Structural Basis of Ca2+-Dependent Self-Processing Activity of Repeat-in-Toxin Proteins

. 2020 Mar 17 ; 11 (2) : . [epub] 20200317

Jazyk angličtina Země Spojené státy americké Médium electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid32184239

The posttranslational Ca2+-dependent "clip-and-link" activity of large repeat-in-toxin (RTX) proteins starts by Ca2+-dependent structural rearrangement of a highly conserved self-processing module (SPM). Subsequently, an internal aspartate-proline (Asp-Pro) peptide bond at the N-terminal end of SPM breaks, and the liberated C-terminal aspartyl residue can react with a free ε-amino group of an adjacent lysine residue to form a new isopeptide bond. Here, we report a solution structure of the calcium-loaded SPM (Ca-SPM) derived from the FrpC protein of Neisseria meningitidis The Ca-SPM structure defines a unique protein architecture and provides structural insight into the autocatalytic cleavage of the Asp-Pro peptide bond through a "twisted-amide" activation. Furthermore, in-frame deletion of the SPM domain from the ApxIVA protein of Actinobacillus pleuropneumoniae attenuated the virulence of this porcine pathogen in a pig respiratory challenge model. We hypothesize that the Ca2+-dependent clip-and-link activity represents an unconventional strategy for Gram-negative pathogens to adhere to the host target cell surface.IMPORTANCE The Ca2+-dependent clip-and-link activity of large repeat-in-toxin (RTX) proteins is an exceptional posttranslational process in which an internal domain called a self-processing module (SPM) mediates Ca2+-dependent processing of a highly specific aspartate-proline (Asp-Pro) peptide bond and covalent linkage of the released aspartyl to an adjacent lysine residue through an isopeptide bond. Here, we report the solution structures of the Ca2+-loaded SPM (Ca-SPM) defining the mechanism of the autocatalytic cleavage of the Asp414-Pro415 peptide bond of the Neisseria meningitidis FrpC exoprotein. Moreover, deletion of the SPM domain in the ApxIVA protein, the FrpC homolog of Actinobacillus pleuropneumoniae, resulted in attenuation of virulence of the bacterium in a pig infection model, indicating that the Ca2+-dependent clip-and-link activity plays a role in the virulence of Gram-negative pathogens.

Zobrazit více v PubMed

Osicka R, Prochazkova K, Sulc M, Linhartova I, Havlicek V, Sebo P. 2004. A novel “clip-and-link” activity of repeat in toxin (RTX) proteins from gram-negative pathogens. Covalent protein cross-linking by an Asp-Lys isopeptide bond upon calcium-dependent processing at an Asp-Pro bond. J Biol Chem 279:24944–24956. doi:10.1074/jbc.M314013200. PubMed DOI

Matyska Liskova P, Fiser R, Macek P, Chmelik J, Sykora J, Bednarova L, Konopasek I, Bumba L. 2016. Probing the Ca2+-assisted π-π interaction during Ca2+-dependent protein folding. Soft Matter 12:531–541. doi:10.1039/c5sm01796c. PubMed DOI

Linhartová I, Bumba L, Mašín J, Basler M, Osička R, Kamanová J, Procházková K, Adkins I, Hejnová-Holubová J, Sadílková L, Morová J, Sebo P. 2010. RTX proteins: a highly diverse family secreted by a common mechanism. FEMS Microbiol Rev 34:1076–1112. doi:10.1111/j.1574-6976.2010.00231.x. PubMed DOI PMC

Bumba L, Masin J, Macek P, Wald T, Motlova L, Bibova I, Klimova N, Bednarova L, Veverka V, Kachala M, Svergun DI, Barinka C, Sebo P. 2016. Calcium-driven folding of RTX domain β-rolls ratchets translocation of RTX proteins through Type I secretion ducts. Mol Cell 62:47–62. doi:10.1016/j.molcel.2016.03.018. PubMed DOI

