Apoptosis Regulatory Proteins/chemistry/metabolism; Binding Sites; Carrier Proteins/chemistry/metabolism; Cell Line; HSP72 Heat-Shock Proteins/metabolism; HSP90 Heat-Shock Proteins/metabolism; Humans; Models, Molecular; Protein Binding; Protein Conformation; Protein Domains; Protein Isoforms/chemistry/metabolism; Protein Multimerization; ATPase; HSP70; HSP90; NMR; PIH1D1; R2TP; RPAP3; RUVBL; X-ray; chaperones; machinery assembly
Abstract :
[en] RPAP3 and PIH1D1 are part of the HSP90 co-chaperone R2TP complex involved in the assembly process of many molecular machines. In this study, we performed a deep structural investigation of the HSP binding abilities of the two TPR domains of RPAP3. We combined 3D NMR, non-denaturing MS, and ITC techniques with Y2H, IP-LUMIER, FRET, and ATPase activity assays and explain the fundamental role played by the second TPR domain of RPAP3 in the specific recruitment of HSP90. We also established the 3D structure of an RPAP3:PIH1D1 sub-complex demonstrating the need for a 34-residue insertion, specific of RPAP3 isoform 1, for the tight binding of PIH1D1. We also confirm the existence of a complex lacking PIH1D1 in human cells (R2T), which shows differential binding to certain clients. These results highlight similarities and differences between the yeast and human R2TP complexes, and document the diversification of this family of co-chaperone complexes in human.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Henri, Julien ; Université de Liège - ULiège > HEC Liège : UER > UER Finance et Droit : Gestion financière
Chagot, Marie-Eve
Bourguet, Maxime
Abel, Yoann
Terral, Guillaume
Maurizy, Chloé ; Université de Liège - ULiège > GIGA Stem Cells - Medical Chemistry
Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66 (2010), 213–221.
Afonine, P.V., Grosse-Kunstleve, R.W., Echols, N., Headd, J.J., Moriarty, N.W., Mustyakimov, M., Terwilliger, T.C., Urzhumtsev, A., Zwart, P.H., Adams, P.D., Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D Biol. Crystallogr. 68 (2012), 352–367.
Anthis, N.J., Clore, G.M., Sequence-specific determination of protein and peptide concentrations by absorbance at 205 nm. Protein Sci. 22 (2013), 851–858.
Back, R., Dominguez, C., Rothe, B., Bobo, C., Beaufils, C., Morera, S., Meyer, P., Charpentier, B., Branlant, C., Allain, F.H., et al. High-resolution structural analysis shows how Tah1 tethers Hsp90 to the R2TP complex. Structure 21 (2013), 1834–1847.
Benbahouche Nel, H., Iliopoulos, I., Torok, I., Marhold, J., Henri, J., Kajava, A.V., Farkas, R., Kempf, T., Schnolzer, M., Meyer, P., et al. Drosophila Spag is the homolog of RNA polymerase II-associated protein 3 (RPAP3) and recruits the heat shock proteins 70 and 90 (Hsp70 and Hsp90) during the assembly of cellular machineries. J. Biol. Chem. 289 (2014), 6236–6247.
Bertini, I., Luchinat, C., Parigi, G., Ravera, E., Reif, B., Turano, P., Solid-state NMR of proteins sedimented by ultracentrifugation. Proc. Natl. Acad. Sci. USA 108 (2011), 10396–10399.
Blundell, K.L., Pal, M., Roe, S.M., Pearl, L.H., Prodromou, C., The structure of FKBP38 in complex with the MEEVD tetratricopeptide binding-motif of Hsp90. PLoS One, 12, 2017, e0173543.
Boulon, S., Marmier-Gourrier, N., Pradet-Balade, B., Wurth, L., Verheggen, C., Jady, B.E., Rothe, B., Pescia, C., Robert, M.C., Kiss, T., et al. The Hsp90 chaperone controls the biogenesis of L7Ae RNPs through conserved machinery. J. Cell Biol. 180 (2008), 579–595.
Boulon, S., Pradet-Balade, B., Verheggen, C., Molle, D., Boireau, S., Georgieva, M., Azzag, K., Robert, M.C., Ahmad, Y., Neel, H., et al. HSP90 and its R2TP/Prefoldin-like cochaperone are involved in the cytoplasmic assembly of RNA polymerase II. Mol. Cell 39 (2010), 912–924.
Chagot, M.E., Jacquemin, C., Branlant, C., Charpentier, B., Manival, X., Quinternet, M., (1)H, (15)N and (13)C resonance assignments of the two TPR domains from the human RPAP3 protein. Biomol. NMR Assign. 9 (2015), 99–102.
Eckert, K., Saliou, J.M., Monlezun, L., Vigouroux, A., Atmane, N., Caillat, C., Quevillon-Cheruel, S., Madiona, K., Nicaise, M., Lazereg, S., et al. The Pih1-Tah1 cochaperone complex inhibits Hsp90 molecular chaperone ATPase activity. J. Biol. Chem. 285 (2010), 31304–31312.
Emsley, P., Cowtan, K., Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60 (2004), 2126–2132.
Jecklin, M.C., Touboul, D., Bovet, C., Wortmann, A., Zenobi, R., Which electrospray-based ionization method best reflects protein-ligand interactions found in solution? A comparison of ESI, nanoESI, and ESSI for the determination of dissociation constants with mass spectrometry. J. Am. Soc. Mass Spectrom. 19 (2008), 332–343.
