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Silverio MP, Neumann T, Schaubruch K, Heermann R, Pérez-García P, Chow J, Streit WR. Metagenome-derived SusD-homologs affiliated with Bacteroidota bind to synthetic polymers. Appl Environ Microbiol 2024; 90:e0093324. [PMID: 38953372 PMCID: PMC11267923 DOI: 10.1128/aem.00933-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 06/04/2024] [Indexed: 07/04/2024] Open
Abstract
Starch utilization system (Sus)D-homologs are well known for their carbohydrate-binding capabilities and are part of the sus operon in microorganisms affiliated with the phylum Bacteroidota. Until now, SusD-like proteins have been characterized regarding their affinity toward natural polymers. In this study, three metagenomic SusD homologs (designated SusD1, SusD38489, and SusD70111) were identified and tested with respect to binding to natural and non-natural polymers. SusD1 and SusD38489 are cellulose-binding modules, while SusD70111 preferentially binds chitin. Employing translational fusion proteins with superfolder GFP (sfGFP), pull-down assays, and surface plasmon resonance (SPR) has provided evidence for binding to polyethylene terephthalate (PET) and other synthetic polymers. Structural analysis suggested that a Trp triad might be involved in protein adsorption. Mutation of these residues to Ala resulted in an impaired adsorption to microcrystalline cellulose (MC), but not so to PET and other synthetic polymers. We believe that the characterized SusDs, alongside the methods and considerations presented in this work, will aid further research regarding bioremediation of plastics. IMPORTANCE SusD1 and SusD38489 can be considered for further applications regarding their putative adsorption toward fossil-fuel based polymers. This is the first time that SusD homologs from the polysaccharide utilization loci (PUL), largely described for the phylum Bacteroidota, are characterized as synthetic polymer-binding proteins.
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Affiliation(s)
| | - Tabea Neumann
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Kirsten Schaubruch
- Institute of Molecular Physiology, Johannes-Gutenberg University of Mainz, Mainz, Germany
| | - Ralf Heermann
- Institute of Molecular Physiology, Johannes-Gutenberg University of Mainz, Mainz, Germany
| | - Pablo Pérez-García
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Wolfgang R. Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
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2
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Li X, Lippens G, Parrou JL, Cioci G, Esque J, Wang Z, Laville E, Potocki-Veronese G, Labourel A. Biochemical characterization of a SusD-like protein involved in β-1,3-glucan utilization by an uncultured cow rumen Bacteroides. mSphere 2024:e0027824. [PMID: 39012103 DOI: 10.1128/msphere.00278-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/18/2024] [Indexed: 07/17/2024] Open
Abstract
In ruminants, the rumen is a specialized stomach that is adapted to the breakdown of plant-derived complex polysaccharides through the coordinated activities of a diverse microbial community. Bacteroidota is a major phylum in this bovine rumen microbiota. They contain several clusters of genes called polysaccharide utilization loci (PULs) that encode proteins working in concert to capture, degrade, and transport polysaccharides. Despite the critical role of SusD-like proteins for efficient substrate transport, they remain largely unexplored. Here, we present the biochemical characterization of a SusD-like protein encoded by a β-glucan utilization locus from an Escherichia coli metagenomic clone previously isolated by functional screening of the bovine rumen microbiome. In this study, we show that clone 41O1 can grow on laminaritriose, cellotriose, and a mixture of cellobiosyl-cellobiose and glucosyl-cellotriose as sole carbon sources. Based on this, we used various in vitro analyses to investigate the binding ability of 41O1_SusD-like towards these oligosaccharides and the corresponding polysaccharides. We observed a clear binding affinity for β-1,6 branched β-1,3-glucans (laminarins, yeast β-glucan) and laminaritriose. Comparison of the AlphaFold2 model of 41O1_SusD-like with its closest structural homologs highlights a similar pattern of substrate recognition. In particular, three tryptophan residues are shown to be crucial for laminarin recognition. In the context of the cow rumen, we discuss the possible substrates targeted by the 41O1_PUL, such as the (1,3;1,4)-β-d-glucans present in cereal grains or the β-1,3- and (1,3;1,6)-β-d-glucans that are components of the cell wall of ruminal yeasts.IMPORTANCEThe rumen microbiota can majorly impact overall animal health, feed efficiency, and release of harmful substances into the environment. This microbiota is involved in the fermentation of organic matter to provide the host with valuable and assimilable nutrients. Bacteroidota efficiently captures, breaks down, and imports complex polysaccharides through the concerted action of proteins encoded by polysaccharide utilization loci (PULs). Within this system, SusD-like protein has proven necessary for the active internalization of the substrate. Nevertheless, the vast majority of SusD-like proteins characterized to date originate from cultured bacteria. With regard to the diversity and importance of uncultured bacteria in the rumen, further studies are required to better understand the role of polysaccharide utilization loci in ruminal polysaccharide degradation. Our detailed characterization of the 41O1_SusD-like therefore contributes to a better understanding of the carbohydrate metabolism of an uncultured Bacteroides from the cow rumen.
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Affiliation(s)
- Xiaoqian Li
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Guy Lippens
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Jean-Luc Parrou
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Gianluca Cioci
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Jérémy Esque
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Zhi Wang
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | | | - Aurore Labourel
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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3
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Zühlke MK, Ficko-Blean E, Bartosik D, Terrapon N, Jeudy A, Jam M, Wang F, Welsch N, Dürwald A, Martin LT, Larocque R, Jouanneau D, Eisenack T, Thomas F, Trautwein-Schult A, Teeling H, Becher D, Schweder T, Czjzek M. Unveiling the role of novel carbohydrate-binding modules in laminarin interaction of multimodular proteins from marine Bacteroidota during phytoplankton blooms. Environ Microbiol 2024; 26:e16624. [PMID: 38757353 DOI: 10.1111/1462-2920.16624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Laminarin, a β(1,3)-glucan, serves as a storage polysaccharide in marine microalgae such as diatoms. Its abundance, water solubility and simple structure make it an appealing substrate for marine bacteria. Consequently, many marine bacteria have evolved strategies to scavenge and decompose laminarin, employing carbohydrate-binding modules (CBMs) as crucial components. In this study, we characterized two previously unassigned domains as laminarin-binding CBMs in multimodular proteins from the marine bacterium Christiangramia forsetii KT0803T, thereby introducing the new laminarin-binding CBM families CBM102 and CBM103. We identified four CBM102s in a surface glycan-binding protein (SGBP) and a single CBM103 linked to a glycoside hydrolase module from family 16 (GH16_3). Our analysis revealed that both modular proteins have an elongated shape, with GH16_3 exhibiting greater flexibility than SGBP. This flexibility may aid in the recognition and/or degradation of laminarin, while the constraints in SGBP could facilitate the docking of laminarin onto the bacterial surface. Exploration of bacterial metagenome-assembled genomes (MAGs) from phytoplankton blooms in the North Sea showed that both laminarin-binding CBM families are widespread among marine Bacteroidota. The high protein abundance of CBM102- and CBM103-containing proteins during phytoplankton blooms further emphasizes their significance in marine laminarin utilization.
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Affiliation(s)
- Marie-Katherin Zühlke
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Elizabeth Ficko-Blean
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Daniel Bartosik
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université (AMU, UMR7257), CNRS, Marseille, France
| | - Alexandra Jeudy
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Murielle Jam
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Fengqing Wang
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Norma Welsch
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Alexandra Dürwald
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Helmholtz Institute for One Health, Helmholtz Centre for Infection Research HZI, Greifswald, Germany
| | - Laura Torres Martin
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
| | - Robert Larocque
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Diane Jouanneau
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Tom Eisenack
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
| | - François Thomas
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Anke Trautwein-Schult
- Microbial Proteomics, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Dörte Becher
- Microbial Proteomics, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Mirjam Czjzek
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
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4
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Photenhauer AL, Villafuerte-Vega RC, Cerqueira FM, Armbruster KM, Mareček F, Chen T, Wawrzak Z, Hopkins JB, Vander Kooi CW, Janeček Š, Ruotolo BT, Koropatkin NM. The Ruminococcus bromii amylosome protein Sas6 binds single and double helical α-glucan structures in starch. Nat Struct Mol Biol 2024; 31:255-265. [PMID: 38177679 PMCID: PMC11081458 DOI: 10.1038/s41594-023-01166-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 10/27/2023] [Indexed: 01/06/2024]
Abstract
Resistant starch is a prebiotic accessed by gut bacteria with specialized amylases and starch-binding proteins. The human gut symbiont Ruminococcus bromii expresses Sas6 (Starch Adherence System member 6), which consists of two starch-specific carbohydrate-binding modules from family 26 (RbCBM26) and family 74 (RbCBM74). Here, we present the crystal structures of Sas6 and of RbCBM74 bound with a double helical dimer of maltodecaose. The RbCBM74 starch-binding groove complements the double helical α-glucan geometry of amylopectin, suggesting that this module selects this feature in starch granules. Isothermal titration calorimetry and native mass spectrometry demonstrate that RbCBM74 recognizes longer single and double helical α-glucans, while RbCBM26 binds short maltooligosaccharides. Bioinformatic analysis supports the conservation of the amylopectin-targeting platform in CBM74s from resistant-starch degrading bacteria. Our results suggest that RbCBM74 and RbCBM26 within Sas6 recognize discrete aspects of the starch granule, providing molecular insight into how this structure is accommodated by gut bacteria.
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Affiliation(s)
- Amanda L Photenhauer
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Filipe M Cerqueira
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Krista M Armbruster
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tiantian Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Zdzislaw Wawrzak
- Northwestern Synchrotron Research Center-LS-CAT, Northwestern University, Argonne, IL, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Craig W Vander Kooi
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Nicole M Koropatkin
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
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5
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Cha QQ, Liu SS, Dang YR, Ren XB, Xu F, Li PY, Chen XL, Wang P, Zhang XY, Zhang YZ, Qin QL. Ecological function and interaction of different bacterial groups during alginate processing in coastal seawater community. ENVIRONMENT INTERNATIONAL 2023; 182:108325. [PMID: 37995388 DOI: 10.1016/j.envint.2023.108325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/25/2023]
Abstract
The degradation of high molecular weight organic matter (HMWOM) is a core process of oceanic carbon cycle, which is determined by the activity of microbial communities harboring hundreds of different species. Illustrating the active microbes and their interactions during HMWOM processing can provide key information for revealing the relationship between community composition and its ecological functions. In this study, the genomic and transcriptional responses of microbial communities to the availability of alginate, an abundant HMWOM in coastal ecosystem, were elucidated. The main degraders transcribing alginate lyase (Aly) genes came from genera Alteromonas, Psychrosphaera and Colwellia. Meanwhile, some strains, mainly from the Rhodobacteraceae family, did not transcribe Aly gene but could utilize monosaccharides to grow. The co-culture experiment showed that the activity of Aly-producing strain could promote the growth of Aly-non-producing strain when alginate was the sole carbon source. Interestingly, this interaction did not reduce the alginate degradation rate, possibly due to the easily degradable nature of alginate. This study can improve our understanding of the relationship between microbial community activity and alginate metabolism function as well as further manipulation of microbial community structure for alginate processing.
