251
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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: 1707] [Impact Index Per Article: 243.9] [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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252
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Viver T, Orellana LH, Hatt JK, Urdiain M, Díaz S, Richter M, Antón J, Avian M, Amann R, Konstantinidis KT, Rosselló-Móra R. The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa. Environ Microbiol 2017; 19:3039-3058. [PMID: 28419691 DOI: 10.1111/1462-2920.13763] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/10/2017] [Indexed: 01/06/2023]
Abstract
Cotylorhiza tuberculata is an important scyphozoan jellyfish producing population blooms in the Mediterranean probably due to pelagic ecosystem's decay. Its gastric cavity can serve as a simple model of microbial-animal digestive associations, yet poorly characterized. Using state-of-the-art metagenomic population binning and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), we show that only four novel clonal phylotypes were consistently associated with multiple jellyfish adults. Two affiliated close to Spiroplasma and Mycoplasma genera, one to chlamydial 'Candidatus Syngnamydia', and one to bacteroidetal Tenacibaculum, and were at least one order of magnitude more abundant than any other bacteria detected. Metabolic modelling predicted an aerobic heterotrophic lifestyle for the chlamydia, which were found intracellularly in Onychodromopsis-like ciliates. The Spiroplasma-like organism was predicted to be an anaerobic fermenter associated to some jellyfish cells, whereas the Tenacibaculum-like as free-living aerobic heterotroph, densely colonizing the mesogleal axis inside the gastric filaments. The association between the jellyfish and its reduced microbiome was close and temporally stable, and possibly related to food digestion and protection from pathogens. Based on the genomic and microscopic data, we propose three candidate taxa: 'Candidatus Syngnamydia medusae', 'Candidatus Medusoplasma mediterranei' and 'Candidatus Tenacibaculum medusae'.
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Affiliation(s)
- Tomeu Viver
- Mediterranean Institute for Advanced Studies (IMEDEA; CSIC-UIB), Marine Microbiology Group, Esporles, E-07190, Spain
| | - Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr. NW, Atlanta, GA, 30332, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr. NW, Atlanta, GA, 30332, USA
| | - Mercedes Urdiain
- Mediterranean Institute for Advanced Studies (IMEDEA; CSIC-UIB), Marine Microbiology Group, Esporles, E-07190, Spain
| | - Sara Díaz
- Mediterranean Institute for Advanced Studies (IMEDEA; CSIC-UIB), Marine Microbiology Group, Esporles, E-07190, Spain
| | | | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, and Multidisciplinary Institute for Environmental Studies Ramon Margalef, University of Alicante, Alicante, Spain
| | - Massimo Avian
- Department of Life Science, University of Trieste, Via L. Giorgieri 10, Trieste, 34127, Italy
| | - Rudolf Amann
- Department of Molecular Ecology, Max-Planck-Institut für Marine Mikrobiologie, Bremen, D-28359, Germany
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr. NW, Atlanta, GA, 30332, USA.,School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr. NW, Atlanta, GA, 30332, USA
| | - Ramon Rosselló-Móra
- Mediterranean Institute for Advanced Studies (IMEDEA; CSIC-UIB), Marine Microbiology Group, Esporles, E-07190, Spain
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253
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Manresa MC, Taylor CT. Hypoxia Inducible Factor (HIF) Hydroxylases as Regulators of Intestinal Epithelial Barrier Function. Cell Mol Gastroenterol Hepatol 2017; 3:303-315. [PMID: 28462372 PMCID: PMC5404106 DOI: 10.1016/j.jcmgh.2017.02.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/09/2017] [Indexed: 12/12/2022]
Abstract
Human health is dependent on the ability of the body to extract nutrients, fluids, and oxygen from the external environment while at the same time maintaining a state of internal sterility. Therefore, the cell layers that cover the surface areas of the body such as the lung, skin, and gastrointestinal mucosa provide vital semipermeable barriers that allow the transport of essential nutrients, fluid, and waste products, while at the same time keeping the internal compartments free of microbial organisms. These epithelial surfaces are highly specialized and differ in their anatomic structure depending on their location to provide appropriate and effective site-specific barrier function. Given this important role, it is not surprising that significant disease often is associated with alterations in epithelial barrier function. Examples of such diseases include inflammatory bowel disease, chronic obstructive pulmonary disease, and atopic dermatitis. These chronic inflammatory disorders often are characterized by diminished tissue oxygen levels (hypoxia). Hypoxia triggers an adaptive transcriptional response governed by hypoxia-inducible factors (HIFs), which are repressed by a family of oxygen-sensing HIF hydroxylases. Here, we review recent evidence suggesting that pharmacologic hydroxylase inhibition may be of therapeutic benefit in inflammatory bowel disease through the promotion of intestinal epithelial barrier function through both HIF-dependent and HIF-independent mechanisms.
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Key Words
- CD, Crohn’s disease
- DMOG, dimethyloxalylglycine
- DSS, dextran sodium sulfate
- Epithelial Barrier
- FIH, factor inhibiting hypoxia-inducible factor
- HIF, hypoxia-inducible factor
- Hypoxia
- Hypoxia-Inducible Factor (HIF) Hydroxylases
- IBD, inflammatory bowel disease
- IL, interleukin
- Inflammatory Bowel Disease
- NF-κB, nuclear factor-κB
- PHD, hypoxia-inducible factor–prolyl hydroxylases
- TFF, trefoil factor
- TJ, tight junction
- TLR, Toll-like receptor
- TNF-α, tumor necrosis factor α
- UC, ulcerative colitis
- ZO, zonula occludens
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Affiliation(s)
- Mario C. Manresa
- Conway Institute of Biomolecular and Biomedical Research, Belfield, Dublin, Ireland
- Charles Institute of Dermatology, Belfield, Dublin, Ireland
| | - Cormac T. Taylor
- Conway Institute of Biomolecular and Biomedical Research, Belfield, Dublin, Ireland
- Charles Institute of Dermatology, Belfield, Dublin, Ireland
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
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254
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Huynh TG, Shiu YL, Nguyen TP, Truong QP, Chen JC, Liu CH. Current applications, selection, and possible mechanisms of actions of synbiotics in improving the growth and health status in aquaculture: A review. FISH & SHELLFISH IMMUNOLOGY 2017; 64:367-382. [PMID: 28336489 DOI: 10.1016/j.fsi.2017.03.035] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/16/2017] [Accepted: 03/17/2017] [Indexed: 06/06/2023]
Abstract
Synbiotics, a conjunction between prebiotics and probiotics, have been used in aquaculture for over 10 years. However, the mechanisms of how synbiotics work as growth and immunity promoters are far from being unraveled. Here, we show that a prebiotic as part of a synbiotic is hydrolyzed to mono- or disaccharides as the sole carbon source with diverse mechanisms, thereby increasing biomass and colonization that is established by specific crosstalk between probiotic bacteria and the surface of intestinal epithelial cells of the host. Synbiotics may indirectly and directly promote the growth of aquatic animals through releasing extracellular bacterial enzymes and bioactive products from synbiotic metabolic processes. These compounds may activate precursors of digestive enzymes of the host and augment the nutritional absorptive ability that contributes to the efficacy of food utilization. In fish immune systems, synbiotics cause intestinal epithelial cells to secrete cytokines which modulate immune functional cells as of dendritic cells, T cells, and B cells, and induce the ability of lipopolysaccharides to trigger tumor necrosis factor-α and Toll-like receptor 2 gene transcription leading to increased respiratory burst activity, phagocytosis, and nitric oxide production. In shellfish, synbiotics stimulate the proliferation and degranulation of hemocytes of shrimp due to the presence of bacterial cell walls. Pathogen-associated molecular patterns are subsequently recognized and bound by specific pattern-recognition proteins, triggering melanization and phagocytosis processes.
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Affiliation(s)
- Truong-Giang Huynh
- Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung 912, Taiwan, ROC; College of Aquaculture and Fisheries, CanTho University, CanTho, Viet Nam
| | - Ya-Li Shiu
- Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung 912, Taiwan, ROC
| | | | - Quoc-Phu Truong
- College of Aquaculture and Fisheries, CanTho University, CanTho, Viet Nam
| | - Jiann-Chu Chen
- Department of Aquaculture, College of Life Sciences, National Taiwan Ocean University, Keelung 202, Taiwan, ROC
| | - Chun-Hung Liu
- Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung 912, Taiwan, ROC.
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255
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Lim B, Zimmermann M, Barry NA, Goodman AL. Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut. Cell 2017; 169:547-558.e15. [PMID: 28431252 PMCID: PMC5532740 DOI: 10.1016/j.cell.2017.03.045] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/28/2017] [Accepted: 03/27/2017] [Indexed: 12/15/2022]
Abstract
The gut microbiota is implicated in numerous aspects of health and disease, but dissecting these connections is challenging because genetic tools for gut anaerobes are limited. Inducible promoters are particularly valuable tools because these platforms allow real-time analysis of the contribution of microbiome gene products to community assembly, host physiology, and disease. We developed a panel of tunable expression platforms for the prominent genus Bacteroides in which gene expression is controlled by a synthetic inducer. In the absence of inducer, promoter activity is fully repressed; addition of inducer rapidly increases gene expression by four to five orders of magnitude. Because the inducer is absent in mice and their diets, Bacteroides gene expression inside the gut can be modulated by providing the inducer in drinking water. We use this system to measure the dynamic relationship between commensal sialidase activity and liberation of mucosal sialic acid, a receptor and nutrient for pathogens. VIDEO ABSTRACT.
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Affiliation(s)
- Bentley Lim
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536-0812, USA
| | - Michael Zimmermann
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536-0812, USA
| | - Natasha A Barry
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536-0812, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536-0812, USA.
