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Falaleeva M, Welden JR, Duncan MJ, Stamm S. C/D-box snoRNAs form methylating and non-methylating ribonucleoprotein complexes: Old dogs show new tricks. Bioessays 2017; 39:10.1002/bies.201600264. [PMID: 28505386 PMCID: PMC5586538 DOI: 10.1002/bies.201600264] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
C/D box snoRNAs (SNORDs) are an abundantly expressed class of short, non-coding RNAs that have been long known to perform 2'-O-methylation of rRNAs. However, approximately half of human SNORDs have no predictable rRNA targets, and numerous SNORDs have been associated with diseases that show no defects in rRNAs, among them Prader-Willi syndrome, Duplication 15q syndrome and cancer. This apparent discrepancy has been addressed by recent studies showing that SNORDs can act to regulate pre-mRNA alternative splicing, mRNA abundance, activate enzymes, and be processed into shorter ncRNAs resembling miRNAs and piRNAs. Furthermore, recent biochemical studies have shown that a given SNORD can form both methylating and non-methylating ribonucleoprotein complexes, providing an indication of the likely physical basis for such diverse new functions. Thus, SNORDs are more structurally and functionally diverse than previously thought, and their role in gene expression is under-appreciated. The action of SNORDs in non-methylating complexes can be substituted with oligonucleotides, allowing devising therapies for diseases like Prader-Willi syndrome.
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Affiliation(s)
- Marina Falaleeva
- University Kentucky, Institute for Biochemistry, Lexington, KY, USA
| | - Justin R. Welden
- University Kentucky, Institute for Biochemistry, Lexington, KY, USA
| | | | - Stefan Stamm
- University Kentucky, Institute for Biochemistry, Lexington, KY, USA
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52
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Cloutier P, Poitras C, Durand M, Hekmat O, Fiola-Masson É, Bouchard A, Faubert D, Chabot B, Coulombe B. R2TP/Prefoldin-like component RUVBL1/RUVBL2 directly interacts with ZNHIT2 to regulate assembly of U5 small nuclear ribonucleoprotein. Nat Commun 2017; 8:15615. [PMID: 28561026 PMCID: PMC5460035 DOI: 10.1038/ncomms15615] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 04/12/2017] [Indexed: 01/11/2023] Open
Abstract
The R2TP/Prefoldin-like (R2TP/PFDL) complex has emerged as a cochaperone complex involved in the assembly of a number of critical protein complexes including snoRNPs, nuclear RNA polymerases and PIKK-containing complexes. Here we report on the use of multiple target affinity purification coupled to mass spectrometry to identify two additional complexes that interact with R2TP/PFDL: the TSC1–TSC2 complex and the U5 small nuclear ribonucleoprotein (snRNP). The interaction between R2TP/PFDL and the U5 snRNP is mostly mediated by the previously uncharacterized factor ZNHIT2. A more general function for the zinc-finger HIT domain in binding RUVBL2 is exposed. Disruption of ZNHIT2 and RUVBL2 expression impacts the protein composition of the U5 snRNP suggesting a function for these proteins in promoting the assembly of the ribonucleoprotein. A possible implication of R2TP/PFDL as a major effector of stress-, energy- and nutrient-sensing pathways that regulate anabolic processes through the regulation of its chaperoning activity is discussed. The R2TP/Prefoldin-like cochaperone complex is involved in the assembly of a number of protein complexes. Here the authors provide evidence that RUVBL1/RUVBL2, subunits of that cochaperone complex, directly interact with ZNHIT2 to regulate assembly of U5 small ribonucleoprotein.
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Affiliation(s)
- Philippe Cloutier
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7
| | - Christian Poitras
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7
| | - Mathieu Durand
- Laboratory of Functional Genomics, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1E 4K8
| | - Omid Hekmat
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7
| | - Émilie Fiola-Masson
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7
| | - Annie Bouchard
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7
| | - Denis Faubert
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7
| | - Benoit Chabot
- Laboratory of Functional Genomics, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1E 4K8.,Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1E 4K8
| | - Benoit Coulombe
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7.,Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada H3T 1J4
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53
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Malinová A, Cvačková Z, Matějů D, Hořejší Z, Abéza C, Vandermoere F, Bertrand E, Staněk D, Verheggen C. Assembly of the U5 snRNP component PRPF8 is controlled by the HSP90/R2TP chaperones. J Cell Biol 2017; 216:1579-1596. [PMID: 28515276 PMCID: PMC5461031 DOI: 10.1083/jcb.201701165] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/22/2017] [Accepted: 04/04/2017] [Indexed: 12/23/2022] Open
Abstract
The pre-mRNA splicing factor PRPF8 is a crucial component of the U5 snRNP. Using quantitative proteomics, Malinová et al. show that assembly of the U5 snRNP is controlled by the HSP90/R2TP chaperones and that Retinitis pigmentosa–associated mutations in PRPF8 impair PRPF8 quality control and U5 snRNP chaperone-mediated assembly. Splicing is catalyzed by the spliceosome, a complex of five major small nuclear ribonucleoprotein particles (snRNPs). The pre-mRNA splicing factor PRPF8 is a crucial component of the U5 snRNP, and together with EFTUD2 and SNRNP200, it forms a central module of the spliceosome. Using quantitative proteomics, we identified assembly intermediates containing PRPF8, EFTUD2, and SNRNP200 in association with the HSP90/R2TP complex, its ZNHIT2 cofactor, and additional proteins. HSP90 and R2TP bind unassembled U5 proteins in the cytoplasm, stabilize them, and promote the formation of the U5 snRNP. We further found that PRPF8 mutants causing Retinitis pigmentosa assemble less efficiently with the U5 snRNP and bind more strongly to R2TP, with one mutant retained in the cytoplasm in an R2TP-dependent manner. We propose that the HSP90/R2TP chaperone system promotes the assembly of a key module of U5 snRNP while assuring the quality control of PRPF8. The proteomics data further reveal new interactions between R2TP and the tuberous sclerosis complex (TSC), pointing to a potential link between growth signals and the assembly of key cellular machines.
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Affiliation(s)
- Anna Malinová
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic.,Faculty of Science, Charles University in Prague, 128 00 Prague, Czech Republic
| | - Zuzana Cvačková
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Daniel Matějů
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Zuzana Hořejší
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Claire Abéza
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, University of Montpellier, 34293 Montpellier, France
| | - Franck Vandermoere
- Institut de Génomique Fonctionnelle, Centre National de la Recherche Scientifique, University of Montpellier, 34090 Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, University of Montpellier, 34293 Montpellier, France
| | - David Staněk
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Céline Verheggen
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, University of Montpellier, 34293 Montpellier, France
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54
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Abstract
The heat shock protein 90 (HSP90) chaperone machinery is a key regulator of proteostasis under both physiological and stress conditions in eukaryotic cells. As HSP90 has several hundred protein substrates (or 'clients'), it is involved in many cellular processes beyond protein folding, which include DNA repair, development, the immune response and neurodegenerative disease. A large number of co-chaperones interact with HSP90 and regulate the ATPase-associated conformational changes of the HSP90 dimer that occur during the processing of clients. Recent progress has allowed the interactions of clients with HSP90 and its co-chaperones to be defined. Owing to the importance of HSP90 in the regulation of many cellular proteins, it has become a promising drug target for the treatment of several diseases, which include cancer and diseases associated with protein misfolding.
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Affiliation(s)
- Florian H Schopf
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching, Germany
| | - Maximilian M Biebl
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching, Germany
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55
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Pires ES. The Unmysterious Roles of HSP90: Ovarian Pathology and Autoantibodies. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2017; 222:29-44. [PMID: 28389749 DOI: 10.1007/978-3-319-51409-3_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The heat shock proteins (HSPs) are a group of evolutionarily conserved proteins with important physiological functions, whose synthesis is enhanced by elevated temperature or other stresses. HSPs show high sequence homology between different species, from bacteria to humans. Despite the significant degree of evolutionary conservation, HSPs are highly immunogenic. Of the several HSPs, HSP90 is an abundant, constitutively expressed chaperone constituting around 1-2% of total cellular protein under non-stress conditions. This protein from even the most distantly related eukaryotes has 50% amino acid identity, and all have more than 40% identity with the Escherichia coli protein. They are immunodominant antigens for many common microbes, and thus their epitopes are recognized by the immune system. As HSPs are overexpressed at sites of acute and chronic inflammation, individuals are likely to be sensitized during the course of a microbial infection encountered during life. This chapter considers the evidence of a role for HSP90 in autoimmune ovarian failure, where autoantibodies to it have been observed in patients, and has been correlated to infertility.
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Affiliation(s)
- Eusebio S Pires
- Department of Obstetrics and Gynecology, School of Medicine, University of Virginia, 800732, Jordan Hall, Charlottesville, VA, 22908, USA.
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56
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Affiliation(s)
- Céline Verheggen
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Montpellier, France
| | - Bérengère Pradet-Balade
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Montpellier, France
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57
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Quinternet M, Chagot ME, Rothé B, Tiotiu D, Charpentier B, Manival X. Structural Features of the Box C/D snoRNP Pre-assembly Process Are Conserved through Species. Structure 2016; 24:1693-1706. [PMID: 27594683 DOI: 10.1016/j.str.2016.07.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 11/15/2022]
Abstract
Box C/D small nucleolar ribonucleoparticles (snoRNPs) support 2'-O-methylation of several target RNAs. They share a common set of four core proteins (SNU13, NOP58, NOP56, and FBL) that are assembled on different guide small nucleolar RNAs. Assembly of these entities involves additional protein factors that are absent in the mature active particle. In this context, the platform protein NUFIP1/Rsa1 establishes direct and simultaneous contacts with core proteins and with the components of the assembly machinery. Here, we solve the nuclear magnetic resonance (NMR) structure of a complex resulting from interaction between protein fragments of human NUFIP1 and its cofactor ZNHIT3, and emphasize their imbrication. Using yeast two-hybrid and complementation assays, protein co-expression, isothermal titration calorimetry, and NMR, we demonstrate that yeast and human complexes involving NUFIP1/Rsa1p, ZNHIT3/Hit1p, and SNU13/Snu13p share strong structural similarities, suggesting that the initial steps of the box C/D snoRNP assembly process are conserved among species.
