Cell-surface xyloglucan recognition and hydrolysis by the human gut commensal Bacteroides uniformis

2021 ◽  
Author(s):  
Julie M. Grondin ◽  
Guillaume Déjean ◽  
Filip Van Petegem ◽  
Harry Brumer
Keyword(s):  
Cell Wall ◽  
Gut Microbiota ◽  
Plant Cell ◽  
Binding Proteins ◽  
Plant Cell Wall ◽  
Binding Capacity ◽  
Gene Clusters ◽  
Titration Calorimetry ◽  
Glycoside Hydrolase Family ◽  
Human Gut

Xyloglucan (XyG) is a ubiquitous plant cell wall hemicellulose that is targeted by a range of syntenic, microheterogeneous xyloglucan utilization loci (XyGUL) in Bacteroidetes species of the human gut microbiota (HGM), including Bacteroides ovatus and B. uniformis . Comprehensive biochemical and biophysical analyses have identified key differences in the protein complements of each locus that confer differential access to structurally-diverse XyG sidechain variants. A second, non-syntenic XyGUL was previously identified in B. uniformis , although its function in XyG utilization compared to its syntenic counterpart was unclear. Here, complimentary enzymatic product profiles and bacterial growth curves showcase the notable preference of Bu XyGUL2 surface glycan-binding proteins (SGBPs) to bind full-length XyG, as well as a range of oligosaccharides produced by the glycoside hydrolase family 5 (GH5_4) endo -xyloglucanase from this locus. We use isothermal titration calorimetry (ITC) to characterize this binding capacity and pinpoint the specific contributions of each protein to nutrient capture. The high-resolution structure of Bu XyGUL2 SGBP-B reveals remarkable putative binding site conservation with the canonical XyG-binding Bo XyGUL SGBP-B, supporting similar roles for these proteins in glycan capture. Together, these data underpin the central role of complimentary XyGUL function in B. uniformis , and broaden our systems-based and mechanistic understanding of XyG utilization in the HGM. Importance The omnipresence of xyloglucans in the human diet has led to the evolution of heterogeneous gene clusters in several Bacteroidetes species in the HGM, each specially tuned to respond to the structural variations of these complex plant cell wall polysaccharides. Our research illuminates the complimentary roles of syntenic and non-syntenic XyGUL in B. uniformis in conferring growth on a variety of XyG-derived substrates, providing evidence of glycan-binding protein microadaptation within a single species. These data serve as a comprehensive overview of the binding capacities of the SGBPs from a non-syntenic B. uniformis XyGUL and will inform future studies on the roles of complimentary loci in glycan targeting by key HGM species. Keywordshuman gut microbiota, microbiome, carbohydrate-active enzymes, carbohydrate-binding proteins, Bacteroidetes, CAZymes, polysaccharide utilization loci, xyloglucan

scholarly journals PUL-Mediated Plant Cell Wall Polysaccharide Utilization in the Gut Bacteroidetes

2021 ◽  
Vol 22 (6) ◽  
pp. 3077
Author(s):  
Zhenzhen Hao ◽  
Xiaolu Wang ◽  
Haomeng Yang ◽  
Tao Tu ◽  
Jie Zhang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Cell Wall Polysaccharide ◽  
Prominent Feature ◽  
Cell Wall Polysaccharides ◽  
Gut Microbial Community

Plant cell wall polysaccharides (PCWP) are abundantly present in the food of humans and feed of livestock. Mammalians by themselves cannot degrade PCWP but rather depend on microbes resident in the gut intestine for deconstruction. The dominant Bacteroidetes in the gut microbial community are such bacteria with PCWP-degrading ability. The polysaccharide utilization systems (PUL) responsible for PCWP degradation and utilization are a prominent feature of Bacteroidetes. In recent years, there have been tremendous efforts in elucidating how PULs assist Bacteroidetes to assimilate carbon and acquire energy from PCWP. Here, we will review the PUL-mediated plant cell wall polysaccharides utilization in the gut Bacteroidetes focusing on cellulose, xylan, mannan, and pectin utilization and discuss how the mechanisms can be exploited to modulate the gut microbiota.

