251
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Wei CY, Liao NB, Zhang Y, Ye XQ, Li S, Hu YQ, Liu DH, Linhardt RJ, Wang X, Chen SG. In vitro fermentation behaviors of fucosylated chondroitin sulfate from Pearsonothuria graeffei by human gut microflora. Int J Biol Macromol 2017; 102:1195-1201. [DOI: 10.1016/j.ijbiomac.2017.04.036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/14/2017] [Accepted: 04/10/2017] [Indexed: 02/08/2023]
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252
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Orita T, Sakka M, Kimura T, Sakka K. Characterization of Ruminiclostridium josui arabinoxylan arabinofuranohydrolase, RjAxh43B, and RjAxh43B-containing xylanolytic complex. Enzyme Microb Technol 2017. [DOI: 10.1016/j.enzmictec.2017.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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253
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Spiga L, Winter MG, Furtado de Carvalho T, Zhu W, Hughes ER, Gillis CC, Behrendt CL, Kim J, Chessa D, Andrews-Polymenis HL, Beiting DP, Santos RL, Hooper LV, Winter SE. An Oxidative Central Metabolism Enables Salmonella to Utilize Microbiota-Derived Succinate. Cell Host Microbe 2017; 22:291-301.e6. [PMID: 28844888 DOI: 10.1016/j.chom.2017.07.018] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 06/23/2017] [Accepted: 07/28/2017] [Indexed: 12/31/2022]
Abstract
The mucosal inflammatory response induced by Salmonella serovar Typhimurium creates a favorable niche for this gut pathogen. Conventional wisdom holds that S. Typhimurium undergoes an incomplete tricarboxylic acid (TCA) cycle in the anaerobic mammalian gut. One change during S. Typhimurium-induced inflammation is the production of oxidized compounds by infiltrating neutrophils. We show that inflammation-derived electron acceptors induce a complete, oxidative TCA cycle in S. Typhimurium, allowing the bacteria to compete with the microbiota for colonization. A complete TCA cycle facilitates utilization of the microbiota-derived fermentation product succinate as a carbon source. S. Typhimurium succinate utilization genes contribute to efficient colonization in conventionally raised mice, but provide no growth advantage in germ-free mice. Mono-association of gnotobiotic mice with Bacteroides, a major succinate producer, restores succinate utilization in S. Typhimurium. Thus, oxidative central metabolism enables S. Typhimurium to utilize a variety of carbon sources, including microbiota-derived succinate.
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Affiliation(s)
- Luisella Spiga
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria G Winter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tatiane Furtado de Carvalho
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Wenhan Zhu
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizabeth R Hughes
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Caroline C Gillis
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cassie L Behrendt
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Department of Clinical Science, Quantitative Biomedical Research Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniela Chessa
- Department of Biomedical Science, School of Medicine, University of Sassari, Sassari, Italy
| | - Helene L Andrews-Polymenis
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University System Health Science Center, Bryan, TX 77807, USA
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Renato L Santos
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Lora V Hooper
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sebastian E Winter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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254
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Tannock GW, Taylor MW. Embracing the co-operative society to better understand assembly of the gut microbiota. Environ Microbiol 2017; 19:2924-2925. [PMID: 28401677 DOI: 10.1111/1462-2920.13752] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Gerald W Tannock
- Department of Microbiology & Immunology, & Microbiome Otago, University of Otago, Dunedin, New Zealand
- Riddet Centre of Research Excellence, Massey University, New Zealand
| | - Michael W Taylor
- School of Biological Sciences & Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
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255
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Svartström O, Alneberg J, Terrapon N, Lombard V, de Bruijn I, Malmsten J, Dalin AM, El Muller E, Shah P, Wilmes P, Henrissat B, Aspeborg H, Andersson AF. Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation. ISME JOURNAL 2017; 11:2538-2551. [PMID: 28731473 DOI: 10.1038/ismej.2017.108] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/05/2017] [Accepted: 05/30/2017] [Indexed: 12/25/2022]
Abstract
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.
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Affiliation(s)
- Olov Svartström
- School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Alneberg
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Nicolas Terrapon
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Vincent Lombard
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Ino de Bruijn
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Jonas Malmsten
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden.,Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ann-Marie Dalin
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emilie El Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pranjul Shah
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Henrik Aspeborg
- School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders F Andersson
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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256
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Abstract
The complex carbohydrates of terrestrial and marine biomass represent a rich nutrient source for free-living and mutualistic microbes alike. The enzymatic saccharification of these diverse substrates is of critical importance for fueling a variety of complex microbial communities, including marine, soil, ruminant, and monogastric microbiota. Consequently, highly specific carbohydrate-active enzymes, recognition proteins, and transporters are enriched in the genomes of certain species and are of critical importance in competitive environments. In Bacteroidetes bacteria, these systems are organized as polysaccharide utilization loci (PULs), which are strictly regulated, colocalized gene clusters that encode enzyme and protein ensembles required for the saccharification of complex carbohydrates. This review provides historical perspectives and summarizes key findings in the study of these systems, highlighting a critical shift from sequence-based PUL discovery to systems-based analyses combining reverse genetics, biochemistry, enzymology, and structural biology to precisely illuminate the molecular mechanisms underpinning PUL function. The ecological implications of dynamic PUL deployment by key species in the human gastrointestinal tract are explored, as well as the wider distribution of these systems in other gut, terrestrial, and marine environments.
