Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

Abstract

Gut microbes supply the human body with energy from dietary polysaccharides through carbohydrate active enzymes, or CAZymes1, which are absent in the human genome. These enzymes target polysaccharides from terrestrial plants that dominated diet throughout human evolution2. The array of CAZymes in gut microbes is highly diverse, exemplified by the human gut symbiont Bacteroides thetaiotaomicron3, which contains 261 glycoside hydrolases and polysaccharide lyases, as well as 208 homologues of susC and susD-genes coding for two outer membrane proteins involved in starch utilization1,4. A fundamental question that, to our knowledge, has yet to be addressed is how this diversity evolved by acquiring new genes from microbes living outside the gut. Here we characterize the first porphyranases from a member of the marine Bacteroidetes, Zobellia galactanivorans, active on the sulphated polysaccharide porphyran from marine red algae of the genus Porphyra. Furthermore, we show that genes coding for these porphyranases, agarases and associated proteins have been transferred to the gut bacterium Bacteroides plebeius isolated from Japanese individuals5. Our comparative gut metagenome analyses show that porphyranases and agarases are frequent in the Japanese population6 and that they are absent in metagenome data7 from North American individuals. Seaweeds make an important contribution to the daily diet in Japan (14.2 g per person per day)8, and Porphyra spp. (nori) is the most important nutritional seaweed, traditionally used to prepare sushi9,10. This indicates that seaweeds with associated marine bacteria may have been the route by which these novel CAZymes were acquired in human gut bacteria, and that contact with non-sterile food may be a general factor in CAZyme diversity in human gut microbes.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Activity screening on natural algal polysaccharides reveals porphyranase activity.
Figure 2: Structural determinants of porphyran active enzymes.
Figure 3: Phylogenetic analysis of GH16 galactanases reveals porphyranases in many marine bacteria and in the Japanese gut bacterium B. plebeius.
Figure 4: Upstream and downstream of the porphyranase gene ( Bp1689 ), the genome of B. plebeius contains carbohydrate-related genes that share highest identity with proteins used for red-algal galactan degradation in two marine Bacteroidetes.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited at the Protein Data Bank under accession codes 3ILF (PorA_E139S) and 3JUU (PorB).

References

  1. Cantarel, B. L. et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37, D233–D238 (2009)

    Article  CAS  Google Scholar 

  2. Ley, R. E., Lozupone, C. A., Hamady, M., Knight, R. & Gordon, J. I. Worlds within worlds: evolution of the vertebrate gut microbiota. Nature Rev. Microbiol. 6, 776–778 (2008)

    Article  CAS  Google Scholar 

  3. Xu, J. et al. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299, 2074–2076 (2003)

    Article  ADS  CAS  Google Scholar 

  4. Martens, E. C., Koropatkin, N. M., Smith, T. J. & Gordon J. I Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J. Biol. Chem. 284, 24673–24677 (2009)

    Article  CAS  Google Scholar 

  5. Kitahara, M., Sakamoto, M., Ike, M., Sakata, S. & Benno, Y. Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces. Int. J. Syst. Evol. Microbiol. 55, 2143–2147 (2005)

    Article  CAS  Google Scholar 

  6. Kurokawa, K. et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14, 169–181 (2007)

    Article  CAS  Google Scholar 

  7. Turnbaugh, P. J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480–484 (2009)

    Article  ADS  CAS  Google Scholar 

  8. Fukuda, S. et al. Pattern of dietary fiber intake among the Japanese general population. Eur. J. Clin. Nutr. 61, 99–103 (2007)

    Article  CAS  Google Scholar 

  9. Nisizawa, K., Noda, H., Kikuchi, R. & Watanabe, T. The main seaweed foods in Japan. Hydrobiologia 151–152, 5–29 (1987)

    Article  Google Scholar 

  10. Mc Hugh, D. J. in FAO Fisheries Technical Paper No 441 (FAO, 2003)

    Google Scholar 

  11. Kloareg, B. & Quatrano, R. S. Structure of the cell walls of marine algae and ecophysiological functions of the matrix polysaccharides. Oceanogr. Mar. Biol Annu. Rev. 26, 259–315 (1988)

