1
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Warnock JL, Ball JA, Najmi SM, Henes M, Vazquez A, Koshnevis S, Wieden HJ, Conn GL, Ghalei H. Differential roles of putative arginine fingers of AAA + ATPases Rvb1 and Rvb2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593962. [PMID: 38798342 PMCID: PMC11118528 DOI: 10.1101/2024.05.13.593962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The evolutionarily conserved AAA+ ATPases Rvb1 and Rvb2 proteins form a heteromeric complex (Rvb1/2) required for assembly or remodeling of macromolecular complexes in essential cellular processes ranging from chromatin remodeling to ribosome biogenesis. Rvb1 and Rvb2 have a high degree of sequence and structural similarity, and both contain the classical features of ATPases of their clade, including an N-terminal AAA+ subdomain with the Walker A motif, an insertion domain that typically interacts with various binding partners, and a C-terminal AAA+ subdomain containing a Walker B motif, the Sensor I and II motifs, and an arginine finger. In this study, we find that despite the high degree of structural similarity, Rvb1 and Rvb2 have distinct active sites that impact their activities and regulation within the Rvb1/2 complex. Using a combination of biochemical and genetic approaches, we show that replacing the homologous arginine fingers of Rvb1 and Rvb2 with different amino acids not only has distinct effects on the catalytic activity of the complex, but also impacts cell growth, and the Rvb1/2 interactions with binding partners. Using molecular dynamics simulations, we find that changes near the active site of Rvb1 and Rvb2 cause long-range effects on the protein dynamics in the insertion domain, suggesting a molecular basis for how enzymatic activity within the catalytic site of ATP hydrolysis can be relayed to other domains of the Rvb1/2 complex to modulate its function. Further, we show the impact that the arginine finger variants have on snoRNP biogenesis and validate the findings from molecular dynamics simulations using a targeted genetic screen. Together, our results reveal new aspects of the regulation of the Rvb1/2 complex by identifying a relay of long-range molecular communication from the ATPase active site of the complex to the binding site of cofactors. Most importantly, our findings suggest that despite high similarity and cooperation within the same protein complex, the two proteins have evolved with unique properties critical for the regulation and function of the Rvb1/2 complex.
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Affiliation(s)
- Jennifer L. Warnock
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Jacob A. Ball
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Saman M. Najmi
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Mina Henes
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
- Graduate Program in Biochemistry, Cell & Developmental Biology (BCDB), Emory University, Atlanta, Georgia, USA
- Medical Scientist Training Program, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Amanda Vazquez
- Department of Microbiology, Faculty of Science, University of Manitoba, Manitoba, Canada
| | - Sohail Koshnevis
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Hans-Joachim Wieden
- Department of Microbiology, Faculty of Science, University of Manitoba, Manitoba, Canada
| | - Graeme L. Conn
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Homa Ghalei
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
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2
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Herranz-Montoya I, Park S, Djouder N. A comprehensive analysis of prefoldins and their implication in cancer. iScience 2021; 24:103273. [PMID: 34761191 PMCID: PMC8567396 DOI: 10.1016/j.isci.2021.103273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Prefoldins (PFDNs) are evolutionary conserved co-chaperones, initially discovered in archaea but universally present in eukaryotes. PFDNs are prevalently organized into hetero-hexameric complexes. Although they have been overlooked since their discovery and their functions remain elusive, several reports indicate they act as co-chaperones escorting misfolded or non-native proteins to group II chaperonins. Unlike the eukaryotic PFDNs which interact with cytoskeletal components, the archaeal PFDNs can bind and stabilize a wide range of substrates, possibly due to their great structural diversity. The discovery of the unconventional RPB5 interactor (URI) PFDN-like complex (UPC) suggests that PFDNs have versatile functions and are required for different cellular processes, including an important role in cancer. Here, we summarize their functions across different species. Moreover, a comprehensive analysis of PFDNs genomic alterations across cancer types by using large-scale cancer genomic data indicates that PFDNs are a new class of non-mutated proteins significantly overexpressed in some cancer types.
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Affiliation(s)
- Irene Herranz-Montoya
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Solip Park
- Computational Cancer Genomics Group, Structural Biology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Nabil Djouder
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
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3
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Czekay DP, Kothe U. H/ACA Small Ribonucleoproteins: Structural and Functional Comparison Between Archaea and Eukaryotes. Front Microbiol 2021; 12:654370. [PMID: 33776984 PMCID: PMC7991803 DOI: 10.3389/fmicb.2021.654370] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 02/18/2021] [Indexed: 01/04/2023] Open
Abstract
During ribosome synthesis, ribosomal RNA is modified through the formation of many pseudouridines and methylations which contribute to ribosome function across all domains of life. In archaea and eukaryotes, pseudouridylation of rRNA is catalyzed by H/ACA small ribonucleoproteins (sRNPs) utilizing different H/ACA guide RNAs to identify target uridines for modification. H/ACA sRNPs are conserved in archaea and eukaryotes, as they share a common general architecture and function, but there are also several notable differences between archaeal and eukaryotic H/ACA sRNPs. Due to the higher protein stability in archaea, we have more information on the structure of archaeal H/ACA sRNPs compared to eukaryotic counterparts. However, based on the long history of yeast genetic and other cellular studies, the biological role of H/ACA sRNPs during ribosome biogenesis is better understood in eukaryotes than archaea. Therefore, this review provides an overview of the current knowledge on H/ACA sRNPs from archaea, in particular their structure and function, and relates it to our understanding of the roles of eukaryotic H/ACA sRNP during eukaryotic ribosome synthesis and beyond. Based on this comparison of our current insights into archaeal and eukaryotic H/ACA sRNPs, we discuss what role archaeal H/ACA sRNPs may play in the formation of ribosomes.