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Affiliation(s)
- Marc Quinternet
- FR CNRS-3209 Bioingénierie Moléculaire, Cellulaire et Thérapeutique (BMCT), CNRS, Université de Lorraine, Biopôle, Campus Biologie-Santé, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Marie-Eve Chagot
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Benjamin Rothé
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France; Ecole polytechnique fédérale de Lausanne (EPFL) SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Decebal Tiotiu
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France.
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58
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Verma S, Goyal S, Jamal S, Singh A, Grover A. Hsp90: Friends, clients and natural foes. Biochimie 2016; 127:227-40. [DOI: 10.1016/j.biochi.2016.05.018] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/29/2016] [Indexed: 12/13/2022]
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59
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Bragantini B, Tiotiu D, Rothé B, Saliou JM, Marty H, Cianférani S, Charpentier B, Quinternet M, Manival X. Functional and Structural Insights of the Zinc-Finger HIT protein family members Involved in Box C/D snoRNP Biogenesis. J Mol Biol 2016; 428:2488-2506. [DOI: 10.1016/j.jmb.2016.04.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 04/20/2016] [Accepted: 04/23/2016] [Indexed: 11/29/2022]
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60
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Paci A, Liu PXH, Zhang L, Zhao R. The Proteasome Subunit Rpn8 Interacts with the Small Nucleolar RNA Protein (snoRNP) Assembly Protein Pih1 and Mediates Its Ubiquitin-independent Degradation in Saccharomyces cerevisiae. J Biol Chem 2016; 291:11761-75. [PMID: 27053109 DOI: 10.1074/jbc.m115.702043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Indexed: 11/06/2022] Open
Abstract
Pih1 is a scaffold protein of the Rvb1-Rvb2-Tah1-Pih1 (R2TP) protein complex, which is conserved in fungi and animals. The chaperone-like activity of the R2TP complex has been implicated in the assembly of multiple protein complexes, such as the small nucleolar RNA protein complex. However, the mechanism of the R2TP complex activity in vivo and the assembly of the complex itself are still largely unknown. Pih1 is an unstable protein and tends to aggregate when expressed alone. The C-terminal fragment of Pih1 contains multiple destabilization factors and acts as a degron when fused to other proteins. In this study, we investigated Pih1 interactors and identified a specific interaction between Pih1 and the proteasome subunit Rpn8 in yeast Saccharomyces cerevisiae when HSP90 co-chaperone Tah1 is depleted. By analyzing truncation mutants, we identified that the C-terminal 30 amino acids of Rpn8 are sufficient for the binding to Pih1 C terminus. With in vitro and in vivo degradation assays, we showed that the Pih1 C-terminal fragment Pih1(282-344) is able to induce a ubiquitin-independent degradation of GFP. Additionally, we demonstrated that truncation of the Rpn8 C-terminal disordered region does not affect proteasome assembly but specifically inhibits the degradation of the GFP-Pih1(282-344) fusion protein in vivo and Pih1 in vitro We propose that Pih1 is a ubiquitin-independent proteasome substrate, and the direct interaction with Rpn8 C terminus mediates its proteasomal degradation.
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Affiliation(s)
- Alexandr Paci
- From the Department of Biological Sciences, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Peter X H Liu
- From the Department of Biological Sciences, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Lingjie Zhang
- From the Department of Biological Sciences, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Rongmin Zhao
- From the Department of Biological Sciences, University of Toronto, Toronto, Ontario M1C 1A4, Canada
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61
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Lakshminarasimhan M, Boanca G, Banks CAS, Hattem GL, Gabriel AE, Groppe BD, Smoyer C, Malanowski KE, Peak A, Florens L, Washburn MP. Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components. Mol Cell Proteomics 2016; 15:960-74. [PMID: 26831523 DOI: 10.1074/mcp.m115.053165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 11/06/2022] Open
Abstract
The highly conserved yeast R2TP complex, consisting of Rvb1, Rvb2, Pih1, and Tah1, participates in diverse cellular processes ranging from assembly of protein complexes to apoptosis. Rvb1 and Rvb2 are closely related proteins belonging to the AAA+ superfamily and are essential for cell survival. Although Rvbs have been shown to be associated with various protein complexes including the Ino80 and Swr1chromatin remodeling complexes, we performed a systematic quantitative proteomic analysis of their associated proteins and identified two additional complexes that associate with Rvb1 and Rvb2: the chaperonin-containing T-complex and the 19S regulatory particle of the proteasome complex. We also analyzed Rvb1 and Rvb2 purified from yeast strains devoid of PIH1 and TAH1. These analyses revealed that both Rvb1 and Rvb2 still associated with Hsp90 and were highly enriched with RNA polymerase II complex components. Our analyses also revealed that both Rvb1 and Rvb2 were recruited to the Ino80 and Swr1 chromatin remodeling complexes even in the absence of Pih1 and Tah1 proteins. Using further biochemical analysis, we showed that Rvb1 and Rvb2 directly interacted with Hsp90 as well as with the RNA polymerase II complex. RNA-Seq analysis of the deletion strains compared with the wild-type strains revealed an up-regulation of ribosome biogenesis and ribonucleoprotein complex biogenesis genes, down-regulation of response to abiotic stimulus genes, and down-regulation of response to temperature stimulus genes. A Gene Ontology analysis of the 80 proteins whose protein associations were altered in the PIH1 or TAH1 deletion strains found ribonucleoprotein complex proteins to be the most enriched category. This suggests an important function of the R2TP complex in ribonucleoprotein complex biogenesis at both the proteomic and genomic levels. Finally, these results demonstrate that deletion network analyses can provide novel insights into cellular systems.
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Affiliation(s)
| | - Gina Boanca
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Charles A S Banks
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Gaye L Hattem
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Ana E Gabriel
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Brad D Groppe
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Christine Smoyer
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Kate E Malanowski
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Allison Peak
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Laurence Florens
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Michael P Washburn
- From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and §Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
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62
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A Novel Interaction of Ecdysoneless (ECD) Protein with R2TP Complex Component RUVBL1 Is Required for the Functional Role of ECD in Cell Cycle Progression. Mol Cell Biol 2015; 36:886-99. [PMID: 26711270 DOI: 10.1128/mcb.00594-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/18/2015] [Indexed: 12/21/2022] Open
Abstract
Ecdysoneless (ECD) is an evolutionarily conserved protein whose germ line deletion is embryonic lethal. Deletion of Ecd in cells causes cell cycle arrest, which is rescued by exogenous ECD, demonstrating a requirement of ECD for normal mammalian cell cycle progression. However, the exact mechanism by which ECD regulates cell cycle is unknown. Here, we demonstrate that ECD protein levels and subcellular localization are invariant during cell cycle progression, suggesting a potential role of posttranslational modifications or protein-protein interactions. Since phosphorylated ECD was recently shown to interact with the PIH1D1 adaptor component of the R2TP cochaperone complex, we examined the requirement of ECD phosphorylation in cell cycle progression. Notably, phosphorylation-deficient ECD mutants that failed to bind to PIH1D1 in vitro fully retained the ability to interact with the R2TP complex and yet exhibited a reduced ability to rescue Ecd-deficient cells from cell cycle arrest. Biochemical analyses demonstrated an additional phosphorylation-independent interaction of ECD with the RUVBL1 component of the R2TP complex, and this interaction is essential for ECD's cell cycle progression function. These studies demonstrate that interaction of ECD with RUVBL1, and its CK2-mediated phosphorylation, independent of its interaction with PIH1D1, are important for its cell cycle regulatory function.
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63
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Abstract
Cancer cells have the unusual capacity to limit the cost of the mutation load that they harbor and simultaneously harness its evolutionary potential. This property fuels drug resistance, a key failure mode in oncogene-directed therapy. However, the factors that regulate this capacity might also provide an Achilles' heel that could be exploited therapeutically. Recently, insight has come from a seemingly distant field: protein folding. It is now clear that protein homeostasis broadly supports malignancy and fuels the rapid evolution of drug resistance. Among protein homeostatic mechanisms that influence cancer biology, the essential ATP-driven molecular chaperone heat-shock protein 90 (Hsp90) is especially important. Hsp90 catalyzes folding of many proteins that regulate growth and development. These "client" kinases, transcription factors, and ubiquitin ligases often play critical roles in human disease, especially cancer. Studies in a wide range of systems-from single-celled organisms to human tumor samples-suggest that Hsp90 can broadly reshape the map between genotype and phenotype, acting as a "capacitor" and "potentiator" of genetic variation. Indeed, it has likely done so to such a degree that it has left an impress on diverse genome sequences. Hsp90 can constitute as much as 5% of total protein in transformed cells and increased levels of heat-shock activation correlate with poor prognosis in breast cancer. These findings and others have motivated a flurry of interest in Hsp90 inhibitors as cancer therapeutics, which have met with rather limited success as single agents, but may eventually prove invaluable in limiting the emergence of resistance to other chemotherapeutics, both genotoxic and molecularly targeted. Here, we provide an overview of Hsp90 function, review its relationship to genetic variation and the evolution of new traits, and discuss the importance of these findings for cancer biology and future efforts to drug this pathway.
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Affiliation(s)
- Daniel Jarosz
- Chemical & Systems Biology, Stanford University School of Medicine, Stanford, California, USA; Developmental Biology, Stanford University School of Medicine, Stanford, California, USA.
