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Rizzolo K, Huen J, Kumar A, Phanse S, Vlasblom J, Kakihara Y, Zeineddine HA, Minic Z, Snider J, Wang W, Pons C, Seraphim TV, Boczek EE, Alberti S, Costanzo M, Myers CL, Stagljar I, Boone C, Babu M, Houry WA. Features of the Chaperone Cellular Network Revealed through Systematic Interaction Mapping. Cell Rep 2018; 20:2735-2748. [PMID: 28903051 DOI: 10.1016/j.celrep.2017.08.074] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/21/2017] [Accepted: 08/23/2017] [Indexed: 10/18/2022] Open
Abstract
A comprehensive view of molecular chaperone function in the cell was obtained through a systematic global integrative network approach based on physical (protein-protein) and genetic (gene-gene or epistatic) interaction mapping. This allowed us to decipher interactions involving all core chaperones (67) and cochaperones (15) of Saccharomyces cerevisiae. Our analysis revealed the presence of a large chaperone functional supercomplex, which we named the naturally joined (NAJ) chaperone complex, encompassing Hsp40, Hsp70, Hsp90, AAA+, CCT, and small Hsps. We further found that many chaperones interact with proteins that form foci or condensates under stress conditions. Using an in vitro reconstitution approach, we demonstrate condensate formation for the highly conserved AAA+ ATPases Rvb1 and Rvb2, which are part of the R2TP complex that interacts with Hsp90. This expanded view of the chaperone network in the cell clearly demonstrates the distinction between chaperones having broad versus narrow substrate specificities in protein homeostasis.
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Affiliation(s)
- Kamran Rizzolo
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Jennifer Huen
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Ashwani Kumar
- Department of Computer Science, University of Regina, Regina, SK S4S 0A2, Canada
| | - Sadhna Phanse
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - James Vlasblom
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Yoshito Kakihara
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | | | - Zoran Minic
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Jamie Snider
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Wen Wang
- Department of Computer Science & Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA; Program in Bioinformatics and Computational Biology, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Thiago V Seraphim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Edgar Erik Boczek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Costanzo
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Chad L Myers
- Department of Computer Science & Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA; Program in Bioinformatics and Computational Biology, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - Igor Stagljar
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada.
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
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Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones. Cell Rep 2018; 19:2033-2044. [PMID: 28591576 DOI: 10.1016/j.celrep.2017.05.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 04/05/2017] [Accepted: 05/09/2017] [Indexed: 12/18/2022] Open
Abstract
The hexameric AAA+ ATPases Rvb1 and Rvb2 (Rvbs) are essential for diverse processes ranging from metabolic signaling to chromatin remodeling, but their functions are unknown. While originally thought to act as helicases, recent proposals suggest that Rvbs act as protein assembly chaperones. However, experimental evidence for chaperone-like behavior is lacking. Here, we identify a potent protein activator of the Rvbs, a domain in the Ino80 ATPase subunit of the INO80 chromatin-remodeling complex, termed Ino80INS. Ino80INS stimulates Rvbs' ATPase activity by 16-fold while concomitantly promoting their dodecamerization. Using mass spectrometry, cryo-EM, and integrative modeling, we find that Ino80INS binds asymmetrically along the dodecamerization interface, resulting in a conformationally flexible dodecamer that collapses into hexamers upon ATP addition. Our results demonstrate the chaperone-like potential of Rvb1/Rvb2 and suggest a model where binding of multiple clients such as Ino80 stimulates ATP-driven cycling between hexamers and dodecamers, providing iterative opportunities for correct subunit assembly.
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Affiliation(s)
- Coral Y Zhou
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jonathan B Johnston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eugene Palovcak
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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3
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Tian S, Yu G, He H, Zhao Y, Liu P, Marshall AG, Demeler B, Stagg SM, Li H. Pih1p-Tah1p Puts a Lid on Hexameric AAA+ ATPases Rvb1/2p. Structure 2017; 25:1519-1529.e4. [PMID: 28919439 PMCID: PMC6625358 DOI: 10.1016/j.str.2017.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/11/2017] [Accepted: 08/07/2017] [Indexed: 11/21/2022]
Abstract
The Saccharomyces cerevisiae (Sc) R2TP complex affords an Hsp90-mediated and nucleotide-driven chaperone activity to proteins of small ribonucleoprotein particles (snoRNPs). The current lack of structural information on the ScR2TP complex, however, prevents a mechanistic understanding of this biological process. We characterized the structure of the ScR2TP complex made up of two AAA+ ATPases, Rvb1/2p, and two Hsp90 binding proteins, Tah1p and Pih1p, and its interaction with the snoRNP protein Nop58p by a combination of analytical ultracentrifugation, isothermal titration calorimetry, chemical crosslinking, hydrogen-deuterium exchange, and cryoelectron microscopy methods. We find that Pih1p-Tah1p interacts with Rvb1/2p cooperatively through the nucleotide-sensitive domain of Rvb1/2p. Nop58p further binds Pih1p-Tahp1 on top of the dome-shaped R2TP. Consequently, nucleotide binding releases Pih1p-Tah1p from Rvb1/2p, which offers a mechanism for nucleotide-driven binding and release of snoRNP intermediates.
