Crystal structure of c5321: a protective antigen present in uropathogenic Escherichia coli strains displaying an SLR fold

BMC Structural Biology

Xavier Daura¹  Marco Soriani⁵  Laura Serino⁵  David Reverter²  Ainars Leonchiks³  Jean-Didier Maréchal⁴  Dmitrijs Zhulenkovs³  Lionel Costenaro²  Elena Cartocci⁵  Ilaria Pastorello⁵  Mario Ferrer-Navarro²  Dunja Urosev² 

[1] Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain;Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain;ASLA Biotech Ltd, Ratsupites 1, Riga 1067, Latvia;Department of Chemistry, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain;Novartis Vaccines and Diagnostics Srl, Via Fiorentina 1, Siena 53100, Italy

关键词: Uropathogenic Escherichia coli;    Antigen;    Super-helical fold;    Crystal structure;    Sel1-like repeat;    c5321;   

Others  :  793924
DOI  :  10.1186/1472-6807-13-19

 received in 2013-07-06, accepted in 2013-10-03,  发布年份 2013

【 摘 要 】

Background

Increasing rates of antimicrobial resistance among uropathogens led, among other efforts, to the application of subtractive reverse vaccinology for the identification of antigens present in extraintestinal pathogenic E. coli (ExPEC) strains but absent or variable in non-pathogenic strains, in a quest for a broadly protective Escherichia coli vaccine. The protein coded by locus c5321 from CFT073 E. coli was identified as one of nine potential vaccine candidates against ExPEC and was able to confer protection with an efficacy of 33% in a mouse model of sepsis. c5321 (known also as EsiB) lacks functional annotation and structurally belongs to the Sel1-like repeat (SLR) family. Herein, as part of the general characterization of this potential antigen, we have focused on its structural properties.

Results

We report the 1.74 Å-resolution crystal structure of c5321 from CFT073 E. coli determined by Se-Met SAD phasing. The structure is composed of 11 SLR units in a topological organisation that highly resembles that found in HcpC from Helicobacter pylori, with the main difference residing in how the super-helical fold is stabilised. The stabilising effect of disulfide bridges in HcpC is replaced in c5321 by a strengthening of the inter-repeat hydrophobic core. A metal-ion binding site, uncharacteristic of SLR proteins, is detected between SLR units 3 and 4 in the region of the inter-repeat hydrophobic core. Crystal contacts are observed between the C-terminal tail of one molecule and the C-terminal amphipathic groove of a neighbouring one, resembling interactions between ligand and proteins containing tetratricopeptide-like repeats.

Conclusions

The structure of antigen c5321 presents a mode of stabilization of the SLR fold different from that observed in close homologs of known structure. The location of the metal-ion binding site and the observed crystal contacts suggest a potential role in regulation of conformational flexibility and interaction with yet unidentified target proteins, respectively. These findings open new perspectives in both antigen design and for the identification of a functional role for this protective antigen.