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257
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Cartmell A, Lowe EC, Baslé A, Firbank SJ, Ndeh DA, Murray H, Terrapon N, Lombard V, Henrissat B, Turnbull JE, Czjzek M, Gilbert HJ, Bolam DN. How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans. Proc Natl Acad Sci U S A 2017; 114:7037-7042. [PMID: 28630303 PMCID: PMC5502631 DOI: 10.1073/pnas.1704367114] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human microbiota, which plays an important role in health and disease, uses complex carbohydrates as a major source of nutrients. Utilization hierarchy indicates that the host glycosaminoglycans heparin (Hep) and heparan sulfate (HS) are high-priority carbohydrates for Bacteroides thetaiotaomicron, a prominent member of the human microbiota. The sulfation patterns of these glycosaminoglycans are highly variable, which presents a significant enzymatic challenge to the polysaccharide lyases and sulfatases that mediate degradation. It is possible that the bacterium recruits lyases with highly plastic specificities and expresses a repertoire of enzymes that target substructures of the glycosaminoglycans with variable sulfation or that the glycans are desulfated before cleavage by the lyases. To distinguish between these mechanisms, the components of the B. thetaiotaomicron Hep/HS degrading apparatus were analyzed. The data showed that the bacterium expressed a single-surface endo-acting lyase that cleaved HS, reflecting its higher molecular weight compared with Hep. Both Hep and HS oligosaccharides imported into the periplasm were degraded by a repertoire of lyases, with each enzyme displaying specificity for substructures within these glycosaminoglycans that display a different degree of sulfation. Furthermore, the crystal structures of a key surface glycan binding protein, which is able to bind both Hep and HS, and periplasmic sulfatases reveal the major specificity determinants for these proteins. The locus described here is highly conserved within the human gut Bacteroides, indicating that the model developed is of generic relevance to this important microbial community.
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Affiliation(s)
- Alan Cartmell
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Elisabeth C Lowe
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Susan J Firbank
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Didier A Ndeh
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Heath Murray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
- Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jeremy E Turnbull
- Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Mirjam Czjzek
- Sorbonne Universités, Université Pierre-et-Marie-Curie, Université Paris 06, F-29688 Roscoff cedex, Bretagne, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff cedex, Bretagne, France
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom;
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258
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Munoz-Munoz J, Cartmell A, Terrapon N, Baslé A, Henrissat B, Gilbert HJ. An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins. J Biol Chem 2017. [PMID: 28637865 DOI: 10.1074/jbc.m117.794578] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human gut microbiota utilizes complex carbohydrates as major nutrients. The requirement for efficient glycan degrading systems exerts a major selection pressure on this microbial community. Thus, we propose that this microbial ecosystem represents a substantial resource for discovering novel carbohydrate active enzymes. To test this hypothesis we screened the potential enzymatic functions of hypothetical proteins encoded by genes of Bacteroides thetaiotaomicron that were up-regulated by arabinogalactan proteins or AGPs. Although AGPs are ubiquitous in plants, there is a paucity of information on their detailed structure, the function of these glycans in planta, and the mechanisms by which they are depolymerized in microbial ecosystems. Here we have discovered a new polysaccharide lyase family that is specific for the l-rhamnose-α1,4-d-glucuronic acid linkage that caps the side chains of complex AGPs. The reaction product generated by the lyase, Δ4,5-unsaturated uronic acid, is removed from AGP by a glycoside hydrolase located in family GH105, producing the final product 4-deoxy-β-l-threo-hex-4-enepyranosyl-uronic acid. The crystal structure of a member of the novel lyase family revealed a catalytic domain that displays an (α/α)6 barrel-fold. In the center of the barrel is a deep pocket, which, based on mutagenesis data and amino acid conservation, comprises the active site of the lyase. A tyrosine is the proposed catalytic base in the β-elimination reaction. This study illustrates how highly complex glycans can be used as a scaffold to discover new enzyme families within microbial ecosystems where carbohydrate metabolism is a major evolutionary driver.
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Affiliation(s)
- José Munoz-Munoz
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Alan Cartmell
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicolas Terrapon
- the Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Arnaud Baslé
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Bernard Henrissat
- the Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France.,the USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France, and.,the Department of Biological Sciences, King Abdulaziz University, 23218 Jeddah, Saudi Arabia
| | - Harry J Gilbert
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom,
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259
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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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260
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Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, Young VB, Henrissat B, Wilmes P, Stappenbeck TS, Núñez G, Martens EC. A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility. Cell 2017; 167:1339-1353.e21. [PMID: 27863247 DOI: 10.1016/j.cell.2016.10.043] [Citation(s) in RCA: 1659] [Impact Index Per Article: 237.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/13/2016] [Accepted: 10/21/2016] [Indexed: 02/07/2023]
Abstract
Despite the accepted health benefits of consuming dietary fiber, little is known about the mechanisms by which fiber deprivation impacts the gut microbiota and alters disease risk. Using a gnotobiotic mouse model, in which animals were colonized with a synthetic human gut microbiota composed of fully sequenced commensal bacteria, we elucidated the functional interactions between dietary fiber, the gut microbiota, and the colonic mucus barrier, which serves as a primary defense against enteric pathogens. We show that during chronic or intermittent dietary fiber deficiency, the gut microbiota resorts to host-secreted mucus glycoproteins as a nutrient source, leading to erosion of the colonic mucus barrier. Dietary fiber deprivation, together with a fiber-deprived, mucus-eroding microbiota, promotes greater epithelial access and lethal colitis by the mucosal pathogen, Citrobacter rodentium. Our work reveals intricate pathways linking diet, the gut microbiome, and intestinal barrier dysfunction, which could be exploited to improve health using dietary therapeutics.
