Dataset Information

A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation.

ABSTRACT: Glycans are major nutrients for the human gut microbiota (HGM). Arabinogalactan proteins (AGPs) comprise a heterogenous group of plant glycans in which a ?1,3-galactan backbone and ?1,6-galactan side chains are conserved. Diversity is provided by the variable nature of the sugars that decorate the galactans. The mechanisms by which nutritionally relevant AGPs are degraded in the HGM are poorly understood. Here we explore how the HGM organism Bacteroides thetaiotaomicron metabolizes AGPs. We propose a sequential degradative model in which exo-acting glycoside hydrolase (GH) family 43 ?1,3-galactanases release the side chains. These oligosaccharide side chains are depolymerized by the synergistic action of exo-acting enzymes in which catalytic interactions are dependent on whether degradation is initiated by a lyase or GH. We identified two GHs that establish two previously undiscovered GH families. The crystal structures of the exo-?1,3-galactanases identified a key specificity determinant and departure from the canonical catalytic apparatus of GH43 enzymes. Growth studies of Bacteroidetes spp. on complex AGP revealed 3 keystone organisms that facilitated utilization of the glycan by 17 recipient bacteria, which included B. thetaiotaomicron. A surface endo-?1,3-galactanase, when engineered into B. thetaiotaomicron, enabled the bacterium to utilize complex AGPs and act as a keystone organism.

SUBMITTER: Cartmell A

PROVIDER: S-EPMC6217937 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation.

Cartmell Alan A Muñoz-Muñoz Jose J Briggs Jonathon A JA Ndeh Didier A DA Lowe Elisabeth C EC Baslé Arnaud A Terrapon Nicolas N Stott Katherine K Heunis Tiaan T Gray Joe J Yu Li L Dupree Paul P Fernandes Pearl Z PZ Shah Sayali S Williams Spencer J SJ Labourel Aurore A Trost Matthias M Henrissat Bernard B Gilbert Harry J HJ

Nature microbiology 20181022 11

Glycans are major nutrients for the human gut microbiota (HGM). Arabinogalactan proteins (AGPs) comprise a heterogenous group of plant glycans in which a β1,3-galactan backbone and β1,6-galactan side chains are conserved. Diversity is provided by the variable nature of the sugars that decorate the galactans. The mechanisms by which nutritionally relevant AGPs are degraded in the HGM are poorly understood. Here we explore how the HGM organism Bacteroides thetaiotaomicron metabolizes AGPs. We prop ...[more]

PMID: 30349080

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Project description:The human gut microbiota (HGM) contributes to the physiology and health of its host. The health benefits provided by dietary manipulation of the HGM require knowledge of how glycans, the major nutrients available to this ecosystem, are metabolized. Arabinogalactan proteins (AGPs) are a ubiquitous feature of plant polysaccharides available to the HGM. Although the galactan backbone and galactooligosaccharide side chains of AGPs are conserved, the decorations of these structures are highly variable. Here, we tested the hypothesis that these variations in arabinogalactan decoration provide a selection mechanism for specific Bacteroides species within the HGM. The data showed that only a single bacterium, B. plebeius, grew on red wine AGP (Wi-AGP) and seaweed AGP (SW-AGP) in mono- or mixed culture. Wi-AGP thus acts as a privileged nutrient for a Bacteroides species within the HGM that utilizes marine and terrestrial plant glycans. The B. plebeius polysaccharide utilization loci (PULs) upregulated by AGPs encoded a polysaccharide lyase, located in the enzyme family GH145, which hydrolyzed Rha-Glc linkages in Wi-AGP. Further analysis of GH145 identified an enzyme with two active sites that displayed glycoside hydrolase and lyase activities, respectively, which conferred substrate flexibility for different AGPs. The AGP-degrading apparatus of B. plebeius also contained a sulfatase, BpS1_8, active on SW-AGP and Wi-AGP, which played a pivotal role in the utilization of these glycans by the bacterium. BpS1_8 enabled other Bacteroides species to access the sulfated AGPs, providing a route to introducing privileged nutrient utilization into probiotic and commensal organisms that could improve human health. IMPORTANCE Dietary manipulation of the HGM requires knowledge of how glycans available to this ecosystem are metabolized. The variable structures that decorate the core component of plant AGPs may influence their utilization by specific organisms within the HGM. Here, we evaluated the ability of Bacteroides species to utilize a marine and terrestrial AGP. The data showed that a single bacterium, B. plebeius, grew on Wi-AGP and SW-AGP in mono- or mixed culture. Wi-AGP is thus a privileged nutrient for a Bacteroides species that utilizes marine and terrestrial plant glycans. A key component of the AGP-degrading apparatus of B. plebeius is a sulfatase that conferred the ability of the bacterium to utilize these glycans. The enzyme enabled other Bacteroides species to access the sulfated AGPs, providing a route to introducing privileged nutrient utilization into probiotic and commensal organisms that could improve human health.