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64
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Quinternet M, Rothé B, Barbier M, Bobo C, Saliou JM, Jacquemin C, Back R, Chagot ME, Cianférani S, Meyer P, Branlant C, Charpentier B, Manival X. 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 2015. [PMID: 26210662 DOI: 10.1016/j.jmb.2015.07.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In eukaryotes, nucleotide post-transcriptional modifications in RNAs play an essential role in cell proliferation by contributing to pre-ribosomal RNA processing, ribosome assembly and activity. Box C/D small nucleolar ribonucleoparticles catalyze site-specific 2'-O-methylation of riboses, one of the most prevalent RNA modifications. They contain one guide RNA and four core proteins and their in vivo assembly requires numerous factors including (HUMAN/Yeast) BCD1/Bcd1p, NUFIP1/Rsa1p, ZNHIT3/Hit1p, the R2TP complex composed of protein PIH1D1/Pih1p and RPAP3/Tah1p that bridges the R2TP complex to the HSP90/Hsp82 chaperone and two AAA+ ATPases. We show that Tah1p can stabilize Pih1p in the absence of Hsp82 activity during the stationary phase of growth and consequently that the Tah1p:Pih1p interaction is sufficient for Pih1p stability. This prompted us to establish the solution structure of the Tah1p:Pih1p complex by NMR. The C-terminal tail S93-S111 of Tah1p snakes along Pih1p264-344 folded in a CS domain to form two intermolecular β-sheets and one covering loop. However, a thorough inspection of the NMR and crystal structures revealed structural differences that may be of functional importance. In addition, our NMR and isothermal titration calorimetry data revealed the formation of direct contacts between Pih1p257-344 and the Hsp82MC domain in the presence of Tah1p. By co-expression in Escherichia coli, we demonstrate that Pih1p has two other direct partners, the Rsa1p assembly factor and the Nop58p core protein, and in vivo and in vitro experiments mapped the required binding domains. Our data suggest that these two interactions are mutually exclusive. The implication of this finding for box C/D small nucleolar ribonucleoparticle assembly is discussed.
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Affiliation(s)
- Marc Quinternet
- FR 3209 CNRS-Université de Lorraine, Bioingénierie Moléculaire, Cellulaire et Thérapeutique, Biopôle, Campus Biologie-Santé, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Benjamin Rothé
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Muriel Barbier
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Claude Bobo
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Jean-Michel Saliou
- BioOrganic Mass Spectrometry Laboratory, IPHC-DSA, UMR 7178 Université de Strasbourg-CNRS, 25 rue Becquerel, 67087 Strasbourg, France
| | - Clémence Jacquemin
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Régis Back
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Marie-Eve Chagot
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Sarah Cianférani
- BioOrganic Mass Spectrometry Laboratory, IPHC-DSA, UMR 7178 Université de Strasbourg-CNRS, 25 rue Becquerel, 67087 Strasbourg, France
| | - Philippe Meyer
- Sorbonne Universités, UPMC University Paris 6, CNRS, UMR 8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France.
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Khurana N, Bhattacharyya S. Hsp90, the concertmaster: tuning transcription. Front Oncol 2015; 5:100. [PMID: 25973397 PMCID: PMC4412016 DOI: 10.3389/fonc.2015.00100] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 04/14/2015] [Indexed: 01/07/2023] Open
Abstract
In the last decade, Hsp90 has emerged as a major regulator of cancer cell growth and proliferation. In cancer cells, it assists in giving maturation to oncogenic proteins including several kinases and transcription factors (TF). Recent studies have shown that apart from its chaperone activity, it also imparts regulation of transcription machinery and thereby alters the cellular physiology. Hsp90 and its co-chaperones modulate transcription at least at three different levels. In the first place, they alter the steady-state levels of certain TFs in response to various physiological cues. Second, they modulate the activity of certain epigenetic modifiers, such as histone deacetylases or DNA methyl transferases, and thereby respond to the change in the environment. Third, they participate in the eviction of histones from the promoter region of certain genes and thereby turn on gene expression. In this review, we discuss the role of Hsp90 in all the three aforementioned mechanisms of transcriptional control, taking examples from various model organisms with a special emphasis on cancer progression.
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Affiliation(s)
- Nidhi Khurana
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad , Hyderabad , India
| | - Sunanda Bhattacharyya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad , Hyderabad , India
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66
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Manival X, Jacquemin C, Charpentier B, Quinternet M. (1)H, (15)N and (13)C resonance assignments of the yeast Pih1 and Tah1 C-terminal domains complex. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:71-73. [PMID: 24493341 DOI: 10.1007/s12104-014-9547-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/27/2014] [Indexed: 06/03/2023]
Abstract
We report the nearly complete (1)H, (15)N and (13)C resonance assignment of the complex formed by the C-terminal domains of Pih1 and Tah1 from S. cerevisiae and evidence the folding ability of Tah1 under complex formation.
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Affiliation(s)
- Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS, Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505, Vandœuvre-lès-Nancy, France
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67
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Prieto MB, Georg RC, Gonzales-Zubiate FA, Luz JS, Oliveira CC. Nop17 is a key R2TP factor for the assembly and maturation of box C/D snoRNP complex. BMC Mol Biol 2015; 16:7. [PMID: 25888478 PMCID: PMC4377001 DOI: 10.1186/s12867-015-0037-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/24/2015] [Indexed: 11/24/2022] Open
Abstract
Background Box C/D snoRNPs are responsible for rRNA methylation and processing, and are formed by snoRNAs and four conserved proteins, Nop1, Nop56, Nop58 and Snu13. The snoRNP assembly is a stepwise process, involving other protein complexes, among which the R2TP and Hsp90 chaperone. Nop17, also known as Pih1, has been shown to be a constituent of the R2TP (Rvb1, Rvb2, Tah1, Pih1) and to participate in box C/D snoRNP assembly by its interaction with Nop58. The molecular function of Nop17, however, has not yet been described. Results To shed light on the role played by Nop17 in the maturation of snoRNP, here we analyzed the interactions domains of Nop58 – Nop17 – Tah1 and the importance of ATP to the interaction between Nop17 and the ATPase Rvb1/2. Conclusions Based on the results shown here, we propose a model for the assembly of box C/D snoRNP, according to which R2TP complex is important for reducing the affinity of Nop58 for snoRNA, and for the binding of the other snoRNP subunits. Electronic supplementary material The online version of this article (doi:10.1186/s12867-015-0037-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marcela B Prieto
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil.
| | - Raphaela C Georg
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil. .,Present address: Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil.
| | - Fernando A Gonzales-Zubiate
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil.
| | - Juliana S Luz
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil. .,Present address: Department of Biological Sciences, School of Pharmacy, São Paulo State University, Araraquara, Brazil.
| | - Carla C Oliveira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil.
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68
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Lafontaine DLJ. Noncoding RNAs in eukaryotic ribosome biogenesis and function. Nat Struct Mol Biol 2015; 22:11-9. [PMID: 25565028 DOI: 10.1038/nsmb.2939] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 11/26/2014] [Indexed: 12/22/2022]
Abstract
The ribosome, central to protein synthesis in all cells, is a complex multicomponent assembly with rRNA at its functional core. During the process of ribosome biogenesis, diverse noncoding RNAs participate in controlling the quantity and quality of this rRNA. In this Review, I discuss the multiple roles assumed by noncoding RNAs during the different steps of ribosome biogenesis and how they contribute to the generation of ribosome heterogeneity, which affects normal and pathophysiological processes.
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Affiliation(s)
- Denis L J Lafontaine
- RNA Molecular Biology, Fonds National de la Recherche Scientifique, Université Libre de Bruxelles, Brussels, Belgium
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69
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von Morgen P, Hořejší Z, Macurek L. Substrate recognition and function of the R2TP complex in response to cellular stress. Front Genet 2015; 6:69. [PMID: 25767478 PMCID: PMC4341119 DOI: 10.3389/fgene.2015.00069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/10/2015] [Indexed: 11/18/2022] Open
Abstract
The R2TP complex is a HSP90 co-chaperone, which consists of four subunits: PIH1D1, RPAP3, RUVBL1, and RUVBL2. It is involved in the assembly of large protein or protein–RNA complexes such as RNA polymerase, small nucleolar ribonucleoproteins (snoRNPs), phosphatidylinositol 3 kinase-related kinases (PIKKs), and their complexes. While RPAP3 has a HSP90 binding domain and the RUVBLs comprise ATPase activities important for R2TP functions, PIH1D1 contains a PIH-N domain that specifically recognizes phosphorylated substrates of the R2TP complex. In this review we provide an overview of the current knowledge of the R2TP complex with the focus on the recently identified structural and mechanistic features of the R2TP complex functions. We also discuss the way R2TP regulates cellular response to stress caused by low levels of nutrients or by DNA damage and its possible exploitation as a target for anti-cancer therapy.
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Affiliation(s)
- Patrick von Morgen
- Department of Cancer Cell Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague Czech Republic
| | - Zuzana Hořejší
- Department of Cancer Cell Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague Czech Republic ; DNA Damage Response Laboratory, London Research Institute, London UK
| | - Libor Macurek
- Department of Cancer Cell Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague Czech Republic
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70
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Jeganathan A, Leong V, Zhao L, Huen J, Nano N, Houry WA, Ortega J. Yeast rvb1 and rvb2 proteins oligomerize as a conformationally variable dodecamer with low frequency. J Mol Biol 2015; 427:1875-86. [PMID: 25636407 DOI: 10.1016/j.jmb.2015.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 12/16/2014] [Accepted: 01/16/2015] [Indexed: 01/10/2023]
Abstract
Rvb1 and Rvb2 are conserved AAA+ (ATPases associated with diverse cellular activities) proteins found at the core of large multicomponent complexes that play key roles in chromatin remodeling, integrity of the telomeres, ribonucleoprotein complex biogenesis and other essential cellular processes. These proteins contain an AAA+ domain for ATP binding and hydrolysis and an insertion domain proposed to bind DNA/RNA. Yeast Rvb1 and Rvb2 proteins oligomerize primarily as heterohexameric rings. The six AAA+ core domains form the body of the ring and the insertion domains protrude from one face of the ring. Conversely, human Rvbs form a mixture of hexamers and dodecamers made of two stacked hexamers interacting through the insertion domains. Human dodecamers adopt either a contracted or a stretched conformation. Here, we found that yeast Rvb1/Rvb2 complexes when assembled in vivo mainly form hexamers but they also assemble as dodecamers with a frequency lower than 10%. Yeast dodecamers adopt not only the stretched and contracted structures that have been described for human Rvb1/Rvb2 dodecamers but also intermediate conformations in between these two extreme states. The orientation of the insertion domains of Rvb1 and Rvb2 proteins in these conformers changes as the dodecamer transitions from the stretched structure to a more contracted structure. Finally, we observed that for the yeast proteins, oligomerization as a dodecamer inhibits the ATPase activity of the Rvb1/Rvb2 complex. These results indicate that although human and yeast Rvb1 and Rvb2 proteins share high degree of homology, there are significant differences in their oligomeric behavior and dynamics.
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Affiliation(s)
- Ajitha Jeganathan
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Vivian Leong
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Liang Zhao
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Jennifer Huen
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Nardin Nano
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1.