    Google Scholar 

  12. Michel, G., Nyvall-Collen, P., Barbeyron, T., Czjzek, M. & Helbert, W. Bioconversion of red seaweed galactans: a focus on bacterial agarases and carrageenases. Appl. Microbiol. Biotechnol. 71, 23–33 (2006)

    Article  CAS  Google Scholar 

  13. Gilbert, H. J., Stalbrand, H. & Brumer, H. How the walls come crumbling down: recent structural biochemistry of plant polysaccharide degradation. Curr. Opin. Plant Biol. 11, 338–348 (2008)

    Article  CAS  Google Scholar 

  14. Barbeyron, T. et al. Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of [Cytophaga] uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Zobellia uliginosa gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 51, 985–987 (2001)

    Article  CAS  Google Scholar 

  15. Barbeyron, T., Gerard, A., Potin, P., Henrissat, B. & Kloareg, B. The κ-carrageenase of the marine bacterium Cytophaga drobachiensis. Structural and phylogenetic relationships within family-16 glycoside hydrolases. Mol. Biol. Evol. 15, 528–537 (1998)

    Article  CAS  Google Scholar 

  16. Jam, M. et al. The endo-β-agarases AgaA and AgaB from the marine bacterium Zobellia galactanivorans: two paralogue enzymes with different molecular organizations and catalytic behaviours. Biochem. J. 385, 703–713 (2005)

    Article  CAS  Google Scholar 

  17. Allouch, J. et al. The three-dimensional structures of two β-agarases. J. Biol. Chem. 278, 47171–47180 (2003)

    Article  CAS  Google Scholar 

  18. Maciel, J. S. et al. Structural characterization of cold extracted fraction of soluble sulfated polysaccharide from the red seaweed Gracilaria birdiae . Carbohydr. Polym. 71, 559–565 (2008)

    Article  CAS  Google Scholar 

  19. Turvey, J. R. & Rees, D. A. Isolation of l-galactose-6-sulphate from a seaweed polysaccharide. Nature 189, 831–832 (1961)

    Article  ADS  CAS  Google Scholar 

  20. Anderson, N. S. & Rees, D. A. Porphyran — a polysaccharide with a masked repeating structure. J. Chem. Soc. 5880–5887 (1965)

  21. Garcillán-Barcia, M. P., Francia, M. V. & de la Cruz, F. The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiol. Rev. 33, 657–687 (2009)

    Article  Google Scholar 

  22. Zhong, Z. et al. Sequence analysis of a 101-kilobase plasmid required for agar degradation by a Microscilla isolate. Appl. Environ. Microbiol. 67, 5771–5779 (2001)

    Article  ADS  CAS  Google Scholar 

  23. Fisher, R. A. On the interpretation of χ2 from contingency tables, and the calculation of P. J. R. Stat. Soc. 85, 87–94 (1922)

    Article  Google Scholar 

  24. Kuo, C. H. & Ochman, H. Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biol. Direct 4, 35 (2009)

    Article  Google Scholar 

  25. Ishihara, K., Oyamada, C., Matsushima, R., Murata, M. & Muraoka, T. Inhibitory effect of porphyran, prepared from dried “nori”, on contact hypersensitivity in mice. Biosci. Biotechnol. Biochem. 69, 1824–1830 (2005)

    Article  CAS  Google Scholar 

  26. Kidby, D. K. & Davidson, D. J. A convenient ferricyanide estimation of reducing sugars in the nanomole range. Anal. Biochem. 55, 321–325 (1973)

    Article  CAS  Google Scholar 

  27. Pape, T. & Schneider, T. R. HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs. J. Appl. Cryst. 37, 843–844 (2004)

    Article  CAS  Google Scholar 

  28. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997)