Project description:Glycans, the major source of energy for the human gut microbiota (HGM), are metabolised by numerous members of the Bacteroides genus. Arabinogalactan proteins (AGPs) are a ubiquitous and highly heterogenous group of plant glycans in which a B1,3-galactan backbone and B1,6-galactan side chains are conserved features. Diversity is provided by the extensive and highly variable nature of the sugars that decorate both the backbone and side chain galactans. The mechanisms by which nutritionally relevant AGPs are degraded at a cellular and biochemical level are poorly understood, as is the impact of this process on the ecology of the HGM. Here we have explored how the HGM organism Bacteroides thetaiotaomicron metabolises simple and highly complex AGPs. We propose a sequential degradative model in which a repertoire of exo-acting family GH43 B1,3-galactanases releases backbone galactose units that are attached to the side chains. The oligosaccharide side chains are depolymerized by the synergistic action of exo-acting enzymes in which catalytic interactions are dependent on whether degradation is initiated by a lyase or glycoside hydrolase. We identified an a-L-arabinofuranosidase and B-D-glucuronidase that are the founders of two previously undiscovered glycoside hydrolase families. The crystal structures of the backbone exo-B1,3-galactanases identified a key specificity determinant and reveals significant departure from the canonical catalytic apparatus of other family GH43 enzymes. Growth studies of 20 HGM Bacteroidetes species on a complex AGP revealed three keystone organisms that facilitated utilisation of fragments of the glycan by the 17 other bacteria, which thus acted as recipients. The ability to function as a keystone organism was conferred by a surface endo-B1,3-galactanase, which, when engineered into a recipient enabled this bacterium to utilise complex AGPs and facilitate the growth of the other Bacteroidetes species. This study underpins future pre- and probiotic strategies to exploit AGPs to manipulate the function of the HGM.

Project description:Bacteroides thetaiotaomicron is commonly found in the human colon and stabilizes its ecosystem by catabolism of various polysaccharides. A model of cross-talk between the metabolism of amino acids and fructans in B. thetaiotaomicron was proposed. The growth of B. thetaiotaomicron DSM 2079 in two defined media containing mineral salts and vitamins, and supplemented with either 20 or 2 amino acids, was studied in an isothermal microcalorimeter. The polyfructans inulin (from chicory) and levan (synthesized using levansucrase from Pseudomonas syringae), two fructooligosaccharide preparations with different composition, sucrose and fructose were tested as substrates. The calorimetric power-time curves were substrate specific and typically multiauxic. A surplus of amino acids reduced the consumption of longer oligosaccharides (degree of polymerization > 3). Bacterial growth was not detected either in the carbohydrate free medium containing amino acids or in the medium with inulin as a sole carbohydrate. In amino acid-restricted medium, fermentation leading to acetic acid formation was dominant at the beginning of growth (up to 24 h), followed by increased lactic acid production, and mainly propionic and succinic acids were produced at the end of fermentation. In the medium supplemented with 20 amino acids, the highest production of d-lactate (82 ± 33 mmol/gDW) occurred in parallel with extensive consumption (up to 17 mmol/gDW) of amino acids, especially Ser, Thr, and Asp. The production of Ala and Glu was observed at growth on all substrates, and the production was enhanced under amino acid deficiency. The study revealed the influence of amino acids on fructan metabolism in B. thetaiotaomicron and showed that defined growth media are invaluable in elucidating quantitative metabolic profiles of the bacteria. Levan was shown to act as an easily degradable substrate for B. thetaiotaomicron. The effect of levan on balancing or modifying colon microbiota will be studied in further experiments.

Dataset Information

A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation.

Publications

A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation.

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