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Affiliation(s)
- Mahesh S Desai
- Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette 4362, Luxembourg; University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg.
| | - Anna M Seekatz
- University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Nobuhiko Kamada
- University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
| | | | - Sho Kitamoto
- University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Arnaud Muller
- Department of Oncology, Luxembourg Institute of Health, Luxembourg 1526, Luxembourg
| | - Vincent B Young
- University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette 4362, Luxembourg
| | | | - Gabriel Núñez
- University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Eric C Martens
- University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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261
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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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262
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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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263
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Senf D, Ruprecht C, de Kruijff GHM, Simonetti SO, Schuhmacher F, Seeberger PH, Pfrengle F. Active Site Mapping of Xylan-Deconstructing Enzymes with Arabinoxylan Oligosaccharides Produced by Automated Glycan Assembly. Chemistry 2017; 23:3197-3205. [PMID: 28092124 DOI: 10.1002/chem.201605902] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Indexed: 11/10/2022]
Abstract
Xylan-degrading enzymes are crucial for the deconstruction of hemicellulosic biomass, making the hydrolysis products available for various industrial applications such as the production of biofuel. To determine the substrate specificities of these enzymes, we prepared a collection of complex xylan oligosaccharides by automated glycan assembly. Seven differentially protected building blocks provided the basis for the modular assembly of 2-substituted, 3-substituted, and 2-/3-substituted arabino- and glucuronoxylan oligosaccharides. Elongation of the xylan backbone relied on iterative additions of C4-fluorenylmethoxylcarbonyl (Fmoc) protected xylose building blocks to a linker-functionalized resin. Arabinofuranose and glucuronic acid residues have been selectively attached to the backbone using fully orthogonal 2-(methyl)naphthyl (Nap) and 2-(azidomethyl)benzoyl (Azmb) protecting groups at the C2 and C3 hydroxyls of the xylose building blocks. The arabinoxylan oligosaccharides are excellent tools to map the active site of glycosyl hydrolases involved in xylan deconstruction. The substrate specificities of several xylanases and arabinofuranosidases were determined by analyzing the digestion products after incubation of the oligosaccharides with glycosyl hydrolases.
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Affiliation(s)
- Deborah Senf
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Colin Ruprecht
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Goswinus H M de Kruijff
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany.,Current address: Institute of Organic Chemistry, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Sebastian O Simonetti
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Current address: Rosario Chemistry Institute (IQUIR, CONICET-UNR), Suipacha 570, S2002LRK, Rosario, Argentina
| | - Frank Schuhmacher
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Fabian Pfrengle
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
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264
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Schwalm ND, Townsend GE, Groisman EA. Prioritization of polysaccharide utilization and control of regulator activation in Bacteroides thetaiotaomicron. Mol Microbiol 2017; 104:32-45. [PMID: 28009067 DOI: 10.1111/mmi.13609] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2016] [Indexed: 12/30/2022]
Abstract
Bacteroides thetaiotaomicron is a human gut symbiotic bacterium that utilizes a myriad of host dietary and mucosal polysaccharides. The proteins responsible for the uptake and breakdown of many of these polysaccharides are transcriptionally regulated by hybrid two-component systems (HTCSs). These systems consist of a single polypeptide harboring the domains of sensor kinases and response regulators, and thus, are thought to autophosphorylate in response to specific signals. We now report that the HTCS BT0366 is phosphorylated in vivo when B. thetaiotaomicron experiences the BT0366 inducer arabinan but not when grown in the presence of glucose. BT0366 phosphorylation and transcription of BT0366-activated genes requires the conserved predicted sites of phosphorylation in BT0366. When chondroitin sulfate is added to arabinan-containing cultures, BT0366 phosphorylation and transcription of BT0366-activated genes are inhibited and the bacterium exhibits diauxic growth. Whereas 20 additional combinations of polysaccharides also give rise to diauxic growth, other combinations result in synergistic or unaltered growth relative to bacteria experiencing a single polysaccharide. The different strategies employed by B. thetaiotaomicron when faced with multiple polysaccharides may aid its competitiveness in the mammalian gut.
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Affiliation(s)
- Nathan D Schwalm
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.,Yale Microbial Sciences Institute, West Haven, CT, USA
| | - Guy E Townsend
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.,Yale Microbial Sciences Institute, West Haven, CT, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.,Yale Microbial Sciences Institute, West Haven, CT, USA
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265
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Centanni M, Hutchison JC, Carnachan SM, Daines AM, Kelly WJ, Tannock GW, Sims IM. Differential growth of bowel commensal Bacteroides species on plant xylans of differing structural complexity. Carbohydr Polym 2017; 157:1374-1382. [DOI: 10.1016/j.carbpol.2016.11.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/25/2016] [Accepted: 11/04/2016] [Indexed: 01/30/2023]
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266
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Patrascu O, Béguet-Crespel F, Marinelli L, Le Chatelier E, Abraham AL, Leclerc M, Klopp C, Terrapon N, Henrissat B, Blottière HM, Doré J, Béra-Maillet C. A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Sci Rep 2017; 7:40248. [PMID: 28091525 PMCID: PMC5238381 DOI: 10.1038/srep40248] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/05/2016] [Indexed: 12/26/2022] Open
Abstract
The digestion of dietary fibers is a major function of the human intestinal microbiota. So far this function has been attributed to the microorganisms inhabiting the colon, and many studies have focused on this distal part of the gastrointestinal tract using easily accessible fecal material. However, microbial fermentations, supported by the presence of short-chain fatty acids, are suspected to occur in the upper small intestine, particularly in the ileum. Using a fosmid library from the human ileal mucosa, we screened 20,000 clones for their activities against carboxymethylcellulose and xylans chosen as models of the major plant cell wall (PCW) polysaccharides from dietary fibres. Eleven positive clones revealed a broad range of CAZyme encoding genes from Bacteroides and Clostridiales species, as well as Polysaccharide Utilization Loci (PULs). The functional glycoside hydrolase genes were identified, and oligosaccharide break-down products examined from different polysaccharides including mixed-linkage β-glucans. CAZymes and PULs were also examined for their prevalence in human gut microbiome. Several clusters of genes of low prevalence in fecal microbiome suggested they belong to unidentified strains rather specifically established upstream the colon, in the ileum. Thus, the ileal mucosa-associated microbiota encompasses the enzymatic potential for PCW polysaccharide degradation in the small intestine.
