• A Corrigendum to this article was published on 23 August 2017

This article has been updated

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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Change history

  • 05 April 2017

    The PDB code ‘5MQP’ was added to the Data Availability section; and reference citations were corrected in the final paragraph of the main text.

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Acknowledgements

This work was supported in part by a grant to H.J.G. and B.H. from the European Research Council (grant no. 322820). B.H. was also funded by Agence Nationale de la Recherche under grant number ANR 12-BIME-0006-01. H.J.G was also supported by Biotechnology and Biological Research Council (grant numbers BB/K020358/1 and BB/K001949/1), the Wellcome Trust (grant no. WT097907MA) and, with X.Z., M.-C.R. and F.B., was funded by the European Union Seventh Framework Programme under the WallTraC project (grant agreement number 263916). M.A.O and B.R.U. were supported in part by grant DE-FG02-12ER16324 from The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the US Department of Energy. I.V. was in receipt of a Marie Skłodowska-Curie Fellowship (grant no. 707922). G.J.D. is a Royal Society Ken Murray Research Professor. D.W.A. was supported by a grant from the Beef and Cattle Research Council (FDE.15.13). We thank Diamond Light Source for access to beamline I02, I04-1 and I24 (mx1960, mx7854 and mx9948) that contributed to the results presented here, and to T. Doco and S. J. Charnock who supplied the partially purified apple RG-II.

Author information

Author notes

    • Artur Rogowski
    •  & Fanny Buffetto

    Present addresses: Megazyme, Bray, Co. Wicklow, A98 YV29, Ireland (A.R.); Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Matieland 7602, South Africa (F.B.).

    • Didier Ndeh
    • , Artur Rogowski
    • , Alan Cartmell
    •  & Ana S. Luis

    These authors contributed equally to this work.

Affiliations

  1. Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK

    • Didier Ndeh
    • , Artur Rogowski
    • , Alan Cartmell
    • , Ana S. Luis
    • , Arnaud Baslé
    • , Joseph Gray
    • , Immacolata Venditto
    • , Jonathon Briggs
    • , Xiaoyang Zhang
    • , Aurore Labourel
    •  & Harry J. Gilbert
  2. Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, F-13288 Marseille, France

    • Nicolas Terrapon
    •  & Bernard Henrissat
  3. INRA, UR1268 Biopolymères Interactions Assemblages, 44300 Nantes, France

    • Fanny Buffetto
    •  & Marie-Christine Ralet
  4. Department of Biological Chemistry, John Innes Centre Norwich Research Park, Norwich NR4 7UH, UK

    • Sergey Nepogodiev
    •  & Robert A. Field
  5. Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109 USA

    • Yao Xiao
    •  & Eric C. Martens
  6. Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, USA

    • Yanping Zhu
    • , Malcolm A. O’Neill
    • , Breeanna R. Urbanowicz
    •  & William S. York
  7. Department of Chemistry, University of York, York YO10 5DD, UK

    • Gideon J. Davies
  8. Lethbridge Research Centre, Lethbridge, Alberta T1J 4B1, Canada

    • D. Wade Abbott
  9. INRA, USC 1408 AFMB, F-13288 Marseille, France

    • Bernard Henrissat
  10. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia

    • Bernard Henrissat

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Contributions

Enzyme characterization was by D.N., A.R., A.C., A.S.L., I.V., A.L., D.W.A., Y.Z. and X.Z. Crystallographic studies were by A.C., A.B., A.S.L., D.N. and I.V. Purification of RG-II and oligosaccharide products was by M.A.O., A.R., D.N., A.C, A.L., A.S.L., F.B. and M.-C.R. HPLC analysis was by A.R., D.N., A.C. and A.S.L., while mass spectrometry analysis was by A.R. and J.G. Chemical synthesis was by S.N. and R.A.F. Growth analysis on purified RG-II performed by D.N. and A.R. Gene deletion strains were created and characterized by D.N and I.V. Bioinformatics and genomic annotation were by N.T. and B.H. Bacterial growth and transcriptomic experiments were by J.B., Y.X. and E.C.M. Experiments were designed by D.N., A.R., A.C., A.S.L., E.C.M. and H.J.G. The manuscript was written by H.J.G. with contributions from G.J.D., B.H., M.A.O, B.R.U., E.C.M. and W.S.Y. Figures were prepared by A.R., A.L., D.N. and A.S.L.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Harry J. Gilbert.

Reviewer Information Nature thanks M. Czjzek, S. Duncan and S. Withers for their contribution to the peer review of this work.

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