Crystal structure of the Yersinia enterocolitica type III secretion chaperone SycD in complex with a peptide of the minor translocator YopD

BMC Structural Biology

Hartmut H Niemann¹  Madeleine Schreiner¹ 

[1] Department of Chemistry, Bielefeld University, PO Box 10 01 31, 33501, Bielefeld, Germany

关键词: Type III secretion;    Translocator;    Tetratricopeptide repeat;    Protein-protein interaction;    Peptide binding;    Dimer;    Crystal structure;    Complex;    Chaperone;    Bacterial virulence factor;   

Others  :  1092203
DOI  :  10.1186/1472-6807-12-13

 received in 2012-03-08, accepted in 2012-06-18,  发布年份 2012

【 摘 要 】

Background

Type III secretion systems are used by Gram-negative bacteria as “macromolecular syringes” to inject effector proteins into eukaryotic cells. Two hydrophobic proteins called translocators form the necessary pore in the host cell membrane. Both translocators depend on binding to a single chaperone in the bacterial cytoplasm to ensure their stability and efficient transport through the secretion needle. It was suggested that the conserved chaperones bind the more divergent translocators via a hexapeptide motif that is found in both translocators and conserved between species.

Results

We crystallized a synthetic decapeptide from the Yersinia enterocolitica minor type III secretion translocator YopD bound to its cognate chaperone SycD and determined the complex structure at 2.5 Å resolution. The structure of peptide-bound SycD is almost identical to that of apo SycD with an all helical fold consisting of three tetratricopeptide repeats (TPRs) and an additional C-terminal helix. Peptide-bound SycD formed a kinked head-to-head dimer that had previously been observed for the apo form of SycD. The homodimer interface comprises both helices of the first tetratricopeptide repeat. The YopD peptide bound in extended conformation into a mainly hydrophobic groove on the concave side of SycD. TPRs 1 and 2 of SycD form three hydrophobic pockets that accommodated the conserved hydrophobic residues at position 1, 3 and 6 of the translocator hexapeptide sequence. Two tyrosines that are highly conserved among translocator chaperones contribute to the hydrophobic patches but also form hydrogen bonds to the peptide backbone.

Conclusions

The interaction between SycD and YopD is very similar to the binding of the Pseudomonas minor translocator PopD to its chaperone PcrH and the Shigella major translocator IpaB to its chaperone IpgC. This confirms the prediction made by Kolbe and co-workers that a hexapeptide with hydrophobic residues at three positions is a conserved chaperone binding motif. Because the hydrophobic groove on the concave side of translocator chaperones is involved in binding of the major and the minor translocator, simultaneous binding of both translocators to a single type III secretion class II chaperone appears unlikely.

【 授权许可】

   
2012 Schreiner and Niemann.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1 .

Figure 2 .

Figure 3 .

