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How Members of the Human Gut Microbiota Overcome the Sulfation Problem Posed by Glycosaminoglycans

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How Members of the Human Gut Microbiota Overcome the Sulfation Problem Posed by Glycosaminoglycans How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans Alan Cartmella,1, Elisabeth C. Lowea,1, Arnaud Basléa, Susan J. Firbanka, Didier A. Ndeha, Heath Murraya, Nicolas Terraponb, Vincent Lombardb, Bernard Henrissatb,c,d, Jeremy E. Turnbulle, Mirjam Czjzekf,g, Harry J. Gilberta, and David N. Bolama,2 aInstitute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom; bArchitecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France; cInstitut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France; dDepartment of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; eCentre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom; fSorbonne Universités, Université Pierre-et-Marie-Curie, Université Paris 06, F-29688 Roscoff cedex, Bretagne, France; and gCNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff cedex, Bretagne, France Edited by Carolyn R. Bertozzi, Stanford University, Stanford, CA, and approved May 23, 2017 (received for review March 17, 2017) The human microbiota, which plays an important role in health and by the CM. HS is a major component of the extracellular matrix of disease, uses complex carbohydrates as a major source of nutrients. mammalian cells and therefore, likely to be available to the gut Utilization hierarchy indicates that the host glycosaminoglycans microbiota via turnover of epithelial cells, whereas Hep is released heparin (Hep) and heparan sulfate (HS) are high-priority carbohy- from mast cells at sites of injury and therefore, may not be as drates for Bacteroides thetaiotaomicron, a prominent member of the prevalent as HS in the gut (10, 11). human microbiota. The sulfation patterns of these glycosaminogly- Microbial utilization of Hep and HS poses significant biological cans are highly variable, which presents a significant enzymatic chal- challenges. Both glycans differ significantly in their degree of po- lenge to the polysaccharide lyases and sulfatases that mediate lymerization (DP), which suggests that degradation may occur in degradation. It is possible that the bacterium recruits lyases with different cellular locations, whereas sulfation patterns and the highly plastic specificities and expresses a repertoire of enzymes that uronic acid (UA) are also variable (Fig. 1) (10). This substantial target substructures of the glycosaminoglycans with variable sulfa- heterogeneity indicates that either a complex portfolio of enzymes tion or that the glycans are desulfated before cleavage by the lyases. is required to deconstruct these acidicglycansortheenzymesthat To distinguish between these mechanisms, the components of the mediate this process display significant substrate promiscuity. The B. thetaiotaomicron Hep/HS degrading apparatus were analyzed. depolymerization of UA-containing glycans, such as Hep/HS, is The data showed that the bacterium expressed a single-surface mediated by glycoside hydrolases (GHs) and/or polysaccharide ly- endo-acting lyase that cleaved HS, reflecting its higher molecular ases (PLs) that are grouped into sequence-based families in the weight compared with Hep. Both Hep and HS oligosaccharides imported into the periplasm were degraded by a repertoire of lyases, CAZy database (12). Hep/HS are degraded by bacterial PLs be- with each enzyme displaying specificity for substructures within these longing to families PL12, -13, and -21. Based on specificity, these glycosaminoglycans that display a different degree of sulfation. Fur- PLs can be further broadly grouped into three functional groups, thermore, the crystal structures of a key surface glycan binding protein, which is able to bind both Hep and HS, and periplasmic sulfatases Significance reveal the major specificity determinants for these proteins. The locus described here is highly conserved within the human gut Bacteroides, The major nutrients available to the human microbiota are com- indicating that the model developed is of generic relevance to this plex carbohydrates. Host glycans are important to this microbial important microbial community. community, particularly when dietary carbohydrates are scarce. The host glycans heparin and heparan sulfate are high-priority human gut microbiota | glycosaminoglycan degradation | heparin | carbohydrates for Bacteroides thetaiotaomicron, a member of the heparan sulfate | Bacteroides thetaiotaomicron human microbiota. The degradation of these complex carbohy- drates is challenging, reflecting their highly variable sulfation