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71
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Bizarro J, Charron C, Boulon S, Westman B, Pradet-Balade B, Vandermoere F, Chagot ME, Hallais M, Ahmad Y, Leonhardt H, Lamond A, Manival X, Branlant C, Charpentier B, Verheggen C, Bertrand E. Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control. ACTA ACUST UNITED AC 2014; 207:463-80. [PMID: 25404746 PMCID: PMC4242836 DOI: 10.1083/jcb.201404160] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
During small nucleolar ribonucleoprotein complex assembly, a pre-snoRNP complex consisting only of protein components forms first, followed by displacement of the ZNHIT3 subunit when C/D snoRNAs bind and dynamic loading and unloading of RuvBL AAA+ ATPases. In vitro, assembly of box C/D small nucleolar ribonucleoproteins (snoRNPs) involves the sequential recruitment of core proteins to snoRNAs. In vivo, however, assembly factors are required (NUFIP, BCD1, and the HSP90–R2TP complex), and it is unknown whether a similar sequential scheme applies. In this paper, we describe systematic quantitative stable isotope labeling by amino acids in cell culture proteomic experiments and the crystal structure of the core protein Snu13p/15.5K bound to a fragment of the assembly factor Rsa1p/NUFIP. This revealed several unexpected features: (a) the existence of a protein-only pre-snoRNP complex containing five assembly factors and two core proteins, 15.5K and Nop58; (b) the characterization of ZNHIT3, which is present in the protein-only complex but gets released upon binding to C/D snoRNAs; (c) the dynamics of the R2TP complex, which appears to load/unload RuvBL AAA+ adenosine triphosphatase from pre-snoRNPs; and (d) a potential mechanism for preventing premature activation of snoRNP catalytic activity. These data provide a framework for understanding the assembly of box C/D snoRNPs.
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Affiliation(s)
- Jonathan Bizarro
- Equipe labellisée Ligue contre le Cancer, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, Institut de Génétique Moléculaire de Montpellier, 34293 Montpellier, Cedex 5, France
| | - Christophe Charron
- Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Séverine Boulon
- Centre de Recherches de Biochimie Macromoléculaire, Unité Mixte de Recherche 5237, 34293 Montpellier, Cedex 5, France
| | - Belinda Westman
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Bérengère Pradet-Balade
- Equipe labellisée Ligue contre le Cancer, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, Institut de Génétique Moléculaire de Montpellier, 34293 Montpellier, Cedex 5, France
| | - Franck Vandermoere
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 5203, Institut de Génomique Fonctionnelle, F-34000 Montpellier, France Institut National de la Santé et de la Recherche Médicale, U661, F-34000 Montpellier, France Unité Mixte de Recherche 5203, Université de Montpellier 1 and Université de Montpellier 2, F-34000 Montpellier, France
| | - Marie-Eve Chagot
- Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Marie Hallais
- Equipe labellisée Ligue contre le Cancer, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, Institut de Génétique Moléculaire de Montpellier, 34293 Montpellier, Cedex 5, France
| | - Yasmeen Ahmad
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Heinrich Leonhardt
- Munich Center for Integrated Protein Science (CiPS) and Department of Biology, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany Munich Center for Integrated Protein Science (CiPS) and Department of Biology, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Angus Lamond
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Céline Verheggen
- Equipe labellisée Ligue contre le Cancer, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, Institut de Génétique Moléculaire de Montpellier, 34293 Montpellier, Cedex 5, France
| | - Edouard Bertrand
- Equipe labellisée Ligue contre le Cancer, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, Institut de Génétique Moléculaire de Montpellier, 34293 Montpellier, Cedex 5, France
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72
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Westman BJ, Lamond AI. A role for SUMOylation in snoRNP biogenesis revealed by quantitative proteomics. Nucleus 2014. [DOI: 10.4161/nucl.14437] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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73
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Gopinath RK, You ST, Chien KY, Swamy KBS, Yu JS, Schuyler SC, Leu JY. The Hsp90-dependent proteome is conserved and enriched for hub proteins with high levels of protein-protein connectivity. Genome Biol Evol 2014; 6:2851-65. [PMID: 25316598 PMCID: PMC4224352 DOI: 10.1093/gbe/evu226] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hsp90 is one of the most abundant and conserved proteins in the cell. Reduced levels or activity of Hsp90 causes defects in many cellular processes and also reveals genetic and nongenetic variation within a population. Despite information about Hsp90 protein–protein interactions, a global view of the Hsp90-regulated proteome in yeast is unavailable. To investigate the degree of dependency of individual yeast proteins on Hsp90, we used the “stable isotope labeling by amino acids in cell culture” method coupled with mass spectrometry to quantify around 4,000 proteins in low-Hsp90 cells. We observed that 904 proteins changed in their abundance by more than 1.5-fold. When compared with the transcriptome of the same population of cells, two-thirds of the misregulated proteins were observed to be affected posttranscriptionally, of which the majority were downregulated. Further analyses indicated that the downregulated proteins are highly conserved and assume central roles in cellular networks with a high number of protein interacting partners, suggesting that Hsp90 buffers genetic and nongenetic variation through regulating protein network hubs. The downregulated proteins were enriched for essential proteins previously not known to be Hsp90-dependent. Finally, we observed that downregulation of transcription factors and mating pathway components by attenuating Hsp90 function led to decreased target gene expression and pheromone response, respectively, providing a direct link between observed proteome regulation and cellular phenotypes.
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Affiliation(s)
- Rajaneesh Karimpurath Gopinath
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Ting You
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Kun-Yi Chien
- Molecular Medicine Research Center, Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | | | - Jau-Song Yu
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Scott C Schuyler
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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74
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Rothé B, Saliou JM, Quinternet M, Back R, Tiotiu D, Jacquemin C, Loegler C, Schlotter F, Peña V, Eckert K, Moréra S, Dorsselaer AV, Branlant C, Massenet S, Sanglier-Cianférani S, Manival X, Charpentier B. Protein Hit1, a novel box C/D snoRNP assembly factor, controls cellular concentration of the scaffolding protein Rsa1 by direct interaction. Nucleic Acids Res 2014; 42:10731-47. [PMID: 25170085 PMCID: PMC4176330 DOI: 10.1093/nar/gku612] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 01/09/2023] Open
Abstract
Biogenesis of eukaryotic box C/D small nucleolar ribonucleoprotein particles (C/D snoRNPs) involves conserved trans-acting factors, which are proposed to facilitate the assembly of the core proteins Snu13p/15.5K, Nop58p/NOP58, Nop56p/NOP56 and Nop1p/Fibrillarin on box C/D small nucleolar RNAs (C/D snoRNAs). In yeast, protein Rsa1 acts as a platform, interacting with both the RNA-binding core protein Snu13 and protein Pih1 of the Hsp82-R2TP chaperone complex. In this work, a proteomic approach coupled with functional and structural studies identifies protein Hit1 as a novel Rsa1p-interacting partner involved in C/D snoRNP assembly. Hit1p contributes to in vivo C/D snoRNA stability and pre-RNA maturation kinetics. It associates with U3 snoRNA precursors and influences its 3'-end processing. Remarkably, Hit1p is required to maintain steady-state levels of Rsa1p. This stabilizing activity is likely to be general across eukaryotic species, as the human protein ZNHIT3(TRIP3) showing sequence homology with Hit1p regulates the abundance of NUFIP1, the Rsa1p functional homolog. The nuclear magnetic resonance solution structure of the Rsa1p317-352-Hit1p70-164 complex reveals a novel mode of protein-protein association explaining the strong stability of the Rsa1p-Hit1p complex. Our biochemical data show that C/D snoRNAs and the core protein Nop58 can interact with the purified Snu13p-Rsa1p-Hit1p heterotrimer.
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Affiliation(s)
- Benjamin Rothé
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Jean-Michel Saliou
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg. CNRS, UMR 7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Marc Quinternet
- FR CNRS-3209 Bioingénierie Moléculaire, Cellulaire et Thérapeutique (BMCT), CNRS, Université de Lorraine, Biopôle, Campus Biologie Santé, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Régis Back
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Decebal Tiotiu
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Clémence Jacquemin
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Christine Loegler
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Florence Schlotter
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Vlad Peña
- Max-Planck-Institut für biophysikalische Chemie, Abtl. Röntgenkristallographie, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kelvin Eckert
- Laboratoire d'Enzymologie et Biochimie Structurales (LEBS), CNRS, 1 Avenue de Terrasse, 91198 Gif-sur Yvette, France
| | - Solange Moréra
- Laboratoire d'Enzymologie et Biochimie Structurales (LEBS), CNRS, 1 Avenue de Terrasse, 91198 Gif-sur Yvette, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg. CNRS, UMR 7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Sarah Sanglier-Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg. CNRS, UMR 7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
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75
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Peng Y, Yu G, Tian S, Li H. Co-expression and co-purification of archaeal and eukaryal box C/D RNPs. PLoS One 2014; 9:e103096. [PMID: 25078083 PMCID: PMC4117494 DOI: 10.1371/journal.pone.0103096] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/27/2014] [Indexed: 11/18/2022] Open
Abstract
Box C/D ribonucleoprotein particles (RNPs) are 2'-O-methylation enzymes required for maturation of ribosomal and small nuclear RNA. Previous biochemical and structural studies of the box C/D RNPs were limited by the unavailability of purified intact RNPs. We developed a bacterial co-expression strategy based on the combined use of a multi-gene expression system and a tRNA-scaffold construct that allowed the expression and purification of homogeneous archaeal and human box C/D RNPs. While the co-expressed and co-purified archaeal box C/D RNP was found to be fully active in a 2'-O-methylation assay, the intact human U14 box C/D RNP showed no detectable catalytic activity, consistent with the earlier findings that assembly of eukaryotic box C/D RNPs is nonspontaneous and requires additional protein factors. Our systems provide a means for further biochemical and structural characterization of box C/D RNPs and their assembly factors.