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256
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Ndeh D, Rogowski A, Cartmell A, Luis AS, Baslé A, Gray J, Venditto I, Briggs J, Zhang X, Labourel A, Terrapon N, Buffetto F, Nepogodiev S, Xiao Y, Field RA, Zhu Y, O’Neil MA, Urbanowicz BR, York WS, Davies GJ, Abbott DW, Ralet MC, Martens EC, Henrissat B, Gilbert HJ. Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Nature 2017; 544:65-70. [PMID: 28329766 PMCID: PMC5388186 DOI: 10.1038/nature21725] [Citation(s) in RCA: 395] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/27/2017] [Indexed: 12/30/2022]
Abstract
The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here we show that the gut bacterium Bacteroides thetaiotaomicron uses the most structurally complex glycan known: the plant pectic polysaccharide rhamnogalacturonan-II, cleaving all but 1 of its 21 distinct glycosidic linkages. The deconstruction of rhamnogalacturonan-II side chains and backbone are coordinated to overcome steric constraints, and the degradation involves previously undiscovered enzyme families and catalytic activities. The degradation system informs revision of the current structural model of rhamnogalacturonan-II and highlights how individual gut bacteria orchestrate manifold enzymes to metabolize the most challenging glycan in the human diet.
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Affiliation(s)
- Didier Ndeh
- Institute for Cell and Molecular Biosciences, Newcastle University,
Newcastle upon Tyne NE2 4HH, U.K
| | - Artur Rogowski
- Institute for Cell and Molecular Biosciences, Newcastle University,
Newcastle upon Tyne NE2 4HH, U.K
| | - Alan Cartmell
- Institute for Cell and Molecular Biosciences, Newcastle University,
Newcastle upon Tyne NE2 4HH, U.K
| | - Ana S. Luis
- Institute for Cell and Molecular Biosciences, Newcastle University,
Newcastle upon Tyne NE2 4HH, U.K
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University,
Newcastle upon Tyne NE2 4HH, U.K
| | - Joseph Gray
- Institute for Cell and Molecular Biosciences, Newcastle University,
Newcastle upon Tyne NE2 4HH, U.K
| | - Immacolata Venditto
- Institute for Cell and Molecular Biosciences, Newcastle University,
Newcastle upon Tyne NE2 4HH, U.K
| | - Jonathon Briggs
- Institute for Cell and Molecular Biosciences, Newcastle University,
Newcastle upon Tyne NE2 4HH, U.K
| | - Xiaoyang Zhang
- Institute for Cell and Molecular Biosciences, Newcastle University,
Newcastle upon Tyne NE2 4HH, U.K
| | - Aurore Labourel
- Institute for Cell and Molecular Biosciences, Newcastle University,
Newcastle upon Tyne NE2 4HH, U.K
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques,
Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University,
F-13288 Marseille, France
| | - Fanny Buffetto
- INRA, UR1268 Biopolymères Interactions Assemblages, 44300
Nantes, France
| | - Sergey Nepogodiev
- Department of Biological Chemistry, John Innes Centre Norwich
Research Park, Norwich NR4 7UH, UK
| | - Yao Xiao
- Department of Microbiology and Immunology, University of Michigan
Medical School, Ann Arbor, MI, USA
| | - Robert A. Field
- Department of Biological Chemistry, John Innes Centre Norwich
Research Park, Norwich NR4 7UH, UK
| | - Yanping Zhu
- Complex Carbohydrate Research Center, The University of Georgia, 315
Riverbend Road, Athens, GA 30602, USA
| | - Malcolm A. O’Neil
- Complex Carbohydrate Research Center, The University of Georgia, 315
Riverbend Road, Athens, GA 30602, USA
| | - Breeana R. Urbanowicz
- Complex Carbohydrate Research Center, The University of Georgia, 315
Riverbend Road, Athens, GA 30602, USA
| | - William S. York
- Complex Carbohydrate Research Center, The University of Georgia, 315
Riverbend Road, Athens, GA 30602, USA
| | | | | | | | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan
Medical School, Ann Arbor, MI, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques,
Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University,
F-13288 Marseille, France
- INRA, USC 1408 AFMB, F-13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University,
Jeddah, Saudi Arabia
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University,
Newcastle upon Tyne NE2 4HH, U.K
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257
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Hehemann JH, Truong LV, Unfried F, Welsch N, Kabisch J, Heiden SE, Junker S, Becher D, Thürmer A, Daniel R, Amann R, Schweder T. Aquatic adaptation of a laterally acquired pectin degradation pathway in marine gammaproteobacteria. Environ Microbiol 2017; 19:2320-2333. [PMID: 28276126 DOI: 10.1111/1462-2920.13726] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 03/03/2017] [Accepted: 03/05/2017] [Indexed: 01/09/2023]
Abstract
Mobile genomic islands distribute functional traits between microbes and habitats, yet it remains unclear how their proteins adapt to new environments. Here we used a comparative phylogenomic and proteomic approach to show that the marine bacterium Pseudoalteromonas haloplanktis ANT/505 acquired a genomic island with a functional pathway for pectin catabolism. Bioinformatics and biochemical experiments revealed that this pathway encodes a series of carbohydrate-active enzymes including two multi-modular pectate lyases, PelA and PelB. PelA is a large enzyme with a polysaccharide lyase family 1 (PL1) domain and a carbohydrate esterase family 8 domain, and PelB contains a PL1 domain and two carbohydrate-binding domains of family 13. Comparative phylogenomic analyses indicate that the pathway was most likely acquired from terrestrial microbes, yet we observed multi-modular orthologues only in marine bacteria. Proteomic experiments showed that P. haloplanktis ANT/505 secretes both pectate lyases into the environment in the presence of pectin. These multi-modular enzymes may therefore represent a marine innovation that enhances physical interaction with pectins to reduce loss of substrate and enzymes by diffusion. Our results revealed that marine bacteria can catabolize pectin, and highlight enzyme fusion as a potential adaptation that may facilitate microbial consumption of polymeric substrates in aquatic environments.
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Affiliation(s)
- Jan-Hendrik Hehemann
- MARUM, Center for Marine Environmental Sciences at the University of Bremen, Leobener Strasse, Bremen, D-28359, Germany.,Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Le Van Truong
- Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Institute of Biotechnology, Vietnamese Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam
| | - Frank Unfried
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany.,Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Norma Welsch
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Johannes Kabisch
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany.,Department of Biology, Computer-aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 10, Darmstadt, D-64287, Germany
| | - Stefan E Heiden
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Sabryna Junker
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, D-17487, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, D-17487, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory (G2L), Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory (G2L), Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Thomas Schweder
- Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
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258
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Ali-Ahmad A, Garron ML, Zamboni V, Lenfant N, Nurizzo D, Henrissat B, Berrin JG, Bourne Y, Vincent F. Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2. J Struct Biol 2017; 197:227-235. [DOI: 10.1016/j.jsb.2016.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/18/2016] [Accepted: 11/19/2016] [Indexed: 12/16/2022]
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259
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Tang K, Lin Y, Han Y, Jiao N. Characterization of Potential Polysaccharide Utilization Systems in the Marine Bacteroidetes Gramella Flava JLT2011 Using a Multi-Omics Approach. Front Microbiol 2017; 8:220. [PMID: 28261179 PMCID: PMC5306329 DOI: 10.3389/fmicb.2017.00220] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/31/2017] [Indexed: 01/26/2023] Open
Abstract
Members of phylum Bacteroidetes are distributed across diverse marine niches and Flavobacteria is often the predominant bacterial class decomposing algae-derived polysaccharides. Here, we report the complete genome of Gramella flava JLT2011 (Flavobacteria) isolated from surface water of the southeastern Pacific. A remarkable genomic feature is that the number of glycoside hydrolase (GH) genes in the genome of G. flava JLT2011 is more than 2-fold higher than that of other Gramella species. The functional profiles of the GHs suggest extensive variation in Gramella species. Growth experiments revealed that G. flava JLT2011 has the ability to utilize a wide range of polysaccharides for growth such as xylan and homogalacturonan in pectin. Nearly half of all GH genes were located on the multi-gene polysaccharide utilization loci (PUL) or PUL-like systems in G. flava JLT2011. This species was also found to harbor the two xylan PULs and a pectin PUL, respectively. Gene expression data indicated that more GHs and sugar-specific outer-membrane susC-susD systems were found in the presence of xylan than in the presence of pectin, suggesting a different strategy for heteropolymeric xylan and homoglacturonan utilization. Multi-omics data (transcriptomics, proteomics, and metabolomics) indicated that xylan PULs and pectin PUL are respectively involved in the catabolism of their corresponding polysaccharides. This work presents a comparison of polysaccharide decomposition within a genus and expands current knowledge on the diversity and function of PULs in marine Bacteroidetes, thereby deepening our understanding of their ecological role in polysaccharide remineralization in the marine system.