    Article  CAS  Google Scholar 

  29. Potterton, L. et al. Developments in the CCP4 molecular-graphics project. Acta Crystallogr. D 60, 2288–2294 (2004)

    Article  Google Scholar 

  30. Boraston, A. B., Bolam, D. N., Gilbert, H. J. & Davies, G. J. Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem. J. 382, 769–781 (2004)

    Article  CAS  Google Scholar 

  31. Studier, F. W. Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005)

    Article  CAS  Google Scholar 

  32. Kabsch, W. Evaluation of single-crystal X-ray-diffraction data from a position-sensitive detector. J. Appl. Cryst. 21, 916–924 (1988)

    Article  CAS  Google Scholar 

  33. Schneider, T. R. & Sheldrick, G. M. Substructure solution with SHELXD. Acta Crystallogr. D 58, 1772–1779 (2002)

    Article  Google Scholar 

  34. Potterton, E., Briggs, P., Turkenburg, M. & Dodson, E. A graphical user interface to the CCP4 program suite. Acta Crystallogr. D 59, 1131–1137 (2003)

    Article  Google Scholar 

  35. Leslie, A. G. W. & Powell, H. R. in Evolving Methods for Macromolecular Crystallography Vol. 245 41–51 (Springer, 2007)

    Book  Google Scholar 

  36. Starr, C. M., Masada, R. I., Hague, C., Skop, E. & Klock, J. C. Fluorophore-assisted carbohydrate electrophoresis in the separation, analysis, and sequencing of carbohydrates. J. Chromatogr. A 720, 295–321 (1996)

    Article  CAS  Google Scholar 

  37. Katoh, K., Misawa, K., Kuma, K.-i. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002)

    Article  CAS  Google Scholar 

  38. Gouet, P., Robert, X. & Courcelle, E. ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res. 31, 3320–3323 (2003)

    Article  CAS  Google Scholar 

  39. Michel, G. et al. The κ-carrageenase of P. carrageenovora features a tunnel-shaped active site: a novel insight in the evolution of Clan-B glycoside hydrolases. Structure 9, 513–525 (2001)

    Article  CAS  Google Scholar 

  40. Guindon, S. & Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696–704 (2003)

    Article  Google Scholar 

  41. Kumar, S., Tamura, K. & Nei, M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5, 150–163 (2004)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank B. Kloareg and C. de Vargas for critical discussions and reading of the manuscript and M. Jam, A. Jeudy and D. Freudenreich for technical assistance. The ‘Marine Plants and Biomolecules’ laboratory is funded by the French national research centre (Centre National de la Recherche Scientifique) and the University Marie Curie; J.-H.H. was supported by a European Marie Curie PhD grant; this work was also funded by the ‘Region Bretagne’ through the program Marine 3D. G.M. was supported by the GIS ‘Genomique Marine’ and the French Research Ministry (ACI Young Researcher). We thank the beamline scientists and staff at the European Synchrotron Radiation Facilities for technical support during data collections, the NMR Service, University Bretagne Occidentale, for access to the Bruker NMR spectrometer and Genoscope for sequencing the Z. galactanivorans genome.

Author Contributions J.-H.H. cloned, purified and crystallized the enzymes and extracted polysaccharides; J.-H.H. and M.C. collected data and solved the crystal structures; G.C. and J.-H.H. purified and characterized oligosaccharides; G.C. and W.H. performed the NMR analysis; G.M., T.B. and J.-H.H. performed the bioinformatic analysis; M.C., T.B., G.M. and J.-H.H. designed the study; J.-H.H., M.C. and G.M. analysed the data and wrote the paper. All authors discussed the results and commented on the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Mirjam Czjzek or Gurvan Michel.

Supplementary information

Supplementary Information

This file contains Supplementary Notes A - C with References, Supplementary Tables 1-7 and Supplementary Figures 1-18 with Legends. (PDF 7309 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hehemann, JH., Correc, G., Barbeyron, T. et al. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464, 908–912 (2010). https://doi.org/10.1038/nature08937

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature08937

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing