roles in gut homeostasis. OMV biogenesis in Bacteroides is a 15 poorly understood process. Here, we revisited the protein composition of B. theta OMVs 16 by mass spectrometry. We confirmed that OMVs produced by this organism contain 17 large quantities of glycosidases and proteases, with most of them being lipoproteins. 18 We found that most of these OMV-enriched lipoproteins are encoded by polysaccharide 19 utilization loci (PULs), such as the sus operon. We examined the subcellular localization 20 of the components of the Sus system, and found that the alpha-amylase SusG is highly 21 enriched in OMVs while the oligosaccharide importer SusC remains mostly in the OM. 22 We show that all OMV-enriched lipoproteins possess a lipoprotein export sequence 23 (LES) that mediates translocation of SusG from the periplasmic face of the OM towards 24 the extracellular milieu and is required for SusG to localize preferentially to OMVs. We 25 also show that surface-exposed SusG in OMVs is active and can rescue growth of 26 bacterial cells incapable of growing on starch as only carbon source. Our results 27 support the role of OMVs as "public goods" that can be utilized by other organisms with 28 different metabolic capabilities. 29 IMPORTANCE 30 Species from the Bacteroides genus are predominant members of the human gut 31 microbiota. OMVs in Bacteroides have been shown to be important for the homeostasis 32 of complex host-commensal relationships, mainly involving immune tolerance and 33 protection from disease. OMVs carry many enzymatic activities involved in the cleavage 34 of complex polysaccharides and have been proposed as public goods that can provide 35 growth to other bacterial species by release of polysaccharide breakdown products into 36 the gut lumen. Nevertheless, the mechanistic nature of OMV biogenesis is unclear for 37Bacteroides spp. This works shows the presence of a negatively-charged rich amino 38 acid dual motif that is required for efficient packing of the surface-exposed alpha-39 amylase SusG into OMVs. Discovery of this motif (LES) is the first step in the 40 generation of tailor made probiotic interventions that can exploit LES-related sequences 41 to generate Bacteroides strains displaying proteins of interest in OMVs.42 Outer membrane vesicles (OMVs) are small spherical structures derived from the outer 44 membrane (OM) of all Gram-negative bacterial species. OMVs are composed of 45 phospholipids, lipopolysaccharide (LPS) or lipooligosaccharide (LOS), and OM and 46 periplasmic proteins (1, 2). OMVs can mediate host-microbe interactions by facilitating 47 long-distance delivery of virulence factors, modulating the host-immune response, and 48 contributing to antibiotic resistance (1, 3-8). Despite these key roles in bacterial 49 p...

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“…GH146 and GH152 are recently created GH families in the CAZy database. The GH146 family comprises b-L-arabinofuranosidase (EC 3.2.1.185) characterized in bacteria of human gut cleaving both b-1,2and b-1,3linked L-Araf branches recently identified in pectic arabinan (Luis et al, 2018). The GH152 family groups stress-induced thaumatin-like proteins that are highly abundant in plants (Trudel et al, 1998).…”

Section: Cazyme Families Identified In Populus Since the Last Whole-gmentioning

confidence: 99%

Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on RNA expression data

et al. 2019

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Summary Carbohydrate‐active enzymes (CAZymes) catalyze the formation and modification of glycoproteins, glycolipids, starch, secondary metabolites and cell wall biopolymers. They are key enzymes for the biosynthesis of food and renewable biomass. Woody biomass is particularly important for long‐term carbon storage and as an abundant renewable natural resource for many industrial applications. This study presents a re‐annotation of CAZyme genes in the current Populus trichocarpa genome assembly and in silico functional characterization, based on high‐resolution RNA‐Seq data sets. Altogether, 1914 CAZyme and expansin genes were annotated in 101 families. About 1797 of these genes were found expressed in at least one Populus organ. We identified genes involved in the biosynthesis of different cell wall polymers and their paralogs. Whereas similar families exist in poplar and Arabidopsis thaliana (with the exception of CBM13 found only in poplar), a few families had significantly different copy numbers between the two species. To identify the transcriptional coordination and functional relatedness within the CAZymes and other proteins, we performed co‐expression network analysis of CAZymes in wood‐forming tissues using the AspWood database (http://aspwood.popgenie.org/aspwood-v3.0/) for Populus tremula. This provided an overview of the transcriptional changes in CAZymes during the transition from primary to secondary wall formation, and the clustering of transcripts into potential regulons. Candidate enzymes involved in the biosynthesis of polysaccharides were identified along with many tissue‐specific uncharacterized genes and transcription factors. These collections offer a rich source of targets for the modification of secondary cell wall biosynthesis and other developmental processes in woody plants.

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Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides

Cited by 310 publications

References 50 publications

Crystal structure of exo‐rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26

Crystal structure of exo‐rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26

A dual motif mediates outer-membrane translocation and packing of glycosidases intoBacteroidesOuter Membrane Vesicles

Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on RNA expression data

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