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Affiliation(s)
- Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Sha-Sha Liu
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Xue-Bing Ren
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Fei Xu
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China; MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China.
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6
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Dutschei T, Beidler I, Bartosik D, Seeßelberg JM, Teune M, Bäumgen M, Ferreira SQ, Heldmann J, Nagel F, Krull J, Berndt L, Methling K, Hein M, Becher D, Langer P, Delcea M, Lalk M, Lammers M, Höhne M, Hehemann JH, Schweder T, Bornscheuer UT. Marine Bacteroidetes enzymatically digest xylans from terrestrial plants. Environ Microbiol 2023; 25:1713-1727. [PMID: 37121608 DOI: 10.1111/1462-2920.16390] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
Marine Bacteroidetes that degrade polysaccharides contribute to carbon cycling in the ocean. Organic matter, including glycans from terrestrial plants, might enter the oceans through rivers. Whether marine bacteria degrade structurally related glycans from diverse sources including terrestrial plants and marine algae was previously unknown. We show that the marine bacterium Flavimarina sp. Hel_I_48 encodes two polysaccharide utilization loci (PULs) which degrade xylans from terrestrial plants and marine algae. Biochemical experiments revealed activity and specificity of the encoded xylanases and associated enzymes of these PULs. Proteomics indicated that these genomic regions respond to glucuronoxylans and arabinoxylans. Substrate specificities of key enzymes suggest dedicated metabolic pathways for xylan utilization. Some of the xylanases were active on different xylans with the conserved β-1,4-linked xylose main chain. Enzyme activity was consistent with growth curves showing Flavimarina sp. Hel_I_48 uses structurally different xylans. The observed abundance of related xylan-degrading enzyme repertoires in genomes of other marine Bacteroidetes indicates similar activities are common in the ocean. The here presented data show that certain marine bacteria are genetically and biochemically variable enough to access parts of structurally diverse xylans from terrestrial plants as well as from marine algal sources.
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Affiliation(s)
- Theresa Dutschei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Irena Beidler
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Daniel Bartosik
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Julia-Maria Seeßelberg
- Department of Protein Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michelle Teune
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Marcus Bäumgen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Soraia Querido Ferreira
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Julia Heldmann
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Felix Nagel
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Joris Krull
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Leona Berndt
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Karen Methling
- Department of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Martin Hein
- Department of Organic Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Peter Langer
- Department of Organic Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Mihaela Delcea
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michael Lalk
- Department of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michael Lammers
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Matthias Höhne
- Department of Protein Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Thomas Schweder
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
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7
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Nakamura S, Kurata R, Tonozuka T, Funane K, Park EY, Miyazaki T. Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria. J Biol Chem 2023:104885. [PMID: 37269952 PMCID: PMC10316084 DOI: 10.1016/j.jbc.2023.104885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/05/2023] Open
Abstract
Dextran is an α-(1→6)-glucan that is synthesized by some lactic acid bacteria, and branched dextran with α-(1→2)-, α-(1→3)-, and α-(1→4)-linkages are often produced. Although many dextranases are known to act on the α-(1→6)-linkage of dextran, few studies have functionally analyzed the proteins involved in degrading branched dextran. The mechanism by which bacteria utilize branched dextran is unknown. Earlier, we identified dextranase (FjDex31A) and kojibiose hydrolase (FjGH65A) in the dextran utilization locus (FjDexUL) of a soil Bacteroidota Flavobacterium johnsoniae and hypothesized that FjDexUL is involved in the degradation of α-(1→2)-branched dextran. In this study, we demonstrate that FjDexUL proteins recognize and degrade α-(1→2)- and α-(1→3)-branched dextrans produced by Leuconostoc citreum S-32 (S-32 α-glucan). The FjDexUL gene was significantly upregulated when S-32 α-glucan was the carbon source compared with α-glucooligosaccharides and α-glucans, such as linear dextran and branched α-glucan from L. citreum S-64. FjDexUL GHs synergistically degraded S-32 α-glucan. The crystal structure of FjGH66 shows that some sugar-binding subsites can accommodate α-(1→2)- and α-(1→3)-branches. The structure of FjGH65A in complex with isomaltose supports that FjGH65A acts on α-(1→2)-glucosyl isomaltooligosaccharides. Furthermore, two cell surface sugar-binding proteins (FjDusD and FjDusE) were characterized, and FjDusD showed affinity for isomaltooligosaccharides and FjDusE for dextran, including linear and branched dextrans. Collectively, FjDexUL proteins are suggested to be involved in the degradation of α-(1→2)- and α-(1→3)-branched dextrans. Our results will be helpful in understanding the bacterial nutrient requirements and symbiotic relationships between bacteria at the molecular level.
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Affiliation(s)
- Shuntaro Nakamura
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan
| | - Rikuya Kurata
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Takashi Tonozuka
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Kazumi Funane
- Faculty of Life and Environmental Sciences, University of Yamanashi, 4-4-37, Takeda-cho, Kofu, Yamanashi, 400-8510, Japan
| | - Enoch Y Park
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan; Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Takatsugu Miyazaki
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan; Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
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8
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Gu Y, Guberman-Pfeffer MJ, Srikanth V, Shen C, Giska F, Gupta K, Londer Y, Samatey FA, Batista VS, Malvankar NS. Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity. Nat Microbiol 2023; 8:284-298. [PMID: 36732469 PMCID: PMC9999484 DOI: 10.1038/s41564-022-01315-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 12/20/2022] [Indexed: 02/04/2023]
Abstract
OmcZ nanowires produced by Geobacter species have high electron conductivity (>30 S cm-1). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire-forming cytochrome essential for the formation of high-current-density biofilms that require long-distance (>10 µm) extracellular electron transport. However, the mechanisms underlying OmcZ nanowire assembly and high conductivity are unknown. Here we report a 3.5-Å-resolution cryogenic electron microscopy structure for OmcZ nanowires. Our structure reveals linear and closely stacked haems that may account for conductivity. Surface-exposed haems and charge interactions explain how OmcZ nanowires bind to diverse extracellular electron acceptors and how organization of nanowire network re-arranges in different biochemical environments. In vitro studies explain how G. sulfurreducens employ a serine protease to control the assembly of OmcZ monomers into nanowires. We find that both OmcZ and serine protease are widespread in environmentally important bacteria and archaea, thus establishing a prevalence of nanowire biogenesis across diverse species and environments.
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Affiliation(s)
- Yangqi Gu
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- PNAC division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Matthew J Guberman-Pfeffer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vishok Srikanth
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Microbiology, Yale University, New Haven, CT, USA
| | - Fabian Giska
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Kallol Gupta
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Yuri Londer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Fadel A Samatey
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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9
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Modesto JL, Pearce VH, Townsend GE. Harnessing gut microbes for glycan detection and quantification. Nat Commun 2023; 14:275. [PMID: 36650134 PMCID: PMC9845299 DOI: 10.1038/s41467-022-35626-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 12/13/2022] [Indexed: 01/19/2023] Open
Abstract
Glycans facilitate critical biological functions and control the mammalian gut microbiota composition by supplying differentially accessible nutrients to distinct microbial subsets. Therefore, identifying unique glycan substrates that support defined microbial populations could inform therapeutic avenues to treat diseases via modulation of the gut microbiota composition and metabolism. However, examining heterogeneous glycan mixtures for individual microbial substrates is hindered by glycan structural complexity and diversity, which presents substantial challenges to glycomics approaches. Fortuitously, gut microbes encode specialized sensor proteins that recognize unique glycan structures and in-turn activate predictable, specific, and dynamic transcriptional responses. Here, we harness this microbial machinery to indicate the presence and abundance of compositionally similar, yet structurally distinct glycans, using a transcriptional reporter we develop. We implement these tools to examine glycan mixtures, isolate target molecules for downstream characterization, and quantify the recovered products. We assert that this toolkit could dramatically enhance our understanding of the mammalian intestinal environment and identify host-microbial interactions critical for human health.
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Affiliation(s)
- Jennifer L Modesto
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA.,Penn State Microbiome Center, The Pennsylvania State University, State College, PA, 16802, USA.,Center for Molecular Carcinogenesis and Toxicology, The Pennsylvania State University, State College, PA, 16802, USA
| | - Victoria H Pearce
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA.,Penn State Microbiome Center, The Pennsylvania State University, State College, PA, 16802, USA.,Center for Molecular Carcinogenesis and Toxicology, The Pennsylvania State University, State College, PA, 16802, USA
| | - Guy E Townsend
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA. .,Penn State Microbiome Center, The Pennsylvania State University, State College, PA, 16802, USA. .,Center for Molecular Carcinogenesis and Toxicology, The Pennsylvania State University, State College, PA, 16802, USA.
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10
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Couture G, Luthria DL, Chen Y, Bacalzo NP, Tareq FS, Harnly J, Phillips KM, Pehrsson PR, McKillop K, Fukagawa NK, Lebrilla CB. Multi-Glycomic Characterization of Fiber from AOAC Methods Defines the Carbohydrate Structures. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14559-14570. [PMID: 36382383 DOI: 10.1021/acs.jafc.2c06191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Dietary fiber has long been known to be an essential component of a healthy diet, and recent investigations into the gut microbiome-health paradigm have identified fiber as a prime determinant in this interaction. Further, fiber is now known to impact the gut microbiome in a structure-specific manner, conferring differential bioactivities to these specific structures. However, current analytical methods for food carbohydrate analysis do not capture this important structural information. To address this need, we utilized rapid-throughput LC-MS methods to develop a novel analytical pipeline to determine the structural composition of soluble and insoluble fiber fractions from two AOAC methods (991.43 and 2017.16) at the total monosaccharide, glycosidic linkage, and free saccharide level. Two foods were chosen for this proof-of-concept study: oats and potato starch. For oats, both AOAC methods gave similar results. Insoluble fiber was found to be comprised of linkages corresponding to β-glucan, arabinoxylan, xyloglucan, and mannan, while soluble fiber was found to be mostly β-glucan, with small amounts of arabinogalactan. For raw potato starch, each AOAC method gave markedly different results in the soluble fiber fractions. These observed differences are attributable to the resistant starch content of potato starch and the different starch digestion conditions used in each method. Together, these tools are a means to obtain the complex structures present within dietary fiber while retaining "classical" determinations such as soluble and insoluble fiber. These efforts will provide an analytical framework to connect gravimetric fiber determinations with their constituent structures to better inform gut microbiome and clinical nutrition studies.
