Structural basis of mammalian high-mannose N-glycan processing by human gut Bacteroides

Trastoy, Beatriz; Du, Jonathan J.; Klontz, Erik H.; Li, Chao; Cifuente, Javier O.; Wang, Lai-Xi; Sundberg, Eric J.; Guerin, Marcelo E.

doi:10.1038/s41467-020-14754-7

Cited by 33 publications

(48 citation statements)

References 73 publications

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“…Glycoside hydrolases can work on the peripheral side of the mucin, i.e., α- D -galactosidase, α- L -fucosidase and N -acetyl-α- D -galactosaminidase, as well as in the core molecule, i.e., β- D -galactosidase, β- D -fucosidase, N -acetyl-β- D -glucosaminidase, N -acetyl-β- D -galactosaminidase, β- D -glucosidase, and β- D -mannosidase 83 . Several gut microbes have developed a complex enzymatic machinery that degrades mucin, such as the B. thetaiotaomicron , which contains polysaccharide utilization loci (PULs) that encode highly specific carbohydrate-active enzymes, surface glycan-binding proteins and transporters 22 – 24 . As mentioned above, BT4244 is an O -glycopeptidase from B. thetaiotaomicron comprised in PUL78, which also contains two genes, BT4241 and BT4243, encoding a GH2 and a GH109 glycoside hydrolases, respectively 84 .…”

Section: Discussionmentioning

confidence: 99%

“…Bacteroides thetaiotaomicron represents a paradigm on how a prominent gut Bacteroidetes is able to catabolize dietary glycans 20 , 21 . The B. thetaiotaomicron genome contains polysaccharide utilization loci (PULs) that encode highly specific carbohydrate-active enzymes, surface glycan-binding proteins and transporters, with each PUL coordinating the degradation of a given glycan 22 – 24 . The gene products of PULs have been termed Sus-like systems because they are reminiscent of the starch utilization system (Sus), but harbor enzymes that are predicted to target non-starch glycans 25 .…”

Section: Introductionmentioning

confidence: 99%

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Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila

et al. 2020

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Akkermansia muciniphila is a mucin-degrading bacterium commonly found in the human gut that promotes a beneficial effect on health, likely based on the regulation of mucus thickness and gut barrier integrity, but also on the modulation of the immune system. In this work, we focus in OgpA from A. muciniphila, an O-glycopeptidase that exclusively hydrolyzes the peptide bond N-terminal to serine or threonine residues substituted with an O-glycan. We determine the high-resolution X-ray crystal structures of the unliganded form of OgpA, the complex with the glycodrosocin O-glycopeptide substrate and its product, providing a comprehensive set of snapshots of the enzyme along the catalytic cycle. In combination with O-glycopeptide chemistry, enzyme kinetics, and computational methods we unveil the molecular mechanism of O-glycan recognition and specificity for OgpA. The data also contribute to understanding how A. muciniphila processes mucins in the gut, as well as analysis of post-translational O-glycosylation events in proteins.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila

et al. 2020

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“…Man5N2-Asn (Man5GlcNAc2-Asn) were prepared from Man9GlcNAc2-Asn isolated from soybean agglutinin (108). The crude soybean agglutinin isolated from soybean flour was digested with pronase (Sigma Aldrich) and purified to afford Man9GlcNAc2-Asn, which was subsequently treated with B. thetaiotaomicron α1,2mannosidase to provide Man5N2-Asn.…”

Section: Nm5n2-asn (Glcnacman5glcnac2-asn) Andmentioning

confidence: 99%

Characterizing human α-1,6-fucosyltransferase (FUT8) substrate specificity and structural similarities with related fucosyltransferases

