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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: 32] [Impact Index Per Article: 5.3] [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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52
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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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53
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Navigating the Gut Buffet: Control of Polysaccharide Utilization in Bacteroides spp. Trends Microbiol 2017; 25:1005-1015. [DOI: 10.1016/j.tim.2017.06.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/09/2017] [Accepted: 06/20/2017] [Indexed: 12/26/2022]
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54
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Frank SA. Receptor uptake arrays for vitamin B 12, siderophores, and glycans shape bacterial communities. Ecol Evol 2017; 7:10175-10195. [PMID: 29238546 PMCID: PMC5723603 DOI: 10.1002/ece3.3544] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/20/2017] [Accepted: 09/28/2017] [Indexed: 01/15/2023] Open
Abstract
Molecular variants of vitamin B12, siderophores, and glycans occur. To take up variant forms, bacteria may express an array of receptors. The gut microbe Bacteroides thetaiotaomicron has three different receptors to take up variants of vitamin B12 and 88 receptors to take up various glycans. The design of receptor arrays reflects key processes that shape cellular evolution. Competition may focus each species on a subset of the available nutrient diversity. Some gut bacteria can take up only a narrow range of carbohydrates, whereas species such as B. thetaiotaomicron can digest many different complex glycans. Comparison of different nutrients, habitats, and genomes provides opportunity to test hypotheses about the breadth of receptor arrays. Another important process concerns fluctuations in nutrient availability. Such fluctuations enhance the value of cellular sensors, which gain information about environmental availability and adjust receptor deployment. Bacteria often adjust receptor expression in response to fluctuations of particular carbohydrate food sources. Some species may adjust expression of uptake receptors for specific siderophores. How do cells use sensor information to control the response to fluctuations? This question about regulatory wiring relates to problems that arise in control theory and artificial intelligence. Control theory clarifies how to analyze environmental fluctuations in relation to the design of sensors and response systems. Recent advances in deep learning studies of artificial intelligence focus on the architecture of regulatory wiring and the ways in which complex control networks represent and classify environmental states. I emphasize the similar design problems that arise in cellular evolution, control theory, and artificial intelligence. I connect those broad conceptual aspects to many testable hypotheses for bacterial uptake of vitamin B12, siderophores, and glycans.
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Affiliation(s)
- Steven A. Frank
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaIrvineCAUSA
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55
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Abstract
The complex carbohydrates of terrestrial and marine biomass represent a rich nutrient source for free-living and mutualistic microbes alike. The enzymatic saccharification of these diverse substrates is of critical importance for fueling a variety of complex microbial communities, including marine, soil, ruminant, and monogastric microbiota. Consequently, highly specific carbohydrate-active enzymes, recognition proteins, and transporters are enriched in the genomes of certain species and are of critical importance in competitive environments. In Bacteroidetes bacteria, these systems are organized as polysaccharide utilization loci (PULs), which are strictly regulated, colocalized gene clusters that encode enzyme and protein ensembles required for the saccharification of complex carbohydrates. This review provides historical perspectives and summarizes key findings in the study of these systems, highlighting a critical shift from sequence-based PUL discovery to systems-based analyses combining reverse genetics, biochemistry, enzymology, and structural biology to precisely illuminate the molecular mechanisms underpinning PUL function. The ecological implications of dynamic PUL deployment by key species in the human gastrointestinal tract are explored, as well as the wider distribution of these systems in other gut, terrestrial, and marine environments.
