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.

  • Article
  • Published:

Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides

Abstract

The major nutrients available to human colonic Bacteroides species are glycans, exemplified by pectins, a network of covalently linked plant cell wall polysaccharides containing galacturonic acid (GalA). Metabolism of complex carbohydrates by the Bacteroides genus is orchestrated by polysaccharide utilization loci (PULs). In Bacteroides thetaiotaomicron, a human colonic bacterium, the PULs activated by different pectin domains have been identified; however, the mechanism by which these loci contribute to the degradation of these GalA-containing polysaccharides is poorly understood. Here we show that each PUL orchestrates the metabolism of specific pectin molecules, recruiting enzymes from two previously unknown glycoside hydrolase families. The apparatus that depolymerizes the backbone of rhamnogalacturonan-I is particularly complex. This system contains several glycoside hydrolases that trim the remnants of other pectin domains attached to rhamnogalacturonan-I, and nine enzymes that contribute to the degradation of the backbone that makes up a rhamnose-GalA repeating unit. The catalytic properties of the pectin-degrading enzymes are optimized to protect the glycan cues that activate the specific PULs ensuring a continuous supply of inducing molecules throughout growth. The contribution of Bacteroides spp. to metabolism of the pectic network is illustrated by cross-feeding between organisms.

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

Fig. 1: Genomic organization of pectin PULs.
Fig. 2: Depolymerization of pectins at the cell surface of B. thetaiotaomicron cell surface.
Fig. 3: Signal molecule protection.
Fig. 4: Cross-feeding of polysaccharide breakdown products between Bacteroides species.
Fig. 5: Model of pectin utilization by B. thetaiotaomicron.

Similar content being viewed by others

References

  1. Caffall, K. H. & Mohnen, D. The structure, function, and biosynthesis of plant cell wall pectic polysaccharides. Carbohyd. Res. 344, 1879–1900 (2009).

    Article  CAS  PubMed  Google Scholar 

  2. Gilbert, J. A. et al. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature 535, 94–103 (2016).

    Article  CAS  PubMed  Google Scholar 

  3. Sonnenburg, J. L. & Backhed, F. Diet-microbiota interactions as moderators of human metabolism. Nature 535, 56–64 (2016).

    Article  CAS  PubMed  Google Scholar 

  4. Koropatkin, N. M., Cameron, E. A. & Martens, E. C. How glycan metabolism shapes the human gut microbiota. Nat. Rev. Microbiol. 10, 323–335 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Desai, M. S. et al. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 167, 1339–1353 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Wu, M. et al. Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides. Science 350, aac5992 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  7. Cartmell, A. et al. How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans. Proc. Natl Acad. Sci. USA 114, 7037–7042 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Cuskin, F. et al. Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature 517, 165–169 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Larsbrink, J. et al. A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Nature 506, 498–502 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Ndeh, D. et al. Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Nature 544, 65–70 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M. & Henrissat, B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, 490–495 (2014).

    Article  CAS  PubMed  Google Scholar 

  12. Gilbert, H. J. The biochemistry and structural biology of plant cell wall deconstruction. Plant Physiol. 153, 444–455 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Lau, J. M., Mcneil, M., Darvill, A. G. & Albersheim, P. Treatment of rhamnogalacturonan-I with lithium in ethylenediamine. Carbohyd. Res. 168, 245–274 (1987).

    Article  CAS  Google Scholar 

  14. Coenen, G. J., Bakx, E. J., Verhoef, R. P., Schols, H. A. & Voragen, A. G. J. Identification of the connecting linkage between homo- or xylogalacturonan and rhamnogalacturonan type I. Carbohyd. Polym. 70, 224–235 (2007).

    Article  CAS  Google Scholar 

  15. Bonnin, E., Garnier, C. & Ralet, M. C. Pectin-modifying enzymes and pectin-derived materials: applications and impacts. App. Microbiol. Biotechnol. 98, 519–532 (2014).

    Article  CAS  PubMed  Google Scholar 

  16. Martens, E. C. et al. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. 9, e1001221 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. 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  PubMed  PubMed Central  Google Scholar 

  18. Glenwright, A. J. et al. Structural basis for nutrient acquisition by dominant members of the human gut microbiota. Nature 541, 407–411 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  20. Cartmell, A. et al. The structure and function of an arabinan-specific α-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases. J. Biol. Chem. 286, 15483–15495 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Pickersgill, R., Smith, D., Worboys, K. & Jenkins, J. Crystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora. J. Biol. Chem. 273, 24660–24664 (1998).

    Article  CAS  PubMed  Google Scholar 

  22. van Santen, Y. et al. 1.68-angstrom crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis. J. Biol. Chem. 274, 30474–30480 (1999).

    Article  PubMed  Google Scholar 

  23. Sengkhamparn, N. et al. Okra pectin contains an unusual substitution of its rhamnosyl residues with acetyl and alpha-linked galactosyl groups. Carbohyd. Res. 344, 1842–1851 (2009).

    Article  CAS  PubMed  Google Scholar 

  24. Renard, C. M., Crepeau, M. J. & Thibault, J. F. Glucuronic acid directly linked to galacturonic acid in the rhamnogalacturonan backbone of beet pectins. Eur. J. Biochem. 266, 566–574 (1999).

    Article  CAS  PubMed  Google Scholar 

  25. Raghavan, V., Lowe, E. C., Townsend, G. E. 2nd, Bolam, D. N. & Groisman, E. A. Tuning transcription of nutrient utilization genes to catabolic rate promotes growth in a gut bacterium. Mol. Microbiol. 93, 1010–1025 (2014).