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Affiliation(s)
- Yu Peng
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America
| | - Ge Yu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, United States of America
| | - Shaoxiong Tian
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, United States of America
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, United States of America
- * E-mail:
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76
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Kakihara Y, Makhnevych T, Zhao L, Tang W, Houry WA. Nutritional status modulates box C/D snoRNP biogenesis by regulated subcellular relocalization of the R2TP complex. Genome Biol 2014; 15:404. [PMID: 25060708 PMCID: PMC4165372 DOI: 10.1186/s13059-014-0404-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Box C/D snoRNPs, which are typically composed of box C/D snoRNA and the four core protein components Nop1, Nop56, Nop58, and Snu13, play an essential role in the modification and processing of pre-ribosomal RNA. The highly conserved R2TP complex, comprising the proteins Rvb1, Rvb2, Tah1, and Pih1, has been shown to be required for box C/D snoRNP biogenesis and assembly; however, the molecular basis of R2TP chaperone-like activity is not yet known. RESULTS Here, we describe an unexpected finding in which the activity of the R2TP complex is required for Nop58 protein stability and is controlled by the dynamic subcellular redistribution of the complex in response to growth conditions and nutrient availability. In growing cells, the complex localizes to the nucleus and interacts with box C/D snoRNPs. This interaction is significantly reduced in poorly growing cells as R2TP predominantly relocalizes to the cytoplasm. The R2TP-snoRNP interaction is mainly mediated by Pih1. CONCLUSIONS The R2TP complex exerts a novel regulation on box C/D snoRNP biogenesis that affects their assembly and consequently pre-rRNA maturation in response to different growth conditions.
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77
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Hořejší Z, Stach L, Flower TG, Joshi D, Flynn H, Skehel JM, O'Reilly NJ, Ogrodowicz RW, Smerdon SJ, Boulton SJ. Phosphorylation-dependent PIH1D1 interactions define substrate specificity of the R2TP cochaperone complex. Cell Rep 2014; 7:19-26. [PMID: 24656813 PMCID: PMC3989777 DOI: 10.1016/j.celrep.2014.03.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/04/2014] [Accepted: 03/07/2014] [Indexed: 12/21/2022] Open
Abstract
The R2TP cochaperone complex plays a critical role in the assembly of multisubunit machines, including small nucleolar ribonucleoproteins (snoRNPs), RNA polymerase II, and the mTORC1 and SMG1 kinase complexes, but the molecular basis of substrate recognition remains unclear. Here, we describe a phosphopeptide binding domain (PIH-N) in the PIH1D1 subunit of the R2TP complex that preferentially binds to highly acidic phosphorylated proteins. A cocrystal structure of a PIH-N domain/TEL2 phosphopeptide complex reveals a highly specific phosphopeptide recognition mechanism in which Lys57 and 64 in PIH1D1, along with a conserved DpSDD phosphopeptide motif within TEL2, are essential and sufficient for binding. Proteomic analysis of PIH1D1 interactors identified R2TP complex substrates that are recruited by the PIH-N domain in a sequence-specific and phosphorylation-dependent manner suggestive of a common mechanism of substrate recognition. We propose that protein complexes assembled by the R2TP complex are defined by phosphorylation of a specific motif and recognition by the PIH1D1 subunit.
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Affiliation(s)
- Zuzana Hořejší
- DNA Damage Response Laboratory, London Research Institute, Clare Hall, South Mimms EN6 3LD, UK
| | - Lasse Stach
- MRC National Institute for Medical Research, Division of Molecular Structure, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Thomas G Flower
- MRC National Institute for Medical Research, Division of Molecular Structure, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Dhira Joshi
- Peptide Chemistry, London Research Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Helen Flynn
- DNA Damage Response Laboratory, London Research Institute, Clare Hall, South Mimms EN6 3LD, UK
| | - J Mark Skehel
- DNA Damage Response Laboratory, London Research Institute, Clare Hall, South Mimms EN6 3LD, UK; Biological Mass Spectrometry and Proteomics Group, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Nicola J O'Reilly
- DNA Damage Response Laboratory, London Research Institute, Clare Hall, South Mimms EN6 3LD, UK
| | - Roksana W Ogrodowicz
- MRC National Institute for Medical Research, Division of Molecular Structure, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Stephen J Smerdon
- MRC National Institute for Medical Research, Division of Molecular Structure, The Ridgeway, Mill Hill, London NW7 1AA, UK.
| | - Simon J Boulton
- DNA Damage Response Laboratory, London Research Institute, Clare Hall, South Mimms EN6 3LD, UK.
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78
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Co-chaperones of Hsp90 in Plasmodium falciparum and their concerted roles in cellular regulation. Parasitology 2014; 141:1177-91. [PMID: 24560171 DOI: 10.1017/s0031182013002084] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Co-chaperones are well-known regulators of heat shock protein 90 (Hsp90). Hsp90 is a molecular chaperone that is essential in the eukaryotes for the folding and activation of numerous proteins involved in important cellular processes such as signal transduction, growth and developmental regulation. Co-chaperones assist Hsp90 in the protein folding process by modulating conformational changes to promote client protein interaction and functional maturation. With the recognition of Plasmodium falciparum Hsp90 (PfHsp90) as a potential antimalarial drug target, there is obvious interest in the study of its co-chaperones in their partnership in regulating cellular processes in malaria parasite. Previous studies on PfHsp90 have identified more than 10 co-chaperones in P. falciparum genome. However, many of them remained annotated as putative proteins as their functionality has not been validated experimentally. So far, only five co-chaperones, PfHop, Pfp23, PfAha1, PfPP5 and PfFKBP35 have been characterized and shown to interact with PfHsp90. This review will summarize current knowledge on the co-chaperones in P. falciparum and discuss their regulatory roles on PfHsp90. As certain eukaryotic co-chaperones have also been implicated in altering the affinity of Hsp90 for its inhibitor, this review will also examine plasmodial co-chaperones' potential influence on approaches towards designing antimalarials targeting PfHsp90.
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79
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Amaya C, Kurisetty V, Stiles J, Nyakeriga AM, Arumugam A, Lakshmanaswamy R, Botez CE, Mitchell DC, Bryan BA. A genomics approach to identify susceptibilities of breast cancer cells to "fever-range" hyperthermia. BMC Cancer 2014; 14:81. [PMID: 24511912 PMCID: PMC3931319 DOI: 10.1186/1471-2407-14-81] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 01/22/2014] [Indexed: 12/22/2022] Open
Abstract
Background Preclinical and clinical studies have shown for decades that tumor cells demonstrate significantly enhanced sensitivity to “fever range” hyperthermia (increasing the intratumoral temperature to 42-45°C) than normal cells, although it is unknown why cancer cells exhibit this distinctive susceptibility. Methods To address this issue, mammary epithelial cells and three malignant breast cancer lines were subjected to hyperthermic shock and microarray, bioinformatics, and network analysis of the global transcription changes was subsequently performed. Results Bioinformatics analysis differentiated the gene expression patterns that distinguish the heat shock response of normal cells from malignant breast cancer cells, revealing that the gene expression profiles of mammary epithelial cells are completely distinct from malignant breast cancer lines following this treatment. Using gene network analysis, we identified altered expression of transcripts involved in mitotic regulators, histones, and non-protein coding RNAs as the significant processes that differed between the hyperthermic response of mammary epithelial cells and breast cancer cells. We confirmed our data via qPCR and flow cytometric analysis to demonstrate that hyperthermia specifically disrupts the expression of key mitotic regulators and G2/M phase progression in the breast cancer cells. Conclusion These data have identified molecular mechanisms by which breast cancer lines may exhibit enhanced susceptibility to hyperthermic shock.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Brad A Bryan
- Department of Biomedical Sciences, Paul L, Foster School of Medicine, Texas Tech University Health Sciences Center, 5001 El Paso Drive, MSB1 Room 2111, El Paso, Texas 79905, USA.
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80
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Dong F, Shinohara K, Botilde Y, Nabeshima R, Asai Y, Fukumoto A, Hasegawa T, Matsuo M, Takeda H, Shiratori H, Nakamura T, Hamada H. Pih1d3 is required for cytoplasmic preassembly of axonemal dynein in mouse sperm. ACTA ACUST UNITED AC 2014; 204:203-13. [PMID: 24421334 PMCID: PMC3897177 DOI: 10.1083/jcb.201304076] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Pih1d3 promotes the stability and assembly of axonemal outer and inner dynein arms to allow for cytoplasmic preassembly of dynein complexes in spermatogenic cells. Axonemal dynein complexes are preassembled in the cytoplasm before their transport to cilia, but the mechanism of this process remains unclear. We now show that mice lacking Pih1d3, a PIH1 domain–containing protein, develop normally but manifest male sterility. Pih1d3−/− sperm were immotile and fragile, with the axoneme of the flagellum lacking outer dynein arms (ODAs) and inner dynein arms (IDAs) and showing a disturbed 9+2 microtubule organization. Pih1d3 was expressed specifically in spermatogenic cells, with the mRNA being most abundant in pachytene spermatocytes. Pih1d3 localized to the cytoplasm of spermatogenic cells but was not detected in spermatids or mature sperm. The levels of ODA and IDA proteins were reduced in the mutant testis and sperm, and Pih1d3 was found to interact with an intermediate chain of ODA as well as with Hsp70 and Hsp90. Our results suggest that Pih1d3 contributes to cytoplasmic preassembly of dynein complexes in spermatogenic cells by stabilizing and promoting complex formation by ODA and IDA proteins.
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Affiliation(s)
- Fenglan Dong
- Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), 1-3 Yamada-oka, Suita, Osaka 565-0871, Japan
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81
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Benbahouche NEH, Iliopoulos I, Török I, Marhold J, Henri J, Kajava AV, Farkaš R, Kempf T, Schnölzer M, Meyer P, Kiss I, Bertrand E, Mechler BM, Pradet-Balade B. 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 2014; 289:6236-47. [PMID: 24394412 DOI: 10.1074/jbc.m113.499608] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The R2TP is a recently identified Hsp90 co-chaperone, composed of four proteins as follows: Pih1D1, RPAP3, and the AAA(+)-ATPases RUVBL1 and RUVBL2. In mammals, the R2TP is involved in the biogenesis of cellular machineries such as RNA polymerases, small nucleolar ribonucleoparticles and phosphatidylinositol 3-kinase-related kinases. Here, we characterize the spaghetti (spag) gene of Drosophila, the homolog of human RPAP3. This gene plays an essential function during Drosophila development. We show that Spag protein binds Drosophila orthologs of R2TP components and Hsp90, like its yeast counterpart. Unexpectedly, Spag also interacts and stimulates the chaperone activity of Hsp70. Using null mutants and flies with inducible RNAi, we show that spaghetti is necessary for the stabilization of snoRNP core proteins and target of rapamycin activity and likely the assembly of RNA polymerase II. This work highlights the strong conservation of both the HSP90/R2TP system and its clients and further shows that Spag, unlike Saccharomyces cerevisiae Tah1, performs essential functions in metazoans. Interaction of Spag with both Hsp70 and Hsp90 suggests a model whereby R2TP would accompany clients from Hsp70 to Hsp90 to facilitate their assembly into macromolecular complexes.