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Affiliation(s)
- Orlane Patrascu
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Fabienne Béguet-Crespel
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Ludovica Marinelli
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | - Anne-Laure Abraham
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Marion Leclerc
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Christophe Klopp
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | - Nicolas Terrapon
- CNRS UMR 7257, Université Aix-Marseille, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Bernard Henrissat
- CNRS UMR 7257, Université Aix-Marseille, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hervé M Blottière
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.,Metagenopolis, INRA, 78350 Jouy-en-Josas, France
| | - Joël Doré
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.,Metagenopolis, INRA, 78350 Jouy-en-Josas, France
| | - Christel Béra-Maillet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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267
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Lammerts van Bueren A, Mulder M, Leeuwen SV, Dijkhuizen L. Prebiotic galactooligosaccharides activate mucin and pectic galactan utilization pathways in the human gut symbiont Bacteroides thetaiotaomicron. Sci Rep 2017; 7:40478. [PMID: 28091546 PMCID: PMC5238430 DOI: 10.1038/srep40478] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/06/2016] [Indexed: 12/18/2022] Open
Abstract
Galactooligosaccharides (GOS) are prebiotic carbohydrates that impart changes in the gut bacterial composition of formula-fed infants to more closely resemble that of breast-fed infants. Consuming human milk oligosaccharides (HMOs) provides specific bacterial strains with an advantage for colonizing the infant intestine. These same effects are seen in infants after GOS consumption, however GOS are very complex mixtures and the underlying molecular mechanisms of how GOS mimic HMOs are relatively unknown. Here we studied the effects of GOS utilization on a prominent gut symbiont, Bacteroides thetaiotaomicron, which has been previously shown to consume HMOs via mucin O-glycan degradation pathways. We show that several pathways for targeting O-mucin glycans are activated in B. thetaiotaomicron by GOS, as well as the galactan utilization sytem. Characterization of the endo-galactanase from this system identified activity on various longer GOS substrates while a subset of GOS compounds were identified as potential activators of mucin glycan metabolism in B. thetaiotaomicron. Our results show that GOS functions as an inducer of mucin-glycan pathways while providing a nutrient source in the form of β-(1 → 4)-galactan. These metabolic features of GOS mixtures may serve to explain the beneficial effects that are seen for GOS supplemented infant formula.
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Affiliation(s)
- Alicia Lammerts van Bueren
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Marieke Mulder
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Sander van Leeuwen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
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268
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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: 150] [Impact Index Per Article: 21.4] [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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269
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McLean R, Inglis GD, Mosimann SC, Uwiera RRE, Abbott DW. Determining the Localization of Carbohydrate Active Enzymes Within Gram-Negative Bacteria. Methods Mol Biol 2017; 1588:199-208. [PMID: 28417370 DOI: 10.1007/978-1-4939-6899-2_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Investigating the subcellular location of secreted proteins is valuable for illuminating their biological function. Although several bioinformatics programs currently exist to predict the destination of a trafficked protein using its signal peptide sequence, these programs have limited accuracy and often require experimental validation. Here, we present a systematic method to fractionate gram-negative cells and characterize the subcellular localization of secreted carbohydrate active enzymes (CAZymes). This method involves four parallel approaches that reveal the relative abundance of protein within the cytoplasm, periplasm, outer membrane, and extracellular environment. Cytoplasmic and periplasmic proteins are fractionated by lysis and osmotic shock, respectively. Outer membrane bound proteins are determined by comparing cells before and after exoproteolytic digestion. Extracellularly secreted proteins are collected from the media and concentrated. These four different fractionations can then be probed for the presence and quantity of target proteins using immunochemical methods such as Western blots and ELISAs, or enzyme activity assays.
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Affiliation(s)
- Richard McLean
- Functional Genomics of Complex Carbohydrate Utilization, Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave. South, Lethbridge, T1J 4B1 AB, Canada.,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, T1K 3M4 AB, Canada
| | - G Douglas Inglis
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, T1K 3M4 AB, Canada
| | - Steven C Mosimann
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, T1K 3M4 AB, Canada
| | - Richard R E Uwiera
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G 2P5
| | - D Wade Abbott
- Functional Genomics of Complex Carbohydrate Utilization, Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave. South, Lethbridge, T1J 4B1 AB, Canada. .,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, T1K 3M4 AB, Canada.