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Affiliation(s)
- Kai Tang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University Xiamen, China
| | - Yingfan Lin
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University Xiamen, China
| | - Yu Han
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University Xiamen, China
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260
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Han YB, Chen LQ, Li Z, Tan YM, Feng Y, Yang GY. Structural Insights into the Broad Substrate Specificity of a Novel Endoglycoceramidase I Belonging to a New Subfamily of GH5 Glycosidases. J Biol Chem 2017; 292:4789-4800. [PMID: 28179425 DOI: 10.1074/jbc.m116.763821] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/11/2017] [Indexed: 01/27/2023] Open
Abstract
Endoglycoceramidases (EGCases) specifically hydrolyze the glycosidic linkage between the oligosaccharide and the ceramide moieties of various glycosphingolipids, and they have received substantial attention in the emerging field of glycosphingolipidology. However, the mechanism regulating the strict substrate specificity of these GH5 glycosidases has not been identified. In this study, we report a novel EGCase I from Rhodococcus equi 103S (103S_EGCase I) with remarkably broad substrate specificity. Based on phylogenetic analyses, the enzyme may represent a new subfamily of GH5 glycosidases. The X-ray crystal structures of 103S_EGCase I alone and in complex with its substrates monosialodihexosylganglioside (GM3) and monosialotetrahexosylganglioside (GM1) enabled us to identify several structural features that may account for its broad specificity. Compared with EGCase II from Rhodococcus sp. M-777 (M777_EGCase II), which possesses strict substrate specificity, 103S_EGCase I possesses a longer α7-helix and a shorter loop 4, which forms a larger substrate-binding pocket that could accommodate more extended oligosaccharides. In addition, loop 2 and loop 8 of the enzyme adopt a more open conformation, which also enlarges the oligosaccharide-binding cavity. Based on this knowledge, a rationally designed experiment was performed to examine the substrate specificity of EGCase II. The truncation of loop 4 in M777_EGCase II increased its activity toward GM1 (163%). Remarkably, the S63G mutant of M777_EGCase II showed a broader substrate spectra and significantly increased activity toward bulky substrates (up to >1370-fold for fucosyl-GM1). Collectively, the results presented here reveal the exquisite substrate recognition mechanism of EGCases and provide an opportunity for further engineering of these enzymes.
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Affiliation(s)
- Yun-Bin Han
- From the State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,the Shanghai Institute for Advanced Immunological Studies, ShanghaiTech University, Shanghai 200031, China, and
| | - Liu-Qing Chen
- From the State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhuo Li
- From the State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu-Meng Tan
- From the State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- From the State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guang-Yu Yang
- From the State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China, .,the Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), East China University of Science and Technology, Shanghai 200237, China
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261
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Wang B, Yao M, Lv L, Ling Z, Li L. The Human Microbiota in Health and Disease. ENGINEERING 2017; 3:71-82. [DOI: 10.1016/j.eng.2017.01.008] [Citation(s) in RCA: 445] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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262
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Glenwright AJ, Pothula KR, Bhamidimarri SP, Chorev DS, Baslé A, Firbank SJ, Zheng H, Robinson CV, Winterhalter M, Kleinekathöfer U, Bolam DN, van den Berg B. Structural basis for nutrient acquisition by dominant members of the human gut microbiota. Nature 2017; 541:407-411. [PMID: 28077872 DOI: 10.1038/nature20828] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 11/24/2016] [Indexed: 12/30/2022]
Abstract
The human large intestine is populated by a high density of microorganisms, collectively termed the colonic microbiota, which has an important role in human health and nutrition. The survival of microbiota members from the dominant Gram-negative phylum Bacteroidetes depends on their ability to degrade dietary glycans that cannot be metabolized by the host. The genes encoding proteins involved in the degradation of specific glycans are organized into co-regulated polysaccharide utilization loci, with the archetypal locus sus (for starch utilisation system) encoding seven proteins, SusA-SusG. Glycan degradation mainly occurs intracellularly and depends on the import of oligosaccharides by an outer membrane protein complex composed of an extracellular SusD-like lipoprotein and an integral membrane SusC-like TonB-dependent transporter. The presence of the partner SusD-like lipoprotein is the major feature that distinguishes SusC-like proteins from previously characterized TonB-dependent transporters. Many sequenced gut Bacteroides spp. encode over 100 SusCD pairs, of which the majority have unknown functions and substrate specificities. The mechanism by which extracellular substrate binding by SusD proteins is coupled to outer membrane passage through their cognate SusC transporter is unknown. Here we present X-ray crystal structures of two functionally distinct SusCD complexes purified from Bacteroides thetaiotaomicron and derive a general model for substrate translocation. The SusC transporters form homodimers, with each β-barrel protomer tightly capped by SusD. Ligands are bound at the SusC-SusD interface in a large solvent-excluded cavity. Molecular dynamics simulations and single-channel electrophysiology reveal a 'pedal bin' mechanism, in which SusD moves away from SusC in a hinge-like fashion in the absence of ligand to expose the substrate-binding site to the extracellular milieu. These data provide mechanistic insights into outer membrane nutrient import by members of the microbiota, an area of major importance for understanding human-microbiota symbiosis.
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Affiliation(s)
- Amy J Glenwright
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Karunakar R Pothula
- Jacobs University Bremen, Department of Physics & Earth Sciences, 28759 Bremen, Germany
| | - Satya P Bhamidimarri
- Jacobs University Bremen, Department of Life Sciences & Chemistry, 28759 Bremen, Germany
| | - Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Susan J Firbank
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Hongjun Zheng
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Mathias Winterhalter
- Jacobs University Bremen, Department of Life Sciences & Chemistry, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Jacobs University Bremen, Department of Physics & Earth Sciences, 28759 Bremen, Germany
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Bert van den Berg
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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263
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McKee LS. Measuring Enzyme Kinetics of Glycoside Hydrolases Using the 3,5-Dinitrosalicylic Acid Assay. Methods Mol Biol 2017; 1588:27-36. [PMID: 28417358 DOI: 10.1007/978-1-4939-6899-2_3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Use of the 3,5-dinitrosalicylic acid reagent allows the simple and rapid quantification of reducing sugars. The method can be used for analysis of biological samples or in the characterization of enzyme reactions. Presented here is an application of the method in measuring the kinetics of a glycoside hydrolase reaction, including the optimization of the DNSA reagent, and the production of a standard curve of absorbance and sugar concentration.
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Affiliation(s)
- Lauren S McKee
- Division of Glycoscience, School of Biotechnology, KTH, Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden.
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264
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Sheflin AM, Melby CL, Carbonero F, Weir TL. Linking dietary patterns with gut microbial composition and function. Gut Microbes 2016; 8:113-129. [PMID: 27960648 PMCID: PMC5390824 DOI: 10.1080/19490976.2016.1270809] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Emerging insights have implicated the gut microbiota as an important factor in the maintenance of human health. Although nutrition research has focused on how direct interactions between dietary components and host systems influence human health, it is becoming increasingly important to consider nutrient effects on the gut microbiome for a more complete picture. Understanding nutrient-host-microbiome interactions promises to reveal novel mechanisms of disease etiology and progression, offers new disease prevention strategies and therapeutic possibilities, and may mandate alternative criteria to evaluate the safety of food ingredients. Here we review the current literature on diet effects on the microbiome and the generation of microbial metabolites of dietary constituents that may influence human health. We conclude with a discussion of the relevance of these studies to nutrition and public health and summarize further research needs required to realize the potential of exploiting diet-microbiota interactions for improved health.
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Affiliation(s)
- Amy M. Sheflin
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, USA
| | - Christopher L. Melby
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, CO, USA
| | - Franck Carbonero
- Department of Food Science, University of Arkansas, Fayetteville, AR, USA
| | - Tiffany L. Weir
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, CO, USA,CONTACT Tiffany L. Weir 210 Gifford Building, 1571 Campus Delivery, Colorado State University, Fort Collins, CO 80521-1571, USA
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265
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Bågenholm V, Reddy SK, Bouraoui H, Morrill J, Kulcinskaja E, Bahr CM, Aurelius O, Rogers T, Xiao Y, Logan DT, Martens EC, Koropatkin NM, Stålbrand H. Galactomannan Catabolism Conferred by a Polysaccharide Utilization Locus of Bacteroides ovatus: ENZYME SYNERGY AND CRYSTAL STRUCTURE OF A β-MANNANASE. J Biol Chem 2016; 292:229-243. [PMID: 27872187 PMCID: PMC5217682 DOI: 10.1074/jbc.m116.746438] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 11/18/2016] [Indexed: 01/15/2023] Open
Abstract
A recently identified polysaccharide utilization locus (PUL) from Bacteroides ovatus ATCC 8483 is transcriptionally up-regulated during growth on galacto- and glucomannans. It encodes two glycoside hydrolase family 26 (GH26) β-mannanases, BoMan26A and BoMan26B, and a GH36 α-galactosidase, BoGal36A. The PUL also includes two glycan-binding proteins, confirmed by β-mannan affinity electrophoresis. When this PUL was deleted, B. ovatus was no longer able to grow on locust bean galactomannan. BoMan26A primarily formed mannobiose from mannan polysaccharides. BoMan26B had higher activity on galactomannan with a high degree of galactosyl substitution and was shown to be endo-acting generating a more diverse mixture of oligosaccharides, including mannobiose. Of the two β-mannanases, only BoMan26B hydrolyzed galactoglucomannan. A crystal structure of BoMan26A revealed a similar structure to the exo-mannobiohydrolase CjMan26C from Cellvibrio japonicus, with a conserved glycone region (−1 and −2 subsites), including a conserved loop closing the active site beyond subsite −2. Analysis of cellular location by immunolabeling and fluorescence microscopy suggests that BoMan26B is surface-exposed and associated with the outer membrane, although BoMan26A and BoGal36A are likely periplasmic. In light of the cellular location and the biochemical properties of the two characterized β-mannanases, we propose a scheme of sequential action by the glycoside hydrolases encoded by the β-mannan PUL and involved in the β-mannan utilization pathway in B. ovatus. The outer membrane-associated BoMan26B initially acts on the polysaccharide galactomannan, producing comparably large oligosaccharide fragments. Galactomanno-oligosaccharides are further processed in the periplasm, degalactosylated by BoGal36A, and subsequently hydrolyzed into mainly mannobiose by the β-mannanase BoMan26A.