Baumann U. 2019. Structure-function relationships of the repeat domains of RTX toxins. Toxins 11:657. doi:10.3390/toxins11110657. PubMed DOI PMC

Sviridova E, Rezacova P, Bondar A, Veverka V, Novak P, Schenk G, Svergun DI, Kuta Smatanova I, Bumba L. 2017. Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis. Sci Rep 7:40408. doi:10.1038/srep40408. PubMed DOI PMC

Sadilkova L, Osicka R, Sulc M, Linhartova I, Novak P, Sebo P. 2008. Single-step affinity purification of recombinant proteins using a self-excising module from Neisseria meningitidis FrpC. Protein Sci 17:1834–1843. doi:10.1110/ps.035733.108. PubMed DOI PMC

Kula RJ, Sawyer DT, Chan SI, Finley CM. 1963. Nuclear magnetic resonance studies of metal-ethylenediaminetetraacetic acid complexes. J Am Chem Soc 85:2930–2936. doi:10.1021/ja00902a016. DOI

Julenius K, Robblee J, Thulin E, Finn BE, Fairman R, Linse S. 2002. Coupling of ligand binding and dimerization of helix-loop-helix peptides: spectroscopic and sedimentation analyses of calbindin D9k EF-hands. Proteins 47:323–333. doi:10.1002/prot.10080. PubMed DOI

Villalobo A, González-Muñoz M, Berchtold MW. 2019. Proteins with calmodulin-like domains: structures and functional roles. Cell Mol Life Sci 76:2299–2328. doi:10.1007/s00018-019-03062-z. PubMed DOI PMC

Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, Lehtinen S, Studer RA, Thornton J, Orengo CA. 2015. CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res 43:D376–D381. doi:10.1093/nar/gku947. PubMed DOI PMC

Roy A, Yang J, Zhang Y. 2012. COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res 40:W471–W477. doi:10.1093/nar/gks372. PubMed DOI PMC

Holm L, Rosenstrom P. 2010. Dali server: conservation mapping in 3D. Nucleic Acids Res 38:W545–W549. doi:10.1093/nar/gkq366. PubMed DOI PMC

Krissinel E, Henrick K. 2004. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60:2256–2268. doi:10.1107/S0907444904026460. PubMed DOI

Schaller A, Kuhn R, Kuhnert P, Nicolet J, Anderson TJ, Maclnnes JI, Segers R, Frey J. 1999. Characterization of apxlVA, a new RTX determinant of Actinobacillus pleuropneumoniae. Microbiology 145:2105–2116. doi:10.1099/13500872-145-8-2105. PubMed DOI

Thomas S, Holland IB, Schmitt L. 2014. The Type 1 secretion pathway—the hemolysin system and beyond. Biochim Biophys Acta 1843:1629–1641. doi:10.1016/j.bbamcr.2013.09.017. PubMed DOI

Lamed R, Kenig R, Morag E, Yaron S, Shoham Y, Bayer EA. 2001. Nonproteolytic cleavage of aspartyl proline bonds in the cellulosomal scaffoldin subunit from Clostridium thermocellum. Appl Biochem Biotechnol 90:67–73. doi:10.1385/abab:90:1:67. PubMed DOI

Piszkiewicz D, Landon M, Smith EL. 1970. Anomalous cleavage of aspartyl-proline peptide bonds during amino acid sequence determinations. Biochem Biophys Res Commun 40:1173–1178. doi:10.1016/0006-291x(70)90918-6. PubMed DOI

Oliyai C, Borchardt RT. 1993. Chemical pathways of peptide degradation. IV. Pathways, kinetics, and mechanism of degradation of an aspartyl residue in a model hexapeptide. Pharm Res 10:95–102. doi:10.1023/A:1018981231468. PubMed DOI