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270
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Lim SH, Kim Y, Yun KN, Kim JY, Jang JH, Han MJ, Lee J. Plant-based foods containing cell wall polysaccharides rich in specific active monosaccharides protect against myocardial injury in rat myocardial infarction models. Sci Rep 2016; 6:38728. [PMID: 27929093 PMCID: PMC5143980 DOI: 10.1038/srep38728] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/11/2016] [Indexed: 12/31/2022] Open
Abstract
Many cohort studies have shown that consumption of diets containing a higher composition of foods derived from plants reduces mortality from coronary heart disease (CHD). Here, we examined the active components of a plant-based diet and the underlying mechanisms that reduce the risk of CHD using three rat models and a quantitative proteomics approach. In a short-term myocardial infarction (MI) model, intake of wheat extract (WE), the representative cardioprotectant identified by screening approximately 4,000 samples, reduced myocardial injury by inhibiting apoptosis, enhancing ATP production, and maintaining protein homeostasis. In long-term post-MI models, this myocardial protection resulted in ameliorating adverse left-ventricular remodelling, which is a predictor of heart failure. Among the wheat components, arabinose and xylose were identified as active components responsible for the observed efficacy of WE, which was administered via ingestion and tail-vein injections. Finally, the food components of plant-based diets that contained cell wall polysaccharides rich in arabinose, xylose, and possibly fucose were found to confer protection against myocardial injury. These results show for the first time that specific monosaccharides found in the cell wall polysaccharides in plant-based diets can act as active ingredients that reduce CHD by inhibiting postocclusion steps, including MI and heart failure.
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Affiliation(s)
- Sun Ha Lim
- Department of Biochemistry, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea
| | | | - Ki Na Yun
- Biomedical Omics Group, Korea Basic Science Institute, Ochang 28119, Korea
- Sogang University, Seoul 04107, Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute, Ochang 28119, Korea
| | - Jung-Hee Jang
- Department of Pharmacology, School of Medicine, Keimyung University, Daegu 42601, Korea
| | - Mee-Jung Han
- Department of Biomolecular and Chemical Engineering, Dongyang University, Yeongju, Gyeongbuk 36040, Korea
| | - Jongwon Lee
- Department of Biochemistry, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea
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271
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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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272
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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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273
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Bacteroides intestinalis DSM 17393, a member of the human colonic microbiome, upregulates multiple endoxylanases during growth on xylan. Sci Rep 2016; 6:34360. [PMID: 27681607 PMCID: PMC5041131 DOI: 10.1038/srep34360] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/13/2016] [Indexed: 12/19/2022] Open
Abstract
Many human diets contain arabinoxylan, and the ease of genome sequencing coupled with reduced cost have led to unraveling the arsenal of genes utilized by the colonic Bacteroidetes to depolymerize this polysaccharide. The colonic Bacteroidetes with potential to ferment arabinoxylans include Bacteroides intestinalis. In this study, we analyzed the hydrolytic activities of members of a xylan degradation cluster encoded on the genome of Bacteroides intestinalis DSM 17393. Here, it is demonstrated that a cocktail of the xylanolytic enzymes completely hydrolyze arabinoxylans found in human diets. We show that this bacterium and relatives have evolved and secrete a unique bifunctional endoxylanase/arabinofuranosidase in the same polypeptide. The bifunctional enzyme and other secreted enzymes attack the polysaccharides extracellularly to remove the side-chains, exposing the xylan backbone for cleavage to xylo-oligosaccharides and xylose. These end products are
transported into the cell where a β-xylosidase cleaves the oligosaccharides to fermentable sugars. While our experiments focused on B. intestinalis, it is likely that the extracellular enzymes also release nutrients to members of the colonic microbial community that practice cross-feeding. The presence of the genes characterized in this study in other colonic Bacteroidetes suggests a conserved strategy for energy acquisition from arabinoxylan, a component of human diets.
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274
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Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes. Nat Commun 2016; 7:12860. [PMID: 27653556 PMCID: PMC5036157 DOI: 10.1038/ncomms12860] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 08/09/2016] [Indexed: 11/17/2022] Open
Abstract
Adaptive radiations are important drivers of niche filling, since they rapidly adapt a single clade of organisms to ecological opportunities. Although thought to be common for animals and plants, adaptive radiations have remained difficult to document for microbes in the wild. Here we describe a recent adaptive radiation leading to fine-scale ecophysiological differentiation in the degradation of an algal glycan in a clade of closely related marine bacteria. Horizontal gene transfer is the primary driver in the diversification of the pathway leading to several ecophysiologically differentiated Vibrionaceae populations adapted to different physical forms of alginate. Pathway architecture is predictive of function and ecology, underscoring that horizontal gene transfer without extensive regulatory changes can rapidly assemble fully functional pathways in microbes. Adaptive radiations are well-known for animals and plants, but not for microbes. Here, Hehemann et al. show that there has been a recent adaptive radiation of bacteria in the Vibrionaceae to use different forms of alginate and that this radiation has been mediated by horizontal gene transfer.