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Affiliation(s)
- Shaoxiong Tian
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Ge Yu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Huan He
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Yu Zhao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Peilu Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Ion Cyclotron Resonance Program, The National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Scott M Stagg
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hong Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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Rivera-Calzada A, Pal M, Muñoz-Hernández H, Luque-Ortega JR, Gil-Carton D, Degliesposti G, Skehel JM, Prodromou C, Pearl LH, Llorca O. The Structure of the R2TP Complex Defines a Platform for Recruiting Diverse Client Proteins to the HSP90 Molecular Chaperone System. Structure 2017. [PMID: 28648606 PMCID: PMC5501727 DOI: 10.1016/j.str.2017.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The R2TP complex, comprising the Rvb1p-Rvb2p AAA-ATPases, Tah1p, and Pih1p in yeast, is a specialized Hsp90 co-chaperone required for the assembly and maturation of multi-subunit complexes. These include the small nucleolar ribonucleoproteins, RNA polymerase II, and complexes containing phosphatidylinositol-3-kinase-like kinases. The structure and stoichiometry of yeast R2TP and how it couples to Hsp90 are currently unknown. Here, we determine the 3D organization of yeast R2TP using sedimentation velocity analysis and cryo-electron microscopy. The 359-kDa complex comprises one Rvb1p/Rvb2p hetero-hexamer with domains II (DIIs) forming an open basket that accommodates a single copy of Tah1p-Pih1p. Tah1p-Pih1p binding to multiple DII domains regulates Rvb1p/Rvb2p ATPase activity. Using domain dissection and cross-linking mass spectrometry, we identified a unique region of Pih1p that is essential for interaction with Rvb1p/Rvb2p. These data provide a structural basis for understanding how R2TP couples an Hsp90 dimer to a diverse set of client proteins and complexes. Rvb1p-Rvb2p forms a hetero-hexamer with DII domains recruiting a single Tah1p-Pih1p Residues 230–250 in Pih1p are essential to bind Rvb1p-Rvb2p 3D structure of yeast R2TP couples an Hsp90 dimer to client proteins Tah1p-Pih1p binding to flexible DII domains stimulates Rvb1p-Rvb2p ATPase activity
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Affiliation(s)
- Angel Rivera-Calzada
- Centro de Investigaciones Biológicas (CIB), Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Mohinder Pal
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Hugo Muñoz-Hernández
- Centro de Investigaciones Biológicas (CIB), Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Juan R Luque-Ortega
- Centro de Investigaciones Biológicas (CIB), Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - David Gil-Carton
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | | | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Chrisostomos Prodromou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
| | - Laurence H Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
| | - Oscar Llorca
- Centro de Investigaciones Biológicas (CIB), Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain.
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Matias PM, Baek SH, Bandeiras TM, Dutta A, Houry WA, Llorca O, Rosenbaum J. The AAA+ proteins Pontin and Reptin enter adult age: from understanding their basic biology to the identification of selective inhibitors. Front Mol Biosci 2015; 2:17. [PMID: 25988184 PMCID: PMC4428354 DOI: 10.3389/fmolb.2015.00017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 04/19/2015] [Indexed: 11/13/2022] Open
Abstract
Pontin and Reptin are related partner proteins belonging to the AAA+ (ATPases Associated with various cellular Activities) family. They are implicated in multiple and seemingly unrelated processes encompassing the regulation of gene transcription, the remodeling of chromatin, DNA damage sensing and repair, and the assembly of protein and ribonucleoprotein complexes, among others. The 2nd International Workshop on Pontin and Reptin took place at the Instituto de Tecnologia Química e Biológica António Xavier in Oeiras, Portugal on October 10-12, 2014, and reported significant new advances on the mechanisms of action of these two AAA+ ATPases. The major points under discussion were related to the mechanisms through which these proteins regulate gene transcription, their roles as co-chaperones, and their involvement in pathophysiology, especially in cancer and ciliary biology and disease. Finally, they may become anticancer drug targets since small chemical inhibitors were shown to produce anti-tumor effects in animal models.
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Affiliation(s)
- Pedro M Matias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal ; Instituto de Biologia Experimental e Tecnológica Oeiras, Portugal
| | - Sung Hee Baek
- Creative Research Initiative Center for Chromatin Dynamics, School of Biological Sciences, Seoul National University Seoul, South Korea
| | | | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia Charlottesville, VA, USA
| | - Walid A Houry
- Department of Biochemistry, University of Toronto Toronto, ON, Canada
| | - Oscar Llorca
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council, CSIC) Madrid, Spain
| | - Jean Rosenbaum
- INSERM, U1053 Bordeaux, France ; Groupe de Recherches pour l'Etude du Foie, Université de Bordeaux Bordeaux, France
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