Solubilisation of Ferulic Acid from Plant Cell Wall Materials in a Model Human Gut System

1996 ◽  
Vol 24 (3) ◽  
pp. 384S-384S ◽  
Author(s):  
PAUL A KROON ◽  
CRAIG B FAULDS ◽  
PETER RYDEN ◽  
GARY WILLIAMSON
Keyword(s):  
Cell Wall ◽  
Ferulic Acid ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Human Gut ◽  
Wall Materials ◽  
Cell Wall Materials

scholarly journals Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity

2019 ◽  
Vol 85 (20) ◽  
Author(s):  
Guillaume Déjean ◽  
Alexandra S. Tauzin ◽  
Stuart W. Bennett ◽  
A. Louise Creagh ◽  
Harry Brumer
Keyword(s):  
Gut Microbiota ◽  
Community Dynamics ◽  
Gene Clusters ◽  
Individual Species ◽  
Glycoside Hydrolase Family ◽  
Backbone Cleavage ◽  
Structural Variations ◽  
Human Gut ◽  
Complex Carbohydrates

ABSTRACT Genome sequencing has revealed substantial variation in the predicted abilities of individual species within animal gut microbiota to metabolize the complex carbohydrates comprising dietary fiber. At the same time, a currently limited body of functional studies precludes a richer understanding of how dietary glycan structures affect the gut microbiota composition and community dynamics. Here, using biochemical and biophysical techniques, we identified and characterized differences among recombinant proteins from syntenic xyloglucan utilization loci (XyGUL) of three Bacteroides and one Dysgonomonas species from the human gut, which drive substrate specificity and access to distinct polysaccharide side chains. Enzymology of four syntenic glycoside hydrolase family 5 subfamily 4 (GH5_4) endo-xyloglucanases revealed surprising differences in xyloglucan (XyG) backbone cleavage specificity, including the ability of some homologs to hydrolyze congested branched positions. Further, differences in the complement of GH43 alpha-l-arabinofuranosidases and GH95 alpha-l-fucosidases among syntenic XyGUL confer distinct abilities to fully saccharify plant species-specific arabinogalactoxyloglucan and/or fucogalactoxyloglucan. Finally, characterization of highly sequence-divergent cell surface glycan-binding proteins (SGBPs) across syntenic XyGUL revealed a novel group of XyG oligosaccharide-specific SGBPs encoded within select Bacteroides. IMPORTANCE The catabolism of complex carbohydrates that otherwise escape the endogenous digestive enzymes of humans and other animals drives the composition and function of the gut microbiota. Thus, detailed molecular characterization of dietary glycan utilization systems is essential both to understand the ecology of these complex communities and to manipulate their compositions, e.g., to benefit human health. Our research reveals new insight into how ubiquitous members of the human gut microbiota have evolved a set of microheterogeneous gene clusters to efficiently respond to the structural variations of plant xyloglucans. The data here will enable refined functional prediction of xyloglucan utilization among diverse environmental taxa in animal guts and beyond.

scholarly journals Crystallization and preliminary crystallographic studies of a novel noncatalytic carbohydrate-binding module from theRuminococcus flavefacienscellulosome

2015 ◽  
Vol 71 (1) ◽  
pp. 45-48 ◽  
Author(s):  
Immacolata Venditto ◽  
Arun Goyal ◽  
Andrew Thompson ◽  
Luis M. A. Ferreira ◽  
Carlos M. G. A. Fontes ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Catalytic Domain ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Cellulolytic Bacterium ◽  
Modular Architecture ◽  
Carbohydrate Binding Modules ◽  
Fundamental Biological Process

Microbial degradation of the plant cell wall is a fundamental biological process with considerable industrial importance. Hydrolysis of recalcitrant polysaccharides is orchestrated by a large repertoire of carbohydrate-active enzymes that display a modular architecture in which a catalytic domain is connectedvialinker sequences to one or more noncatalytic carbohydrate-binding modules (CBMs). CBMs direct the appended catalytic modules to their target substrates, thus potentiating catalysis. The genome of the most abundant ruminal cellulolytic bacterium,Ruminococcus flavefaciensstrain FD-1, provides an opportunity to discover novel cellulosomal proteins involved in plant cell-wall deconstruction. It encodes a modular protein comprising a glycoside hydrolase family 9 catalytic module (GH9) linked to two unclassified tandemly repeated CBMs (termed CBM-Rf6A and CBM-Rf6B) and a C-terminal dockerin. The novel CBM-Rf6A from this protein has been crystallized and data were processed for the native and a selenomethionine derivative to 1.75 and 1.5 Å resolution, respectively. The crystals belonged to orthorhombic and cubic space groups, respectively. The structure was solved by a single-wavelength anomalous dispersion experiment using theCCP4 program suite andSHELXC/D/E.