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Affiliation(s)
- Nour El Houda Benbahouche
- From the Equipe Labellisée Ligue Contre le Cancer, Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
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82
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Yu YT, Meier UT. RNA-guided isomerization of uridine to pseudouridine--pseudouridylation. RNA Biol 2014; 11:1483-94. [PMID: 25590339 PMCID: PMC4615163 DOI: 10.4161/15476286.2014.972855] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 09/12/2014] [Indexed: 01/13/2023] Open
Abstract
Box H/ACA ribonucleoproteins (RNPs), each consisting of one unique guide RNA and 4 common core proteins, constitute a family of complex enzymes that catalyze, in an RNA-guided manner, the isomerization of uridines to pseudouridines (Ψs) in RNAs, a reaction known as pseudouridylation. Over the years, box H/ACA RNPs have been extensively studied revealing many important aspects of these RNA modifying machines. In this review, we focus on the composition, structure, and biogenesis of H/ACA RNPs. We explain the mechanism of how this enzyme family recognizes and specifies its target uridine in a substrate RNA. We discuss the substrates of box H/ACA RNPs, focusing on rRNA (rRNA) and spliceosomal small nuclear RNA (snRNA). We describe the modification product Ψ and its contribution to RNA function. Finally, we consider possible mechanisms of the bone marrow failure syndrome dyskeratosis congenita and of prostate and other cancers linked to mutations in H/ACA RNPs.
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Key Words
- DC, dyskeratosis congenita
- H/ACA
- HH, hoyeraal-hreidarsson syndrome
- PIKK, phosphatidylinositol 3-kinase-related kinase
- PUA, pseudouridylase and archaeosine transglycosylase
- RNA modification
- RNA-guided
- RNP, ribonucleoprotein
- SMN, survival of motor neuron protein
- SSD, SHQ1 specific domain
- U, uridine
- X-DC, X-linked dyskeratosis congenita
- dyskeratosis congenita
- prostate cancer
- pseudouridine
- rRNA
- rRNA, ribosomal RNA
- ribonucleoproteins
- sca, small Cajal body
- snRNA, small nuclear RNA
- sno, small nucleolar
- snoRNA
- snoRNA, small nucleolar RNA
- spliceosomal small nuclear RNA
- tRNA, transfer RNA
- ψ, pseudouridine, 5-ribosyluracil
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MESH Headings
- Dyskeratosis Congenita/genetics
- Dyskeratosis Congenita/metabolism
- Dyskeratosis Congenita/pathology
- Humans
- Isomerism
- Male
- Mutation
- Nucleic Acid Conformation
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Pseudouridine/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Uridine/metabolism
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Yi-Tao Yu
- University of Rochester Medical Center; Department of Biochemistry and Biophysics; Center for RNA Biology; Rochester, NY USA
| | - U Thomas Meier
- Albert Einstein College of Medicine; Department of Anatomy and Structural Biology; Bronx, NY USA
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83
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Rothé B, Back R, Quinternet M, Bizarro J, Robert MC, Blaud M, Romier C, Manival X, Charpentier B, Bertrand E, Branlant C. Characterization of the interaction between protein Snu13p/15.5K and the Rsa1p/NUFIP factor and demonstration of its functional importance for snoRNP assembly. Nucleic Acids Res 2013; 42:2015-36. [PMID: 24234454 PMCID: PMC3919607 DOI: 10.1093/nar/gkt1091] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The yeast Snu13p protein and its 15.5K human homolog both bind U4 snRNA and box C/D snoRNAs. They also bind the Rsa1p/NUFIP assembly factor, proposed to scaffold immature snoRNPs and to recruit the Hsp90-R2TP chaperone complex. However, the nature of the Snu13p/15.5K–Rsa1p/NUFIP interaction and its exact role in snoRNP assembly remained to be elucidated. By using biophysical, molecular and imaging approaches, here, we identify residues needed for Snu13p/15.5K–Rsa1p/NUFIP interaction. By NMR structure determination and docking approaches, we built a 3D model of the Snup13p–Rsa1p interface, suggesting that residues R249, R246 and K250 in Rsa1p and E72 and D73 in Snu13p form a network of electrostatic interactions shielded from the solvent by hydrophobic residues from both proteins and that residue W253 of Rsa1p is inserted in a hydrophobic cavity of Snu13p. Individual mutations of residues in yeast demonstrate the functional importance of the predicted interactions for both cell growth and snoRNP formation. Using archaeal box C/D sRNP 3D structures as templates, the association of Snu13p with Rsa1p is predicted to be exclusive of interactions in active snoRNPs. Rsa1p and NUFIP may thus prevent premature activity of pre-snoRNPs, and their removal may be a key step for active snoRNP production.
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Affiliation(s)
- Benjamin Rothé
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 avenue de la forêt de Haye, BP 184, 54505 Vandœuvre-lès-Nancy, France, FR CNRS-3209 (Ingénierie Moléculaire et Thérapeutique), CNRS, Université de Lorraine, Faculté de Médecine, Bâtiment Biopôle, BP 184, 54505 Vandœuvre-lès-Nancy Cedex, France, Equipe labellisée Ligue contre le Cancer, IGMM (Institut de Génétique Moléculaire de Montpellier), Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5535, Montpellier Cedex 5, France and IGBMC (Institut de Génétique et Biologie Moléculaire et Cellulaire), Département de Biologie et Génomique Structurales, Université de Strasbourg, CNRS, INSERM, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, France
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84
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PIH1D1 interacts with mTOR complex 1 and enhances ribosome RNA transcription. FEBS Lett 2013; 587:3303-8. [DOI: 10.1016/j.febslet.2013.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/30/2013] [Accepted: 09/01/2013] [Indexed: 02/07/2023]
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85
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Back R, Dominguez C, Rothé B, Bobo C, Beaufils C, Moréra S, Meyer P, Charpentier B, Branlant C, Allain FHT, Manival X. High-resolution structural analysis shows how Tah1 tethers Hsp90 to the R2TP complex. Structure 2013; 21:1834-47. [PMID: 24012479 DOI: 10.1016/j.str.2013.07.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 07/03/2013] [Accepted: 07/10/2013] [Indexed: 11/30/2022]
Abstract
The ubiquitous Hsp90 chaperone participates in snoRNP and RNA polymerase assembly through interaction with the R2TP complex. This complex includes the proteins Tah1, Pih1, Rvb1, and Rvb2. Tah1 bridges Hsp90 to R2TP. Its minimal TPR domain includes two TPR motifs and a capping helix. We established the high-resolution solution structures of Tah1 free and in complex with the Hsp90 C-terminal peptide. The TPR fold is similar in the free and bound forms and we show experimentally that in addition to its solvating/stabilizing role, the capping helix is essential for the recognition of the Hsp90 (704)EMEEVD(709) motif. In addition to Lys79 and Arg83 from the carboxylate clamp, this helix bears Tyr82 forming a π/S-CH3 interaction with Hsp90 M(705) from the peptide 310 helix. The Tah1 C-terminal region is unfolded, and we demonstrate that it is essential for the recruitment of the Pih1 C-terminal domain and folds upon binding.
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Affiliation(s)
- Régis Back
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 Université de Lorraine-CNRS, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 Avenue de la forêt de Haye, BP 184, 54505 Vandœuvre-lès-Nancy, France
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86
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Ahmad M, Afrin F, Tuteja R. Identification of R2TP complex of Leishmania donovani and Plasmodium falciparum using genome wide in-silico analysis. Commun Integr Biol 2013; 6:e26005. [PMID: 24505500 PMCID: PMC3913666 DOI: 10.4161/cib.26005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/01/2013] [Accepted: 08/01/2013] [Indexed: 12/22/2022] Open
Abstract
Recently discovered R2TP complex is an important multiprotein complex involved in multiple cellular process like snoRNP biogenesis, PIKK signaling, RNA polymerase II assembly and apoptosis. Within R2TP complex, Pih1 tightly interacts with Rvb1/Rvb2 and with Tah1 to form R2TP macromolecular complex. R2TP complex further interacts with Hsp90 to form R2TP-Hsp90 complex, which has been found critical in many cellular process. The genome wide screening of Leishmania donovani and Plasmodium falciparum led to the identification of RuvB like1, RuvB like 2, Pih1, and Tah1. Therefore, we speculate that this complex is also important for these parasites as in the yeast. The detailed analysis of crucial components of R2TP complex, Ld-RuvB like 1, and Ld-RuvB like 2, revealed the presence of characteristic motifs like DNA binding motif and ATPase motifs. Hsp90 is also reported from Leishmania donovani and Plasmodium falciparum suggesting that the R2TP complex further interacts with Hsp90 to form R2TP-Hsp90 complex. Recently it has been discovered that RuvB like proteins are overexpressed in many cancers and their ATPase activity is crucial for cancer cell proliferation and the human RuvBs have been proposed as suitable drug target for cancer. Similarly one of the Plasmodium falciparum RuvB like protein (PfRuvB3) has been found to be specific to the stage where nuclear division led multiplication of parasite take place. Considering all these it seems that the R2TP complex may be playing some critical role both in the cancer cell proliferation in human and rapid multiplication of the parasites Leishmania donovani and Plasmodium falciparum.
