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

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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.

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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.

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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

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.

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

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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) doi:10.1038/s41564-017-0079-1

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