Boruah

Kadirvelraj

Liu

et al. 2020

Journal of Biological Chemistry

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Mammalian Asn-linked glycans are extensively processed as they transit the secretory pathway to generate diverse glycans on cell surface and secreted glycoproteins. Additional modification of the glycan core by α-1,6-fucose addition to the innermost GlcNAc residue (core fucosylation) is catalyzed by an α-1,6-fucosyltransferase (FUT8). The importance of core fucosylation can be seen in the complex pathological phenotypes of FUT8 null mice, which display defects in cellular signaling, development, and subsequent neonatal lethality. Elevated core fucosylation has also been identified in several human cancers. However, the structural basis for FUT8 substrate specificity remains unknown. Here, using various crystal structures of FUT8 in complex with a donor substrate analog, and with four distinct glycan acceptors, we identify the molecular basis for FUT8 specificity and activity. The ordering of three active site loops corresponds to an increased occupancy for bound GDP, suggesting an induced-fit folding of the donor binding subsite. Structures of the various acceptor complexes were compared with kinetic data on FUT8 active site mutants and with specificity data from a library of glycan acceptors to reveal how binding site complementarity and steric hindrance can tune substrate affinity. The FUT8 structure was also compared with other known fucosyltransferases to identify conserved and divergent structural features for donor and acceptor recognition and catalysis. These data provide insights into the evolution of modular templates for donor and acceptor recognition among GT-B fold glycosyltransferases in the synthesis of diverse glycan structures in biological systems.

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“…Among the functions associated with "carbohydrate", a particular increase in the LE dataset was observed in the "monosaccharide" (level 2) turnover-associated genes (HE: 3%, LE: 4% Figure 6). Indeed, gut-associated Bacteroides species carry a specific genetic machinery to degrade plant-derived mannans or human high-mannose-type N-glycans, stemming from mucosal secretions and secreted epithelial cells [45,46].…”

Section: He Microbiomes Are Specialized On C1-c3 Compound Turnovermentioning

confidence: 99%

“…Especially mannose metabolism (level 3; HE: 0.8%, LE: 1%), including the metabolism of alpha-1,2-mannosidase (level 4; HE: 0.6%, LE: 0.9%), was found to be increased in LE samples (Supplementary Figure 6). Indeed, gut-associated Bacteroides species carry a specific genetic machinery to degrade plant-derived mannans or human high-mannose-type N-glycans, stemming from mucosal secretions and secreted epithelial cells [45,46].…”

Section: He Microbiomes Are Specialized On C1-c3 Compound Turnovermentioning

confidence: 99%

Reduced B12 Uptake and Increased Gastrointestinal Formate Drive Archaeome-Mediated Breath Methane Emission in Humans

Kumpitsch

Fischmeister

Mahnert

et al. 2021

Preprint

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Background Methane is an end product of microbial fermentation in the human gastrointestinal tract. This gas is solely produced by an archaeal subpopulation of the human microbiome. Increased methane production has been associated with abdominal pain, bloating, constipation, IBD, CRC or other conditions. Twenty percent of the (healthy) Western populations innately exhale substantially higher amounts (>5 ppm) of this gas. The underlying principle for differential methane emission and its effect on human health was still not sufficiently understood. Results We assessed the breath methane content, gastrointestinal microbiome, metagenome, metabolome, and eating behavior of one-hundred healthy young adults (female: n = 52, male: n = 48; mean age =24.1). On the basis of the amount of methane emitted, participants were grouped into high methane emitters (CH4 breath content 5-75 ppm) and low emitters (CH4 < 5 ppm). The microbiomes of high methane emitters were characterized by a 1000-fold increase in Methanobrevibacter smithii. This archaeon co-occurred with a bacterial community specialized on dietary fibre degradation, which included members of Ruminococcaceae and Christensenellaceae. As confirmed by metagenomics and metabolomics, the biology of high methane producers was further characterized by increased formate and acetate levels in the gut. These metabolites were strongly correlated with dietary habits, such as vitamin, fat and fibre intake, host genetics, and microbiome function, altogether driving archaeal methanogenesis. Conclusions This study enlightens the complex, multi-level interplay of host diet, genetics and microbiome composition/function leading to two fundamentally different gastrointestinal phenotypes and identifies novel points of therapeutic action in methane-associated disorders.

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Structural basis of mammalian high-mannose N-glycan processing by human gut Bacteroides

Cited by 33 publications

References 73 publications

Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila

Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila

Characterizing human α-1,6-fucosyltransferase (FUT8) substrate specificity and structural similarities with related fucosyltransferases

Reduced B12 Uptake and Increased Gastrointestinal Formate Drive Archaeome-Mediated Breath Methane Emission in Humans

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