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A coiled-coil domain acts as a molecular ruler to regulate O-antigen chain length in lipopolysaccharide

Abstract

Long-chain bacterial polysaccharides have important roles in pathogenicity. In Escherichia coli O9a, a model for ABC transporter–dependent polysaccharide assembly, a large extracellular carbohydrate with a narrow size distribution is polymerized from monosaccharides by a complex of two proteins, WbdA (polymerase) and WbdD (terminating protein). Combining crystallography and small-angle X-ray scattering, we found that the C-terminal domain of WbdD contains an extended coiled-coil that physically separates WbdA from the catalytic domain of WbdD. The effects of insertions and deletions in the coiled-coil region were analyzed in vivo, revealing that polymer size is controlled by varying the length of the coiled-coil domain. Thus, the coiled-coil domain of WbdD functions as a molecular ruler that, along with WbdA:WbdD stoichiometry, controls the chain length of a model bacterial polysaccharide.

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Figure 1: Biosynthesis of modally distributed O-antigen–modified LPS chains in E. coli O9a.
Figure 2: The low-resolution structure of WbdD reveals new functional details.
Figure 3: Solution scattering of WbdD1–556 construct.
Figure 4: Deletions and insertions in the coiled-coil lead to changes in the size of the O-antigen–modified LPS molecule.
Figure 5: Proposed model for elongation and termination of the O9a antigen.

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References

  1. Raetz, C.R.H. & Whitfield, C. Lipopolysaccharide endotoxins. Annu. Rev. Biochem. 71, 635–700 (2002).

    Article  CAS  PubMed  Google Scholar 

  2. Whitfield, C. & Trent, M.S. Biosynthesis and export of bacterial lipopolysaccharides. Annu. Rev. Biochem. 83, 99–128 (2014).

    Article  CAS  PubMed  Google Scholar 

  3. Stenutz, R., Weintraub, A. & Widmalm, G. The structures of Escherichia coli O-polysaccharide antigens. FEMS Microbiol. Rev. 30, 382–403 (2006).

    Article  CAS  PubMed  Google Scholar 

  4. Joiner, K.A. Complement evasion by bacteria and parasites. Annu. Rev. Microbiol. 42, 201–230 (1988).

    Article  CAS  PubMed  Google Scholar 

  5. Katsura, I. Mechanism of length determination in bacteriophage lambda tails. Adv. Biophys. 26, 1–18 (1990).

    Article  CAS  PubMed  Google Scholar 

  6. Journet, L., Agrain, C., Broz, P. & Cornelis, G.R. The needle length of bacterial injectisomes is determined by a molecular ruler. Science 302, 1757–1760 (2003).

    Article  CAS  PubMed  Google Scholar 

  7. Greenfield, L.K. & Whitfield, C. Synthesis of lipopolysaccharide O-antigens by ABC transporter–dependent pathways. Carbohydr. Res. 356, 12–24 (2012).

    Article  CAS  PubMed  Google Scholar 

  8. Greenfield, L.K. et al. Biosynthesis of the polymannose lipopolysaccharide O antigens from Escherichia coli serotypes O8 and O9a requires a unique combination of single- and multi-active site mannosyltransferases. J. Biol. Chem. 287, 35078–35091 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Greenfield, L.K. et al. Domain organization of the polymerizing mannosyltransferases involved in synthesis of the Escherichia coli O8 and O9a lipopolysaccharide O-antigens. J. Biol. Chem. 287, 38135–38149 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Clarke, B.R., Cuthbertson, L. & Whitfield, C. Nonreducing terminal modifications determine the chain length of polymannose O antigens of Escherichia coli and couple chain termination to polymer export via an ATP-binding cassette transporter. J. Biol. Chem. 279, 35709–35718 (2004).