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Affiliation(s)
- Moaz Ahmad
- Malaria Group; International Centre for Genetic Engineering and Biotechnology; Aruna Asaf Ali Marg; New Delhi, India ; Department of Biotechnology; Jamia Hamdard; Hamdard Nagar; New Delhi, India
| | - Farhat Afrin
- Department of Biotechnology; Jamia Hamdard; Hamdard Nagar; New Delhi, India
| | - Renu Tuteja
- Malaria Group; International Centre for Genetic Engineering and Biotechnology; Aruna Asaf Ali Marg; New Delhi, India
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87
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Saeki M, Egusa H, Kamano Y, Kakihara Y, Houry WA, Yatani H, Noguchi S, Kamisaki Y. Exosome-bound WD repeat protein Monad inhibits breast cancer cell invasion by degrading amphiregulin mRNA. PLoS One 2013; 8:e67326. [PMID: 23844004 PMCID: PMC3701000 DOI: 10.1371/journal.pone.0067326] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/17/2013] [Indexed: 11/19/2022] Open
Abstract
Increased stabilization of mRNA coding for key cancer genes can contribute to invasiveness. This is achieved by down-regulation of exosome cofactors, which bind to 3'-UTR in cancer-related genes. Here, we identified amphiregulin, an EGFR ligand, as a target of WD repeat protein Monad, a component of R2TP/prefoldin-like complex, in MDA-MB-231 breast cancer cells. Monad specifically interacted with both the 3'-UTR of amphiregulin mRNA and the RNA degrading exosome, and enhanced decay of amphiregulin transcripts. Knockdown of Monad increased invasion and this effect was abolished with anti-amphiregulin neutralizing antibody. These results suggest that Monad could prevent amphiregulin-mediated invasion by degrading amphiregulin mRNA.
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Affiliation(s)
- Makio Saeki
- Department of Pharmacology, Graduate School of Dentistry, Osaka University, Suita, Osaka, Japan.
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88
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Nano N, Houry WA. Chaperone-like activity of the AAA+ proteins Rvb1 and Rvb2 in the assembly of various complexes. Philos Trans R Soc Lond B Biol Sci 2013; 368:20110399. [PMID: 23530256 DOI: 10.1098/rstb.2011.0399] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Rvb1 and Rvb2 are highly conserved and essential eukaryotic AAA+ proteins linked to a wide range of cellular processes. AAA+ proteins are ATPases associated with diverse cellular activities and are characterized by the presence of one or more AAA+ domains. These domains have the canonical Walker A and Walker B nucleotide binding and hydrolysis motifs. Rvb1 and Rvb2 have been found to be part of critical cellular complexes: the histone acetyltransferase Tip60 complex, chromatin remodelling complexes Ino80 and SWR-C, and the telomerase complex. In addition, Rvb1 and Rvb2 are components of the R2TP complex that was identified by our group and was determined to be involved in the maturation of box C/D small nucleolar ribonucleoprotein (snoRNP) complexes. Furthermore, the Rvbs have been associated with mitotic spindle assembly, as well as phosphatidylinositol 3-kinase-related protein kinase (PIKK) signalling. This review sheds light on the potential role of the Rvbs as chaperones in the assembly and remodelling of these critical complexes.
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Affiliation(s)
- Nardin Nano
- Department of Biochemistry, University of Toronto, , Toronto, Ontario, Canada M5S 1A8
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89
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Rtp1p is a karyopherin-like protein required for RNA polymerase II biogenesis. Mol Cell Biol 2013; 33:1756-67. [PMID: 23438601 DOI: 10.1128/mcb.01449-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The assembly and nuclear transport of RNA polymerase II (RNA pol II) are processes that require the participation of many auxiliary factors. In a yeast genetic screen, we identified a previously uncharacterized gene, YMR185w (renamed RTP1), which encodes a protein required for the nuclear import of RNA pol II. Using protein affinity purification coupled to mass spectrometry, we identified interactions between Rtp1p and members of the R2TP complex. Rtp1p also interacts, to a different extent, with several RNA pol II subunits. The pattern of interactions is compatible with a role for Rtp1p as an assembly factor that participates in the formation of the Rpb2/Rpb3 subassembly complex and its binding to the Rpb1p-containing subcomplex. Besides, Rtp1p has a molecular architecture characteristic of karyopherins, composed of HEAT repeats, and is able to interact with phenylalanine-glycine-containing nucleoporins. Our results define Rtp1p as a new component of the RNA pol II biogenesis machinery that plays roles in subunit assembly and likely in transport through the nuclear pore complex.
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90
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Abstract
RVB1/RVB2 (RuvBL1/RuvBL2 or pontin/reptin) are enigmatic AAA(+) ATPase proteins that are present in multiple cellular complexes. Although they have been implicated in many cellular functions, the exact molecular function of RVB proteins in the various complexes is not clear. TIP60 complex (TIP60.com) is a tumor suppressor chromatin-remodeling complex containing RVB proteins. RVBs are required for the lysine acetyltransferase activity of TIP60.com but not for that of the pure recombinant TIP60 polypeptide. Here we describe two molecular functions of RVBs in TIP60.com. First, RVBs negate the repression of catalytic activity of TIP60 by another protein in TIP60.com, p400. RVBs competitively displace the SNF2 domain of p400 from the TIP60 polypeptide. In addition RVBs are also required for heat stability of TIP60.com by a p400-independent pathway. RVB1 and RVB2 are redundant with each other for these functions and do not require their ATPase activities. Thus, RVB proteins act as molecular adaptors that can substitute for one another to facilitate the optimal assembly, heat stability, and function of the TIP60 complex.
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91
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Izumi N, Yamashita A, Ohno S. Integrated regulation of PIKK-mediated stress responses by AAA+ proteins RUVBL1 and RUVBL2. Nucleus 2012; 3:29-43. [PMID: 22540023 PMCID: PMC3337166 DOI: 10.4161/nucl.18926] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Proteins of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family are activated by various cellular stresses, including DNA damage, premature termination codon and nutritional status, and induce appropriate cellular responses. The importance of PIKK functions in the maintenance of genome integrity, accurate gene expression and the proper control of cell growth/proliferation is established. Recently, ATPase associated diverse cellular activities (AAA+) proteins RUVBL1 and RUVBL2 (RUVBL1/2) have been shown to be common regulators of PIKKs. The RUVBL1/2 complex regulates PIKK-mediated stress responses through physical interactions with PIKKs and by controlling PIKK mRNA levels. In this review, the functions of PIKKs in stress responses are outlined and the physiological significance of the integrated regulation of PIKKs by the RUVBL1/2 complex is presented. We also discuss a putative "PIKK regulatory chaperone complex" including other PIKK regulators, Hsp90 and the Tel2 complex.
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Affiliation(s)
- Natsuko Izumi
- Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama, Japan
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92
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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 2012; 430:320-4. [PMID: 23159623 DOI: 10.1016/j.bbrc.2012.11.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 11/01/2012] [Indexed: 12/19/2022]
Abstract
We previously characterized RNA polymerase II-associated protein 3 (RPAP3) as a cell death enhancer. Here we report the identification and characterization of splicing isoform of RPAP3, isoform 1 and 2. We investigated the interaction between RPAP3 and PIH1 domain containing protein 1 (PIH1D1), and found that RPAP3 isoform 1, but not isoform 2, interacted with PIH1D1. Furthermore, knockdown of RPAP3 isoform 1 by small interfering RNA down-regulated PIH1D1 protein level without affecting PIH1D1 mRNA. RPAP3 isoform 2 potentiated doxorubicin-induced cell death in human breast cancer T-47 cells although isoform 1 showed no effect. These results suggest that R2TP complex is composed of RPAP3 isoform 1 for its stabilization, and that RPAP3 isoform 2 may have a dominant negative effect on the survival potency of R2TP complex.
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Affiliation(s)
- Miki Yoshida
- Department of Pharmacology, Graduate School of Dentistry, Osaka University, Suita, Osaka 565-0871, Japan
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93
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Paci A, Liu XH, Huang H, Lim A, Houry WA, Zhao R. The stability of the small nucleolar ribonucleoprotein (snoRNP) assembly protein Pih1 in Saccharomyces cerevisiae is modulated by its C terminus. J Biol Chem 2012; 287:43205-14. [PMID: 23139418 DOI: 10.1074/jbc.m112.408849] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Pih1 is an unstable protein and a subunit of the R2TP complex that, in yeast Saccharomyces cerevisiae, also contains the helicases Rvb1, Rvb2, and the Hsp90 cofactor Tah1. Pih1 and the R2TP complex are required for the box C/D small nucleolar ribonucleoprotein (snoRNP) assembly and ribosomal RNA processing. Purified Pih1 tends to aggregate in vitro. Molecular chaperone Hsp90 and its cochaperone Tah1 are required for the stability of Pih1 in vivo. We had shown earlier that the C terminus of Pih1 destabilizes the protein and that the C terminus of Tah1 binds to the Pih1 C terminus to form a stable complex. Here, we analyzed the secondary structure of the Pih1 C terminus and identified two intrinsically disordered regions and five hydrophobic clusters. Site-directed mutagenesis indicated that one predicted intrinsically disordered region IDR2 is involved in Tah1 binding, and that the C terminus of Pih1 contains multiple destabilization or degron elements. Additionally, the Pih1 N-terminal domain, Pih1(1-230), was found to be able to complement the physiological role of full-length Pih1 at 37 °C. Pih1(1-230) as well as a shorter Pih1 N-terminal fragment Pih1(1-195) is able to bind Rvb1/Rvb2 heterocomplex. However, the sequence between the two disordered regions in Pih1 significantly enhances the Pih1 N-terminal domain binding to Rvb1/Rvb2. Based on these data, a model of protein-protein interactions within the R2TP complex is proposed.
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Affiliation(s)
- Alexandr Paci
- Department of Biological Sciences, University of Toronto, Toronto, Ontario M1C 1A4, Canada
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94
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Ahmad M, Tuteja R. Plasmodium falciparum RuvB proteins: Emerging importance and expectations beyond cell cycle progression. Commun Integr Biol 2012; 5:350-61. [PMID: 23060959 PMCID: PMC3460840 DOI: 10.4161/cib.20005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The urgent requirement of next generation antimalarials has been of recent interest due to the emergence of drug-resistant parasite. The genome-wide analysis of Plasmodium falciparum helicases revealed three RuvB proteins. Due to the presence of helicase motif I and II in PfRuvBs, there is a high probability that they contain ATPase and possibly helicase activity. The Plasmodium database has homologs of several key proteins that interact with RuvBs and are most likely involved in the cell cycle progression, chromatin remodeling, and other cellular activities. Phylogenetically PfRuvBs are closely related to Saccharomyces cerevisiae RuvB, which is essential for cell cycle progression and survival of yeast. Thus PfRuvBs can serve as potential drug target if they show an essential role in the survival of parasite.