    Article  CAS  PubMed  Google Scholar 

  26. Bagenholm, V. et al. Galactomannan catabolism conferred by a polysaccharide utilization locus of Bacteroides ovatus: enzyme synergy and crystal structure of a beta-mannanase. J. Biol. Chem. 292, 229–243 (2017).

    Article  PubMed  Google Scholar 

  27. Rogowski, A. et al. Glycan complexity dictates microbial resource allocation in the large intestine. Nat. Commun. 6, 7481 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Rakoff-Nahoum, S., Coyne, M. J. & Comstock, L. E. An ecological network of polysaccharide utilization among human intestinal symbionts. Curr. Biol. 24, 40–49 (2014).

    Article  CAS  PubMed  Google Scholar 

  29. Rakoff-Nahoum, S., Foster, K. R. & Comstock, L. E. The evolution of cooperation within the gut microbiota. Nature 533, 255–259 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Foley, M. H., Cockburn, D. W. & Koropatkin, N. M. The Sus operon: a model system for starch uptake by the human gut Bacteroidetes. Cell Mol. Life Sci. 73, 2603–2617 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Miller, G. L. Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal. Chem. 31, 426–428 (1959).

    Article  CAS  Google Scholar 

  32. Cavanagh, J., Fairbrother, W. J., Palmer, A. G. & Skelton, N. J. Protein NMR Spectroscopy: Principles and Practice (Academic Press, Cambridge, 1996).

    Google Scholar 

  33. Vranken, W. F. et al. The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59, 687–696 (2005).

    Article  CAS  PubMed  Google Scholar 

  34. Koropatkin, N. M., Martens, E. C., Gordon, J. I. & Smith, T. J. Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure 16, 1105–1115 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Despres, J. et al. Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics 17, 147 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  36. Winter, G. xia2: an expert system for macromolecular crystallography data reduction. J. Appl. Crystallogr. 43, 186–190 (2010).

    Article  CAS  Google Scholar 

  37. Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution? Acta Crystallogr. D 69, 1204–1214 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Evans, P. R. An introduction to data reduction: space-group determination, scaling and intensity statistics. Acta Crystallogr. D 67, 282–292 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  Google Scholar 

  41. Sheldrick, G. M. Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. D 66, 479–485 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Long, F., Vagin, A. A., Young, P. & Murshudov, G. N. BALBES: a molecular-replacement pipeline. Acta Crystallogr. D 64, 125–132 (2008).

    Article  CAS  PubMed  Google Scholar 

  43. Langer, G., Cohen, S. X., Lamzin, V. S. & Perrakis, A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protoc. 3, 1171–1179 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Cowtan, K. Fitting molecular fragments into electron density. Acta Crystallogr. D 64, 83–89 (2008).

    Article  CAS  PubMed  Google Scholar 

  45. Vagin, A. A. et al. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr. D 60, 2184–2195 (2004).

    Article  PubMed  Google Scholar 

  46. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).

    Article  PubMed  Google Scholar 

  47. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).

    Article  CAS  PubMed  Google Scholar 

  48. Terrapon, N., Lombard, V., Gilbert, H. J. & Henrissat, B. Automatic prediction of polysaccharide utilization loci in Bacteroidetes species. Bioinformatics 31, 647–655 (2015).

    Article  CAS  PubMed  Google Scholar 

  49. Terrapon, N., Weiner, J., Grath, S., Moore, A. D. & Bornberg-Bauer, E. Rapid similarity search of proteins using alignments of domain arrangements. Bioinformatics 30, 274–281 (2014).

    Article  CAS  PubMed  Google Scholar 

  50. Varki, A. et al. Symbol nomenclature for graphical representations of glycans. Glycobiology 25, 1323–1324 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported in part by an Advanced Grant from the European Research Council (Grant No. 322820) awarded to H.J.G. and B.H. supporting A.S.L., D.N., A.C. and N.T., a Wellcome Trust Senior Investigator Award to H.J.G. (grant No. WT097907MA) that supported J.B. and E.C.L. a European Union Seventh Framework Initial Training Network Programme entitled the “WallTraC project” (Grant Agreement number 263916) awarded to M-C.R. and H.J.G, which supported X.Z. and J.S. The Biotechnology and Biological Research Council project ‘Ricefuel’ (grant numbers BB/K020358/1) awarded to H.J.G. supported A.L. 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 J. Gray at Newcastle University for assistance with the mass spectrometry.

Author information

Authors and Affiliations

Authors

Contributions

Enzyme characterization was carried out by A.S.L., J.B., X.Z., A.L., I.V., R.M., K.Sh, B.F. and J.S. The generation of oligosaccharide products was carried out by M-C.R., X.Z., A.S.L., A.C. and D.N. Gene deletion strains were constructed by A.S.L., D.N., R.M., B.F., J.B. and D.W.A. Co-culturing experiments were carried out by J.B. and A.S.L. Phylogenetic reconstruction and metagenomic analysis was by N.T. and B.H. Bacterial growth and transcriptomic experiments were by X.Z., E.C.L. and E.C.M. X-ray protein crystallography was by A.B., A.C., A.S.L. and J.B. NMR experiments were by A.S.L. and K.St. Experiments were designed by D.W.A., H.J.G., E.C.L., S.C.M. and H.J.G. The manuscript was written by H.J.G. with substantial contributions from D.W.A., E.C.L., N.T. and B.H. Figures were prepared by E.C.L. and A.S.L.

Corresponding authors

Correspondence to D. Wade Abbott or Harry J. Gilbert.

Ethics declarations

Competing interests

The authors declare no competing financial interests. 

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Discussion, Tables, Figures and References.

Life Sciences Reporting Summary

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Luis, A.S., Briggs, J., Zhang, X. et al. Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides . Nat Microbiol 3, 210–219 (2018). https://doi.org/10.1038/s41564-017-0079-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41564-017-0079-1

This article is cited by

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