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Affiliation(s)
- Viktoria Bågenholm
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Sumitha K Reddy
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Hanene Bouraoui
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Johan Morrill
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Evelina Kulcinskaja
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Constance M Bahr
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Oskar Aurelius
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Theresa Rogers
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Yao Xiao
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Derek T Logan
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Eric C Martens
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Nicole M Koropatkin
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Henrik Stålbrand
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
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266
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Abstract
Complex carbohydrates are ubiquitous in all kingdoms of life. As major components of the plant cell wall they constitute both a rich renewable carbon source for biotechnological transformation into fuels, chemicals and materials, and also form an important energy source as part of a healthy human diet. In both contexts, there has been significant, sustained interest in understanding how microbes transform these substrates. Classical perspectives of microbial polysaccharide degradation are currently being augmented by recent advances in the discovery of lytic polysaccharide monooxygenases (LPMOs) and polysaccharide utilization loci (PULs). Fundamental discoveries in carbohydrate enzymology are both advancing biological understanding, as well as informing applications in industrial biomass conversion and modulation of the human gut microbiota to mediate health benefits.
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267
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Sulfatases and radical SAM enzymes: emerging themes in glycosaminoglycan metabolism and the human microbiota. Biochem Soc Trans 2016; 44:109-15. [PMID: 26862195 DOI: 10.1042/bst20150191] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Humans live in a permanent association with bacterial populations collectively called the microbiota. In the last 10 years, major advances in our knowledge of the microbiota have shed light on its critical roles in human physiology. The microbiota has also been shown to be a major factor in numerous pathologies including obesity or inflammatory disorders. Despite tremendous progresses, our understanding of the key functions of the human microbiota and the molecular basis of its interactions with the host remain still poorly understood. Among the factors involved in host colonization, two enzymes families, sulfatases and radical S-adenosyl-L-methionine enzymes, have recently emerged as key enzymes.
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268
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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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269
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Sheflin AM, Borresen EC, Kirkwood JS, Boot CM, Whitney AK, Lu S, Brown RJ, Broeckling CD, Ryan EP, Weir TL. Dietary supplementation with rice bran or navy bean alters gut bacterial metabolism in colorectal cancer survivors. Mol Nutr Food Res 2016; 61. [PMID: 27461523 DOI: 10.1002/mnfr.201500905] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/30/2016] [Accepted: 07/04/2016] [Indexed: 12/17/2022]
Abstract
SCOPE Heat-stabilized rice bran (SRB) and cooked navy bean powder (NBP) contain a variety of phytochemicals that are fermented by colonic microbiota and may influence intestinal health. Dietary interventions with these foods should be explored for modulating colorectal cancer risk. METHODS AND RESULTS A randomized-controlled pilot clinical trial investigated the effects of eating SRB (30 g/day) or cooked navy bean powder (35 g/day) on gut microbiota and metabolites (NCT01929122). Twenty-nine overweight/obese volunteers with a prior history of colorectal cancer consumed a study-provided meal and snack daily for 28 days. Volunteers receiving SRB or NBP showed increased gut bacterial diversity and altered gut microbial composition at 28 days compared to baseline. Supplementation with SRB or NBP increased total dietary fiber intake similarly, yet only rice bran intake led to a decreased Firmicutes:Bacteroidetes ratio and increased SCFA (propionate and acetate) in stool after 14 days but not at 28 days. CONCLUSION These findings support modulation of gut microbiota and fermentation byproducts by SRB and suggest that foods with similar ability to increase dietary fiber intake may not have equal effects on gut microbiota and microbial metabolism.
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Affiliation(s)
- Amy M Sheflin
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, CO, USA
| | - Erica C Borresen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jay S Kirkwood
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, USA
| | - Claudia M Boot
- Department of Chemistry, Central Instrument Facility, Colorado State University, Fort Collins, CO, USA
| | - Alyssa K Whitney
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, CO, USA
| | - Shen Lu
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, CO, USA
| | - Regina J Brown
- Department of Medicine, Division of Medical Oncology, University of Colorado Denver and Lone Tree Oncology affiliation of University of Colorado Cancer Center, Aurora, Colorado, USA
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, USA
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Tiffany L Weir
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, CO, USA
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270
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Szewczyk J, Collet JF. The Journey of Lipoproteins Through the Cell: One Birthplace, Multiple Destinations. Adv Microb Physiol 2016; 69:1-50. [PMID: 27720009 DOI: 10.1016/bs.ampbs.2016.07.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bacterial lipoproteins are a very diverse group of proteins characterized by the presence of an N-terminal lipid moiety that serves as a membrane anchor. Lipoproteins have a wide variety of crucial functions, ranging from envelope biogenesis to stress response. In Gram-negative bacteria, lipoproteins can be targeted to various destinations in the cell, including the periplasmic side of the cytoplasmic or outer membrane, the cell surface or the external milieu. The sorting mechanisms have been studied in detail in Escherichia coli, but exceptions to the rules established in this model bacterium exist in other bacteria. In this chapter, we will present the current knowledge on lipoprotein sorting in the cell. Our particular focus will be on the surface-exposed lipoproteins that appear to be much more common than previously assumed. We will discuss the different targeting strategies, provide numerous examples of surface-exposed lipoproteins and discuss the techniques used to assess their surface exposure.
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Affiliation(s)
- J Szewczyk
- WELBIO, Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - J-F Collet
- WELBIO, Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Brussels, Belgium.
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271
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Purification, expression and characterization of a novel α-l-fucosidase from a marine bacteria Wenyingzhuangia fucanilytica. Protein Expr Purif 2016; 129:9-17. [PMID: 27576198 DOI: 10.1016/j.pep.2016.08.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/23/2016] [Accepted: 08/25/2016] [Indexed: 11/22/2022]
Abstract
α-l-Fucosyl residues are frequently found in oligosaccharides, polysaccharides and glycoconjugates which play fundamental roles in various biological processes. α-l-Fucosidases, glycoside hydrolases for catalyzing the removal of α-l-fucose, can serve as desirable tools in the study and the modification of fucose-containing biomolecules. In this study, an α-l-fucosidase named as Alf1_Wf was purified from a marine bacterium Wenyingzhuangia fucanilytica by using a combination of chromatographic procedures. The sequence of Alf1_Wf was identified via proteomics analysis against the predicted proteome of the bacterium. Recombinant Alf1_Wf with 6×His tag was expressed in E. coli and showed α-l-fucosidase activity. Sequence annotation revealed that Alf1_Wf contained a combination of GH29 catalytic domain and CBM35 accessory domain. Alf1_Wf was confirmed as a member of GH29-A subfamily based on the phylogenetic analysis. Furthermore, biochemical properties and kinetic characteristics of the enzyme were also determined. Substrate specificity determination showed that Alf1_Wf was capable in hydrolyzing α1,4-fucosidic linkage and synthetic substrate pNP-fucose. Besides, Alf1_Wf could act on partially degraded fucoidan. This study successfully purified, identified, cloned, expressed and characterized a novel α-l-fucosidase, and meanwhile revealed a new multidomain structure of glycoside hydrolase. The knowledge gained from this study should facilitate the further research and application of α-l-fucosidases.
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272
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Roth C, Petricevic M, John A, Goddard-Borger ED, Davies GJ, Williams SJ. Structural and mechanistic insights into a Bacteroides vulgatus retaining N-acetyl-β-galactosaminidase that uses neighbouring group participation. Chem Commun (Camb) 2016; 52:11096-9. [PMID: 27546776 DOI: 10.1039/c6cc04649e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacteroides vulgatus is a member of the human microbiota whose abundance is increased in patients with Crohn's disease. We show that a B. vulgatus glycoside hydrolase from the carbohydrate active enzyme family GH123, BvGH123, is an N-acetyl-β-galactosaminidase that acts with retention of stereochemistry, and, through a 3-D structure in complex with Gal-thiazoline, provide evidence in support of a neighbouring group participation mechanism.
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Affiliation(s)
- C Roth
- Department of Chemistry, University of York, Heslington, York, UK.
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273
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Fischbach MA, Segre JA. Signaling in Host-Associated Microbial Communities. Cell 2016; 164:1288-1300. [PMID: 26967294 DOI: 10.1016/j.cell.2016.02.037] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Indexed: 12/14/2022]
Abstract
Human-associated microbiota form and stabilize communities based on interspecies interactions. We review how these microbe-microbe and microbe-host interactions are communicated to shape communities over a human's lifespan, including periods of health and disease. Modeling and dissecting signaling in host-associated communities is crucial to understand their function and will open the door to therapies that prevent or correct microbial community dysfunction to promote health and treat disease.
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Affiliation(s)
- Michael A Fischbach
- Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA.
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274
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Recent structural insights into the enzymology of the ubiquitous plant cell wall glycan xyloglucan. Curr Opin Struct Biol 2016; 40:43-53. [PMID: 27475238 DOI: 10.1016/j.sbi.2016.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 01/03/2023]
Abstract
The xyloglucans (XyGs) constitute a family of highly decorated β(1→4)-glucans whose members are widespread and abundant across the plant kingdom. As such, XyGs constitute a significant reserve of metabolically accessible monosaccharides for diverse phytopathogenic, saprophytic, and gut symbiotic micro-organisms. To overcome the intrinsic stability of the diverse glycosidic bonds in XyGs, bacteria and fungi have evolved extensive repertoires of xyloglucan-active enzymes from manifold families, whose exquisitely adapted tertiary structures are recently coming to light.
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275
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Gut microbiota in autoimmunity: potential for clinical applications. Arch Pharm Res 2016; 39:1565-1576. [DOI: 10.1007/s12272-016-0796-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/15/2016] [Indexed: 01/09/2023]
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276
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Functional and modular analyses of diverse endoglucanases from Ruminococcus albus 8, a specialist plant cell wall degrading bacterium. Sci Rep 2016; 6:29979. [PMID: 27439730 PMCID: PMC4954948 DOI: 10.1038/srep29979] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/24/2016] [Indexed: 11/09/2022] Open
Abstract
Ruminococcus albus 8 is a specialist plant cell wall degrading ruminal bacterium capable of utilizing hemicellulose and cellulose. Cellulose degradation requires a suite of enzymes including endoglucanases, exoglucanases, and β-glucosidases. The enzymes employed by R. albus 8 in degrading cellulose are yet to be completely elucidated. Through bioinformatic analysis of a draft genome sequence of R. albus 8, seventeen putatively cellulolytic genes were identified. The genes were heterologously expressed in E. coli, and purified to near homogeneity. On biochemical analysis with cellulosic substrates, seven of the gene products (Ra0185, Ra0259, Ra0325, Ra0903, Ra1831, Ra2461, and Ra2535) were identified as endoglucanases, releasing predominantly cellobiose and cellotriose. Each of the R. albus 8 endoglucanases, except for Ra0259 and Ra0325, bound to the model crystalline cellulose Avicel, confirming functional carbohydrate binding modules (CBMs). The polypeptides for Ra1831 and Ra2535 were found to contain distantly related homologs of CBM65. Mutational analysis of residues within the CBM65 of Ra1831 identified key residues required for binding. Phylogenetic analysis of the endoglucanases revealed three distinct subfamilies of glycoside hydrolase family 5 (GH5). Our results demonstrate that this fibrolytic bacterium uses diverse GH5 catalytic domains appended with different CBMs, including novel forms of CBM65, to degrade cellulose.
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277
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Bennke CM, Krüger K, Kappelmann L, Huang S, Gobet A, Schüler M, Barbe V, Fuchs BM, Michel G, Teeling H, Amann RI. Polysaccharide utilisation loci ofBacteroidetesfrom two contrasting open ocean sites in the North Atlantic. Environ Microbiol 2016; 18:4456-4470. [DOI: 10.1111/1462-2920.13429] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Christin M. Bennke
- Max-Planck-Institute for Marine Microbiology, Department of Molecular Ecology; Celsiusstraße 1 28359 Bremen Germany
| | - Karen Krüger
- Max-Planck-Institute for Marine Microbiology, Department of Molecular Ecology; Celsiusstraße 1 28359 Bremen Germany
| | - Lennart Kappelmann
- Max-Planck-Institute for Marine Microbiology, Department of Molecular Ecology; Celsiusstraße 1 28359 Bremen Germany
| | - Sixing Huang
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures; Inhoffenstraße 7B 38124 Braunschweig Germany
| | - Angélique Gobet
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models; Station Biologique de Roscoff, CS 90074 F-29688 Roscoff cedex Bretagne France
| | - Margarete Schüler
- University of Bayreuth; Biologie / Elektronenmikroskopie B1, Universitätsstraße 30 95447 Bayreuth Germany
| | - Valérie Barbe
- Laboratoire de Biologie Moléculaire pour l'Étude des Génomes, C.E.A, Institut de Génomique - Genoscope; 2 rue Gaston Crémieux 91057 Évry cedex France
| | - Bernhard M. Fuchs
- Max-Planck-Institute for Marine Microbiology, Department of Molecular Ecology; Celsiusstraße 1 28359 Bremen Germany
| | - Gurvan Michel
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models; Station Biologique de Roscoff, CS 90074 F-29688 Roscoff cedex Bretagne France
| | - Hanno Teeling
- Max-Planck-Institute for Marine Microbiology, Department of Molecular Ecology; Celsiusstraße 1 28359 Bremen Germany
| | - Rudolf I. Amann
- Max-Planck-Institute for Marine Microbiology, Department of Molecular Ecology; Celsiusstraße 1 28359 Bremen Germany
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278
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Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing. Sci Rep 2016; 6:29681. [PMID: 27411898 PMCID: PMC4944186 DOI: 10.1038/srep29681] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/20/2016] [Indexed: 02/08/2023] Open
Abstract
Demands for faster and more accurate methods to analyze microbial communities from natural and clinical samples have been increasing in the medical and healthcare industry. Recent advances in next-generation sequencing technologies have facilitated the elucidation of the microbial community composition with higher accuracy and greater throughput than was previously achievable; however, the short sequencing reads often limit the microbial composition analysis at the species level due to the high similarity of 16S rRNA amplicon sequences. To overcome this limitation, we used the nanopore sequencing platform to sequence full-length 16S rRNA amplicon libraries prepared from the mouse gut microbiota. A comparison of the nanopore and short-read sequencing data showed that there were no significant differences in major taxonomic units (89%) except one phylotype and three taxonomic units. Moreover, both sequencing data were highly similar at all taxonomic resolutions except the species level. At the species level, nanopore sequencing allowed identification of more species than short-read sequencing, facilitating the accurate classification of the bacterial community composition. Therefore, this method of full-length 16S rRNA amplicon sequencing will be useful for rapid, accurate and efficient detection of microbial diversity in various biological and clinical samples.
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279
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Ormerod KL, Wood DLA, Lachner N, Gellatly SL, Daly JN, Parsons JD, Dal'Molin CGO, Palfreyman RW, Nielsen LK, Cooper MA, Morrison M, Hansbro PM, Hugenholtz P. Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. MICROBIOME 2016; 4:36. [PMID: 27388460 PMCID: PMC4936053 DOI: 10.1186/s40168-016-0181-2] [Citation(s) in RCA: 426] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/23/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeothermic animals and are increasingly being recognized as a numerically predominant member of the gut microbiota; however, little is known about the nature of their interactions with the host. RESULTS Here, we provide the first whole genome exploration of this family, for which we propose the name "Candidatus Homeothermaceae," using 30 population genomes extracted from fecal samples of four different animal hosts: human, mouse, koala, and guinea pig. We infer the core metabolism of "Ca. Homeothermaceae" to be that of fermentative or nanaerobic bacteria, resembling that of related Bacteroidales families. In addition, we describe three trophic guilds within the family, plant glycan (hemicellulose and pectin), host glycan, and α-glucan, each broadly defined by increased abundance of enzymes involved in the degradation of particular carbohydrates. CONCLUSIONS "Ca. Homeothermaceae" representatives constitute a substantial component of the murine gut microbiota, as well as being present within the human gut, and this study provides important first insights into the nature of their residency. The presence of trophic guilds within the family indicates the potential for niche partitioning and specific roles for each guild in gut health and dysbiosis.
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Affiliation(s)
- Kate L Ormerod
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - David L A Wood
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Nancy Lachner
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Shaan L Gellatly
- Priority Research Centre for Healthy Lungs, The University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Joshua N Daly
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Jeremy D Parsons
- QFAB Bioinformatics, The University of Queensland, Brisbane, Australia
| | - Cristiana G O Dal'Molin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Robin W Palfreyman
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Mark Morrison
- Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, The University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
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280
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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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281
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Foley MH, Cockburn DW, Koropatkin NM. The Sus operon: a model system for starch uptake by the human gut Bacteroidetes. Cell Mol Life Sci 2016; 73:2603-17. [PMID: 27137179 PMCID: PMC4924478 DOI: 10.1007/s00018-016-2242-x] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/16/2022]
Abstract
Resident bacteria in the densely populated human intestinal tract must efficiently compete for carbohydrate nutrition. The Bacteroidetes, a dominant bacterial phylum in the mammalian gut, encode a plethora of discrete polysaccharide utilization loci (PULs) that are selectively activated to facilitate glycan capture at the cell surface. The most well-studied PUL-encoded glycan-uptake system is the starch utilization system (Sus) of Bacteroides thetaiotaomicron. The Sus includes the requisite proteins for binding and degrading starch at the surface of the cell preceding oligosaccharide transport across the outer membrane for further depolymerization to glucose in the periplasm. All mammalian gut Bacteroidetes possess analogous Sus-like systems that target numerous diverse glycans. In this review, we discuss what is known about the eight Sus proteins of B. thetaiotaomicron that define the Sus-like paradigm of nutrient acquisition that is exclusive to the Gram-negative Bacteroidetes. We emphasize the well-characterized outer membrane proteins SusDEF and the α-amylase SusG, each of which have unique structural features that allow them to interact with starch on the cell surface. Despite the apparent redundancy in starch-binding sites among these proteins, each has a distinct role during starch catabolism. Additionally, we consider what is known about how these proteins dynamically interact and cooperate in the membrane and propose a model for the formation of the Sus outer membrane complex.
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Affiliation(s)
- Matthew H Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - 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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282
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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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283
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Reddy SK, Bågenholm V, Pudlo NA, Bouraoui H, Koropatkin NM, Martens EC, Stålbrand H. A β-mannan utilization locus in Bacteroides ovatus involves a GH36 α-galactosidase active on galactomannans. FEBS Lett 2016; 590:2106-18. [PMID: 27288925 PMCID: PMC5094572 DOI: 10.1002/1873-3468.12250] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/07/2016] [Accepted: 06/09/2016] [Indexed: 11/25/2022]
Abstract
The Bacova_02091 gene in the β‐mannan utilization locus of Bacteroides ovatus encodes a family GH36 α‐galactosidase (BoGal36A), transcriptionally upregulated during growth on galactomannan. Characterization of recombinant BoGal36A reveals unique properties compared to other GH36 α‐galactosidases, which preferentially hydrolyse terminal α‐galactose in raffinose family oligosaccharides. BoGal36A prefers hydrolysing internal galactose substitutions from intact and depolymerized galactomannan. BoGal36A efficiently releases (> 90%) galactose from guar and locust bean galactomannans, resulting in precipitation of the polysaccharides. As compared to other GH36 structures, the BoGal36A 3D model displays a loop deletion, resulting in a wider active site cleft which likely can accommodate a galactose‐substituted polymannose backbone.
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Affiliation(s)
- Sumitha K Reddy
- Department of Biochemistry and Structural Biology, Lund University, Sweden
| | - Viktoria Bågenholm
- Department of Biochemistry and Structural Biology, Lund University, Sweden
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Hanene Bouraoui
- Department of Biochemistry and Structural Biology, Lund University, Sweden
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Henrik Stålbrand
- Department of Biochemistry and Structural Biology, Lund University, Sweden
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284
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Gardner JG. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus. World J Microbiol Biotechnol 2016; 32:121. [PMID: 27263016 DOI: 10.1007/s11274-016-2068-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 04/07/2016] [Indexed: 01/10/2023]
Abstract
Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. This review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.
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Affiliation(s)
- Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
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285
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Lobb B, Doxey AC. Novel function discovery through sequence and structural data mining. Curr Opin Struct Biol 2016; 38:53-61. [DOI: 10.1016/j.sbi.2016.05.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/17/2016] [Accepted: 05/24/2016] [Indexed: 01/30/2023]
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286
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Sun C, Fu GY, Zhang CY, Hu J, Xu L, Wang RJ, Su Y, Han SB, Yu XY, Cheng H, Zhang XQ, Huo YY, Xu XW, Wu M. Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci. Appl Environ Microbiol 2016; 82:2975-2987. [PMID: 26969704 PMCID: PMC4959061 DOI: 10.1128/aem.00204-16] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/04/2016] [Indexed: 11/20/2022] Open
Abstract
The members of the phylum Bacteroidetes are recognized as some of the most important specialists for the degradation of polysaccharides. However, in contrast to research on Bacteroidetes in the human gut, research on polysaccharide degradation by marine Bacteroidetes is still rare. The genus Algibacter belongs to the Flavobacteriaceae family of the Bacteroidetes, and most species in this genus are isolated from or near the habitat of algae, indicating a preference for the complex polysaccharides of algae. In this work, a novel brown-seaweed-degrading strain designated HZ22 was isolated from the surface of a brown seaweed (Laminaria japonica). On the basis of its physiological, chemotaxonomic, and genotypic characteristics, it is proposed that strain HZ22 represents a novel species in the genus Algibacter with the proposed name Algibacter alginolytica sp. nov. The genome of strain HZ22, the type strain of this species, harbors 3,371 coding sequences (CDSs) and 255 carbohydrate-active enzymes (CAZymes), including 104 glycoside hydrolases (GHs) and 18 polysaccharide lyases (PLs); this appears to be the highest proportion of CAZymes (∼7.5%) among the reported strains in the class Flavobacteria Seventeen polysaccharide utilization loci (PUL) are predicted to be specific for marine polysaccharides, especially algal polysaccharides from red, green, and brown seaweeds. In particular, PUL N is predicted to be specific for alginate. Taking these findings together with the results of assays of crude alginate lyases, we prove that strain HZ22(T) can completely degrade alginate. This work reveals that strain HZ22(T) has good potential for the degradation of algal polysaccharides and that the structure and related mechanism of PUL in strain HZ22(T) are worth further research.
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Affiliation(s)
- Cong Sun
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Ge-Yi Fu
- Ocean College, Zhejiang University, Hangzhou, People's Republic of China
| | - Chong-Ya Zhang
- Ocean College, Zhejiang University, Hangzhou, People's Republic of China
| | - Jing Hu
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Lin Xu
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Rui-Jun Wang
- Ocean College, Zhejiang University, Hangzhou, People's Republic of China
| | - Yue Su
- Ocean College, Zhejiang University, Hangzhou, People's Republic of China
| | - Shuai-Bo Han
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiao-Yun Yu
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Hong Cheng
- Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou, People's Republic of China
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou, People's Republic of China
| | - Xin-Qi Zhang
- School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Linan, People's Republic of China
| | - Ying-Yi Huo
- Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou, People's Republic of China
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou, People's Republic of China
| | - Xue-Wei Xu
- Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou, People's Republic of China
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou, People's Republic of China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- Ocean College, Zhejiang University, Hangzhou, People's Republic of China
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287
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Abstract
Polysaccharide utilization loci (PUL) within the genomes of resident human gut Bacteroidetes are central to the metabolism of the otherwise indigestible complex carbohydrates known as “dietary fiber.” However, functional characterization of PUL lags significantly behind sequencing efforts, which limits physiological understanding of the human-bacterial symbiosis. In particular, the molecular basis of complex polysaccharide recognition, an essential prerequisite to hydrolysis by cell surface glycosidases and subsequent metabolism, is generally poorly understood. Here, we present the biochemical, structural, and reverse genetic characterization of two unique cell surface glycan-binding proteins (SGBPs) encoded by a xyloglucan utilization locus (XyGUL) from Bacteroides ovatus, which are integral to growth on this key dietary vegetable polysaccharide. Biochemical analysis reveals that these outer membrane-anchored proteins are in fact exquisitely specific for the highly branched xyloglucan (XyG) polysaccharide. The crystal structure of SGBP-A, a SusD homolog, with a bound XyG tetradecasaccharide reveals an extended carbohydrate-binding platform that primarily relies on recognition of the β-glucan backbone. The unique, tetra-modular structure of SGBP-B is comprised of tandem Ig-like folds, with XyG binding mediated at the distal C-terminal domain. Despite displaying similar affinities for XyG, reverse-genetic analysis reveals that SGBP-B is only required for the efficient capture of smaller oligosaccharides, whereas the presence of SGBP-A is more critical than its carbohydrate-binding ability for growth on XyG. Together, these data demonstrate that SGBP-A and SGBP-B play complementary, specialized roles in carbohydrate capture by B. ovatus and elaborate a model of how vegetable xyloglucans are accessed by the Bacteroidetes. The Bacteroidetes are dominant bacteria in the human gut that are responsible for the digestion of the complex polysaccharides that constitute “dietary fiber.” Although this symbiotic relationship has been appreciated for decades, little is currently known about how Bacteroidetes seek out and bind plant cell wall polysaccharides as a necessary first step in their metabolism. Here, we provide the first biochemical, crystallographic, and genetic insight into how two surface glycan-binding proteins from the complex Bacteroides ovatus xyloglucan utilization locus (XyGUL) enable recognition and uptake of this ubiquitous vegetable polysaccharide. Our combined analysis illuminates new fundamental aspects of complex polysaccharide recognition, cleavage, and import at the Bacteroidetes cell surface that may facilitate the development of prebiotics to target this phylum of gut bacteria.
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288
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Wang W, Yan R, Nocek BP, Vuong TV, Di Leo R, Xu X, Cui H, Gatenholm P, Toriz G, Tenkanen M, Savchenko A, Master ER. Biochemical and Structural Characterization of a Five-domain GH115 α-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T. J Biol Chem 2016; 291:14120-14133. [PMID: 27129264 DOI: 10.1074/jbc.m115.702944] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 01/01/2023] Open
Abstract
Glucuronic acid (GlcAp) and/or methylglucuronic acid (MeGlcAp) decorate the major forms of xylan in hardwood and coniferous softwoods as well as many cereal grains. Accordingly, the complete utilization of glucuronoxylans or conversion to sugar precursors requires the action of main chain xylanases as well as α-glucuronidases that release the α- (1→2)-linked (Me)GlcAp side groups. Herein, a family GH115 enzymefrom the marine bacterium Saccharophagus degradans 2-40(T), SdeAgu115A, demonstrated activity toward glucuronoxylan and oligomers thereof with preference toward MeGlcAp linked to internal xylopyranosyl residues. Unique biochemical characteristics of NaCl activation were also observed. The crystal structure of SdeAgu115A revealed a five-domain architecture, with an additional insertion C(+) domain that had significant impact on the domain arrangement of SdeAgu115A monomer and its dimerization. The participation of domain C(+) in substrate binding was supported by reduced substrate inhibition upon introducing W773A, W689A, and F696A substitutions within this domain. In addition to Asp-335, the catalytic essentiality of Glu-216 was revealed by site-specific mutagenesis. A primary sequence analysis suggested that the SdeAgu115A architecture is shared by more than half of GH115 members, thus defining a distinct archetype for GH115 enzymes.
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Affiliation(s)
- Weijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Ruoyu Yan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Boguslaw P Nocek
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Xiaohui Xu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Hong Cui
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Paul Gatenholm
- Department of Chemistry and Chemical Engineering, Wallenberg Wood Science Center and Biopolymer Technology, Chalmers University of Technology, Kemivägen 4, Gothenburg 412 96, Sweden
| | - Guillermo Toriz
- Department of Chemistry and Chemical Engineering, Wallenberg Wood Science Center and Biopolymer Technology, Chalmers University of Technology, Kemivägen 4, Gothenburg 412 96, Sweden,; Department of Wood, Cellulose and Paper Research, University of Guadalajara, Guadalajara 44100, Mexico
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, Helsinki 00014, Finland
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada,.
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada,.
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289
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Matsuzawa T, Kimura N, Suenaga H, Yaoi K. Screening, identification, and characterization of α-xylosidase from a soil metagenome. J Biosci Bioeng 2016; 122:393-9. [PMID: 27074950 DOI: 10.1016/j.jbiosc.2016.03.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 03/04/2016] [Accepted: 03/17/2016] [Indexed: 10/22/2022]
Abstract
A novel α-xylosidase, MeXyl31, was isolated and characterized from a soil metagenomic library. The amino acid sequence of MeXyl31 showed a slight homology with other characterized α-xylosidases. The optimal pH and temperature of recombinant MeXyl31 were pH 5.5 and 45°C, respectively. Recombinant MeXyl31 had a higher α-xylosidase activity toward pNP α-d-xylopyranoside than pNP α-d-glucopyranoside, isoprimeverose, and other xyloglucan oligosaccharides. The kcat/Km value toward pNP α-d-xylopyranoside was about 750-fold higher than that of isoprimeverose. MeXyl31 activity was strongly inactivated in the presence of zinc and copper ions. MeXyl31 is the first α-xylosidase isolated from the metagenome and, relative to other xyloglucan oligosaccharides, shows higher activity toward pNP α-d-xylopyranoside.