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Affiliation(s)
- Garret Couture
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California Davis, Davis, California 95616, United States
| | - Devanand L Luthria
- USDA Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland 20705, United States
| | - Ye Chen
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California Davis, Davis, California 95616, United States
| | - Nikita P Bacalzo
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California Davis, Davis, California 95616, United States
| | - Fakir S Tareq
- USDA Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland 20705, United States
| | - James Harnly
- USDA Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland 20705, United States
| | - Katherine M Phillips
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Pamela R Pehrsson
- USDA Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland 20705, United States
| | - Kyle McKillop
- USDA Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland 20705, United States
| | - Naomi K Fukagawa
- USDA Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland 20705, United States
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California Davis, Davis, California 95616, United States
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11
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Structural and Biochemical Characterization of a Nonbinding SusD-Like Protein Involved in Xylooligosaccharide Utilization by an Uncultured Human Gut Bacteroides Strain. mSphere 2022; 7:e0024422. [PMID: 36043703 PMCID: PMC9599597 DOI: 10.1128/msphere.00244-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the human gut microbiota, Bacteroidetes break down dietary and endogenous glycosides through highly specific polysaccharide utilization loci (PULs). PULs encode a variety of sensor regulators, binding proteins, transporters, and carbohydrate-active enzymes (CAZymes). Surface glycan-binding proteins (SGBPs) are essential for the efficient capture of the glycosides present on the cell surface, providing Bacteroidetes with a competitive advantage in colonizing their habitats. Here, we present the functional and structural characterization of a SusD-like protein encoded by a xylooligosaccharide (XOS) PUL from an uncultured human gut Bacteroides strain. This locus is also conserved in Bacteroides vulgatus, thereby providing new mechanistic insights into the role of SGBPs in the metabolism of dietary fiber of importance for gut health. Various in vitro analyses, including saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy, revealed that the SusD-like protein cannot bind to the cognate substrate of the XOS PUL, although its presence is essential for the PUL to function. Analysis of the crystal structure of the SusD-like protein reveals an unfolded binding surface and the absence or inappropriate orientation of several key residues compared with other known SusD-like structures. These results highlight the critical role of the SusD-like protein in the transport of oligosaccharides and provide fundamental knowledge about the structure-function of SusC/D-like transporters, revealing that the binding specificity of SusD-like SGBPs does not necessarily reflect the uptake specificity of the transporter. IMPORTANCE The metabolization of dietary fiber is a crucial function for many gut bacteria, especially Bacteroidetes, which are particularly well adapted for recognizing, binding, transporting, and degrading glycosides. In this study, we report the functional and structural characterization of a SusD-like protein involved in xylooligosaccharide utilization by an uncultured gut Bacteroides strain. We demonstrate that while this protein is structurally similar to many canonical Bacteroidetes surface glycan-binding proteins, it cannot bind the substrate taken up by the cognate SusC-like transporter. This lack of binding might be explained by the absence of several key residues known to be involved in oligosaccharide binding and/or the possible necessity of the SusC-like protein to be present to create a cooperative binding site. The term “surface glycan-binding proteins” generally used for SusD-like proteins is thus not generic. Overall, this study allowed us to revisit the concept of glycoside utilization by Bacteroidetes, in particular those strains that feed on the short fibers naturally present in some dietary compounds or on the leftovers of other microbes.
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12
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Feng J, Qian Y, Zhou Z, Ertmer S, Vivas EI, Lan F, Hamilton JJ, Rey FE, Anantharaman K, Venturelli OS. Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. Cell Host Microbe 2022; 30:200-215.e12. [PMID: 34995484 PMCID: PMC9060796 DOI: 10.1016/j.chom.2021.12.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/22/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023]
Abstract
Polysaccharide utilization loci (PULs) are co-regulated bacterial genes that sense nutrients and enable glycan digestion. Human gut microbiome members, notably Bacteroides, contain numerous PULs that enable glycan utilization and shape ecological dynamics. To investigate the role of PULs on fitness and inter-species interactions, we develop a CRISPR-based genome editing tool to study 23 PULs in Bacteroides uniformis (BU). BU PULs show distinct glycan-degrading functions and transcriptional coordination that enables the population to adapt upon loss of other PULs. Exploiting a BU mutant barcoding strategy, we demonstrate that in vitro fitness and BU colonization in the murine gut are enhanced by deletion of specific PULs and modulated by glycan availability. PULs mediate glycan-dependent interactions with butyrate producers that depend on the degradation mechanism and glycan utilization ability of the butyrate producer. Thus, PULs determine community dynamics and butyrate production and provide a selective advantage or disadvantage depending on the nutritional landscape.
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Affiliation(s)
- Jun Feng
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yili Qian
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sarah Ertmer
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eugenio I. Vivas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA,Gnotobiotic Animal Core Facility, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Freeman Lan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J. Hamilton
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Federico E. Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ophelia S. Venturelli
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA,Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA,Lead contact,Correspondence:
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13
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Grondin JM, Déjean G, Van Petegem F, Brumer H. Cell Surface Xyloglucan Recognition and Hydrolysis by the Human Gut Commensal Bacteroides uniformis. Appl Environ Microbiol 2022; 88:e0156621. [PMID: 34731054 PMCID: PMC8752140 DOI: 10.1128/aem.01566-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/24/2021] [Indexed: 11/20/2022] Open
Abstract
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 side chain variants. A second, nonsyntenic XyGUL was previously identified in B. uniformis, although its function in XyG utilization compared to its syntenic counterpart was unclear. Here, complementary enzymatic product profiles and bacterial growth curves showcase the notable preference of BuXyGUL2 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 BuXyGUL2 SGBP-B reveals remarkable putative binding site conservation with the canonical XyG-binding BoXyGUL SGBP-B, supporting similar roles for these proteins in glycan capture. Together, these data underpin the central role of complementary 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 complementary roles of syntenic and nonsyntenic 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 nonsyntenic B. uniformis XyGUL and will inform future studies on the roles of complementary loci in glycan targeting by key HGM species.
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Affiliation(s)
- Julie M. Grondin
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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14
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Mapping Molecular Recognition of β1,3-1,4-Glucans by a Surface Glycan-Binding Protein from the Human Gut Symbiont Bacteroides ovatus. Microbiol Spectr 2021; 9:e0182621. [PMID: 34817219 PMCID: PMC8612152 DOI: 10.1128/spectrum.01826-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multigene polysaccharide utilization locus (PUL) encoding enzymes and surface carbohydrate (glycan)-binding proteins (SGBPs) was recently identified in prominent members of Bacteroidetes in the human gut and characterized in Bacteroides ovatus. This PUL-encoded system specifically targets mixed-linkage β1,3-1,4-glucans, a group of diet-derived carbohydrates that promote a healthy microbiota and have potential as prebiotics. The BoSGBPMLG-A protein encoded by the BACOVA_2743 gene is a SusD-like protein that plays a key role in the PUL’s specificity and functionality. Here, we perform a detailed analysis of the molecular determinants underlying carbohydrate binding by BoSGBPMLG-A, combining carbohydrate microarray technology with quantitative affinity studies and a high-resolution X-ray crystallography structure of the complex of BoSGBPMLG-A with a β1,3-1,4-nonasaccharide. We demonstrate its unique binding specificity toward β1,3-1,4-gluco-oligosaccharides, with increasing binding affinities up to the octasaccharide and dependency on the number and position of β1,3 linkages. The interaction is defined by a 41-Å-long extended binding site that accommodates the oligosaccharide in a mode distinct from that of previously described bacterial β1,3-1,4-glucan-binding proteins. In addition to the shape complementarity mediated by CH-π interactions, a complex hydrogen bonding network complemented by a high number of key ordered water molecules establishes additional specific interactions with the oligosaccharide. These support the twisted conformation of the β-glucan backbone imposed by the β1,3 linkages and explain the dependency on the oligosaccharide chain length. We propose that the specificity of the PUL conferred by BoSGBPMLG-A to import long β1,3-1,4-glucan oligosaccharides to the bacterial periplasm allows Bacteroidetes to outcompete bacteria that lack this PUL for utilization of β1,3-1,4-glucans. IMPORTANCE With the knowledge of bacterial gene systems encoding proteins that target dietary carbohydrates as a source of nutrients and their importance for human health, major efforts are being made to understand carbohydrate recognition by various commensal bacteria. Here, we describe an integrative strategy that combines carbohydrate microarray technology with structural studies to further elucidate the molecular determinants of carbohydrate recognition by BoSGBPMLG-A, a key protein expressed at the surface of Bacteroides ovatus for utilization of mixed-linkage β1,3-1,4-glucans. We have mapped at high resolution interactions that occur at the binding site of BoSGBPMLG-A and provide evidence for the role of key water-mediated interactions for fine specificity and affinity. Understanding at the molecular level how commensal bacteria, such as prominent members of Bacteroidetes, can differentially utilize dietary carbohydrates with potential prebiotic activities will shed light on possible ways to modulate the microbiome to promote human health.
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15
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Fultz R, Ticer T, Ihekweazu FD, Horvath TD, Haidacher SJ, Hoch KM, Bajaj M, Spinler JK, Haag AM, Buffington SA, Engevik MA. Unraveling the Metabolic Requirements of the Gut Commensal Bacteroides ovatus. Front Microbiol 2021; 12:745469. [PMID: 34899632 PMCID: PMC8656163 DOI: 10.3389/fmicb.2021.745469] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/29/2021] [Indexed: 01/16/2023] Open
Abstract
Background: Bacteroidetes are the most common bacterial phylum in the mammalian intestine and the effects of several Bacteroides spp. on multiple facets of host physiology have been previously described. Of the Bacteroides spp., Bacteroides ovatus has recently garnered attention due to its beneficial effects in the context of intestinal inflammation. In this study, we aimed to examine model host intestinal physiological conditions and dietary modifications to characterize their effects on B. ovatus growth. Methods and Results: Using Biolog phenotypic microarrays, we evaluated 62 primary carbon sources and determined that B. ovatus ATCC 8384 can use the following carbohydrates as primary carbon sources: 10 disaccharides, 4 trisaccharides, 4 polysaccharides, 4 polymers, 3 L-linked sugars, 6 D-linked sugars, 5 amino-sugars, 6 alcohol sugars, and 15 organic acids. Proteomic profiling of B. ovatus bacteria revealed that a significant portion of the B. ovatus proteome contains proteins important for metabolism. Among the proteins, we found glycosyl hydrolase (GH) familes GH2, GH5, GH20, GH 43, GH88, GH92, and GH95. We also identified multiple proteins with antioxidant properties and reasoned that these proteins may support B. ovatus growth in the GI tract. Upon further testing, we showed that B. ovatus grew robustly in various pH, osmolarity, bile, ethanol, and H2O2 concentrations; indicating that B. ovatus is a well-adapted gut microbe. Conclusion: Taken together, we have demonstrated that key host and diet-derived changes in the intestinal environment influence B. ovatus growth. These data provide the framework for future work toward understanding how diet and lifestyle interventions may promote a beneficial environment for B. ovatus growth.
