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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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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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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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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DOI: https://doi.org/10.1038/nsmb.2935
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