    CAS  PubMed  Google Scholar 

  11. Clarke, B.R., Greenfield, L.K., Bouwman, C. & Whitfield, C. Coordination of polymerization, chain termination, and export in assembly of the Escherichia coli lipopolysaccharide O9a antigen in an ATP-binding cassette transporter-dependent pathway. J. Biol. Chem. 284, 30662–30672 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Clarke, B.R. et al. In vitro reconstruction of the chain termination reaction in biosynthesis of the Escherichia coli O9a O-polysaccharide: the chain-length regulator, WbdD, catalyzes the addition of methyl phosphate to the non-reducing terminus of the growing glycan. J. Biol. Chem. 286, 41391–41401 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Cuthbertson, L., Kimber, M.S. & Whitfield, C. Substrate binding by a bacterial ABC transporter involved in polysaccharide export. Proc. Natl. Acad. Sci. USA 104, 19529–19534 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  14. Cuthbertson, L., Mainprize, I.L., Naismith, J.H. & Whitfield, C. Pivotal roles of the outer membrane polysaccharide export and polysaccharide copolymerase protein families in export of extracellular polysaccharides in gram-negative bacteria. Microbiol. Mol. Biol. Rev. 73, 155–177 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Hagelueken, G. et al. Structure of WbdD: a bifunctional kinase and methyltransferase that regulates the chain length of the O antigen in Escherichia coli O9a. Mol. Microbiol. 86, 730–742 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. King, J.D., Berry, S., Clarke, B.R., Morris, R.J. & Whitfield, C. Lipopolysaccharide O antigen size distribution is determined by a chain extension complex of variable stoichiometry in Escherichia coli O9a. Proc. Natl. Acad. Sci. USA 111, 6407–6412 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Hagelueken, G. et al. Crystallization, dehydration and experimental phasing of WbdD, a bifunctional kinase and methyltransferase from Escherichia coli O9a. Acta Crystallogr. D Biol. Crystallogr. 68, 1371–1379 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Schröder, G.F., Levitt, M. & Brunger, A.T. Super-resolution biomolecular crystallography with low-resolution data. Nature 464, 1218–1222 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Lupas, A.N. & Gruber, M. The structure of α-helical coiled coils. Adv. Protein Chem. 70, 37–38 (2005).

    Article  CAS  PubMed  Google Scholar 

  20. Grigoryan, G. & DeGrado, W.F. Probing designability via a generalized model of helical bundle geometry. J. Mol. Biol. 405, 1079–1100 (2011).

    Article  CAS  PubMed  Google Scholar 

  21. Strelkov, S.V. & Burkhard, P. Analysis of α-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation. J. Struct. Biol. 137, 54–64 (2002).

    Article  CAS  PubMed  Google Scholar 

  22. Wood, C.W. et al. CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies. Bioinformatics 30, 3029–3035 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Petoukhov, M.V. & Svergun, D.I. Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys. J. 89, 1237–1250 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. van Stokkum, I.H., Spoelder, H.J., Bloemendal, M., van Grondelle, R. & Groen, F.C. Estimation of protein secondary structure and error analysis from circular dichroism spectra. Anal. Biochem. 191, 110–118 (1990).

    Article  CAS  PubMed  Google Scholar 

  25. Sreerama, N. & Woody, R.W. Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal. Biochem. 287, 252–260 (2000).

    Article  CAS  PubMed  Google Scholar 

  26. King, J. Bacteriophage T4 tail assembly: four steps in core formation. J. Mol. Biol. 58, 693–709 (1971).

    Article  CAS  PubMed  Google Scholar 

  27. Marshall, W.F. Cellular length control systems. Annu. Rev. Cell Dev. Biol. 20, 677–693 (2004).

    Article  CAS  PubMed  Google Scholar 

  28. Makishima, S., Komoriya, K., Yamaguchi, S. & Aizawa, S.-I. Length of the flagellar hook and the capacity of the type III export apparatus. Science 291, 2411–2413 (2001).