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Affiliation(s)
- Robert Fultz
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, TX, United States
| | - Taylor Ticer
- Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina, Charleston, SC, United States
| | - Faith D. Ihekweazu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
- Section of Gastroenterology, Hepatology, and Nutrition, Texas Children’s Hospital, Houston, TX, United States
| | - Thomas D. Horvath
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
| | - Sigmund J. Haidacher
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
| | - Kathleen M. Hoch
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
| | - Meghna Bajaj
- Department of Chemistry and Physics and Department of Biotechnology, Alcorn State University, Lorman, MS, United States
| | - Jennifer K. Spinler
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
| | - Anthony M. Haag
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
| | - Shelly A. Buffington
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, TX, United States
| | - Melinda A. Engevik
- Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina, Charleston, SC, United States
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16
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Golisch B, Lei Z, Tamura K, Brumer H. Configured for the Human Gut Microbiota: Molecular Mechanisms of Dietary β-Glucan Utilization. ACS Chem Biol 2021; 16:2087-2102. [PMID: 34709792 DOI: 10.1021/acschembio.1c00563] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The β-glucans are a disparate group of structurally diverse polysaccharides, whose members are widespread in human diets as components of the cell walls of plants, algae, and fungi (including yeasts), and as bacterial exopolysaccharides. Individual β-glucans from these sources have long been associated with positive effects on human health through metabolic and immunological effects. Remarkably, the β-configured glucosidic linkages that define these polysaccharides render them inaccessible to the limited repertoire of digestive enzymes encoded by the human genome. As a result, the various β-glucans become fodder for the human gut microbiota (HGM) in the lower gastrointestinal tract, where they influence community composition and metabolic output, including fermentation to short chain fatty acids (SCFAs). Only recently, however, have the specific molecular systems that enable the utilization of β-glucans by select members of the HGM been fully elucidated by combined genetic, biochemical, and structural biological approaches. In the context of β-glucan structures and their effects on human nutrition and health, we summarize here the functional characterization of individual polysaccharide utilization loci (PULs) responsible for the saccharification of mixed-linkage β(1→3)/β(1→4)-glucans, β(1→6)-glucans, β(1→3)-glucans, β(1→2)-glucans, and xyloglucans in symbiotic human gut bacteria. These exemplar PULs serve as well-defined biomarkers for the prediction of β-glucan metabolic capability in individual bacterial taxa and across the global human population.
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17
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Li M, Li S, Guo X, Guo C, Wang Y, Du Z, Zhang Z, Xie C, Ding K. Discrete genetic loci in human gut Bacteroides thetaiotaomicron confer pectin metabolism. Carbohydr Polym 2021; 272:118534. [PMID: 34420703 DOI: 10.1016/j.carbpol.2021.118534] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/26/2021] [Accepted: 08/02/2021] [Indexed: 02/09/2023]
Abstract
Although the polysaccharide utilization loci (PULs) activated by pectin have been defined, due to the complex of side-chain structure, the degradative mechanisms still remain vague. Thus, we hypothesize that there may have other specific PULs to target pectin. Here, we characterize loci-encoded proteins expressed by Bacteroides thetaiotaomicron (BT) that are involved in the pectin capturing, importation, de-branching and degradation into monosaccharides. Totally, four PULs contain ten enzymes and four glycan binding proteins which including a novel surface enzyme and a surface glycan binding protein are identified. Notably, PUL2 and PUL3 have not been reported so far. Further, we show that the degradation products support the growth of other Bacteroides spp. and probiotics. In addition, genes involved in this process are conservative in other Bacteroides spp. Our results further highlight the contribution of Bacteroides spp. to metabolism the pectic network.
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Affiliation(s)
- Meixia Li
- Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China
| | - Saijuan Li
- Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China
| | - Xiaozhen Guo
- Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China
| | - Ciliang Guo
- Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China
| | - Yeqin Wang
- Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China
| | - Zhenyun Du
- Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China
| | - Zhenqing Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Cen Xie
- Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China; University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, PR China.
| | - Kan Ding
- Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China; University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, PR China.
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18
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McKee LS, La Rosa SL, Westereng B, Eijsink VG, Pope PB, Larsbrink J. Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:559-581. [PMID: 34036727 DOI: 10.1111/1758-2229.12980] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
The Bacteroidetes phylum is renowned for its ability to degrade a wide range of complex carbohydrates, a trait that has enabled its dominance in many diverse environments. The best studied species inhabit the human gut microbiome and use polysaccharide utilization loci (PULs), discrete genetic structures that encode proteins involved in the sensing, binding, deconstruction, and import of target glycans. In many environmental species, polysaccharide degradation is tightly coupled to the phylum-exclusive type IX secretion system (T9SS), which is used for the secretion of certain enzymes and is linked to gliding motility. In addition, within specific species these two adaptive systems (PULs and T9SS) are intertwined, with PUL-encoded enzymes being secreted by the T9SS. Here, we discuss the most noteworthy PUL and non-PUL mechanisms that confer specific and rapid polysaccharide degradation capabilities to the Bacteroidetes in a range of environments. We also acknowledge that the literature showcasing examples of PULs is rapidly expanding and developing a set of assumptions that can be hard to track back to original findings. Therefore, we present a simple universal description of conserved PUL functions and how they are determined, while proposing a common nomenclature describing PULs and their components, to simplify discussion and understanding of PUL systems.
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Affiliation(s)
- Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, 106 91, Sweden
- Wallenberg Wood Science Center, Stockholm, 100 44, Sweden
| | | | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Stockholm, 100 44, Sweden
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, 412 96, Sweden
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19
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Krska D, Mazurkewich S, Brown HA, Theibich Y, Poulsen JCN, Morris AL, Koropatkin NM, Lo Leggio L, Larsbrink J. Structural and Functional Analysis of a Multimodular Hyperthermostable Xylanase-Glucuronoyl Esterase from Caldicellulosiruptor kristjansonii. Biochemistry 2021; 60:2206-2220. [PMID: 34180241 PMCID: PMC8280721 DOI: 10.1021/acs.biochem.1c00305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The hyperthermophilic bacterium Caldicellulosiruptor kristjansonii encodes an unusual enzyme, CkXyn10C-GE15A, which
incorporates two catalytic domains, a xylanase and a glucuronoyl esterase,
and five carbohydrate-binding modules (CBMs) from families 9 and 22.
The xylanase and glucuronoyl esterase catalytic domains were recently
biochemically characterized, as was the ability of the individual
CBMs to bind insoluble polysaccharides. Here, we further probed the
abilities of the different CBMs from CkXyn10C-GE15A
to bind to soluble poly- and oligosaccharides using affinity gel electrophoresis,
isothermal titration calorimetry, and differential scanning fluorimetry.
The results revealed additional binding properties of the proteins
compared to the former studies on insoluble polysaccharides. Collectively,
the results show that all five CBMs have their own distinct binding
preferences and appear to complement each other and the catalytic
domains in targeting complex cell wall polysaccharides. Additionally,
through renewed efforts, we have achieved partial structural characterization
of this complex multidomain protein. We have determined the structures
of the third CBM9 domain (CBM9.3) and the glucuronoyl esterase (GE15A)
by X-ray crystallography. CBM9.3 is the second CBM9 structure determined
to date and was shown to bind oligosaccharide ligands at the same
site but in a different binding mode compared to that of the previously
determined CBM9 structure from Thermotoga maritima. GE15A represents a unique intermediate between reported fungal
and bacterial glucuronoyl esterase structures as it lacks two inserted
loop regions typical of bacterial enzymes and a third loop has an
atypical structure. We also report small-angle X-ray scattering measurements
of the N-terminal CBM22.1–CBM22.2–Xyn10C construct,
indicating a compact arrangement at room temperature.
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Affiliation(s)
- Daniel Krska
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Scott Mazurkewich
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Yusuf Theibich
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | | | - Adeline L Morris
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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20
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Cockburn DW, Kibler R, Brown HA, Duvall R, Moraïs S, Bayer E, Koropatkin NM. Structure and substrate recognition by the Ruminococcus bromii amylosome pullulanases. J Struct Biol 2021; 213:107765. [PMID: 34186214 DOI: 10.1016/j.jsb.2021.107765] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/11/2021] [Accepted: 06/23/2021] [Indexed: 01/15/2023]
Abstract
Pullulanases are glycoside hydrolase family 13 (GH13) enzymes that target α1,6 glucosidic linkages within starch and aid in the degradation of the α1,4- and α1,6- linked glucans pullulan, glycogen and amylopectin. The human gut bacterium Ruminococcus bromii synthesizes two extracellular pullulanases, Amy10 and Amy12, that are incorporated into the multiprotein amylosome complex that enables the digestion of granular resistant starch from the diet. Here we provide a comparative biochemical analysis of these pullulanases and the x-ray crystal structures of the wild type and the nucleophile mutant D392A of Amy12 complexed with maltoheptaose and 63-α-D glucosyl-maltotriose. While Amy10 displays higher catalytic efficiency on pullulan and cleaves only α1,6 linkages, Amy12 has some activity on α1,4 linkages suggesting that these enzymes are not redundant within the amylosome. Our structures of Amy12 include a mucin-binding protein (MucBP) domain that follows the C-domain of the GH13 fold, an atypical feature of these enzymes. The wild type Amy12 structure with maltoheptaose captured two oligosaccharides in the active site arranged as expected following catalysis of an α1,6 branch point in amylopectin. The nucleophile mutant D392A complexed with maltoheptaose or 63-α-D glucosyl-maltotriose captured β-glucose at the reducing end in the -1 subsite, facilitated by the truncation of the active site aspartate and stabilized by stacking with Y279. The core interface between the co-crystallized ligands and Amy12 occurs within the -2 through + 1 subsites, which may allow for flexible recognition of α1,6 linkages within a variety of starch structures.
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Affiliation(s)
- Darrell W Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Ryan Kibler
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Rebecca Duvall
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Sarah Moraïs
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Edward Bayer
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
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21
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PUL-Mediated Plant Cell Wall Polysaccharide Utilization in the Gut Bacteroidetes. Int J Mol Sci 2021; 22:ijms22063077. [PMID: 33802923 PMCID: PMC8002723 DOI: 10.3390/ijms22063077] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/07/2021] [Accepted: 03/11/2021] [Indexed: 01/16/2023] Open
Abstract
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.
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22
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Kmezik C, Mazurkewich S, Meents T, McKee LS, Idström A, Armeni M, Savolainen O, Brändén G, Larsbrink J. A polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases. J Biol Chem 2021; 296:100500. [PMID: 33667545 PMCID: PMC8040265 DOI: 10.1016/j.jbc.2021.100500] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/27/2021] [Accepted: 03/01/2021] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota plays a central role in human health by enzymatically degrading dietary fiber and concomitantly excreting short chain fatty acids that are associated with manifold health benefits. The polysaccharide xylan is abundant in dietary fiber but noncarbohydrate decorations hinder efficient cleavage by glycoside hydrolases (GHs) and need to be addressed by carbohydrate esterases (CEs). Enzymes from carbohydrate esterase families 1 and 6 (CE1 and 6) perform key roles in xylan degradation by removing feruloyl and acetate decorations, yet little is known about these enzyme families especially with regard to their diversity in activity. Bacteroidetes bacteria are dominant members of the microbiota and often encode their carbohydrate-active enzymes in multigene polysaccharide utilization loci (PULs). Here we present the characterization of three CEs found in a PUL encoded by the gut Bacteroidete Dysgonomonas mossii. We demonstrate that the CEs are functionally distinct, with one highly efficient CE6 acetyl esterase and two CE1 enzymes with feruloyl esterase activities. One multidomain CE1 enzyme contains two CE1 domains: an N-terminal domain feruloyl esterase, and a C-terminal domain with minimal activity on model substrates. We present the structure of the C-terminal CE1 domain with the carbohydrate-binding module that bridges the two CE1 domains, as well as a complex of the same protein fragment with methyl ferulate. The investment of D. mossii in producing multiple CEs suggests that improved accessibility of xylan for GHs and cleavage of covalent polysaccharide-polysaccharide and lignin-polysaccharide bonds are important enzyme activities in the gut environment.