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56
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Cartmell A, Lowe EC, Baslé A, Firbank SJ, Ndeh DA, Murray H, Terrapon N, Lombard V, Henrissat B, Turnbull JE, Czjzek M, Gilbert HJ, Bolam DN. How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans. Proc Natl Acad Sci U S A 2017; 114:7037-7042. [PMID: 28630303 PMCID: PMC5502631 DOI: 10.1073/pnas.1704367114] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human microbiota, which plays an important role in health and disease, uses complex carbohydrates as a major source of nutrients. Utilization hierarchy indicates that the host glycosaminoglycans heparin (Hep) and heparan sulfate (HS) are high-priority carbohydrates for Bacteroides thetaiotaomicron, a prominent member of the human microbiota. The sulfation patterns of these glycosaminoglycans are highly variable, which presents a significant enzymatic challenge to the polysaccharide lyases and sulfatases that mediate degradation. It is possible that the bacterium recruits lyases with highly plastic specificities and expresses a repertoire of enzymes that target substructures of the glycosaminoglycans with variable sulfation or that the glycans are desulfated before cleavage by the lyases. To distinguish between these mechanisms, the components of the B. thetaiotaomicron Hep/HS degrading apparatus were analyzed. The data showed that the bacterium expressed a single-surface endo-acting lyase that cleaved HS, reflecting its higher molecular weight compared with Hep. Both Hep and HS oligosaccharides imported into the periplasm were degraded by a repertoire of lyases, with each enzyme displaying specificity for substructures within these glycosaminoglycans that display a different degree of sulfation. Furthermore, the crystal structures of a key surface glycan binding protein, which is able to bind both Hep and HS, and periplasmic sulfatases reveal the major specificity determinants for these proteins. The locus described here is highly conserved within the human gut Bacteroides, indicating that the model developed is of generic relevance to this important microbial community.
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Affiliation(s)
- Alan Cartmell
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Elisabeth C Lowe
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Susan J Firbank
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Didier A Ndeh
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Heath Murray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
- Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jeremy E Turnbull
- Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Mirjam Czjzek
- Sorbonne Universités, Université Pierre-et-Marie-Curie, Université Paris 06, F-29688 Roscoff cedex, Bretagne, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff cedex, Bretagne, France
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom;
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57
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Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J 2017; 474:1823-1836. [PMID: 28512250 PMCID: PMC5433529 DOI: 10.1042/bcj20160510] [Citation(s) in RCA: 1733] [Impact Index Per Article: 247.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 02/08/2023]
Abstract
The human gastrointestinal (GI) tract harbours a complex and dynamic population of microorganisms, the gut microbiota, which exert a marked influence on the host during homeostasis and disease. Multiple factors contribute to the establishment of the human gut microbiota during infancy. Diet is considered as one of the main drivers in shaping the gut microbiota across the life time. Intestinal bacteria play a crucial role in maintaining immune and metabolic homeostasis and protecting against pathogens. Altered gut bacterial composition (dysbiosis) has been associated with the pathogenesis of many inflammatory diseases and infections. The interpretation of these studies relies on a better understanding of inter-individual variations, heterogeneity of bacterial communities along and across the GI tract, functional redundancy and the need to distinguish cause from effect in states of dysbiosis. This review summarises our current understanding of the development and composition of the human GI microbiota, and its impact on gut integrity and host health, underlying the need for mechanistic studies focusing on host-microbe interactions.
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Affiliation(s)
- Elizabeth Thursby
- The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, U.K
| | - Nathalie Juge
- The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, U.K.