Lalevee, S., Bour, G., Quinternet, M., Samarut, E., Kessler, P., Vitorino, M., Bruck, N., Delsuc, M.A., Vonesch, J.L., Kieffer, B., et al. Vinexinss, an atypical “sensor” of retinoic acid receptor gamma signaling: union and sequestration, separation, and phosphorylation. FASEB J. 24 (2010), 4523–4534.
Li, J., Richter, K., Buchner, J., Mixed Hsp90-cochaperone complexes are important for the progression of the reaction cycle. Nat. Struct. Mol. Biol. 18 (2011), 61–66.
Lopez-Mendez, B., Guntert, P., Automated protein structure determination from NMR spectra. J. Am. Chem. Soc. 128 (2006), 13112–13122.
Martino, F., Pal, M., Munoz-Hernandez, H., Rodriguez, C.F., Nunez-Ramirez, R., Gil-Carton, D., Degliesposti, G., Skehel, J.M., Roe, S.M., Prodromou, C., et al. RPAP3 provides a flexible scaffold for coupling HSP90 to the human R2TP co-chaperone complex. Nat. Commun., 9, 2018, 1501.
Maurizy, C., Quinternet, M., Abel, Y., Verheggen, C., Santo, P.E., Bourguet, M., Paiva, A.C.F., Bragantini, B., Chagot, M.-E., Robert, M.-C., et al. The RPAP3-Cterminal domain identifies R2TP-like quaternary chaperones. Nat. Commun., 2018, 10.1038/s41467-018-04431-1.
Meyer, P., Prodromou, C., Hu, B., Vaughan, C., Roe, S.M., Panaretou, B., Piper, P.W., Pearl, L.H., Structural and functional analysis of the middle segment of hsp90: implications for ATP hydrolysis and client protein and cochaperone interactions. Mol. Cell 11 (2003), 647–658.
Meyer, P., Prodromou, C., Liao, C., Hu, B., Roe, S.M., Vaughan, C.K., Vlasic, I., Panaretou, B., Piper, P.W., Pearl, L.H., Structural basis for recruitment of the ATPase activator Aha1 to the Hsp90 chaperone machinery. EMBO J. 23 (2004), 1402–1410.
Pal, M., Morgan, M., Phelps, S.E., Roe, S.M., Parry-Morris, S., Downs, J.A., Polier, S., Pearl, L.H., Prodromou, C., Structural basis for phosphorylation-dependent recruitment of Tel2 to Hsp90 by Pih1. Structure 6 (2014), 805–818.
Panaretou, B., Sinclair, K., Prodromou, C., Johal, J., Pearl, L., Piper, P.W., The Hsp90 of Candida albicans can confer Hsp90 functions in Saccharomyces cerevisiae: a potential model for the processes that generate immunogenic fragments of this molecular chaperone in C. albicans infections. Microbiology 145:Pt 12 (1999), 3455–3463.
Prodromou, C., Siligardi, G., O'Brien, R., Woolfson, D.N., Regan, L., Panaretou, B., Ladbury, J.E., Piper, P.W., Pearl, L.H., Regulation of Hsp90 ATPase activity by tetratricopeptide repeat (TPR)-domain co-chaperones. EMBO J. 18 (1999), 754–762.
Quinternet, M., Chagot, M.E., Rothe, B., Tiotiu, D., Charpentier, B., Manival, X., Structural features of the box C/D snoRNP pre-assembly process are conserved through species. Structure 24 (2016), 1693–1706.
Quinternet, M., Rothe, B., Barbier, M., Bobo, C., Saliou, J.M., Jacquemin, C., Back, R., Chagot, M.E., Cianferani, S., Meyer, P., et al. Structure/function analysis of protein-protein interactions developed by the yeast Pih1 platform protein and its partners in box C/D snoRNP assembly. J. Mol. Biol. 427 (2015), 2816–2839.
Retzlaff, M., Hagn, F., Mitschke, L., Hessling, M., Gugel, F., Kessler, H., Richter, K., Buchner, J., Asymmetric activation of the Hsp90 dimer by its cochaperone Aha1. Mol. Cell 37 (2010), 344–354.
Rivera-Calzada, A., Pal, M., Munoz-Hernandez, H., Luque-Ortega, J.R., Gil-Carton, D., Degliesposti, G., Skehel, J.M., Prodromou, C., Pearl, L.H., Llorca, O., The structure of the R2TP complex defines a platform for recruiting diverse client proteins to the HSP90 molecular chaperone system. Structure 25 (2017), 1145–1152.e4.
Shen, Y., Delaglio, F., Cornilescu, G., Bax, A., TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J. Biomol. NMR 44 (2009), 213–223.
Tosi, A., Haas, C., Herzog, F., Gilmozzi, A., Berninghausen, O., Ungewickell, C., Gerhold, C.B., Lakomek, K., Aebersold, R., Beckmann, R., et al. Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex. Cell 154 (2013), 1207–1219.
Yoshida, M., Saeki, M., Egusa, H., Irie, Y., Kamano, Y., Uraguchi, S., Sotozono, M., Niwa, H., Kamisaki, Y., RPAP3 splicing variant isoform 1 interacts with PIH1D1 to compose R2TP complex for cell survival. Biochem. Biophys. Res. Commun. 430 (2013), 320–324.
Zhao, R., Houry, W.A., Hsp90: a chaperone for protein folding and gene regulation. Biochem. Cell Biol. 83 (2005), 703–710.
Zhao, R., Kakihara, Y., Gribun, A., Huen, J., Yang, G., Khanna, M., Costanzo, M., Brost, R.L., Boone, C., Hughes, T.R., et al. Molecular chaperone Hsp90 stabilizes Pih1/Nop17 to maintain R2TP complex activity that regulates snoRNA accumulation. J. Cell Biol. 180 (2008), 563–578.