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Affiliation(s)
- Cathleen Kmezik
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Scott Mazurkewich
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tomke Meents
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lauren Sara McKee
- Division of Glycoscience, Department of Chemistry, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden; Wallenberg Wood Science Center, Stockholm, Sweden
| | - Alexander Idström
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Marina Armeni
- Chalmers Mass Spectrometry Infrastructure, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Otto Savolainen
- Chalmers Mass Spectrometry Infrastructure, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Wallenberg Wood Science Center, Stockholm, Sweden.
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23
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Baker JT, Duarte ME, Holanda DM, Kim SW. Friend or Foe? Impacts of Dietary Xylans, Xylooligosaccharides, and Xylanases on Intestinal Health and Growth Performance of Monogastric Animals. Animals (Basel) 2021; 11:609. [PMID: 33652614 PMCID: PMC7996850 DOI: 10.3390/ani11030609] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/11/2021] [Accepted: 02/24/2021] [Indexed: 12/27/2022] Open
Abstract
This paper discusses the structural difference and role of xylan, procedures involved in the production of xylooligosaccharides (XOS), and their implementation into animal feeds. Xylan is non-starch polysaccharides that share a β-(1-4)-linked xylopyranose backbone as a common feature. Due to the myriad of residues that can be substituted on the polymers within the xylan family, more anti-nutritional factors are associated with certain types of xylan than others. XOS are sugar oligomers extracted from xylan-containing lignocellulosic materials, such as crop residues, wood, and herbaceous biomass, that possess prebiotic effects. XOS can also be produced in the intestine of monogastric animals to some extent when exogenous enzymes, such as xylanase, are added to the feed. Xylanase supplementation is a common practice within both swine and poultry production to reduce intestinal viscosity and improve digestive utilization of nutrients. The efficacy of xylanase supplementation varies widely due a number of factors, one of which being the presence of xylanase inhibitors present in common feedstuffs. The use of prebiotics in animal feeding is gaining popularity as producers look to accelerate growth rate, enhance intestinal health, and improve other production parameters in an attempt to provide a safe and sustainable food product. Available research on the impact of xylan, XOS, as well as xylanase on the growth and health of swine and poultry, is also summarized. The response to xylanase supplementation in swine and poultry feeds is highly variable and whether the benefits are a result of nutrient release from NSP, reduction in digesta viscosity, production of short chain xylooligosaccharides or a combination of these is still in question. XOS supplementation seems to benefit both swine and poultry at various stages of production, as well as varying levels of XOS purity and degree of polymerization; however, further research is needed to elucidate the ideal dosage, purity, and degree of polymerization needed to confer benefits on intestinal health and performance in each respective species.
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Affiliation(s)
| | | | | | - Sung Woo Kim
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, USA; (J.T.B.); (M.E.D.); (D.M.H.)
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24
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New Family of Carbohydrate-Binding Modules Defined by a Galactosyl-Binding Protein Module from a Cellvibrio japonicus Endo-Xyloglucanase. Appl Environ Microbiol 2021; 87:e0263420. [PMID: 33355108 DOI: 10.1128/aem.02634-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Carbohydrate-binding modules (CBMs) are usually appended to carbohydrate-active enzymes (CAZymes) and serve to potentiate catalytic activity, for example, by increasing substrate affinity. The Gram-negative soil saprophyte Cellvibrio japonicus is a valuable source for CAZyme and CBM discovery and characterization due to its innate ability to degrade a wide array of plant polysaccharides. Bioinformatic analysis of the CJA_2959 gene product from C. japonicus revealed a modular architecture consisting of a fibronectin type III (Fn3) module, a cryptic module of unknown function (X181), and a glycoside hydrolase family 5 subfamily 4 (GH5_4) catalytic module. We previously demonstrated that the last of these, CjGH5F, is an efficient and specific endo-xyloglucanase (M. A. Attia, C. E. Nelson, W. A. Offen, N. Jain, et al., Biotechnol Biofuels 11:45, 2018, https://doi.org/10.1186/s13068-018-1039-6). In the present study, C-terminal fusion of superfolder green fluorescent protein in tandem with the Fn3-X181 modules enabled recombinant production and purification from Escherichia coli. Native affinity gel electrophoresis revealed binding specificity for the terminal galactose-containing plant polysaccharides galactoxyloglucan and galactomannan. Isothermal titration calorimetry further evidenced a preference for galactoxyloglucan polysaccharide over short oligosaccharides comprising the limit-digest products of CjGH5F. Thus, our results identify the X181 module as the defining member of a new CBM family, CBM88. In addition to directly revealing the function of this CBM in the context of xyloglucan metabolism by C. japonicus, this study will guide future bioinformatic and functional analyses across microbial (meta)genomes. IMPORTANCE This study reveals carbohydrate-binding module family 88 (CBM88) as a new family of galactose-binding protein modules, which are found in series with diverse microbial glycoside hydrolases, polysaccharide lyases, and carbohydrate esterases. The definition of CBM88 in the carbohydrate-active enzymes classification (http://www.cazy.org/CBM88.html) will significantly enable future microbial (meta)genome analysis and functional studies.
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25
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Pollet RM, Martin LM, Koropatkin NM. TonB-dependent transporters in the Bacteroidetes: Unique domain structures and potential functions. Mol Microbiol 2021; 115:490-501. [PMID: 33448497 DOI: 10.1111/mmi.14683] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/26/2022]
Abstract
The human gut microbiota endows the host with a wealth of metabolic functions central to health, one of which is the degradation and fermentation of complex carbohydrates. The Bacteroidetes are one of the dominant bacterial phyla of this community and possess an expanded capacity for glycan utilization. This is mediated via the coordinated expression of discrete polysaccharide utilization loci (PUL) that invariantly encode a TonB-dependent transporter (SusC) that works with a glycan-capturing lipoprotein (SusD). More broadly within Gram-negative bacteria, TonB-dependent transporters (TBDTs) are deployed for the uptake of not only sugars, but also more often for essential nutrients such as iron and vitamins. Here, we provide a comprehensive look at the repertoire of TBDTs found in the model gut symbiont Bacteroides thetaiotaomicron and the range of predicted functional domains associated with these transporters and SusD proteins for the uptake of both glycans and other nutrients. This atlas of the B. thetaiotaomicron TBDTs reveals that there are at least three distinct subtypes of these transporters encoded within its genome that are presumably regulated in different ways to tune nutrient uptake.
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Affiliation(s)
| | - Lauryn M Martin
- Department of Biology, Alcorn State University, Alcorn, MS, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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26
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Cha QQ, Wang XJ, Ren XB, Li D, Wang P, Li PY, Fu HH, Zhang XY, Chen XL, Zhang YZ, Xu F, Qin QL. Comparison of Alginate Utilization Pathways in Culturable Bacteria Isolated From Arctic and Antarctic Marine Environments. Front Microbiol 2021; 12:609393. [PMID: 33584613 PMCID: PMC7874173 DOI: 10.3389/fmicb.2021.609393] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
Alginate, mainly derived from brown algae, is an important carbon source that can support the growth of marine microorganisms in the Arctic and Antarctic regions. However, there is a lack of systematic investigation and comparison of alginate utilization pathways in culturable bacteria from both polar regions. In this study, 88 strains were isolated from the Arctic and Antarctic regions, of which 60 strains could grow in the medium with alginate as the sole carbon source. These alginate-utilizing strains belong to 9 genera of the phyla Proteobacteria and Bacteroidetes. The genomes of 26 alginate-utilizing strains were sequenced and genomic analyses showed that they all contain the gene clusters related to alginate utilization. The alginate transport systems of Proteobacteria differ from those of Bacteroidetes and there may be unique transport systems among different genera of Proteobacteria. The biogeographic distribution pattern of alginate utilization genes was further investigated. The alginate utilization genes are found to cluster according to bacterial taxonomy rather than geographic location, indicating that the alginate utilization genes do not evolve independently in both polar regions. This study systematically illustrates the alginate utilization pathways in culturable bacteria from the Arctic and Antarctic regions, shedding light into the distribution and evolution of alginate utilization pathways in polar bacteria.
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Affiliation(s)
- Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Juan Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xue-Bing Ren
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Dong Li
- Department of Molecular Biology, Qingdao Vland Biotech Group Inc., Qingdao, China
| | - Peng Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hui-Hui Fu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Fei Xu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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27
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Gray DA, White JBR, Oluwole AO, Rath P, Glenwright AJ, Mazur A, Zahn M, Baslé A, Morland C, Evans SL, Cartmell A, Robinson CV, Hiller S, Ranson NA, Bolam DN, van den Berg B. Insights into SusCD-mediated glycan import by a prominent gut symbiont. Nat Commun 2021; 12:44. [PMID: 33398001 PMCID: PMC7782687 DOI: 10.1038/s41467-020-20285-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/19/2020] [Indexed: 01/29/2023] Open
Abstract
In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a "pedal bin" transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the β2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to ~2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism.
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Affiliation(s)
- Declan A Gray
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Joshua B R White
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Abraham O Oluwole
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK
| | | | - Amy J Glenwright
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Adam Mazur
- Biozentrum, University of Basel, Basel, Switzerland
| | - Michael Zahn
- Biozentrum, University of Basel, Basel, Switzerland
| | - Arnaud Baslé
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Carl Morland
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Sasha L Evans
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Alan Cartmell
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK
| | | | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David N Bolam
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Bert van den Berg
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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Tamura K, Dejean G, Van Petegem F, Brumer H. Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota. J Biol Chem 2021; 296:100415. [PMID: 33587952 PMCID: PMC7974029 DOI: 10.1016/j.jbc.2021.100415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 12/12/2022] Open
Abstract
Complex glycans that evade our digestive system are major nutrients that feed the human gut microbiota (HGM). The prevalence of Bacteroidetes in the HGM of populations worldwide is engendered by the evolution of polysaccharide utilization loci (PULs), which encode concerted protein systems to utilize the myriad complex glycans in our diets. Despite their crucial roles in glycan recognition and transport, cell-surface glycan-binding proteins (SGBPs) remained understudied cogs in the PUL machinery. Here, we report the structural and biochemical characterization of a suite of SGBP-A and SGBP-B structures from three syntenic β(1,3)-glucan utilization loci (1,3GULs) from Bacteroides thetaiotaomicron (Bt), Bacteroides uniformis (Bu), and B. fluxus (Bf), which have varying specificities for distinct β-glucans. Ligand complexes provide definitive insight into β(1,3)-glucan selectivity in the HGM, including structural features enabling dual β(1,3)-glucan/mixed-linkage β(1,3)/β(1,4)-glucan-binding capability in some orthologs. The tertiary structural conservation of SusD-like SGBPs-A is juxtaposed with the diverse architectures and binding modes of the SGBPs-B. Specifically, the structures of the trimodular BtSGBP-B and BuSGBP-B revealed a tandem repeat of carbohydrate-binding module-like domains connected by long linkers. In contrast, BfSGBP-B comprises a bimodular architecture with a distinct β-barrel domain at the C terminus that bears a shallow binding canyon. The molecular insights obtained here contribute to our fundamental understanding of HGM function, which in turn may inform tailored microbial intervention therapies.