    Article  CAS  PubMed  Google Scholar 

  29. Erhardt, M., Singer, H.M., Wee, D.H., Keener, J.P. & Hughes, K.T. An infrequent molecular ruler controls flagellar hook length in Salmonella enterica. EMBO J. 30, 2948–2961 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Agrain, C., Sorg, I., Paroz, C. & Cornelis, G.R. Secretion of YscP from Yersinia enterocolitica is essential to control the length of the injectisome needle but not to change the type III secretion substrate specificity. Mol. Microbiol. 57, 1415–1427 (2005).

    Article  CAS  PubMed  Google Scholar 

  31. Wagner, S., Stenta, M., Metzger, L.C., Dal Peraro, M. & Cornelis, G.R. Length control of the injectisome needle requires only one molecule of Yop secretion protein P (YscP). Proc. Natl. Acad. Sci. USA 107, 13860–13865 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  32. Wagner, S. et al. The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome. Mol. Microbiol. 71, 692–701 (2009).

    Article  CAS  PubMed  Google Scholar 

  33. Hatoum-Aslan, A., Samai, P., Maniv, I., Jiang, W. & Marraffini, L.A. A ruler protein in a complex for antiviral defense determines the length of small interfering CRISPR RNAs. J. Biol. Chem. 288, 27888–27897 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Hinz, A. et al. Structural basis of HIV-1 tethering to membranes by the BST-2/tetherin ectodomain. Cell Host Microbe 7, 314–323 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Kim, J.-S. et al. Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Proc. Natl. Acad. Sci. USA 102, 3248–3253 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Price, C., Lingner, J., Bickle, T.A., Firman, K. & Glover, S.W. Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 type I DNA restriction and modification enzymes. J. Mol. Biol. 205, 115–125 (1989).

    Article  CAS  PubMed  Google Scholar 

  37. Kido, N., Sugiyama, T., Yokochi, T., Kobayashi, H. & Okawa, Y. Synthesis of Escherichia coli O9a polysaccharide requires the participation of two domains of WbdA, a mannosyltransferase encoded within the wb* gene cluster. Mol. Microbiol. 27, 1213–1221 (1998).

    Article  CAS  PubMed  Google Scholar 

  38. Kubler-Kielb, J., Whitfield, C., Katzenellenbogen, E. & Vinogradov, E. Identification of the methyl phosphate substituent at the non-reducing terminal mannose residue of the O-specific polysaccharides of Klebsiella pneumoniae O3, Hafnia alvei PCM 1223 and Escherichia coli O9/O9a LPS. Carbohydr. Res. 347, 186–188 (2012).

    Article  CAS  PubMed  Google Scholar 

  39. Steiner, K. et al. Molecular basis of S-layer glycoprotein glycan biosynthesis in Geobacillus stearothermophilus. J. Biol. Chem. 283, 21120–21133 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Vinogradov, E. et al. Structures of lipopolysaccharides from Klebsiella pneumoniae. Eluicidation of the structure of the linkage region between core and polysaccharide O chain and identification of the residues at the non-reducing termini of the O chains. J. Biol. Chem. 277, 25070–25081 (2002).

    Article  CAS  PubMed  Google Scholar 

  41. Mertens, K. et al. Antiserum against Raoultella terrigena ATCC 33257 identifies a large number of Raoultella and Klebsiella clinical isolates as serotype O12. Innate Immun. 16, 366–380 (2010).

    Article  CAS  PubMed  Google Scholar 

  42. Abràmoff, M.D., Magalhães, P.J. & Ram, S.J. Image processing with ImageJ. Biophotonics Int. 11, 36–42 (2004).

    Google Scholar 

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

    Article  CAS  Google Scholar 

  44. McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007).

    Article  CAS  Google Scholar 

  45. Nicholls, R.A., Long, F. & Murshudov, G.N. Low-resolution refinement tools in REFMAC5. Acta Crystallogr. D Biol. Crystallogr. 68, 404–417 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  47. Roessle, M.W. et al. Upgrade of the small-angle X-ray scattering beamline X33 at the European Molecular Biology Laboratory, Hamburg. J. Appl. Crystallogr. 40, 190–194 (2007).