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58
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Tauzin AS, Laville E, Xiao Y, Nouaille S, Le Bourgeois P, Heux S, Portais J, Monsan P, Martens EC, Potocki‐Veronese G, Bordes F. Functional characterization of a gene locus from an uncultured gut
Bacteroides
conferring xylo‐oligosaccharides utilization to
Escherichia coli. Mol Microbiol 2016; 102:579-592. [DOI: 10.1111/mmi.13480] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 08/01/2016] [Accepted: 08/08/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Alexandra S. Tauzin
- LISBP, CNRS, INRA, INSAT, Université de ToulouseToulouse France
- TWB, INRARamonville Saint‐Agne France
| | | | - Yao Xiao
- Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn Arbor MI USA
| | | | | | - Stéphanie Heux
- LISBP, CNRS, INRA, INSAT, Université de ToulouseToulouse France
| | | | | | - Eric C. Martens
- Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn Arbor MI USA
| | | | - Florence Bordes
- LISBP, CNRS, INRA, INSAT, Université de ToulouseToulouse France
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59
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Cockburn DW, Koropatkin NM. Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease. J Mol Biol 2016; 428:3230-3252. [PMID: 27393306 DOI: 10.1016/j.jmb.2016.06.021] [Citation(s) in RCA: 330] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 02/06/2023]
Abstract
Carbohydrates comprise a large fraction of the typical diet, yet humans are only able to directly process some types of starch and simple sugars. The remainder transits the large intestine where it becomes food for the commensal bacterial community. This is an environment of not only intense competition but also impressive cooperation for available glycans, as these bacteria work to maximize their energy harvest from these carbohydrates during their limited transit time through the gut. The species within the gut microbiota use a variety of strategies to process and scavenge both dietary and host-produced glycans such as mucins. Some act as generalists that are able to degrade a wide range of polysaccharides, while others are specialists that are only able to target a few select glycans. All are members of a metabolic network where substantial cross-feeding takes place, as by-products of one organism serve as important resources for another. Much of this metabolic activity influences host physiology, as secondary metabolites and fermentation end products are absorbed either by the epithelial layer or by transit via the portal vein to the liver where they can have additional effects. These microbially derived compounds influence cell proliferation and apoptosis, modulate the immune response, and can alter host metabolism. This review summarizes the molecular underpinnings of these polysaccharide degradation processes, their impact on human health, and how we can manipulate them through the use of prebiotics.
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Affiliation(s)
- Darrell W Cockburn
- 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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60
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Hemsworth GR, Thompson AJ, Stepper J, Sobala ŁF, Coyle T, Larsbrink J, Spadiut O, Goddard-Borger ED, Stubbs KA, Brumer H, Davies GJ. Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut. Open Biol 2016; 6:160142. [PMID: 27466444 PMCID: PMC4967831 DOI: 10.1098/rsob.160142] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/01/2016] [Indexed: 12/22/2022] Open
Abstract
The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are otherwise recalcitrant to assimilation. Indeed, the intrinsic human polysaccharide-degrading enzyme repertoire is limited to various starch-based substrates; more complex polysaccharides demand microbial degradation. Select Bacteroidetes are responsible for the degradation of the ubiquitous vegetable xyloglucans (XyGs), through the concerted action of cohorts of enzymes and glycan-binding proteins encoded by specific xyloglucan utilization loci (XyGULs). Extending recent (meta)genomic, transcriptomic and biochemical analyses, significant questions remain regarding the structural biology of the molecular machinery required for XyG saccharification. Here, we reveal the three-dimensional structures of an α-xylosidase, a β-glucosidase, and two α-l-arabinofuranosidases from the Bacteroides ovatus XyGUL. Aided by bespoke ligand synthesis, our analyses highlight key adaptations in these enzymes that confer individual specificity for xyloglucan side chains and dictate concerted, stepwise disassembly of xyloglucan oligosaccharides. In harness with our recent structural characterization of the vanguard endo-xyloglucanse and cell-surface glycan-binding proteins, the present analysis provides a near-complete structural view of xyloglucan recognition and catalysis by XyGUL proteins.
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Affiliation(s)
- Glyn R Hemsworth
- Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK
| | - Andrew J Thompson
- Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK
| | - Judith Stepper
- Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK
| | - Łukasz F Sobala
- Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK
| | - Travis Coyle
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Johan Larsbrink
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Oliver Spadiut
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden Wallenberg Wood Science Center, Royal Institute of Technology (KTH), Teknikringen 56-58, 100 44 Stockholm, Sweden
| | - Ethan D Goddard-Borger
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville Victoria 3052, Australia
| | - Keith A Stubbs
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Harry Brumer
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Gideon J Davies
- Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK
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