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Affiliation(s)
- Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, The Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guillaume Dejean
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, The Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, The Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
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Tamura K, Brumer H. Glycan utilization systems in the human gut microbiota: a gold mine for structural discoveries. Curr Opin Struct Biol 2020; 68:26-40. [PMID: 33285501 DOI: 10.1016/j.sbi.2020.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/20/2020] [Accepted: 11/01/2020] [Indexed: 12/17/2022]
Abstract
The complex glycans comprising 'dietary fiber' evade the limited repertoire of human digestive enzymes and hence feed the vast community of microbes in the lower gastrointestinal tract. As such, complex glycans drive the composition of the human gut microbiota and, in turn, influence diverse facets of our nutrition and health. To access these otherwise recalcitrant carbohydrates, gut bacteria produce coordinated, substrate-specific arsenals of carbohydrate-active enzymes, glycan-binding proteins, oligosaccharide transporters, and transcriptional regulators. A recent explosion of biochemical and enzymological studies of these systems has led to the discovery of manifold new carbohydrate-active enzyme (CAZyme) families. Crucially underpinned by structural biology, these studies have also provided unprecedented molecular insight into the exquisite specificity of glycan recognition in the diverse CAZymes and non-catalytic proteins from the HGM. The revelation of a multitude of new three-dimensional structures and substrate complexes constitutes a 'gold rush' in the structural biology of the human gut microbiota.
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Affiliation(s)
- Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada; Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
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30
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Briggs JA, Grondin JM, Brumer H. Communal living: glycan utilization by the human gut microbiota. Environ Microbiol 2020; 23:15-35. [PMID: 33185970 DOI: 10.1111/1462-2920.15317] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022]
Abstract
Our lower gastrointestinal tract plays host to a vast consortium of microbes, known as the human gut microbiota (HGM). The HGM thrives on a complex and diverse range of glycan structures from both dietary and host sources, the breakdown of which requires the concerted action of cohorts of carbohydrate-active enzymes (CAZymes), carbohydrate-binding proteins, and transporters. The glycan utilization profile of individual taxa, whether 'specialist' or 'generalist', is dictated by the number and functional diversity of these glycan utilization systems. Furthermore, taxa in the HGM may either compete or cooperate in glycan deconstruction, thereby creating a complex ecological web spanning diverse nutrient niches. As a result, our diet plays a central role in shaping the composition of the HGM. This review presents an overview of our current understanding of glycan utilization by the HGM on three levels: (i) molecular mechanisms of individual glycan deconstruction and uptake by key bacteria, (ii) glycan-mediated microbial interactions, and (iii) community-scale effects of dietary changes. Despite significant recent advancements, there remains much to be discovered regarding complex glycan metabolism in the HGM and its potential to affect positive health outcomes.
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Affiliation(s)
- Jonathon A Briggs
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Julie M Grondin
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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31
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Glowacki RWP, Martens EC. If you eat it, or secrete it, they will grow: the expanding list of nutrients utilized by human gut bacteria. J Bacteriol 2020; 203:JB.00481-20. [PMID: 33168637 PMCID: PMC8092160 DOI: 10.1128/jb.00481-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In order to persist, successful bacterial inhabitants of the human gut need to adapt to changing nutrient conditions, which are influenced by host diet and a variety of other factors. For members of the Bacteroidetes and several other phyla, this has resulted in diversification of a variety of enzyme-based systems that equip them to sense and utilize carbohydrate-based nutrients from host, diet, and bacterial origin. In this review, we focus first on human gut Bacteroides and describe recent findings regarding polysaccharide utilization loci (PULs) and the mechanisms of the multi-protein systems they encode, including their regulation and the expanding diversity of substrates that they target. Next, we highlight previously understudied substrates such as monosaccharides, nucleosides, and Maillard reaction products that can also affect the gut microbiota by feeding symbionts that possess specific systems for their metabolism. Since some pathogens preferentially utilize these nutrients, they may represent nutrient niches competed for by commensals and pathogens. Finally, we address recent work to describe nutrient acquisition mechanisms in other important gut species such as those belonging to the Gram-positive anaerobic phyla Actinobacteria and Firmicutes, as well as the Proteobacteria Because gut bacteria contribute to many aspects of health and disease, we showcase advances in the field of synthetic biology, which seeks to engineer novel, diet-controlled nutrient utilization pathways within gut symbionts to create rationally designed live therapeutics.
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Affiliation(s)
- Robert W. P. Glowacki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Nostoc sphaeroids Kütz polysaccharide and powder enrich a core bacterial community on C57BL/6j mice. Int J Biol Macromol 2020; 162:1734-1742. [PMID: 32781117 DOI: 10.1016/j.ijbiomac.2020.08.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/23/2020] [Accepted: 08/04/2020] [Indexed: 11/22/2022]
Abstract
Gut microbiota is the collection of microbes that lives in the host. Glycan is the major factor to shape the composition of microbial community. Nostoc sphaeroids Kütz (NSK) has been used as food and medicine for thousands of years in Asian countries while the bioactivity on gut microbiota is unclear till now. Here, we used NSK polysaccharide and NSK powder to investigate the bioactivity on the gut microbiota of C57BL/6j mice, respectively. By 16S ribosomal RNA gene sequencing, we found the composition of gut microbiota had been changed and differed from each other. However, the abundance of Bacteroides, Parabacteroides, Escherichia-Shigella and Parasutterella on genus level were significantly increased by NSK polysaccharide and NSK powder. In addition, Akkermansia and Rikenellaceae were enriched by NSK powder. Moreover, we found the IL-1β and IL-6 decreased significantly while TNF-α and IL-10 increased significantly especially in NSK powder group. Intriguingly, the increased microbes were significantly positively co-related with TNF-α and IL-10 while negatively co-related with IL-1β and IL-6 by co-relation and network analysis. The above results suggested that Nostoc sphaeroids Kütz may selectively enrich a "core bacterial community" and add new evidence to discover how Nostoc sphaeroids Kütz has biological function.
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Isolation and structure characterization of a polysaccharide from Crataegus pinnatifida and its bioactivity on gut microbiota. Int J Biol Macromol 2020; 154:82-91. [DOI: 10.1016/j.ijbiomac.2020.03.058] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022]
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34
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Déjean G, Tamura K, Cabrera A, Jain N, Pudlo NA, Pereira G, Viborg AH, Van Petegem F, Martens EC, Brumer H. Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides. mBio 2020; 11:e00095-20. [PMID: 32265336 PMCID: PMC7157763 DOI: 10.1128/mbio.00095-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/09/2020] [Indexed: 01/06/2023] Open
Abstract
The human gut microbiota (HGM) has far-reaching impacts on human health and nutrition, which are fueled primarily by the metabolism of otherwise indigestible complex carbohydrates commonly known as dietary fiber. However, the molecular basis of the ability of individual taxa of the HGM to address specific dietary glycan structures remains largely unclear. In particular, the utilization of β(1,3)-glucans, which are widespread in the human diet as yeast, seaweed, and plant cell walls, had not previously been resolved. Through a systems-based approach, here we show that the symbiont Bacteroides uniformis deploys a single, exemplar polysaccharide utilization locus (PUL) to access yeast β(1,3)-glucan, brown seaweed β(1,3)-glucan (laminarin), and cereal mixed-linkage β(1,3)/β(1,4)-glucan. Combined biochemical, enzymatic, and structural analysis of PUL-encoded glycoside hydrolases (GHs) and surface glycan-binding proteins (SGBPs) illuminates a concerted molecular system by which B. uniformis recognizes and saccharifies these distinct β-glucans. Strikingly, the functional characterization of homologous β(1,3)-glucan utilization loci (1,3GUL) in other Bacteroides further demonstrated that the ability of individual taxa to utilize β(1,3)-glucan variants and/or β(1,3)/β(1,4)-glucans arises combinatorially from the individual specificities of SGBPs and GHs at the cell surface, which feed corresponding signals to periplasmic hybrid two-component sensors (HTCSs) via TonB-dependent transporters (TBDTs). These data reveal the importance of cooperativity in the adaptive evolution of GH and SGBP cohorts to address individual polysaccharide structures. We anticipate that this fine-grained knowledge of PUL function will inform metabolic network analysis and proactive manipulation of the HGM. Indeed, a survey of 2,441 public human metagenomes revealed the international, yet individual-specific, distribution of each 1,3GUL.IMPORTANCEBacteroidetes are a dominant phylum of the human gut microbiota (HGM) that target otherwise indigestible dietary fiber with an arsenal of polysaccharide utilization loci (PULs), each of which is dedicated to the utilization of a specific complex carbohydrate. Here, we provide novel insight into this paradigm through functional characterization of homologous PULs from three autochthonous Bacteroides species, which target the family of dietary β(1,3)-glucans. Through detailed biochemical and protein structural analysis, we observed an unexpected diversity in the substrate specificity of PUL glycosidases and glycan-binding proteins with regard to β(1,3)-glucan linkage and branching patterns. In combination, these individual enzyme and protein specificities support taxon-specific growth on individual β(1,3)-glucans. This detailed metabolic insight, together with a comprehensive survey of individual 1,3GULs across human populations, further expands the fundamental roadmap of the HGM, with potential application to the future development of microbial intervention therapies.
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Affiliation(s)
- Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adriana Cabrera
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Namrata Jain
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Gabriel Pereira
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alexander Holm Viborg
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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35
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Possible beneficial effects of xyloglucan from its degradation by gut microbiota. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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36
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Cerqueira FM, Photenhauer AL, Pollet RM, Brown HA, Koropatkin NM. Starch Digestion by Gut Bacteria: Crowdsourcing for Carbs. Trends Microbiol 2020; 28:95-108. [DOI: 10.1016/j.tim.2019.09.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/29/2019] [Accepted: 09/09/2019] [Indexed: 12/12/2022]
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Abstract
Prebiotics are increasingly used as food supplements, especially in infant formulas, to modify the functioning and composition of the microbiota. However, little is currently known about the mechanisms of prebiotic recognition and transport by gut bacteria, while these steps are crucial in their metabolism. In this study, we established a new strategy to profile the specificity of oligosaccharide transporters, combining microbiomics, genetic locus and strain engineering, and state-of-the art metabolomics. We revisited the transporter classification database and proposed a new way to classify these membrane proteins based on their structural and mechanistic similarities. Based on these developments, we identified and characterized, at the molecular level, a fructooligosaccharide transporting phosphotransferase system, which constitutes a biomarker of diet and gut pathology. The deciphering of this prebiotic metabolization mechanism by a nonbeneficial bacterium highlights the controversial use of prebiotics, especially in the context of chronic gut diseases. Prebiotic oligosaccharides, such as fructooligosaccharides, are increasingly being used to modulate the composition and activity of the gut microbiota. However, carbohydrate utilization analyses and metagenomic studies recently revealed the ability of deleterious and uncultured human gut bacterial species to metabolize these functional foods. Moreover, because of the difficulties of functionally profiling transmembrane proteins, only a few prebiotic transporters have been biochemically characterized to date, while carbohydrate binding and transport are the first and thus crucial steps in their metabolization. Here, we describe the molecular mechanism of a phosphotransferase system, highlighted as a dietary and pathology biomarker in the human gut microbiome. This transporter is encoded by a metagenomic locus that is highly conserved in several human gut Firmicutes, including Dorea species. We developed a generic strategy to deeply analyze, in vitro and in cellulo, the specificity and functionality of recombinant transporters in Escherichia coli, combining carbohydrate utilization locus and host genome engineering and quantification of the binding, transport, and growth rates with analysis of phosphorylated carbohydrates by mass spectrometry. We demonstrated that the Dorea fructooligosaccharide transporter is specific for kestose, whether for binding, transport, or phosphorylation. This constitutes the biochemical proof of effective phosphorylation of glycosides with a degree of polymerization of more than 2, extending the known functional diversity of phosphotransferase systems. Based on these new findings, we revisited the classification of these carbohydrate transporters. IMPORTANCE Prebiotics are increasingly used as food supplements, especially in infant formulas, to modify the functioning and composition of the microbiota. However, little is currently known about the mechanisms of prebiotic recognition and transport by gut bacteria, while these steps are crucial in their metabolism. In this study, we established a new strategy to profile the specificity of oligosaccharide transporters, combining microbiomics, genetic locus and strain engineering, and state-of-the art metabolomics. We revisited the transporter classification database and proposed a new way to classify these membrane proteins based on their structural and mechanistic similarities. Based on these developments, we identified and characterized, at the molecular level, a fructooligosaccharide transporting phosphotransferase system, which constitutes a biomarker of diet and gut pathology. The deciphering of this prebiotic metabolization mechanism by a nonbeneficial bacterium highlights the controversial use of prebiotics, especially in the context of chronic gut diseases.