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275
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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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276
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Individualized Responses of Gut Microbiota to Dietary Intervention Modeled in Humanized Mice. mSystems 2016; 1:mSystems00098-16. [PMID: 27822551 PMCID: PMC5069738 DOI: 10.1128/msystems.00098-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/11/2016] [Indexed: 02/06/2023] Open
Abstract
Diet plays an important role in shaping the structure and function of the gut microbiota. The microbes and microbial products in turn can influence various aspects of host physiology. One promising route to affect host function and restore health is by altering the gut microbiome using dietary intervention. The individuality of the microbiome may pose a significant challenge, so we sought to determine how different microbiotas respond to the same dietary intervention in a controlled setting. We modeled gut microbiotas from three healthy donors in germfree mice and defined compositional and functional alteration following a change in dietary microbiota-accessible carbohydrates (MACs). The three gut communities exhibited responses that differed markedly in magnitude and in the composition of microbiota-derived metabolites. Adjustments in community membership did not correspond to the magnitude of changes in the microbial metabolites, highlighting potential challenges in predicting functional responses from compositional data and the need to assess multiple microbiota parameters following dietary interventions. IMPORTANCE Dietary modification has long been used empirically to modify symptoms in inflammatory bowel disease, irritable bowel syndrome, and a diverse group of diseases with gastrointestinal symptoms. There is both anecdotal and scientific evidence to suggest that individuals respond quite differently to similar dietary changes, and the highly individualized nature of the gut microbiota makes it a prime candidate for these differences. To overcome the typical confounding factors of human dietary interventions, here we employ ex-germfree mice colonized by microbiotas of three different humans to test how different microbiotas respond to a defined change in carbohydrate content of diet by measuring changes in microbiota composition and function using marker gene-based next-generation sequencing and metabolomics. Our findings suggest that the same diet has very different effects on each microbiota's membership and function, which may in turn explain interindividual differences in response to a dietary ingredient.
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277
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CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems. BMC Genomics 2016; 17:671. [PMID: 27552843 PMCID: PMC4994258 DOI: 10.1186/s12864-016-2988-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/02/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Microorganisms constitute a reservoir of enzymes involved in environmental carbon cycling and degradation of plant polysaccharides through their production of a vast variety of Glycoside Hydrolases (GH). The CAZyChip was developed to allow a rapid characterization at transcriptomic level of these GHs and to identify enzymes acting on hydrolysis of polysaccharides or glycans. RESULTS This DNA biochip contains the signature of 55,220 bacterial GHs available in the CAZy database. Probes were designed using two softwares, and microarrays were directly synthesized using the in situ ink-jet technology. CAZyChip specificity and reproducibility was validated by hybridization of known GHs RNA extracted from recombinant E. coli strains, which were previously identified by a functional metagenomic approach. The GHs arsenal was also studied in bioprocess conditions using rumen derived microbiota. CONCLUSIONS The CAZyChip appears to be a user friendly tool for profiling the expression of a large variety of GHs. It can be used to study temporal variations of functional diversity, thereby facilitating the identification of new efficient candidates for enzymatic conversions from various ecosystems.
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278
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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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279
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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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280
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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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281
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Hushegyi A, Pihíková D, Bertok T, Adam V, Kizek R, Tkac J. Ultrasensitive detection of influenza viruses with a glycan-based impedimetric biosensor. Biosens Bioelectron 2016; 79:644-9. [PMID: 26765527 PMCID: PMC4883649 DOI: 10.1016/j.bios.2015.12.102] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/19/2015] [Accepted: 12/29/2015] [Indexed: 12/20/2022]
Abstract
An ultrasensitive impedimetric glycan-based biosensor for reliable and selective detection of inactivated, but intact influenza viruses H3N2 was developed. Such glycan-based approach has a distinct advantage over antibody-based detection of influenza viruses since glycans are natural viral receptors with a possibility to selectively distinguish between potentially pathogenic influenza subtypes by the glycan-based biosensors. Build-up of the biosensor was carefully optimized with atomic force microscopy applied for visualization of the biosensor surface after binding of viruses with the topology of an individual viral particle H3N2 analyzed. The glycan biosensor could detect a glycan binding lectin with a limit of detection (LOD) of 5 aM. The biosensor was finally applied for analysis of influenza viruses H3N2 with LOD of 13 viral particles in 1 μl, what is the lowest LOD for analysis of influenza viral particles by the glycan-based device achieved so far. The biosensor could detect H3N2 viruses selectively with a sensitivity ratio of 30 over influenza viruses H7N7. The impedimetric biosensor presented here is the most sensitive glycan-based device for detection of influenza viruses and among the most sensitive antibody or aptamer based biosensor devices.
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Affiliation(s)
- András Hushegyi
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia
| | - Dominika Pihíková
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia
| | - Tomas Bertok
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - René Kizek
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Jan Tkac
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia.