    Article  CAS  Google Scholar 

  48. Petoukhov, M.V., Konarev, P.V., Kikhney, A.G. & Svergun, D.I. ATSAS2.1 – towards automated and web-supported small-angle scattering data analysis. J. Appl. Crystallogr. 40, 223–228 (2007).

    Article  CAS  Google Scholar 

  49. Konarev, P.V., Volkov, V.V., Sokolova, A.V., Koch, M.H.J. & Svergun, D.I. PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J. Appl. Crystallogr. 36, 1277–1282 (2003).

    Article  CAS  Google Scholar 

  50. Guinier, A. La diffraction des rayons X aux tres petits angles: applications a l'etude de phenomenes ultramicroscopiques. Ann. Phys. (Paris) 12, 161–237 (1939).

    CAS  Google Scholar 

  51. Svergun, D.I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25, 495–503 (1992).

    CAS  Google Scholar 

  52. Petoukhov, M.V. et al. New developments in the ATSAS program package for small-angle scattering data analysis. J. Appl. Crystallogr. 45, 342–350 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Svergun, D., Barberato, C. & Koch, M.H.J. CRYSOL– a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 28, 768–773 (1995).

    Article  CAS  Google Scholar 

  54. Svergun, D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76, 2879–2886 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Kozin, M.B. & Svergun, D.I. Automated matching of high- and low-resolution structural models. J. Appl. Crystallogr. 34, 33–41 (2001).

    Article  CAS  Google Scholar 

  56. Volkov, V.V. & Svergun, D.I. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crystallogr. 36, 860–864 (2003).

    Article  CAS  Google Scholar 

  57. Jávorfi, T., Hussain, R., Myatt, D. & Siligardi, G. Measuring circular dichroism in a capillary cell using the b23 synchrotron radiation CD beamline at diamond light source. Chirality 22 Suppl 1, E149–E153 (2010).

    Article  CAS  PubMed  Google Scholar 

  58. Hussain, R., Jávorfi, T. & Siligardi, G. Spectroscopic analysis: synchrotron radiation circular dichroism. in Comprehensive Chirality (eds. Yamamoto, H. & Carriera, E.M.) 438–448 (Elsevier, 2012).

  59. Hussain, R., Jávorfi, T. & Siligardi, G. Circular dichroism beamline B23 at the diamond light source. J. Synchrotron Radiat. 19, 132–135 (2012).

    Article  PubMed  Google Scholar 

  60. Liu, H. & Naismith, J.H. An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol. BMC Biotechnol. 8, 91 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Whitfield, C., Schoenhals, G. & Graham, L. Mutants of Escherichia coli O9: K30 with Altered synthesis and expression of the capsular K30 antigen. J. Gen. Microbiol. 135, 2589–2599 (1989).

    CAS  PubMed  Google Scholar 

  62. Hitchcock, P.J. & Brown, T.M. Morphological heterogeneity among Salmonella lipopolysaccharide chemotypes in silver-stained polyacrylamide gels. J. Bacteriol. 154, 269–277 (1983).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Tsai, C.M. & Frasch, C.E. A sensitive silver stain for detecting lipopolysaccharides in polyacrylamide gels. Anal. Biochem. 119, 115–119 (1982).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This work was supported by Wellcome Trust grant 081862 (J.H.N. and C.W.), Senior Investigator Award WT100209MA (J.H.N.), the Natural Sciences, Engineering Research Council of Canada (C.W.), and the German Federal Ministry of Education and Research (BMBF) project BioSCAT (contract no: 05K12YE1 (A.T. and D.I.S.). J.H.N. is a Royal Society Wolfson Merit Award Holder and C.W. is a recipient of a Canada Research Chair. We are grateful for beam time on beam lines B23 and IO4 at Diamond and on the beam line X33 of the EMBL at DESY.