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Larsbrink J, McKee LS. Bacteroidetes bacteria in the soil: Glycan acquisition, enzyme secretion, and gliding motility. ADVANCES IN APPLIED MICROBIOLOGY 2020; 110:63-98. [PMID: 32386606 DOI: 10.1016/bs.aambs.2019.11.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The secretion of extracellular enzymes by soil microbes is rate-limiting in the recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant phylum, just like in human and animal intestines. The Bacteroidetes thrive because of their ability to secrete diverse arrays of carbohydrate-active enzymes (CAZymes) that target the highly varied glycans in the soil. Bacteroidetes use an energy-saving system of genomic organization, whereby most of their CAZymes are grouped into Polysaccharide Utilization Loci (PULs). These loci enable high level production of specific CAZymes only when their substrate glycans are abundant in the local environment. This gives the Bacteroidetes a clear advantage over other species in the competitive soil environment, further enhanced by the phylum-specific Type IX Secretion System (T9SS). The T9SS is highly effective at secreting CAZymes and/or tethering them to the cell surface, and is tightly coupled to the ability to rapidly glide over solid surfaces, a connection that promotes an active hunt for nutrition. Although the soil Bacteroidetes are less well studied than human gut symbionts, research is uncovering important biochemical and physiological phenomena. In this review, we summarize the state of the art on research into the CAZymes secreted by soil Bacteroidetes in the contexts of microbial soil ecology and the discovery of novel CAZymes for use in industrial biotechnology. We hope that this review will stimulate further investigations into the somewhat neglected enzymology of non-gut Bacteroidetes.
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Affiliation(s)
- Johan Larsbrink
- Wallenberg Wood Science Center, Gothenburg and Stockholm, Sweden; Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lauren Sara McKee
- Wallenberg Wood Science Center, Gothenburg and Stockholm, Sweden; Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.
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39
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Xyloglucan affects gut-liver circulating bile acid metabolism to improve liver damage in mice fed with high-fat diet. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103651] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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Liu L, Yang J, Yang Y, Luo L, Wang R, Zhang Y, Yuan H. Consolidated bioprocessing performance of bacterial consortium EMSD5 on hemicellulose for isopropanol production. BIORESOURCE TECHNOLOGY 2019; 292:121965. [PMID: 31415990 DOI: 10.1016/j.biortech.2019.121965] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/04/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Consolidated bioprocessing (CBP) of lignocellulose by bacterial consortium for isopropanol production is considered as the most promising strategy. However, low utilization of xylan caused by the complex sidechain structure remains inhibit the conversion of full-biomass. In this study, isopropanol production from different lignocelluloses by the consortium EMSD5 through CBP was performed. A total of 7.00 g/L of isopropanol was obtained from corncob by optimizing fermentation conditions. Isopropanol production by EMSD5 was mainly based on utilizing xylan in corncob and isopropanol titer was increased by 47.71% and reached up to 8.39 g/L using arabinoxylan compared with linear xylan. The analysis of community structures and the isolation of key strain confirmed the enrichment of the isopropanol producer, Clostridium beijierinckii, in the bacterial community when it was incubated with corn glucuronoarabinoxylan and the cooperation between C. beijerinckii and lignocellulose degraders. The unique features of EMSD5 could lead to large-scale isopropanol production using lignocellulose.
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Affiliation(s)
- Liang Liu
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yi Yang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lijin Luo
- Fujian Institute of Microbiology, Fuzhou 350007, China
| | - Ruonan Wang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yu Zhang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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41
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Tamura K, Foley MH, Gardill BR, Dejean G, Schnizlein M, Bahr CME, Louise Creagh A, van Petegem F, Koropatkin NM, Brumer H. Surface glycan-binding proteins are essential for cereal beta-glucan utilization by the human gut symbiont Bacteroides ovatus. Cell Mol Life Sci 2019; 76:4319-4340. [PMID: 31062073 PMCID: PMC6810844 DOI: 10.1007/s00018-019-03115-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/03/2019] [Accepted: 04/23/2019] [Indexed: 02/07/2023]
Abstract
The human gut microbiota, which underpins nutrition and systemic health, is compositionally sensitive to the availability of complex carbohydrates in the diet. The Bacteroidetes comprise a dominant phylum in the human gut microbiota whose members thrive on dietary and endogenous glycans by employing a diversity of highly specific, multi-gene polysaccharide utilization loci (PUL), which encode a variety of carbohydrases, transporters, and sensor/regulators. PULs invariably also encode surface glycan-binding proteins (SGBPs) that play a central role in saccharide capture at the outer membrane. Here, we present combined biophysical, structural, and in vivo characterization of the two SGBPs encoded by the Bacteroides ovatus mixed-linkage β-glucan utilization locus (MLGUL), thereby elucidating their key roles in the metabolism of this ubiquitous dietary cereal polysaccharide. In particular, molecular insight gained through several crystallographic complexes of SGBP-A and SGBP-B with oligosaccharides reveals that unique shape complementarity of binding platforms underpins specificity for the kinked MLG backbone vis-à-vis linear β-glucans. Reverse-genetic analysis revealed that both the presence and binding ability of the SusD homolog BoSGBPMLG-A are essential for growth on MLG, whereas the divergent, multi-domain BoSGBPMLG-B is dispensable but may assist in oligosaccharide scavenging from the environment. The synthesis of these data illuminates the critical role SGBPs play in concert with other MLGUL components, reveals new structure-function relationships among SGBPs, and provides fundamental knowledge to inform future (meta)genomic, biochemical, and microbiological analyses of the human gut microbiota.
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Affiliation(s)
- Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Matthew H Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Bernd R Gardill
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Guillaume Dejean
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Matthew Schnizlein
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Constance M E Bahr
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - A Louise Creagh
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Filip van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
- Department of Botany, University of British Columbia, 3200 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.
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42
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Déjean G, Tauzin AS, Bennett SW, Creagh AL, Brumer H. Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity. Appl Environ Microbiol 2019; 85:e01491-19. [PMID: 31420336 PMCID: PMC6805095 DOI: 10.1128/aem.01491-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/08/2019] [Indexed: 12/16/2022] Open
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 BacteroidesIMPORTANCE 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.
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Affiliation(s)
- Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexandra S Tauzin
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stuart W Bennett
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - A Louise Creagh
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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43
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Singh RP. Glycan utilisation system in Bacteroides and Bifidobacteria and their roles in gut stability and health. Appl Microbiol Biotechnol 2019; 103:7287-7315. [PMID: 31332487 DOI: 10.1007/s00253-019-10012-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 02/07/2023]
Abstract
Gut residential hundred trillion microbial cells are indispensable for maintaining gut homeostasis and impact on host physiology, development and immune systems. Many of them have displayed excellence in utilising dietary- and host-derived complex glycans and are producing useful postbiotics including short-chain fatty acids to primarily fuel different organs of the host. Therefore, employing individual microbiota is nowadays becoming a propitious target in biomedical for improving gut dysbiosis conditions of the host. Among other gut microbial communities, Bacteroides and Bifidobacteria are coevolved to utilise diverse ranges of diet- and host-derived glycans through harmonising distinct glycan utilisation systems. These gut symbionts frequently share digested oligosaccharides, carbohydrate-active enzymes and fermentable intermediate molecules for sustaining gut microbial symbiosis and improving fitness of own or other communities. Genomics approaches have provided unprecedented insights into these functions, but their precise mechanisms of action have poorly known. Sympathetic glycan-utilising strategy of each gut commensal will provide overview of mechanistic dynamic nature of the gut environment and will then assist in applying aptly personalised nutritional therapy. Thus, the review critically summarises cutting edge understanding of major plant- and host-derived glycan-utilising systems of Bacteroides and Bifidobacteria. Their evolutionary adaptation to gut environment and roles of postbiotics in human health are also highlighted.
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Affiliation(s)
- Ravindra Pal Singh
- Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), SAS, Nagar, Punjab, 140306, India.
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44
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Nguyen SN, Flores A, Talamantes D, Dar F, Valdez A, Schwans J, Berlemont R. GeneHunt for rapid domain-specific annotation of glycoside hydrolases. Sci Rep 2019; 9:10137. [PMID: 31300677 PMCID: PMC6626019 DOI: 10.1038/s41598-019-46290-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/26/2019] [Indexed: 12/20/2022] Open
Abstract
The identification of glycoside hydrolases (GHs) for efficient polysaccharide deconstruction is essential for the development of biofuels. Here, we investigate the potential of sequential HMM-profile identification for the rapid and precise identification of the multi-domain architecture of GHs from various datasets. First, as a validation, we successfully reannotated >98% of the biochemically characterized enzymes listed on the CAZy database. Next, we analyzed the 43 million non-redundant sequences from the M5nr data and identified 322,068 unique GHs. Finally, we searched 129 assembled metagenomes retrieved from MG-RAST for environmental GHs and identified 160,790 additional enzymes. Although most identified sequences corresponded to single domain enzymes, many contained several domains, including known accessory domains and some domains never identified in association with GH. Several sequences displayed multiple catalytic domains and few of these potential multi-activity proteins combined potentially synergistic domains. Finally, we produced and confirmed the biochemical activities of a GH5-GH10 cellulase-xylanase and a GH11-CE4 xylanase-esterase. Globally, this "gene to enzyme pipeline" provides a rationale for mining large datasets in order to identify new catalysts combining unique properties for the efficient deconstruction of polysaccharides.
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Affiliation(s)
- S N Nguyen
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - A Flores
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - D Talamantes
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - F Dar
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - A Valdez
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - J Schwans
- Department of Chemistry and Biochemistry, California State University Long Beach, Long Beach, California, USA
| | - R Berlemont
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA.