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Affiliation(s)
- Moaz Ahmad
- Malaria Group; International Centre for Genetic Engineering and Biotechnology; New Delhi, India
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95
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Machado-Pinilla R, Liger D, Leulliot N, Meier UT. Mechanism of the AAA+ ATPases pontin and reptin in the biogenesis of H/ACA RNPs. RNA (NEW YORK, N.Y.) 2012; 18:1833-45. [PMID: 22923768 PMCID: PMC3446707 DOI: 10.1261/rna.034942.112] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The AAA+ ATPases pontin and reptin function in a staggering array of cellular processes including chromatin remodeling, transcriptional regulation, DNA damage repair, and assembly of macromolecular complexes, such as RNA polymerase II and small nucleolar (sno) RNPs. However, the molecular mechanism for all of these AAA+ ATPase associated activities is unknown. Here we document that, during the biogenesis of H/ACA RNPs (including telomerase), the assembly factor SHQ1 holds the pseudouridine synthase NAP57/dyskerin in a viselike grip, and that pontin and reptin (as components of the R2TP complex) are required to pry NAP57 from SHQ1. Significantly, the NAP57 domain captured by SHQ1 harbors most mutations underlying X-linked dyskeratosis congenita (X-DC) implicating the interface between the two proteins as a target of this bone marrow failure syndrome. Homing in on the essential first steps of H/ACA RNP biogenesis, our findings provide the first insight into the mechanism of action of pontin and reptin in the assembly of macromolecular complexes.
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Affiliation(s)
- Rosario Machado-Pinilla
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Dominique Liger
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université de Paris-Sud, CNRS-UMR8619, IFR115, 91405 Orsay Cedex, France
| | - Nicolas Leulliot
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, 75006 Paris, France
| | - U. Thomas Meier
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Corresponding authorE-mail
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96
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Goyal RK, Kumar V, Shukla V, Mattoo R, Liu Y, Chung SH, Giovannoni JJ, Mattoo AK. Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum). PLANTA 2012; 235:453-71. [PMID: 21947620 DOI: 10.1007/s00425-011-1518-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 09/05/2011] [Indexed: 05/03/2023]
Abstract
Physical clustering of genes has been shown in plants; however, little is known about gene clusters that have different functions, particularly those expressed in the tomato fruit. A class I 17.6 small heat shock protein (Sl17.6 shsp) gene was cloned and used as a probe to screen a tomato (Solanum lycopersicum) genomic library. An 8.3-kb genomic fragment was isolated and its DNA sequence determined. Analysis of the genomic fragment identified intronless open reading frames of three class I shsp genes (Sl17.6, Sl20.0, and Sl20.1), the Sl17.6 gene flanked by Sl20.1 and Sl20.0, with complete 5' and 3' UTRs. Upstream of the Sl20.0 shsp, and within the shsp gene cluster, resides a box C/D snoRNA cluster made of SlsnoR12.1 and SlU24a. Characteristic C and D, and C' and D', boxes are conserved in SlsnoR12.1 and SlU24a while the upstream flanking region of SlsnoR12.1 carries TATA box 1, homol-E and homol-D box-like cis sequences, TM6 promoter, and an uncharacterized tomato EST. Molecular phylogenetic analysis revealed that this particular arrangement of shsps is conserved in tomato genome but is distinct from other species. The intronless genomic sequence is decorated with cis elements previously shown to be responsive to cues from plant hormones, dehydration, cold, heat, and MYC/MYB and WRKY71 transcription factors. Chromosomal mapping localized the tomato genomic sequence on the short arm of chromosome 6 in the introgression line (IL) 6-3. Quantitative polymerase chain reaction analysis of gene cluster members revealed differential expression during ripening of tomato fruit, and relatively different abundances in other plant parts.
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Affiliation(s)
- Ravinder K Goyal
- US Department of Agriculture, The Henry A. Wallace Beltsville Agricultural Research Center, Agriculture Research Service, Beltsville, MD 20705-2350, USA
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97
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Zhai N, Zhao ZL, Cheng MB, Di YW, Yan HX, Cao CY, Dai H, Zhang Y, Shen YF. Human PIH1 associates with histone H4 to mediate the glucose-dependent enhancement of pre-rRNA synthesis. J Mol Cell Biol 2012; 4:231-41. [PMID: 22368283 DOI: 10.1093/jmcb/mjs003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ribosome biogenesis is critical in the growth of eukaryotic cells, in which the synthesis of precursor ribosomal RNA is the first and rate-limiting step. Here, we show that human PIH1 domain-containing protein 1 (PIH1) interacts directly with histone H4 and recruits the Brg1-SWI/SNF complex via SNF5 to human rRNA genes. This process is likely involved in PIH1-dependent DNase I-hypersensitive chromatin remodeling at the core promoter of the rRNA genes. PIH1 mediates the occupancy of not only the Brg1 complex but also the Pol I complex at the core promoter and enhances transcription initiation of rRNA genes. Additionally, the interaction between PIH1 and H4K16 expels TIP5, a component of the silencing nucleolar remodeling complex (NoRC), from the core region, suggesting that PIH1 is involved in the derepression of NoRC-silenced rRNA genes. These data indicate that PIH1 is a positive regulator of human rRNA genes and is of great importance for the recovery of human cells from nutrient starvation and the transition to glucose-induced exponential growth in vivo.
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Affiliation(s)
- Niu Zhai
- Department of Biochemistry and Molecular Biology, National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, 5 Dongdan Santiao, Beijing 100005, China
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98
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Boulon S, Bertrand E, Pradet-Balade B. HSP90 and the R2TP co-chaperone complex: building multi-protein machineries essential for cell growth and gene expression. RNA Biol 2012; 9:148-54. [PMID: 22418846 DOI: 10.4161/rna.18494] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
HSP90 (Heat Shock Protein 90) is an essential chaperone involved in the last folding steps of client proteins. It has many clients, and these are often recognized through specific adaptors. Recently, the conserved R2TP complex was identified as a key HSP90 co-chaperone. Current evidences indicate that the HSP90/R2TP system assembles multi-molecular protein complexes. Strikingly, these comprise basic machineries of gene expression: (1) nuclear RNA polymerases; (2) the snoRNPs, essential to produce ribosomes; and (3) mTOR Complex 1 and 2, which control translational activity and cell growth. Another important substrate is the telomerase RNP, required for continuous cell proliferation. We discuss here the assembly of RNA polymerases in bacteria and eukaryotes, the role of HSP90/R2TP in this process and in the assembly of snoRNPs and the PIKK family of TORC1 kinase. Finally, we speculate on the roles of R2TP as a master regulator of cell growth under normal or pathological conditions.
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Affiliation(s)
- Séverine Boulon
- Centre de Recherche de Biochimie Macromoléculaire, CNRS, Université Montpellier; Montpellier, France
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99
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Grandin N, Corset L, Charbonneau M. Genetic and physical interactions between Tel2 and the Med15 Mediator subunit in Saccharomyces cerevisiae. PLoS One 2012; 7:e30451. [PMID: 22291956 PMCID: PMC3265489 DOI: 10.1371/journal.pone.0030451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 12/16/2011] [Indexed: 11/23/2022] Open
Abstract
Background In budding yeast, the highly conserved Tel2 protein is part of several complexes and its main function is now believed to be in the biogenesis of phosphatidyl inositol 3-kinase related kinases. Principal Findings To uncover potentially novel functions of Tel2, we set out to isolate temperature-sensitive (ts) mutant alleles of TEL2 in order to perform genetic screenings. MED15/GAL11, a subunit of Mediator, a general regulator of transcription, was isolated as a suppressor of these mutants. The isolated tel2 mutants exhibited a short telomere phenotype that was partially rescued by MED15/GAL11 overexpression. The tel2-15mutant was markedly deficient in the transcription of EST2, coding for the catalytic subunit of telomerase, potentially explaining the short telomere phenotype of this mutant. In parallel, a two-hybrid screen identified an association between Tel2 and Rvb2, a highly conserved member of the AAA+ family of ATPases further found by in vivo co-immunoprecipitation to be tight and constitutive. Transiently overproduced Tel2 and Med15/Gal11 associated together, suggesting a potential role for Tel2 in transcription. Other Mediator subunits, as well as SUA7/TFIIB, also rescued the tel2-ts mutants. Significance Altogether, the present data suggest the existence of a novel role for Tel2, namely in transcription, possibly in cooperation with Rvb2 and involving the existence of physical interactions with the Med15/Gal11 Mediator subunit.
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Affiliation(s)
- Nathalie Grandin
- UMR CNRS 5239, Ecole Normale Supérieure de Lyon, IFR128 BioSciences Gerland, Lyon, France
- UMR CNRS 6239, Université de Tours, Tours, France
| | | | - Michel Charbonneau
- UMR CNRS 5239, Ecole Normale Supérieure de Lyon, IFR128 BioSciences Gerland, Lyon, France
- UMR CNRS 6239, Université de Tours, Tours, France
- * E-mail:
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100
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Activators of cylindrical proteases as antimicrobials: identification and development of small molecule activators of ClpP protease. ACTA ACUST UNITED AC 2012; 18:1167-78. [PMID: 21944755 DOI: 10.1016/j.chembiol.2011.07.023] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 06/28/2011] [Accepted: 07/13/2011] [Indexed: 11/22/2022]
Abstract
ClpP is a cylindrical serine protease whose ability to degrade proteins is regulated by the unfoldase ATP-dependent chaperones. ClpP on its own can only degrade small peptides. Here, we used ClpP as a target in a high-throughput screen for compounds, which activate the protease and allow it to degrade larger proteins, hence, abolishing the specificity arising from the ATP-dependent chaperones. Our screen resulted in five distinct compounds, which we designate as Activators of Self-Compartmentalizing Proteases 1 to 5 (ACP1 to 5). The compounds are found to stabilize the ClpP double-ring structure. The ACP1 chemical structure was considered to have drug-like characteristics and was further optimized to give analogs with bactericidal activity. Hence, the ACPs represent classes of compounds that can activate ClpP and that can be developed as potential novel antibiotics.
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