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Contributions

G.H., H.H. and J.H.N. carried out the crystallography. A.T., I.D. and D.I.S. carried out SAXS experiments, data analysis and modeling. B.R.C., H.L. and C.W. carried out mutagenesis and in vivo work. H.H. and R.H. carried out CD experiments. All of the authors analyzed data and contributed to writing the paper.

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Correspondence to Chris Whitfield or James H Naismith.

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Integrated supplementary information

Supplementary Figure 1 SAXS data for WbdD1–459 monomer.

Two views (rotated by 90°) of an ab initio model constructed using DAMMIN is shown in the bottom left (grey surfaces). The high-resolution structure of WbdD1-459 shown as cartoon model (purple) is superimposed. Fits of the structural model against the experimental SAXS data (open circles with error bars representing s.d. computed from propagated Poisson counting statistics).

Supplementary Figure 2 Prediction of coiled-coil structures in the C-terminal part of WbdD.

The part of the coiled-coil that has been observed in the low-resolution WbdD1-556 structure (residues up to 506 ordered) is shaded in grey.

Supplementary Figure 3 CD spectra of different WbdD constructs recorded on Diamond beamline B23.

See main text for experimental details and discussion. The experimental helical content and the expected increase with respect to WbdD1-459 (based on the number of inserted or deleted residues) are detailed below the spectra.

Supplementary Figure 4 Effect of His6-WbdD expression level on the chain length of the E. coli O9a O-polysaccharide.

E. coli O9a ΔwbdD [pWQ470] cultures where grown to mid-exponential phase in LB medium containing 0.1% (w/v) D-mannose and varying L-arabinose concentrations (as indicated). Cells equivalent to one A600nm unit were collected from each culture and lysed in SDS-PAGE loading buffer. One half of each sample was treated with proteinase K, separated by SDS-PAGE and the LPS stained with Emerald Pro Q (Life Technologies). The remaining half was separated by SDS-PAGE and His6-WbdD was detected by Western blotting using anti-Penta-His antibody (Qiagen) together with horseradish peroxidase-conjugated goat-anti mouse antibody (Cedar Lane) and Luminata Classico Western HRP substrate (Millipore). Protein levels were quantitated by densitometry and are reported below the figure as the amounts relative to that observed in the sample with the highest expression level (0.05% L-arabinose).

Supplementary Figure 5 Chain length of LPS with mutant WbdD protein.

A) Silver-stained SDS-PAGE showing an incremental decrease in LPS chain-length when His6-WbdD ∆(GHIJ) and (CDEF)2 were over-expressed from the pBAD promoter with various L-arabinose concentrations. In both cases genomic WbdA was constitutively expressed from its native promoter.

B) Plot of LPS length in RU (taken from Figure 3C) versus calculated coiled-coil domain length (taken from Figure 3A). The red line is a linear regression of the plot. The regression parameters are given in the plot.

Supplementary Figure 6 Diagram showing the relative positions of coiled-coil regions within established and putative glycan chain–terminating enzymes.

WbdDO9a and WbdDO8 (GenBank AFQ31610 and BAA28326) possess terminating activity only. The putative coiled-coil of G. stearothermophilus WsaE (ARR99608) separates a chain-terminating methyltransferase domain from two glycosyltransferase domains involved in polysaccharide elongation. The R. terrigena WbbB (AAQ82931) protein has a putative 3-deoxy-D-manno-oct-2-ulosonic acid transferase (pfam05159) domain and two glycosyltransferase domains (pfam 13524 and 01755) separated by a coiled-coil. The putative coiled-coil regions for WbdDO8, WsaE, and WbbB were identified using the COILS program with a window of 28 residues.

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Hagelueken, G., Clarke, B., Huang, H. et al. A coiled-coil domain acts as a molecular ruler to regulate O-antigen chain length in lipopolysaccharide. Nat Struct Mol Biol 22, 50–56 (2015). https://doi.org/10.1038/nsmb.2935

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