he human colonic microbiota (CM) is crucial to health (1–3). patterns. How bacteria have adapted to depolymerize the myriad TThe composition of the CM depends on its ability to access of substructures of this important class of glycosaminoglycan is nutrients, which are primarily dietary and host glycans. Dissecting unknown. Here, we show how enzyme consortia, displaying the mechanisms by which complex carbohydrates are used by the complementary functions, target the different features of these CM is critical to understanding the drivers of the ecology of this host glycans. Structural data reveal that the acidic groups of the BIOCHEMISTRY microbial community and how this process relates to human health. glycans are key specificity determinants for enzymes and binding The major glycan degraders in the CM are the Bacteroidetes (4– proteins that make up the degradative apparatus. 6). These organisms access their target polysaccharides through Author contributions: A.C., E.C.L., H.J.G., and D.N.B. designed research; A.C., E.C.L., A.B., endo-acting enzymes on the bacterial surface followed by import of S.J.F., D.A.N., H.M., N.T., V.L., and M.C. performed research; J.E.T. contributed new the oligosaccharides generated, which are depolymerized in the reagents/analytic tools; A.C., E.C.L., A.B., S.J.F., H.M., N.T., V.L., B.H., M.C., and D.N.B. periplasm. The genes encoding these enzyme systems are physically analyzed data; and A.C., E.C.L., B.H., J.E.T., M.C., H.J.G., and D.N.B. wrote the paper. linked into loci termed polysaccharide utilization loci (PULs) (7). A The authors declare no conflict of interest. significant proportion of the complex carbohydrates available to the This article is a PNAS Direct Submission. CMismammalianinorigin(4).Despitethisknowledge,ourun- Freely available online through the PNAS open access option. derstanding of how the CM accesses host/mammalian glycans is Data deposition: The crystallography, atomic coordinates, and structure factors have been fragmentary. Models for the breakdown of high-mannose and deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 4AK1, 4AK2, 5G2T, complex N-glycans by gut Bacteroides have been proposed (8), and 5G2U, and 5G2V). the ecological significance of removing terminal sialic acid from the 1A.C. and E.C.L. contributed equally to this work. epithelial mucosa is established (9). There is, however, a paucity of 2To whom correspondence should be addressed. Email: [email protected]. information on the mechanism by which glycosaminoglycans This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. (GAGs), such as heparin (Hep) and heparan sulfate (HS), are used 1073/pnas.1704367114/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1704367114 PNAS | July 3, 2017 | vol. 114 | no. 27 | 7037–7042 Downloaded by guest on September 25, 2021 IM sugar ROK family Heparin/HS PUL which the enzymes and binding proteins encoded by this locus fully A transporter TAT protein SusD- SusC- Sulfatase PL15 Sulfatase PL12 GH88 like like SGBP PL12 HTCS PL13 deconstruct these highly variable GAGs and thus, solve the sul- BT1596 4652 46544653 4655 4656 4657 4658 4659 4660 4661 4662 4663 4675 fation problem. Crystal structures of key proteins provide mecha- Locus tag Name Function/Activity BT1596 De-O-Sulfatase Uronic acid 2O-sulfatase nistic insight into substrate and ligand recognition. The data BT4652 Polysaccharide lyase family 15 Lyase with broad specificity for sulfation revealed how the specificity of the apparatus is optimized to target BT4653 Inner membrane transporter Likely monosaccharide transporter BT4654 ROK family protein Glucosamine kinase the repertoire of GAG structures presented to the bacterium at the BT4655 TAT protein Likely glucosamine N-sulfatase BT4656 De-O-Sulfatase Glucosamine 6O-sulfatase different stages of the degradative process. BT4657 Polysaccharide lyase family 12 Lyase that prefers unsulfated substrates BT4658 Glycoside hydrolase family 88 4,5 unsaturated uronic acid hydrolase BT4659 SusD-like Binds heparin/heparan sulfate Results BT4660 SusC-like TonB-dependent transporter BT4661 Surface glycan binding protein Binds heparin/heparan sulfate BT4662 Polysaccharide lyase family 12 Surface lyase producing large oligosaccharides Structure of HS and Hep. Hep and HS are composed of a disac- BT4663 Hybrid two-component system Binds lyase produced disaccharides and upregulates PUL charide repeating unit comprising a UA, D-glucuronic (GlcA), BT4675 Polysaccharide lyase family 13 Lyase that prefers highly sulfated substrates 2S 6S 6S 2S6S 2S or L-iduronic acid (IdoA) alternating with D-glucosamine (GlcN). B NS NS NS GlcN is linked α1,4 to the UA, whereas IdoA and GlcA are linked Low sulfation
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