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282
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Despres J, Forano E, Lepercq P, Comtet-Marre S, Jubelin G, Chambon C, Yeoman CJ, Berg Miller ME, Fields CJ, Martens E, Terrapon N, Henrissat B, White BA, Mosoni P. Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level. BMC Genomics 2016; 17:326. [PMID: 27142817 PMCID: PMC4855328 DOI: 10.1186/s12864-016-2680-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/28/2016] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Plant cell wall (PCW) polysaccharides and especially xylans constitute an important part of human diet. Xylans are not degraded by human digestive enzymes in the upper digestive tract and therefore reach the colon where they are subjected to extensive degradation by some members of the symbiotic microbiota. Xylanolytic bacteria are the first degraders of these complex polysaccharides and they release breakdown products that can have beneficial effects on human health. In order to understand better how these bacteria metabolize xylans in the colon, this study was undertaken to investigate xylan breakdown by the prominent human gut symbiont Bacteroides xylanisolvens XB1A(T). RESULTS Transcriptomic analyses of B. xylanisolvens XB1A(T) grown on insoluble oat-spelt xylan (OSX) at mid- and late-log phases highlighted genes in a polysaccharide utilization locus (PUL), hereafter called PUL 43, and genes in a fragmentary remnant of another PUL, hereafter referred to as rPUL 70, which were highly overexpressed on OSX relative to glucose. Proteomic analyses supported the up-regulation of several genes belonging to PUL 43 and showed the important over-production of a CBM4-containing GH10 endo-xylanase. We also show that PUL 43 is organized in two operons and that the knockout of the PUL 43 sensor/regulator HTCS gene blocked the growth of the mutant on insoluble OSX and soluble wheat arabinoxylan (WAX). The mutation not only repressed gene expression in the PUL 43 operons but also repressed gene expression in rPUL 70. CONCLUSION This study shows that xylan degradation by B. xylanisolvens XB1A(T) is orchestrated by one PUL and one PUL remnant that are linked at the transcriptional level. Coupled to studies on other xylanolytic Bacteroides species, our data emphasize the importance of one peculiar CBM4-containing GH10 endo-xylanase in xylan breakdown and that this modular enzyme may be used as a functional marker of xylan degradation in the human gut. Our results also suggest that B. xylanisolvens XB1A(T) has specialized in the degradation of xylans of low complexity. This functional feature may provide a niche to all xylanolytic bacteria harboring similar PULs. Further functional and ecological studies on fibrolytic Bacteroides species are needed to better understand their role in dietary fiber degradation and their impact on intestinal health.
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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
| | - Gregory Jubelin
- Institut National de la recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France
| | - Christophe Chambon
- INRA, Plate-forme d'Exploration du Métabolisme, 63122, Saint-Genès Champanelle, France
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, 59718, USA
| | - Margaret 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
| | - Eric Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, 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
| | - 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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283
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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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284
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Abstract
PURPOSE OF REVIEW A wide range of dietary carbohydrates, including prebiotic food ingredients, fermentable fibers, and milk oligosaccharides, are able to produce significant changes in the intestinal microbiota. These shifts in the microbial community are often characterized by increased levels of bifidobacteria and lactobacilli. More recent studies have revealed that species of Faecalibacterium, Akkermansia, and other less well studied members may also be enriched. We review the implications of these recent studies on future design of prebiotics and synbiotics to promote gastrointestinal health. RECENT FINDINGS Investigations assessing the clinical outcomes associated with dietary modification of the gut microbiota have shown systemic as well as specific health benefits. Both prebiotic oligosaccharides comprised of a linear arrangement of simple sugars, as well as fiber-rich foods containing complex carbohydrates, have been used in these trials. However, individual variability and nonresponding study participants can make the outcome of dietary interventions less predictable. In contrast, synergistic synbiotics containing prebiotics that specifically stimulate a cognate probiotic provide additional options for personalized gut therapies. SUMMARY This review describes recent research on how prebiotics and fermentable fibers can influence the gut microbiota and result in improvements to human health.
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285
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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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286
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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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287
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Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GCL, Wright AT, Young TD. Tools for the Microbiome: Nano and Beyond. ACS NANO 2016; 10:6-37. [PMID: 26695070 DOI: 10.1021/acsnano.5b07826] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. These technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering. We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.
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Affiliation(s)
- Julie S Biteen
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology , and Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02138, United States
| | - Zoe G Cardon
- The Ecosystems Center, Marine Biological Laboratory , Woods Hole, Massachusetts 02543-1015, United States
| | - Miyoung Chun
- The Kavli Foundation , Oxnard, California 93030, United States
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | | | - Scott E Fraser
- Translational Imaging Center, University of Southern California , Molecular and Computational Biology, Los Angeles, California 90089, United States
| | - Jack A Gilbert
- Institute for Genomic and Systems Biology, Argonne National Laboratory , Argonne, Illinois 60439, United States
- Department of Ecology and Evolution and Department of Surgery, University of Chicago , Chicago, Illinois 60637, United States
| | - Janet K Jansson
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | | | | | | | | | | | - Edward G Ruby
- Kewalo Marine Laboratory, University of Hawaii-Manoa , Honolulu, Hawaii 96813, United States
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | - Sharif Taha
- The Kavli Foundation , Oxnard, California 93030, United States
| | - Ger van den Engh
- Center for Marine Cytometry , Concrete, Washington 98237, United States
- Instituto Milenio de Oceanografía, Universidad de Concepción , Concepción, Chile
| | | | | | - Aaron T Wright
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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288
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Parasuram R, Mills CL, Wang Z, Somasundaram S, Beuning PJ, Ondrechen MJ. Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases. Methods 2016; 93:51-63. [DOI: 10.1016/j.ymeth.2015.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 01/07/2023] Open
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289
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Voiniciuc C, Günl M, Schmidt MHW, Usadel B. Highly Branched Xylan Made by IRREGULAR XYLEM14 and MUCILAGE-RELATED21 Links Mucilage to Arabidopsis Seeds. PLANT PHYSIOLOGY 2015; 169:2481-95. [PMID: 26482889 PMCID: PMC4677919 DOI: 10.1104/pp.15.01441] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/17/2015] [Indexed: 05/07/2023]
Abstract
All cells of terrestrial plants are fortified by walls composed of crystalline cellulose microfibrils and a variety of matrix polymers. Xylans are the second most abundant type of polysaccharides on Earth. Previous studies of Arabidopsis (Arabidopsis thaliana) irregular xylem (irx) mutants, with collapsed xylem vessels and dwarfed stature, highlighted the importance of this cell wall component and revealed multiple players required for its synthesis. Nevertheless, xylan elongation and substitution are complex processes that remain poorly understood. Recently, seed coat epidermal cells were shown to provide an excellent system for deciphering hemicellulose production. Using a coexpression and sequence-based strategy, we predicted several MUCILAGE-RELATED (MUCI) genes that encode glycosyltransferases (GTs) involved in the production of xylan. We now show that MUCI21, a member of an uncharacterized clade of the GT61 family, and IRX14 (GT43 protein) are essential for the synthesis of highly branched xylan in seed coat epidermal cells. Our results reveal that xylan is the most abundant xylose-rich component in Arabidopsis seed mucilage and is required to maintain its architecture. Characterization of muci21 and irx14 single and double mutants indicates that MUCI21 is a Golgi-localized protein that likely facilitates the addition of xylose residues directly to the xylan backbone. These unique branches seem to be necessary for pectin attachment to the seed surface, while the xylan backbone maintains cellulose distribution. Evaluation of muci21 and irx14 alongside mutants that disrupt other wall components suggests that mucilage adherence is maintained by complex interactions between several polymers: cellulose, xylans, pectins, and glycoproteins.