【 授权许可】

   
2013 Urosev et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Welch RA, Burland V, Plunkett G 3rd, Redford P, Roesch P, Rasko D, Buckles EL, Liou S-R, Boutin A, Hackett J, Stroud D, Mayhew GF, Rose DJ, Zhou S, Schwartz DC, Perna NT, Mobley HLT, Donnenberg MS, Blattner FR: Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 2002, 99:17020-17024.
• [2]Moriel DG, Bertoldi I, Spagnuolo A, Marchi S, Rosini R, Nesta B, Pastorello I, Corea VAM, Torricelli G, Cartocci E, Savino S, Scarselli M, Dobrindt U, Hacker J, Tettelin H, Tallon LJ, Sullivan S, Wieler LH, Ewers C, Pickard D, Dougan G, Fontana MR, Rappuoli R, Pizza M, Serino L: Identification of protective and broadly conserved vaccine antigens from the genome of extraintestinal pathogenic Escherichia coli. Proc Natl Acad Sci USA 2010, 107:9072-9077.
• [3]Hagan EC, Mobley HLT: Uropathogenic Escherichia coli outer membrane antigens expressed during urinary tract infection. Infect Immun 2007, 75:3941-3949.
• [4]Pastorello I, Rossi Pacani S, Rosini R, Mattera R, Ferrer Navarro M, Urosev D, Nesta B, Lo Surdo P, Del Vecchio M, Rippa V, Bertoldi I, Gomes Moriel D, Laarman AJ, van Strijp JAG, Daura X, Pizza M, Serino L, Soriani M: EsiB: a novel pathogenic E. coli SIgA-binding protein impairing neutrophil activation. mBio 2013, 4:e00206-e00213.
• [5]Schultz J, Milpetz F, Bork P, Ponting CP: SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci USA 1998, 95:5857-5864.
• [6]Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD: The Pfam protein families database. Nucleic Acids Res 2012, 40:D290-301.
• [7]Grant B, Greenwald I: The Caenorhabditis elegans sel-1 gene, a negative regulator of lin-12 and glp-1, encodes a predicted extracellular protein. Genet 1996, 143:237-247.
• [8]Lüthy L, Grütter MG, Mittl PRE: The crystal structure of Helicobacter pylori cysteine-rich protein B reveals a novel fold for a penicillin-binding protein. J Biol Chem 2002, 277:10187-10193.
• [9]Mittl PRE, Schneider-Brachert W: Sel1-like repeat proteins in signal transduction. Cell Signal 2007, 19:20-31.
• [10]D’Andrea LD, Regan L: TPR proteins: the versatile helix. Trends Biochem Sci 2003, 28:655-662.
• [11]Das AK, Cohen PW, Barford D: The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions. EMBO J 1998, 17:1192-1199.
• [12]Allan RK, Ratajczak T: Versatile TPR domains accommodate different modes of target protein recognition and function. Cell Stress Chaperones 2011, 16:353-367.
• [13]Ramarao MK, Bianchetta MJ, Lanken J, Cohen JB: Role of rapsyn tetratricopeptide repeat and coiled-coil domains in self-association and nicotinic acetylcholine receptor clustering. J Biol Chem 2001, 276:7475-7483.
• [14]Ferreiro DU, Walczak AM, Komives EA, Wolynes PG: The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures. PLoS Comput Biol 2008, 4:e1000070.
• [15]Petersen TN, Brunak S, von Heijne G, Nielsen H: SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011, 8:785-786.
• [16]Lüthy L, Grütter MG, Mittl PRE: The crystal structure of Helicobacter cysteine-rich protein C at 2.0 A resolution: similar peptide-binding sites in TPR and SEL1-like repeat proteins. J Mol Biol 2004, 340:829-841.
• [17]Jínek M, Rehwinkel J, Lazarus BD, Izaurralde E, Hanover JA, Conti E: The superhelical TPR-repeat domain of O-linked GlcNAc transferase exhibits structural similarities to importin alpha. Nat Struct Mol Biol 2004, 11:1001-1007.
• [18]Liang J, Woodward C, Edelsbrunner H: Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Sci 1998, 7:1884-1897.
• [19]Stanley WA, Pursiainen NV, Garman EF, Juffer AH, Wilmanns M, Kursula P: A previously unobserved conformation for the human Pex5p receptor suggests roles for intrinsic flexibility and rigid domain motions in ligand binding. BMC Struct Biol 2007, 7:24. BioMed Central Full Text
• [20]Cliff MJ, Harris R, Barford D, Ladbury JE, Williams MA: Conformational diversity in the TPR domain-mediated interaction of protein phosphatase 5 with Hsp90. Structure 2006, 14:415-426.
• [21]Onuoha SC, Coulstock ET, Grossmann JG, Jackson SE: Structural studies on the co-chaperone Hop and its complexes with Hsp90. J Mol Biol 2008, 379:732-744.
• [22]Alag R, Bharatham N, Dong A, Hills T, Harikishore A, Widjaja AA, Shochat SG, Hui R, Yoon HS: Crystallographic structure of the tetratricopeptide repeat domain of Plasmodium falciparum FKBP35 and its molecular interaction with Hsp90 C-terminal pentapeptide. Protein Sci 2009, 18:2115-2124.
• [23]Ramsey AJ, Russell LC, Chinkers M: C-terminal sequences of hsp70 and hsp90 as non-specific anchors for tetratricopeptide repeat (TPR) proteins. Biochem J 2009, 423:411-419.
• [24]Cortajarena AL, Kajander T, Pan W, Cocco MJ, Regan L: Protein design to understand peptide ligand recognition by tetratricopeptide repeat proteins. Protein Eng Des Sel 2004, 17:399-409.
• [25]Nyarko A, Mosbahi K, Rowe AJ, Leech A, Boter M, Shirasu K, Kleanthous C: TPR-Mediated self-association of plant SGT1. Biochem 2007, 46:11331-11341.
• [26]Zeytuni N, Ozyamak E, Ben-Harush K, Davidov G, Levin M, Gat Y, Moyal T, Brik A, Komeili A, Zarivach R: Self-recognition mechanism of MamA, a magnetosome-associated TPR-containing protein, promotes complex assembly. Proc Natl Acad Sci USA 2011, 108:E480-487.
• [27]Taylor P, Dornan J, Carrello A, Minchin RF, Ratajczak T, Walkinshaw MD: Two structures of cyclophilin 40: folding and fidelity in the TPR domains. Structure 2001, 9:431-438.
• [28]Pizza M, Scarlato V, Masignani V, Giuliani MM, Aricò B, Comanducci M, Jennings GT, Baldi L, Bartolini E, Capecchi B, Galeotti CL, Luzzi E, Manetti R, Marchetti E, Mora M, Nuti S, Ratti G, Santini L, Savino S, Scarselli M, Storni E, Zuo P, Broeker M, Hundt E, Knapp B, Blair E, Mason T, Tettelin H, Hood DW, Jeffries AC, et al.: Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Sci 2000, 287:1816-1820.
• [29]O’Hara AM, Shanahan F: The gut flora as a forgotten organ. EMBO Rep 2006, 7:688-693.
• [30]Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 2010, 66:213-221.
• [31]Cowtan K: The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr D Biol Crystallogr 2006, 62:1002-1011.
• [32]Laskowski R, MacArthur M, Moss D, Thornton J: PROCHECK: A Program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993, 26:283-291.
• [33]Peter JF, Tomer KB: A general strategy for epitope mapping by direct MALDI-TOF mass spectrometry using secondary antibodies and cross-linking. Anal Chem 2001, 73:4012-4019.
• [34]Soriani M, Petit P, Grifantini R, Petracca R, Gancitano G, Frigimelica E, Nardelli F, Garcia C, Spinelli S, Scarabelli G, Fiorucci S, Affentranger R, Ferrer-Navarro M, Zacharias M, Colombo G, Vuillard L, Daura X, Grandi G: Exploiting antigenic diversity for vaccine design: the chlamydia ArtJ paradigm. J Biol Chem 2010, 285:30126-30138.
• [35]McCarthy AA, Brockhauser S, Nurizzo D, Theveneau P, Mairs T, Spruce D, Guijarro M, Lesourd M, Ravelli RBG, McSweeney S: A decade of user operation on the macromolecular crystallography MAD beamline ID14-4 at the ESRF. J Synchrotron Radiat 2009, 16(Pt 6):803-812.