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45
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Foley MH, Déjean G, Hemsworth GR, Davies GJ, Brumer H, Koropatkin NM. A Cell-Surface GH9 Endo-Glucanase Coordinates with Surface Glycan-Binding Proteins to Mediate Xyloglucan Uptake in the Gut Symbiont Bacteroides ovatus. J Mol Biol 2019; 431:981-995. [PMID: 30668971 PMCID: PMC6478033 DOI: 10.1016/j.jmb.2019.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 01/04/2019] [Indexed: 01/07/2023]
Abstract
Dietary fiber is an important food source for members of the human gut microbiome. Members of the dominant Bacteroidetes phylum capture diverse polysaccharides via the action of multiple cell surface proteins encoded within polysaccharide utilization loci (PUL). The independent activities of PUL-encoded glycoside hydrolases (GHs) and surface glycan-binding proteins (SGBPs) for the harvest of various glycans have been studied in detail, but how these proteins work together to coordinate uptake is poorly understood. Here, we combine genetic and biochemical approaches to discern the interplay between the BoGH9 endoglucanase and the xyloglucan-binding proteins SGBP-A and SGBP-B from the Bacteroides ovatus xyloglucan utilization locus (XyGUL). The expression of BoGH9, a weakly active xyloglucanase in isolation, is required in a strain that expresses a non-binding version of SGBP-A (SGBP-A*). The crystal structure of the BoGH9 enzyme suggests the molecular basis for its robust activity on mixed-linkage β-glucan compared to xyloglucan. However, catalytically inactive site-directed mutants of BoGH9 fail to complement the deletion of the active BoGH9 in a SGBP-A* strain. We also find that SGBP-B is needed in an SGBP-A* background to support growth on xyloglucan, but that the non-binding SGBP-B* protein acts in a dominant negative manner to inhibit growth on xyloglucan. We postulate a model whereby the SGBP-A, SGBP-B, and BoGH9 work together at the cell surface, likely within a discrete complex, and that xyloglucan binding by SGBP-B and BoGH9 may facilitate the orientation of the xyloglucan for transfer across the outer membrane.
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Affiliation(s)
- Matthew H Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Glyn R Hemsworth
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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46
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Cheung SG, Goldenthal AR, Uhlemann AC, Mann JJ, Miller JM, Sublette ME. Systematic Review of Gut Microbiota and Major Depression. Front Psychiatry 2019; 10:34. [PMID: 30804820 PMCID: PMC6378305 DOI: 10.3389/fpsyt.2019.00034] [Citation(s) in RCA: 320] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/21/2019] [Indexed: 11/17/2022] Open
Abstract
Background: Recently discovered relationships between the gastrointestinal microbiome and the brain have implications for psychiatric disorders, including major depressive disorder (MDD). Bacterial transplantation from MDD patients to rodents produces depression-like behaviors. In humans, case-control studies have examined the gut microbiome in healthy and affected individuals. We systematically reviewed existing studies comparing gut microbial composition in MDD and healthy volunteers. Methods: A PubMed literature search combined the terms "depression," "depressive disorder," "stool," "fecal," "gut," and "microbiome" to identify human case-control studies that investigated relationships between MDD and microbiota quantified from stool. We evaluated the resulting studies, focusing on bacterial taxa that were different between MDD and healthy controls. Results: Six eligible studies were found in which 50 taxa exhibited differences (p < 0.05) between patients with MDD and controls. Patient characteristics and methodologies varied widely between studies. Five phyla-Bacteroidetes, Firmicutes, Actinobacteria, Fusobacteria, and Protobacteria-were represented; however, divergent results occurred across studies for all phyla. The largest number of differentiating taxa were within phylum Firmicutes, in which nine families and 12 genera differentiated the diagnostic groups. The majority of these families and genera were found to be statistically different between the two groups in two identified studies. Family Lachnospiraceae differentiated the diagnostic groups in four studies (with an even split in directionality). Across all five phyla, nine genera were higher in MDD (Anaerostipes, Blautia, Clostridium, Klebsiella, Lachnospiraceae incertae sedis, Parabacteroides, Parasutterella, Phascolarctobacterium, and Streptococcus), six were lower (Bifidobacterium, Dialister, Escherichia/Shigella, Faecalibacterium, and Ruminococcus), and six were divergent (Alistipes, Bacteroides, Megamonas, Oscillibacter, Prevotella, and Roseburia). We highlight mechanisms and products of bacterial metabolism as they may relate to the etiology of depression. Conclusions: No consensus has emerged from existing human studies of depression and gut microbiome concerning which bacterial taxa are most relevant to depression. This may in part be due to differences in study design. Given that bacterial functions are conserved across taxonomic groups, we propose that studying microbial functioning may be more productive than a purely taxonomic approach to understanding the gut microbiome in depression.
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Affiliation(s)
- Stephanie G. Cheung
- Division of Consultation-Liaison Psychiatry, Columbia University, New York, NY, United States
- Department of Psychiatry, Columbia University, New York, NY, United States
| | - Ariel R. Goldenthal
- Department of Psychiatry, Columbia University, New York, NY, United States
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, New York, NY, United States
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, NY, United States
- Microbiome & Pathogen Genomics Core, Columbia University, New York, NY, United States
| | - J. John Mann
- Department of Psychiatry, Columbia University, New York, NY, United States
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, New York, NY, United States
- Department of Radiology, Columbia University, New York, NY, United States
| | - Jeffrey M. Miller
- Department of Psychiatry, Columbia University, New York, NY, United States
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, New York, NY, United States
| | - M. Elizabeth Sublette
- Department of Psychiatry, Columbia University, New York, NY, United States
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, New York, NY, United States
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47
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Mystkowska AA, Robb C, Vidal-Melgosa S, Vanni C, Fernandez-Guerra A, Höhne M, Hehemann JH. Molecular recognition of the beta-glucans laminarin and pustulan by a SusD-like glycan-binding protein of a marine Bacteroidetes. FEBS J 2018; 285:4465-4481. [PMID: 30300505 DOI: 10.1111/febs.14674] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 09/19/2018] [Accepted: 10/05/2018] [Indexed: 12/26/2022]
Abstract
Marine bacteria catabolize carbohydrate polymers of algae, which synthesize these structurally diverse molecules in ocean surface waters. Although algal glycans are an abundant carbon and energy source in the ocean, the molecular details that enable specific recognition between algal glycans and bacterial degraders remain largely unknown. Here we characterized a surface protein, GMSusD from the planktonic Bacteroidetes-Gramella sp. MAR_2010_102 that thrives during algal blooms. Our biochemical and structural analyses show that GMSusD binds glucose polysaccharides such as branched laminarin and linear pustulan. The 1.8 Å crystal structure of GMSusD indicates that three tryptophan residues form the putative glycan-binding site. Mutagenesis studies confirmed that these residues are crucial for laminarin recognition. We queried metagenomes of global surface water datasets for the occurrence of SusD-like proteins and found sequences with the three structurally conserved residues in different locations in the ocean. The molecular selectivity of GMSusD underscores that specific interactions are required for laminarin recognition. In conclusion, our findings provide insight into the molecular details of β-glucan binding by GMSusD and our bioinformatic analysis reveals that this molecular interaction may contribute to glucan cycling in the surface ocean.
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Affiliation(s)
- Agata Anna Mystkowska
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Craig Robb
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Silvia Vidal-Melgosa
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Chiara Vanni
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Jacobs University Bremen gGmbH, Bremen, Germany
| | - Antonio Fernandez-Guerra
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Jacobs University Bremen gGmbH, Bremen, Germany
| | - Matthias Höhne
- Institute of Biochemistry, Greifswald University, Germany
| | - Jan-Hendrik Hehemann
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
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48
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Molecular Mechanism by which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides. Cell Rep 2018; 21:417-430. [PMID: 29020628 DOI: 10.1016/j.celrep.2017.09.049] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/30/2017] [Accepted: 09/14/2017] [Indexed: 12/18/2022] Open
Abstract
Microbial utilization of complex polysaccharides is a major driving force in shaping the composition of the human gut microbiota. There is a growing appreciation that finely tuned polysaccharide utilization loci enable ubiquitous gut Bacteroidetes to thrive on the plethora of complex polysaccharides that constitute "dietary fiber." Mixed-linkage β(1,3)/β(1,4)-glucans (MLGs) are a key family of plant cell wall polysaccharides with recognized health benefits but whose mechanism of utilization has remained unclear. Here, we provide molecular insight into the function of an archetypal MLG utilization locus (MLGUL) through a combination of biochemistry, enzymology, structural biology, and microbiology. Comparative genomics coupled with growth studies demonstrated further that syntenic MLGULs serve as genetic markers for MLG catabolism across commensal gut bacteria. In turn, we surveyed human gut metagenomes to reveal that MLGULs are ubiquitous in human populations globally, which underscores the importance of gut microbial metabolism of MLG as a common cereal polysaccharide.
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49
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Foley MH, Martens EC, Koropatkin NM. SusE facilitates starch uptake independent of starch binding in B. thetaiotaomicron. Mol Microbiol 2018; 108:551-566. [PMID: 29528148 PMCID: PMC5980745 DOI: 10.1111/mmi.13949] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2018] [Indexed: 12/30/2022]
Abstract
The Bacteroides thetaiotaomicron starch utilization system (Sus) is a model system for nutrient acquisition by gut Bacteroidetes, a dominant phylum of gut bacteria. The Sus includes SusCDEFG, which assemble on the cell surface to capture, degrade and import starch. While SusD is an essential starch-binding protein, the precise role(s) of the partially homologous starch-binding proteins SusE and SusF has remained elusive. We previously reported that a non-binding version of SusD (SusD*) supports growth on starch when other members of the multi-protein complex are present. Here we demonstrate that SusE supports SusD* growth on maltooligosaccharides, and determine the domains of SusE essential for this function. Furthermore, we demonstrate that SusE does not need to bind starch to support growth in the presence of SusD*, suggesting that the assembly of SusCDE is most important for maltooligosaccharide uptake in this context. However, starch binding by proteins SusDEF directs the uptake of maltooligosaccharides of specific lengths, suggesting that these proteins equip the cell to scavenge a range of starch fragments. These data demonstrate that the assembly of core Sus proteins SusCDE is secondary to their glycan binding roles, but glycan binding by Sus proteins may fine tune the selection of glycans from the environment.
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Affiliation(s)
- Matthew H. Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicole M. Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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50
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Champion PA, Shrout JD. The 24th Annual Midwest Microbial Pathogenesis Meeting. J Bacteriol 2018; 200:e000950-18. [PMID: 29483166 PMCID: PMC5952387 DOI: 10.1128/jb.00095-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 24th Annual Midwest Microbial Pathogenesis Conference (MMPC) was held at the University of Notre Dame from August 25-27, 2017. The conference provided an opportunity for scientists from the Midwest to discuss new advances in microbial pathogenesis, including how pathogens promote disease, and how they interact with each other, the microbiome and the host. This commentary highlights the MMPC history, the topics presented at the conference and the reports in this issue.
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Affiliation(s)
- Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Joshua D. Shrout
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
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