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Affiliation(s)
- Cătălin Voiniciuc
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52425 Jülich, Germany (C.V., M.G., M.H.-W.S., B.U.); andInstitute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52074 Aachen, Germany (C.V., M.H.-W.S, B.U.)
| | - Markus Günl
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52425 Jülich, Germany (C.V., M.G., M.H.-W.S., B.U.); andInstitute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52074 Aachen, Germany (C.V., M.H.-W.S, B.U.)
| | - Maximilian Heinrich-Wilhelm Schmidt
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52425 Jülich, Germany (C.V., M.G., M.H.-W.S., B.U.); andInstitute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52074 Aachen, Germany (C.V., M.H.-W.S, B.U.)
| | - Björn Usadel
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52425 Jülich, Germany (C.V., M.G., M.H.-W.S., B.U.); andInstitute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52074 Aachen, Germany (C.V., M.H.-W.S, B.U.)
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290
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Wu M, McNulty NP, Rodionov DA, Khoroshkin MS, Griffin NW, Cheng J, Latreille P, Kerstetter RA, Terrapon N, Henrissat B, Osterman AL, Gordon JI. Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides. Science 2015; 350:aac5992. [PMID: 26430127 DOI: 10.1126/science.aac5992] [Citation(s) in RCA: 178] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Libraries of tens of thousands of transposon mutants generated from each of four human gut Bacteroides strains, two representing the same species, were introduced simultaneously into gnotobiotic mice together with 11 other wild-type strains to generate a 15-member artificial human gut microbiota. Mice received one of two distinct diets monotonously, or both in different ordered sequences. Quantifying the abundance of mutants in different diet contexts allowed gene-level characterization of fitness determinants, niche, stability, and resilience and yielded a prebiotic (arabinoxylan) that allowed targeted manipulation of the community. The approach described is generalizable and should be useful for defining mechanisms critical for sustaining and/or approaches for deliberately reconfiguring the highly adaptive and durable relationship between the human gut microbiota and host in ways that promote wellness.
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Affiliation(s)
- Meng Wu
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA. Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Nathan P McNulty
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, 92037 CA, USA. A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
| | - Matvei S Khoroshkin
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
| | - Nicholas W Griffin
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA. Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jiye Cheng
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA. Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63108, USA
| | | | | | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique et Aix-Marseille Université 13288 Marseille cedex 9, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique et Aix-Marseille Université 13288 Marseille cedex 9, France. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, 92037 CA, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
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291
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Abbott DW, Martens EC, Gilbert HJ, Cuskin F, Lowe EC. Coevolution of yeast mannan digestion: Convergence of the civilized human diet, distal gut microbiome, and host immunity. Gut Microbes 2015; 6:334-9. [PMID: 26440374 PMCID: PMC4826095 DOI: 10.1080/19490976.2015.1091913] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The complex carbohydrates accessible to the distal gut microbiota (DGM) are key drivers in determining the structure of this ecosystem. Typically, plant cell wall polysaccharides and recalcitrant starch (i.e. dietary fiber), in addition to host glycans are considered the primary nutrients for the DGM; however, we recently demonstrated that α-mannans, highly branched polysaccharides that decorate the surface of yeast, are also nutrients for several members of Bacteroides spp. This relationship suggests that the advent of yeast in contemporary food technologies and the colonization of the intestine by endogenous fungi have roles in microbiome structure and function. Here we discuss the process of yeast mannan metabolism, and the intersection between various sources of intestinal fungi and their roles in recognition by the host innate immune system.
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Affiliation(s)
- D Wade Abbott
- Lethbridge Research Center; Agriculture and Agri-Food Canada; Lethbridge, Alberta, Canada,Correspondence to: D Wade Abbott; ; Eric C Martens; ; Harry J Gilbert;
| | - Eric C Martens
- Department of Microbiology and Immunology; University of Michigan Medical School; Ann Arbor, MI USA,Correspondence to: D Wade Abbott; ; Eric C Martens; ; Harry J Gilbert;
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences; The Medical School; Newcastle University; Newcastle upon Tyne, UK,Correspondence to: D Wade Abbott; ; Eric C Martens; ; Harry J Gilbert;
| | - Fiona Cuskin
- Institute for Cell and Molecular Biosciences; The Medical School; Newcastle University; Newcastle upon Tyne, UK
| | - Elisabeth C Lowe
- Institute for Cell and Molecular Biosciences; The Medical School; Newcastle University; Newcastle upon Tyne, UK
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