【 参考文献 】

• [1]Dean P: Functional domains and motifs of bacterial type III effector proteins and their roles in infection. FEMS Microbiol Rev 2011, 35:1100-1125.
• [2]Trosky JE, Liverman ADB, Orth K: Yersinia outer proteins: Yops. Cell Microbiol 2008, 10:557-565.
• [3]Cornelis GR: The type III secretion injectisome. Nat Rev Micro 2006, 4:811-825.
• [4]Izoré T, Job V, Dessen A: Biogenesis, Regulation, and Targeting of the Type III Secretion System. Structure 2011, 19:603-612.
• [5]Troisfontaines P, Cornelis GR: Type III Secretion: More Systems Than You Think. Physiology 2005, 20:326-339.
• [6]Wang Y, Zhang L, Picking WL, Picking WD, de Guzman RN: Structural dissection of the extracellular moieties of the type III secretion apparatus. Mol Biosyst 2008, 4:1176.
• [7]Barta ML, Dickenson NE, Patil M, Keightley A, Wyckoff GJ, Picking WD, Picking WL, Geisbrecht BV: The Structures of Coiled-Coil Domains from Type III Secretion System Translocators Reveal Homology to Pore-Forming Toxins. J Mol Biol 2012, 417:395-405.
• [8]Shaw RK, Daniell S, Ebel F, Frankel G, Knutton S: EspA filament-mediated protein translocation into red blood cells. Cell Microbiol 2001, 3:213-222.
• [9]Hume PJ, McGhie EJ, Hayward RD, Koronakis V: The purified Shigella IpaB and Salmonella SipB translocators share biochemical properties and membrane topology. Mol Microbiol 2003, 49:425-439.
• [10]Goure J, Pastor A, Faudry E, Chabert J, Dessen A, Attree I: The V antigen of Pseudomonas aeruginosa is required for assembly of the functional PopB/PopD translocation pore in host cell membranes. Infect Immun 2004, 72:4741-4750.
• [11]Blocker A, Gounon P, Larquet E, Niebuhr K, Cabiaux V, Parsot C, Sansonetti P: The tripartite type III secreton of Shigella flexneri inserts IpaB and IpaC into host membranes. J Cell Biol 1999, 147:683-693.
• [12]Matteï P, Faudry E, Job V, Izoré T, Attree I, Dessen A: Membrane targeting and pore formation by the type III secretion system translocon. FEBS J 2011, 278:414-426.
• [13]Chen Y, Anderson DM: Expression hierarchy in the Yersinia type III secretion system established through YopD recognition of RNA. Mol Microbiol 2011, 80:966-980.
• [14]Feldman MF, Cornelis GR: The multitalented type III chaperones: all you can do with 15 kDa. FEMS Microbiol Lett 2003, 219:151-158.
• [15]Parsot C: The various and varying roles of specific chaperones in type III secretion systems. Curr Opin Microbiol 2003, 6:7-14.
• [16]Wilharm G, Dittmann S, Schmid A, Heesemann J: On the role of specific chaperones, the specific ATPase, and the proton motive force in type III secretion. Int J Med Microbiol 2007, 297:27-36.
• [17]Akeda Y, Galán JE: Chaperone release and unfolding of substrates in type III secretion. Nature 2005, 437:911-915.
• [18]Galán JE: Energizing type III secretion machines: what is the fuel? Nat Struct Mol Biol 2008, 15:127-128.
• [19]Lorenz C, Buttner D: Functional Characterization of the Type III Secretion ATPase HrcN from the Plant Pathogen Xanthomonas campestris pv. vesicatoria. J Bacteriol 2009, 191:1414-1428.
• [20]Neyt C, Cornelis GR: Role of SycD, the chaperone of the Yersinia Yop translocators YopB and YopD. Mol Microbiol 1999, 31:143-156.
• [21]Büttner CR, Sorg I, Cornelis GR, Heinz DW, Niemann HH: Structure of the Yersinia enterocolitica Type III Secretion Translocator Chaperone SycD. J Mol Biol 2008, 375:997-1012.
• [22]Blatch GL, Lässle M: The tetratricopeptide repeat: a structural motif mediating protein-protein interactions. Bioessays 1999, 21:932-939.
• [23]Chatterjee C, Kumar S, Chakraborty S, Tan YW, Leung KY, Sivaraman J, Mok Y, Cobine P: Crystal Structure of the Heteromolecular Chaperone, AscE-AscG, from the Type III Secretion System in Aeromonas hydrophila. PLoS One 2011, 6:e19208.
• [24]Quinaud M, Ple S, Job V, Contreras-Martel C, Simorre J, Attree I, Dessen A: Structure of the heterotrimeric complex that regulates type III secretion needle formation. Proc Natl Acad Sci 2007, 104:7803-7808.
• [25]Sun P, Tropea JE, Austin BP, Cherry S, Waugh DS: Structural Characterization of the Yersinia pestis Type III Secretion System Needle Protein YscF in Complex with Its Heterodimeric Chaperone YscE/YscG. J Mol Biol 2008, 377:819-830.
• [26]Lunelli M, Lokareddy RK, Zychlinsky A, Kolbe M: IpaB-IpgC interaction defines binding motif for type III secretion translocator. Proc Natl Acad Sci 2009, 106:9661-9666.
• [27]Job V, Mattei P, Lemaire D, Attree I, Dessen A: Structural Basis of Chaperone Recognition of Type III Secretion System Minor Translocator Proteins. J Biol Chem 2010, 285:23224-23232.
• [28]Krissinel E, Henrick K: Inference of macromolecular assemblies from crystalline state. J Mol Biol 2007, 372:774-797.
• [29]Holm L, Park J: DaliLite workbench for protein structure comparison. Bioinformatics 2000, 16:566-567.
• [30]Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH: PHENIX. Acta Crystallogr D: Biol Crystallogr 2010, 66:213-221.
• [31]Xu Q, Canutescu AA, Wang G, Shapovalov M, Obradovic Z, Dunbrack RL: Statistical analysis of interface similarity in crystals of homologous proteins. J Mol Biol 2008, 381:487-507.