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Nobutada Kimura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Hikaru Suenaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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290
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Katayama T. Host-derived glycans serve as selected nutrients for the gut microbe: human milk oligosaccharides and bifidobacteria†. Biosci Biotechnol Biochem 2016; 80:621-32. [DOI: 10.1080/09168451.2015.1132153] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Abstract
Lactation is a common feeding strategy of eutherian mammals, but its functions go beyond feeding the neonates. Ever since Tissier isolated bifidobacteria from the stool of breast-fed infants, human milk has been postulated to contain compounds that selectively stimulate the growth of bifidobacteria in intestines. However, until relatively recently, there have been no reports to link human milk compound(s) with bifidobacterial physiology. Over the past decade, successive studies have demonstrated that infant-gut-associated bifidobacteria are equipped with genetic and enzymatic toolsets dedicated to assimilation of host-derived glycans, especially human milk oligosaccharides (HMOs). Among gut microbes, the presence of enzymes required for degrading HMOs with type-1 chains is essentially limited to infant-gut-associated bifidobacteria, suggesting HMOs serve as selected nutrients for the bacteria. In this study, I shortly discuss the research on bifidobacteria and HMOs from a historical perspective and summarize the roles of bifidobacterial enzymes in the assimilation of HMOs with type-1 chains. Based on this overview, I suggest the co-evolution between bifidobacteria and human beings mediated by HMOs.
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Affiliation(s)
- Takane Katayama
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Japan
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291
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Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. Sci Rep 2016; 6:23473. [PMID: 27032335 PMCID: PMC4817029 DOI: 10.1038/srep23473] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/25/2016] [Indexed: 11/25/2022] Open
Abstract
Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme.
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292
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Attia M, Stepper J, Davies GJ, Brumer H. Functional and structural characterization of a potent GH74 endo-xyloglucanase from the soil saprophyte Cellvibrio japonicus unravels the first step of xyloglucan degradation. FEBS J 2016; 283:1701-19. [PMID: 26929175 DOI: 10.1111/febs.13696] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/09/2016] [Accepted: 02/25/2016] [Indexed: 11/27/2022]
Abstract
UNLABELLED The heteropolysaccharide xyloglucan (XyG) comprises up to one-quarter of the total carbohydrate content of terrestrial plant cell walls and, as such, represents a significant reservoir in the global carbon cycle. The complex composition of XyG requires a consortium of backbone-cleaving endo-xyloglucanases and side-chain cleaving exo-glycosidases for complete saccharification. The biochemical basis for XyG utilization by the model Gram-negative soil saprophytic bacterium Cellvibrio japonicus is incompletely understood, despite the recent characterization of associated side-chain cleaving exo-glycosidases. We present a detailed functional and structural characterization of a multimodular enzyme encoded by gene locus CJA_2477. The CJA_2477 gene product comprises an N-terminal glycoside hydrolase family 74 (GH74) endo-xyloglucanase module in train with two carbohydrate-binding modules (CBMs) from families 10 and 2 (CBM10 and CBM2). The GH74 catalytic domain generates Glc4 -based xylogluco-oligosaccharide (XyGO) substrates for downstream enzymes through an endo-dissociative mode of action. X-ray crystallography of the GH74 module, alone and in complex with XyGO products spanning the entire active site, revealed a broad substrate-binding cleft specifically adapted to XyG recognition, which is composed of two seven-bladed propeller domains characteristic of the GH74 family. The appended CBM10 and CBM2 members notably did not bind XyG, nor other soluble polysaccharides, and instead were specific cellulose-binding modules. Taken together, these data shed light on the first step of xyloglucan utilization by C. japonicus and expand the repertoire of GHs and CBMs for selective biomass analysis and utilization. DATABASE Structural data have been deposited in the RCSB protein database under the Protein Data Bank codes: 5FKR, 5FKS, 5FKT and 5FKQ.
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Affiliation(s)
- Mohamed Attia
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, Canada
| | | | | | - Harry Brumer
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, Canada
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293
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Mechanisms involved in xyloglucan catabolism by the cellulosome-producing bacterium Ruminiclostridium cellulolyticum. Sci Rep 2016; 6:22770. [PMID: 26946939 PMCID: PMC4780118 DOI: 10.1038/srep22770] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/23/2016] [Indexed: 12/23/2022] Open
Abstract
Xyloglucan, a ubiquitous highly branched plant polysaccharide, was found to be rapidly degraded and metabolized by the cellulosome-producing bacterium Ruminiclostridium cellulolyticum. Our study shows that at least four cellulosomal enzymes displaying either endo- or exoxyloglucanase activities, achieve the extracellular degradation of xyloglucan into 4-glucosyl backbone xyloglucan oligosaccharides. The released oligosaccharides (composed of up to 9 monosaccharides) are subsequently imported by a highly specific ATP-binding cassette transporter (ABC-transporter), the expression of the corresponding genes being strongly induced by xyloglucan. This polysaccharide also triggers the synthesis of cytoplasmic β-galactosidase, α-xylosidase, and β-glucosidase that act sequentially to convert the imported oligosaccharides into galactose, xylose, glucose and unexpectedly cellobiose. Thus R. cellulolyticum has developed an energy-saving strategy to metabolize this hemicellulosic polysaccharide that relies on the action of the extracellular cellulosomes, a highly specialized ABC-transporter, and cytoplasmic enzymes acting in a specific order. This strategy appears to be widespread among cellulosome-producing mesophilic bacteria which display highly similar gene clusters encoding the cytosolic enzymes and the ABC-transporter.
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294
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Despres J, Forano E, Lepercq P, Comtet-Marre S, Jubelin G, Yeoman CJ, Miller MEB, Fields CJ, Terrapon N, Le Bourvellec C, Renard CMGC, Henrissat B, White BA, Mosoni P. Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics 2016; 17:147. [PMID: 26920945 PMCID: PMC4769552 DOI: 10.1186/s12864-016-2472-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 02/12/2016] [Indexed: 12/16/2022] Open
Abstract
Background Diet and particularly dietary fibres have an impact on the gut microbiome and play an important role in human health and disease. Pectin is a highly consumed dietary fibre found in fruits and vegetables and is also a widely used additive in the food industry. Yet there is no information on the effect of pectin on the human gut microbiome. Likewise, little is known on gut pectinolytic bacteria and their enzyme systems. This study was undertaken to investigate the mechanisms of pectin degradation by the prominent human gut symbiont Bacteroides xylanisolvens. Results Transcriptomic analyses of B. xylanisolvens XB1A grown on citrus and apple pectins at mid- and late-log phases highlighted six polysaccharide utilization loci (PUL) that were overexpressed on pectin relative to glucose. The PUL numbers used in this report are those given by Terrapon et al. (Bioinformatics 31(5):647-55, 2015) and found in the PUL database: http://www.cazy.org/PULDB/. Based on their CAZyme composition, we propose that PUL 49 and 50, the most overexpressed PULs on both pectins and at both growth phases, are involved in homogalacturonan (HG) and type I rhamnogalacturonan (RGI) degradation, respectively. PUL 13 and PUL 2 could be involved in the degradation of arabinose-containing side chains and of type II rhamnogalacturonan (RGII), respectively. Considering that HG is the most abundant moiety (>70 %) within pectin, the importance of PUL 49 was further investigated by insertion mutagenesis into the susC-like gene. The insertion blocked transcription of the susC-like and the two downstream genes (susD-like/FnIII). The mutant showed strong growth reduction, thus confirming that PUL 49 plays a major role in pectin degradation. Conclusion This study shows the existence of six PULs devoted to pectin degradation by B. xylanisolvens, one of them being particularly important in this function. Hence, this species deploys a very complex enzymatic machinery that probably reflects the structural complexity of pectin. Our findings also highlight the metabolic plasticity of B. xylanisolvens towards dietary fibres that contributes to its competitive fitness within the human gut ecosystem. Wider functional and ecological studies are needed to understand how dietary fibers and especially plant cell wall polysaccharides drive the composition and metabolism of the fibrolytic and non-fibrolytic community within the gut microbial ecosystem. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2472-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jordane Despres
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, 63122, Saint-Genès Champanelle, France.
| | - Evelyne Forano
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, 63122, Saint-Genès Champanelle, France.
| | - Pascale Lepercq
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, 63122, Saint-Genès Champanelle, France.
| | - Sophie Comtet-Marre
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, 63122, Saint-Genès Champanelle, France.
| | - Grégory Jubelin
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, 63122, Saint-Genès Champanelle, France.
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, 59718, USA.
| | - Margret E Berg Miller
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Christopher J Fields
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France. .,INRA, USC 1408 AFMB, 13288, Marseille, France.
| | - Carine Le Bourvellec
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, F-84000, Avignon, France. .,Université d'Avignon et des Pays de Vaucluse, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, F-84000, Avignon, France.
| | - Catherine M G C Renard
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, F-84000, Avignon, France. .,Université d'Avignon et des Pays de Vaucluse, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, F-84000, Avignon, France.
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France. .,INRA, USC 1408 AFMB, 13288, Marseille, France. .,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Bryan A White
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Pascale Mosoni
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, 63122, Saint-Genès Champanelle, France.