Yu W, Vath JE, Huberty MC, Martin SA. 1993. Identification of the facile gas-phase cleavage of the Asp-Pro and Asp-Xxx peptide bonds in matrix-assisted laser desorption time-of-flight mass spectrometry. Anal Chem 65:3015–3023. doi:10.1021/ac00069a014. PubMed DOI

Mahesh S, Tang KC, Raj M. 2018. Amide bond activation of biological molecules. Molecules 23:2615. doi:10.3390/molecules23102615. PubMed DOI PMC

Liu C, Szostak M. 2017. Twisted amides: from obscurity to broadly useful transition-metal-catalyzed reactions by N-C amide bond activation. Chemistry 23:7157–7173. doi:10.1002/chem.201605012. PubMed DOI

Fischer G. 2000. Chemical aspects of peptide bond isomerisation. Chem Soc Rev 29:119–127. doi:10.1039/a803742f. DOI

Brown RS, Bennet AJ, Slebocka-Tilk H. 1992. Recent perspectives concerning the mechanism of H3O+- and hydroxide-promoted amide hydrolysis. Acc Chem Res 25:481–488. doi:10.1021/ar00023a001. DOI

Lizak C, Gerber S, Numao S, Aebi M, Locher KP. 2011. X-ray structure of a bacterial oligosaccharyltransferase. Nature 474:350–355. doi:10.1038/nature10151. PubMed DOI

Xu Q, Buckley D, Guan C, Guo HC. 1999. Structural insights into the mechanism of intramolecular proteolysis. Cell 98:651–661. doi:10.1016/s0092-8674(00)80052-5. PubMed DOI

Prochazkova K, Osicka R, Linhartova I, Halada P, Sulc M, Sebo P. 2005. The Neisseria meningitidis outer membrane lipoprotein FrpD binds the RTX protein FrpC. J Biol Chem 280:3251–3258. doi:10.1074/jbc.M411232200. PubMed DOI

Forman S, Linhartova I, Osicka R, Nassif X, Sebo P, Pelicic V. 2003. Neisseria meningitidis RTX proteins are not required for virulence in infant rats. Infect Immun 71:2253–2257. doi:10.1128/iai.71.4.2253-2257.2003. PubMed DOI PMC

Liu J, Chen X, Tan C, Guo Y, Chen Y, Fu S, Bei W, Chen H. 2009. In vivo induced RTX toxin ApxIVA is essential for the full virulence of Actinobacillus pleuropneumoniae. Vet Microbiol 137:282–289. doi:10.1016/j.vetmic.2009.01.011. PubMed DOI

Chiers K, De Waele T, Pasmans F, Ducatelle R, Haesebrouck F. 2010. Virulence factors of Actinobacillus pleuropneumoniae involved in colonization, persistence and induction of lesions in its porcine host. Vet Res 41:65. doi:10.1051/vetres/2010037. PubMed DOI PMC

Kubáň V, Nováček J, Bumba L, Žídek L. 2015. NMR assignment of intrinsically disordered self-processing module of the FrpC protein of Neisseria meningitidis. Biomol NMR Assign 9:435–440. doi:10.1007/s12104-015-9625-z. PubMed DOI

Sattler M, Schleucher J, Griesinger C. 1999. Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog Nucl Magn Reson Spectrosc 34:93–158. doi:10.1016/S0079-6565(98)00025-9. DOI

Delaglio F, Grzesiek S, Vuister G, Zhu G, Pfeifer J, Bax A. 1995. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293. doi:10.1007/bf00197809. PubMed DOI

Guntert P, Buchner L. 2015. Combined automated NOE assignment and structure calculation with CYANA. J Biomol NMR 62:453–471. doi:10.1007/s10858-015-9924-9. PubMed DOI

Shen Y, Bax A. 2013. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J Biomol NMR 56:227–241. doi:10.1007/s10858-013-9741-y. PubMed DOI PMC

Berendsen HJC, van der Spoel D, van Drunen R. 1995. GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun 91:43–56. doi:10.1016/0010-4655(95)00042-E. DOI