• [32]Schmid A, Dittmann S, Grimminger V, Walter S, Heesemann J, Wilharm G: Yersinia enterocolitica type III secretion chaperone SycD: Recombinant expression, purification and characterization of a homodimer. Protein Expr Purif 2006, 49:176-182.
• [33]Priyadarshi A, Tang L: Crystallization and preliminary crystallographic analysis of the type III secretion translocator chaperone SicA from Salmonella enterica. Acta Crystallogr F: Struct Biol Cryst Commun 2010, 66:1533-1535.
• [34]Basu A, Chatterjee R, Datta S: Expression, Purification, Structural and Functional Analysis of SycB: A Type Three Secretion Chaperone From Yersinia enterocolitica. Protein J 2012, 31:93-107.
• [35]Tan YW, Yu HB, Sivaraman J, Leung KY, Mok Y: Mapping of the chaperone AcrH binding regions of translocators AopB and AopD and characterization of oligomeric and metastable AcrH-AopB-AopD complexes in the type III secretion system of Aeromonas hydrophila. Protein Sci 2009, 18:1724-1734.
• [36]Lokareddy RK, Lunelli M, Eilers B, Wolter V, Kolbe M: Combination of two separate binding domains defines stoichiometry between type III secretion system chaperone IpgC and translocator protein IpaB. J Biol Chem 2010, 285:39965-39975.
• [37]Barta ML, Zhang L, Picking WL, Geisbrecht BV: Evidence for alternative quaternary structure in a bacterial Type III secretion system chaperone. BMC Struct Biol 2010, 10:21. BioMed Central Full Text
• [38]Francis MS, Aili M, Wiklund M, Wolf-Watz H: A study of the YopD-LcrH interaction from Yersinia pseudotuberculosis reveals a role for hydrophobic residues within the amphipathic domain of YopD. Mol Microbiol 2000, 38:85-102.
• [39]Abe Y, Shodai T, Muto T, Mihara K, Torii H, Nishikawa S, Endo T, Kohda D: Structural basis of presequence recognition by the mitochondrial protein import receptor Tom20. Cell 2000, 100:551-560.
• [40]Zhang Y, Chan DC: Structural basis for recruitment of mitochondrial fission complexes by Fis1. Proc Natl Acad Sci 2007, 104:18526-18530.
• [41]Gatto GJ, Geisbrecht BV, Gould SJ, Berg JM: Peroxisomal targeting signal-1 recognition by the TPR domains of human PEX5. Nat Struct Biol 2000, 7:1091-1095.
• [42]Scheufler C, Brinker A, Bourenkov G, Pegoraro S, Moroder L, Bartunik H, Hartl FU, Moarefi I: Structure of TPR domain-peptide complexes: critical elements in the assembly of the Hsp70-Hsp90 multichaperone machine. Cell 2000, 101:199-210.
• [43]Zhang M, Windheim M, Roe SM, Peggie M, Cohen P, Prodromou C, Pearl LH: Chaperoned ubiquitylation–crystal structures of the CHIP U box E3 ubiquitin ligase and a CHIPUbc13-Uev1a complex. Mol Cell 2005, 20:525-538.
• [44]Pallen MJ, Francis MS, Fütterer K: Tetratricopeptide-like repeats in type-III-secretion chaperones and regulators. FEMS Microbiol Lett 2003, 223:53-60.
• [45]Birket SE, Harrington AT, Espina M, Smith ND, Terry CM, Darboe N, Markham AP, Middaugh CR, Picking WL, Picking WD: Preparation and Characterization of Translocator/Chaperone Complexes and Their Component Proteins from Shigella flexneri. Biochemistry 2007, 46:8128-8137.
• [46]Schoehn G, Di Guilmi AM, Lemaire D, Attree I, Weissenhorn W, Dessen A: Oligomerization of type III secretion proteins PopB and PopD precedes pore formation in Pseudomonas. EMBO J 2003, 22:4957-4967.
• [47]Wang B, Mo ZL, Mao YX, Zou YX, Xiao P, Li J, Yang JY, Ye XH, Leung KY, Zhang PJ: Investigation of EscA as a chaperone for the Edwardsiella tarda type III secretion system putative translocon component EseC. Microbiology 2009, 155:1260-1271.
• [48]Zheng J, Li N, Tan YP, Sivaraman J, Mok Y, Mo ZL, Leung KY: EscC is a chaperone for the Edwardsiella tarda type III secretion system putative translocon components EseB and EseD. Microbiology 2007, 153:1953-1962.
• [49]Bogan AA, Thorn KS: Anatomy of hot spots in protein interfaces. J Mol Biol 1998, 280:1-9.
• [50]Edqvist PJ, Broms JE, Betts HJ, Forsberg A, Pallen MJ, Francis MS: Tetratricopeptide repeats in the type III secretion chaperone, LcrH: their role in substrate binding and secretion. Mol Microbiol 2006, 59:31-44.
• [51]Francis MS, Lloyd SA, Wolf-Watz H: The type III secretion chaperone LcrH co-operates with YopD to establish a negative, regulatory loop for control of Yop synthesis in Yersinia pseudotuberculosis. Mol Microbiol 2001, 42:1075-1093.
• [52]Raab R, Swietnicki W: Yersinia pestis YopD 150–287 fragment is partially unfolded in the native state. Protein Expr Purif 2008, 58:53-60.
• [53]Kabsch W: XDS. Acta Crystallogr D: Biol Crystallogr. 2010, 66:125-132.
• [54]Evans P: Scaling and assessment of data quality. Acta Crystallogr D: Biol Crystallogr 2006, 62:72-82.
• [55]Collaborative Computational Project N4: The CCP4 suite: programs for protein crystallography. Acta Crystallogr D: Biol Crystallogr 1994, 50:760-763.
• [56]McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ: Phaser crystallographic software. J Appl Crystallogr 2007, 40:658-674.
• [57]Emsley P, Lohkamp B, Scott WG, Cowtan K: Features and development of Coot. Acta Crystallogr D: Biol Crystallogr 2010, 66:486-501.
• [58]Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC: MolProbity. Acta Crystallogr D: Biol Crystallogr 2010, 66:12-21.
• [59]DeLano Warren L: The PyMOL Molecular Graphics System. LLC, Schrödinger; 2011.
• [60]Baker NA: Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc Natl Acad Sci 2001, 98:10037-10041.