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295
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O Sheridan P, Martin JC, Lawley TD, Browne HP, Harris HMB, Bernalier-Donadille A, Duncan SH, O'Toole PW, P Scott K, J Flint H. Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes. Microb Genom 2016; 2:e000043. [PMID: 28348841 PMCID: PMC5320581 DOI: 10.1099/mgen.0.000043] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/11/2015] [Indexed: 12/25/2022] Open
Abstract
Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the Bacteroidetes, with very little known about the Firmicutes. This work investigates the carbohydrate-active enzymes (CAZymes) in a group of Firmicutes, Roseburia spp. and Eubacterium rectale, which play an important role in producing butyrate from dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representing E. rectale and four Roseburia spp. were analysed for carbohydrate-active genes. Following assembly into a pan-genome, core, variable and unique genes were identified. The 1840 CAZyme genes identified in the pan-genome were assigned to 538 orthologous groups, of which only 26 were present in all strains, indicating considerable inter-strain variability. This analysis was used to categorize the 11 strains into four carbohydrate utilization ecotypes (CUEs), which were shown to correspond to utilization of different carbohydrates for growth. Many glycoside hydrolase genes were found linked to genes encoding oligosaccharide transporters and regulatory elements in the genomes of Roseburia spp. and E. rectale, forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature in Bacteroidetes, key differences were noted in these Firmicutes, including the absence of close homologues of Bacteroides polysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in the Roseburia/E. rectale group are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group.
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Affiliation(s)
- Paul O Sheridan
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Jennifer C Martin
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | | | | | - Hugh M B Harris
- 3 Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Annick Bernalier-Donadille
- 4 Unité de Microbiologie INRA, Centre de Recherche de Clermont-Ferrand/Theix, 63122 Saint Genès Champanelle, France
| | - Sylvia H Duncan
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Paul W O'Toole
- 3 Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Karen P Scott
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Harry J Flint
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
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296
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Abstract
The enzyme-catalysed degradation of oligo and polysaccharides is of considerable interest in many fields ranging from the fundamental–understanding the intrinsic chemical beauty–through to the applied, including diverse practical applications in medicine and biotechnology. Carbohydrates are the most stereochemically-complex biopolymer, and myriad different natural polysaccharides have led to evolution of multifaceted enzyme consortia for their degradation. The glycosidic bonds that link sugar monomers are among the most chemically-stable, yet enzymatically-labile, bonds in the biosphere. That glycoside hydrolases can achieve a rate enhancement (kcat/kuncat) >1017-fold provides testament to their remarkable proficiency and the sophistication of their catalysis reaction mechanisms. The last two decades have seen significant advances in the discovery of new glycosidase sequences, sequence-based classification into families and clans, 3D structures and reaction mechanisms, providing new insights into enzymatic catalysis. New impetus to these studies has been provided by the challenges inherent in plant and microbial polysaccharide degradation, both in the context of environmentally-sustainable routes to foods and biofuels, and increasingly in human nutrition. Study of the reaction mechanism of glycoside hydrolases has also inspired the development of enzyme inhibitors, both as mechanistic probes and increasingly as therapeutic agents. We are on the cusp of a new era where we are learning how to dovetail powerful computational techniques with structural and kinetic data to provide an unprecedented view of conformational details of enzyme action.
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297
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Affiliation(s)
- Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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298
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Direct Image-Based Enumeration of Clostridium phytofermentans Cells on Insoluble Plant Biomass Growth Substrates. Appl Environ Microbiol 2016; 82:972-8. [PMID: 26637592 DOI: 10.1128/aem.03119-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/15/2015] [Indexed: 11/20/2022] Open
Abstract
A dual-fluorescent-dye protocol to visualize and quantify Clostridium phytofermentans ISDg (ATCC 700394) cells growing on insoluble cellulosic substrates was developed by combining calcofluor white staining of the growth substrate with cell staining using the nucleic acid dye Syto 9. Cell growth, cell substrate attachment, and fermentation product formation were investigated in cultures containing either Whatman no. 1 filter paper, wild-type Sorghum bicolor, or a reduced-lignin S. bicolor double mutant (bmr-6 bmr-12 double mutant) as the growth substrate. After 3 days of growth, cell numbers in cultures grown on filter paper as the substrate were 6.0- and 2.2-fold higher than cell numbers in cultures with wild-type sorghum and double mutant sorghum, respectively. However, cells produced more ethanol per cell when grown with either sorghum substrate than with filter paper as the substrate. Ethanol yields of cultures were significantly higher with double mutant sorghum than with wild-type sorghum or filter paper as the substrate. Moreover, ethanol production correlated with cell attachment in sorghum cultures: 90% of cells were directly attached to the double mutant sorghum substrate, while only 76% of cells were attached to wild-type sorghum substrate. With filter paper as the growth substrate, ethanol production was correlated with cell number; however, with either wild-type or mutant sorghum, ethanol production did not correlate with cell number, suggesting that only a portion of the microbial cell population was active during growth on sorghum. The dual-staining procedure described here may be used to visualize and enumerate cells directly on insoluble cellulosic substrates, enabling in-depth studies of interactions of microbes with plant biomass.
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299
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Hutkins RW, Krumbeck JA, Bindels LB, Cani PD, Fahey G, Goh YJ, Hamaker B, Martens EC, Mills DA, Rastal RA, Vaughan E, Sanders ME. Prebiotics: why definitions matter. Curr Opin Biotechnol 2016; 37:1-7. [PMID: 26431716 PMCID: PMC4744122 DOI: 10.1016/j.copbio.2015.09.001] [Citation(s) in RCA: 251] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/21/2015] [Accepted: 09/02/2015] [Indexed: 01/03/2023]
Abstract
The prebiotic concept was introduced twenty years ago, and despite several revisions to the original definition, the scientific community has continued to debate what it means to be a prebiotic. How prebiotics are defined is important not only for the scientific community, but also for regulatory agencies, the food industry, consumers and healthcare professionals. Recent developments in community-wide sequencing and glycomics have revealed that more complex interactions occur between putative prebiotic substrates and the gut microbiota than previously considered. A consensus among scientists on the most appropriate definition of a prebiotic is necessary to enable continued use of the term.
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Affiliation(s)
- Robert W Hutkins
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583-0919, USA.
| | - Janina A Krumbeck
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583-0919, USA; School of Biological Sciences, University of Nebraska, Lincoln, NE 68583-0919, USA
| | - Laure B Bindels
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Patrice D Cani
- Université Catholique de Louvain, Louvain Drug Research Institute, Metabolism and Nutrition Research Group, WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Av. E. Mounier, 73 B1.73.11, B-1200 Brussels, Belgium
| | - George Fahey
- Department of Animal Science, University of Illinois, Urbana, IL 61801, USA
| | - Yong Jun Goh
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Bruce Hamaker
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - David A Mills
- Department of Food Science & Technology, University of California, Davis, CA 95616, USA
| | - Robert A Rastal
- Department of Food and Nutritional Sciences, The University of Reading, PO Box 226, Whiteknights, Reading RG6 6AP, United Kingdom
| | - Elaine Vaughan
- Sensus BV (Royal Cosun), Borchwerf 3, 4704RG Roosendaal, The Netherlands
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300
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Megson ZA, Koerdt A, Schuster H, Ludwig R, Janesch B, Frey A, Naylor K, Wilson IBH, Stafford GP, Messner P, Schäffer C. Characterization of an α-l-fucosidase from the periodontal pathogen Tannerella forsythia. Virulence 2016; 6:282-92. [PMID: 25831954 DOI: 10.1080/21505594.2015.1010982] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The periodontal pathogen Tannerella forsythia expresses several glycosidases which are linked to specific growth requirements and are involved in the invasion of host tissues. α-l-Fucosyl residues are exposed on various host glycoconjugates and, thus, the α-l-fucosidases predicted in the T. forsythia ATCC 43037 genome could potentially serve roles in host-pathogen interactions. We describe the molecular cloning and characterization of the putative fucosidase TfFuc1 (encoded by the bfo_2737 = Tffuc1 gene), previously reported to be present in an outer membrane preparation. In terms of sequence, this 51-kDa protein is a member of the glycosyl hydrolase family GH29. Using an artificial substrate, p-nitrophenyl-α-fucose (KM 670 μM), the enzyme was determined to have a pH optimum of 9.0 and to be competitively inhibited by fucose and deoxyfuconojirimycin. TfFuc1 was shown here to be a unique α(1,2)-fucosidase that also possesses α(1,6) specificity on small unbranched substrates. It is active on mucin after sialidase-catalyzed removal of terminal sialic acid residues and also removes fucose from blood group H. Following knock-out of the Tffuc1 gene and analyzing biofilm formation and cell invasion/adhesion of the mutant in comparison to the wild-type, it is most likely that the enzyme does not act extracellularly. Biochemically interesting as the first fucosidase in T. forsythia to be characterized, the biological role of TfFuc1 may well be in the metabolism of short oligosaccharides in the periplasm, thereby indirectly contributing to the virulence of this organism. TfFuc1 is the first glycosyl hydrolase in the GH29 family reported to be a specific α(1,2)-fucosidase.
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Key Words
- 2) fucosidase
- 4-nitrophenyl-α-l-fucopyranoside
- Amp, ampicillin
- BHI, brain heart infusion medium
- CBB, Coomassie brilliant blue G 250
- DFJ, deoxyfuconojirimycin
- Erm, erythromycin
- FDH, fucose dehydrogenase
- HPAEC, high-performance anion-exchange chromatography with pulsed amperometric detection
- LC-ESI-MS, liquid chromatography-electrospray ionisation-mass spectrometry
- NAM, N-acetylmuramic acid
- PBS, phosphate-buffered saline
- SDS-PAGE, sodium dodecylsulphate polyacrylamide gel electrophoresis
- T. forsythia, Tannerella forsythia ATCC 43037
- TfFuc1, T. forsythia ATCC 43037 fucosidase-1 encoded by the bfo_2737 gene, equally Tffuc1
- WT, wild-type bacterium.
- enzyme activity
- enzyme specificity
- oral pathogen
- pNP-fucose
- periodontitis
- rTfFuc-1, recombinant TfFuc1 enzyme
- tannerella forsythia
- α(1
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Affiliation(s)
- Z A Megson
- a Department of NanoBiotechnology; NanoGlycobiology unit; Universität für Bodenkultur Wien ; Vienna , Austria
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