Lindahl E, Hess B, van der Spoel D. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306–317. doi:10.1007/s008940100045. DOI

Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE. 2010. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 78:1950–1958. doi:10.1002/prot.22711. PubMed DOI PMC

Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. 1983. Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935. doi:10.1063/1.445869. DOI

Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. 1984. Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690. doi:10.1063/1.448118. DOI

Parrinello M, Rahman A. 1981. Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys 52:7182–7190. doi:10.1063/1.328693. DOI

Laskowski R, Rullmann JA, MacArthur M, Kaptein R, Thornton J. 1996. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477–486. doi:10.1007/bf00228148. PubMed DOI

Vriend G. 1990. WHAT IF: a molecular modeling and drug design program. J Mol Graph 8:52–56. doi:10.1016/0263-7855(90)80070-v. PubMed DOI

Doreleijers JF, Sousa da Silva AW, Krieger E, Nabuurs SB, Spronk C, Stevens TJ, Vranken WF, Vriend G, Vuister GW. 2012. CING: an integrated residue-based structure validation program suite. J Biomol NMR 54:267–283. doi:10.1007/s10858-012-9669-7. PubMed DOI PMC

Touw WG, Baakman C, Black J, Te Beek TAH, Krieger E, Joosten RP, Vriend G. 2015. A series of PDB-related databanks for everyday needs. Nucleic Acids Res 43:D364–D368. doi:10.1093/nar/gku1028. PubMed DOI PMC

Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. 2001. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98:10037–10041. doi:10.1073/pnas.181342398. PubMed DOI PMC

Shen Y, Bax A. 2010. SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network. J Biomol NMR 48:13–22. doi:10.1007/s10858-010-9433-9. PubMed DOI PMC

Raiford DS, Fisk CL, Becker ED. 1979. Calibration of methanol and ethylene glycol nuclear magnetic resonance thermometers. Anal Chem 51:2050–2051. doi:10.1021/ac50048a040. DOI

d'Auvergne EJ, Gooley PR. 2008. Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J Biomol NMR 40:121–133. doi:10.1007/s10858-007-9213-3. PubMed DOI PMC

Ferrage F, Cowburn D, Ghose R. 2009. Accurate sampling of high-frequency motions in proteins by steady-state 15N-1H nuclear Overhauser effect measurements in the presence of cross-correlated relaxation. J Am Chem Soc 131:6048–6049. doi:10.1021/ja809526q. PubMed DOI PMC

Lipari G, Szabo A. 1982. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 104:4546–4559. doi:10.1021/ja00381a009. DOI

Berlin K, O'Leary DP, Fushman D. 2011. Fast approximations of the rotational diffusion tensor and their application to structural assembly of molecular complexes. Proteins 79:2268–2281. doi:10.1002/prot.23053. PubMed DOI PMC

Baltes N, Tonpitak W, Hennig-Pauka I, Gruber AD, Gerlach GF. 2003. Actinobacillus pleuropneumoniae serotype 7 siderophore receptor FhuA is not required for virulence. FEMS Microbiol Lett 220:41–48. doi:10.1016/S0378-1097(03)00064-8. PubMed DOI

Faldyna M, Nechvatalova K, Sinkora J, Knotigova P, Leva L, Krejci J, Toman M. 2005. Experimental Actinobacillus pleuropneumoniae infection in piglets with different types and levels of specific protection: immunophenotypic analysis of lymphocyte subsets in the circulation and respiratory mucosal lymphoid tissue. Vet Immunol Immunopathol 107:143–152. doi:10.1016/j.vetimm.2005.04.007. PubMed DOI

Stivala A, Wybrow M, Wirth A, Whisstock JC, Stuckey PJ. 2011. Automatic generation of protein structure cartoons with Pro-origami. Bioinformatics 27:3315–3316. doi:10.1093/bioinformatics/btr575. PubMed DOI

Najít záznam

Citační ukazatele

Nahrávání dat ...

    Možnosti archivace