scholarly journals The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer

2013 ◽  
Vol 280 (1763) ◽  
pp. 20131021 ◽  
Author(s):  
Yannick Pauchet ◽  
David G. Heckel
Keyword(s):  
Cell Wall ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Genetic Material ◽  
Leaf Beetle ◽  
Glycoside Hydrolase Family ◽  
Cell Wall Degrading Enzymes ◽  
Genes Encoding

The primary plant cell wall comprises the most abundant polysaccharides on the Earth and represents a rich source of energy for organisms which have evolved the ability to digest them. Enzymes able to degrade plant cell wall polysaccharides are widely distributed in micro-organisms but are generally absent in animals, although their presence in insects, especially phytophagous beetles from the superfamilies Chrysomeloidea and Curculionoidea, has recently begun to be appreciated. The observed patchy distribution of endogenous genes encoding these enzymes in animals has raised questions about their evolutionary origins. Recent evidence suggests that endogenous plant cell wall degrading enzymes-encoding genes have been acquired by animals through a mechanism known as horizontal gene transfer (HGT). HGT describes how genetic material is moved by means other than vertical inheritance from a parent to an offspring. Here, we provide evidence that the mustard leaf beetle, Phaedon cochleariae , possesses in its genome genes encoding active xylanases from the glycoside hydrolase family 11 (GH11). We also provide evidence that these genes were originally acquired by P. cochleariae from a species of gammaproteobacteria through HGT. This represents the first example of the presence of genes from the GH11 family in animals.

scholarly journals Two new gene clusters involved in the degradation of plant cell wall from the fecal microbiota of Tunisian dromedary

PLoS ONE ◽  
2018 ◽  
Vol 13 (3) ◽  
pp. e0194621 ◽  
Author(s):  
Rihab Ameri ◽  
Elisabeth Laville ◽  
Gabrielle Potocki-Véronèse ◽  
Sahar Trabelsi ◽  
Monia Mezghani ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Gene Clusters ◽  
Fecal Microbiota ◽  
New Gene

scholarly journals EglC, a New Endoglucanase from Aspergillus niger with Major Activity towards Xyloglucan

2002 ◽  
Vol 68 (4) ◽  
pp. 1556-1560 ◽  
Author(s):  
Alinda A. Hasper ◽  
Ester Dekkers ◽  
Marc van Mil ◽  
Peter J. I. van de Vondervoort ◽  
Leo H. de Graaff
Keyword(s):  
Cell Wall ◽  
Aspergillus Niger ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Binding Domain ◽  
Wall Structure ◽  
Glycoside Hydrolase Family ◽  
Cell Wall Polysaccharide ◽  
Cellulose Binding Domain ◽  
Cellulose Binding

ABSTRACT A novel gene, eglC, encoding an endoglucanase, was cloned from Aspergillus niger. Transcription of eglC is regulated by XlnR, a transcriptional activator that controls the degradation of polysaccharides in plant cell walls. EglC is an 858-amino-acid protein and contains a conserved C-terminal cellulose-binding domain. EglC can be classified in glycoside hydrolase family 74. No homology to any of the endoglucanases from Trichoderma reesei was found. In the plant cell wall xyloglucan is closely linked to cellulose fibrils. We hypothesize that the EglC cellulose-binding domain anchors the enzyme to the cellulose chains while it is cleaving the xyloglucan backbone. By this action it may contribute to the degradation of the plant cell wall structure together with other enzymes, including hemicellulases and cellulases. EglC is most active towards xyloglucan and therefore is functionally different from the other two endoglucanases from A. niger, EglA and EglB, which exhibit the greatest activity towards β-glucan. Although the mode of action of EglC is not known, this enzyme represents a new enzyme function involved in plant cell wall polysaccharide degradation by A. niger.

scholarly journals Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts

PLoS Biology ◽  
2011 ◽  
Vol 9 (12) ◽  
pp. e1001221 ◽  
Author(s):  
Eric C. Martens ◽  
Elisabeth C. Lowe ◽  
Herbert Chiang ◽  
Nicholas A. Pudlo ◽  
Meng Wu ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Cell Wall Polysaccharides ◽  
Human Gut ◽  
Gut Symbionts
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