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Affiliation(s)
- Dominic P Czekay
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
| | - Ute Kothe
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
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4
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Wang R, Li X, Sun C, Yu L, Hua D, Shi C, Wang Q, Rao C, Luo W, Jiang Z, Zhou X, Yu S. The ATPase Pontin is a key cell cycle regulator by amplifying E2F1 transcription response in glioma. Cell Death Dis 2021; 12:141. [PMID: 33542204 PMCID: PMC7862657 DOI: 10.1038/s41419-021-03421-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 01/20/2023]
Abstract
Pontin (RUVBL1) is a highly conserved ATPase of the AAA + (ATPases Associated with various cellular Activities) superfamily and is implicated in various biological processes crucial for oncogenesis. Its overexpression is observed in multiple human cancers, whereas the relevance of Pontin to gliomagenesis remains obscure. To gain insights into Pontin involvement in glioma, we performed bioinformatics analyses of Pontin co-expressed genes, Pontin-affected genes, and carried out experimental studies. The results verified that Pontin was upregulated in gliomas. Its higher levels might predict the worse prognosis of glioma patients. The Pontin co-expressed genes were functionally enriched in cell cycle progression and RNA processing. In the nucleus, Pontin promoted cell growth via facilitating cell cycle progression. Using RNA-seq, we found that Pontin knockdown resulted in altered expression of multiple genes, among which the E2F1 targets accounted for a large proportion. Mechanistic studies found that Pontin interacted with E2F1 and markedly amplified the E2F1 transcription response in an ATPase domain-dependent manner. By analyzing the RNA-seq data, we also found that Pontin could impact on the alternative splicing (AS). Both differential expressed genes and AS events affected by Pontin were associated with cell cycle regulation. Taken together, our findings provide novel insights of the importance of Pontin in gliomagenesis by regulating cell cycle and AS, and shed light on the possible application of Pontin as an antineoplastic target in glioma.
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Affiliation(s)
- Run Wang
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Xuebing Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Cuiyun Sun
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Lin Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences of Tianjin Medical University, Tianjin, China
| | - Dan Hua
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Cuijuan Shi
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Qian Wang
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Chun Rao
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Wenjun Luo
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Zhendong Jiang
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China.,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China
| | - Xuexia Zhou
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China. .,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China. .,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China.
| | - Shizhu Yu
- Department of Neuropathology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China. .,Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin, China. .,Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin, China.
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5
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Ojha S, Malla S, Lyons SM. snoRNPs: Functions in Ribosome Biogenesis. Biomolecules 2020; 10:biom10050783. [PMID: 32443616 PMCID: PMC7277114 DOI: 10.3390/biom10050783] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/10/2020] [Accepted: 05/13/2020] [Indexed: 01/18/2023] Open
Abstract
Ribosomes are perhaps the most critical macromolecular machine as they are tasked with carrying out protein synthesis in cells. They are incredibly complex structures composed of protein components and heavily chemically modified RNAs. The task of assembling mature ribosomes from their component parts consumes a massive amount of energy and requires greater than 200 assembly factors. Among the most critical of these are small nucleolar ribonucleoproteins (snoRNPs). These are small RNAs complexed with diverse sets of proteins. As suggested by their name, they localize to the nucleolus, the site of ribosome biogenesis. There, they facilitate multiple roles in ribosomes biogenesis, such as pseudouridylation and 2′-O-methylation of ribosomal (r)RNA, guiding pre-rRNA processing, and acting as molecular chaperones. Here, we reviewed their activity in promoting the assembly of ribosomes in eukaryotes with regards to chemical modification and pre-rRNA processing.
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Affiliation(s)
- Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Sulochan Malla
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Shawn M. Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
- The Genome Science Institute, Boston University School of Medicine, Boston, MA 02115, USA
- Correspondence: ; Tel.: +1-617-358-4280
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6
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Yeast R2TP Interacts with Extended Termini of Client Protein Nop58p. Sci Rep 2019; 9:20228. [PMID: 31882871 PMCID: PMC6934851 DOI: 10.1038/s41598-019-56712-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/13/2019] [Indexed: 01/15/2023] Open
Abstract
The AAA + ATPase R2TP complex facilitates assembly of a number of ribonucleoprotein particles (RNPs). Although the architecture of R2TP is known, its molecular basis for acting upon multiple RNPs remains unknown. In yeast, the core subunit of the box C/D small nucleolar RNPs, Nop58p, is the target for R2TP function. In the recently observed U3 box C/D snoRNP as part of the 90 S small subunit processome, the unfolded regions of Nop58p are observed to form extensive interactions, suggesting a possible role of R2TP in stabilizing the unfolded region of Nop58p prior to its assembly. Here, we analyze the interaction between R2TP and a Maltose Binding Protein (MBP)-fused Nop58p by biophysical and yeast genetics methods. We present evidence that R2TP interacts largely with the unfolded termini of Nop58p. Our results suggest a general mechanism for R2TP to impart specificity by recognizing unfolded regions in its clients.
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7
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Iacovella MG, Bremang M, Basha O, Giacò L, Carotenuto W, Golfieri C, Szakal B, Dal Maschio M, Infantino V, Beznoussenko GV, Joseph CR, Visintin C, Mironov AA, Visintin R, Branzei D, Ferreira-Cerca S, Yeger-Lotem E, De Wulf P. Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae. Nucleic Acids Res 2019; 46:7586-7611. [PMID: 30011030 PMCID: PMC6125641 DOI: 10.1093/nar/gky618] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/28/2018] [Indexed: 12/14/2022] Open
Abstract
The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subunit biogenesis and has not been characterized globally. We show that Rio1 manages directly and via a series of regulators, an essential signaling network at the protein, chromatin and RNA levels. Rio1 orchestrates growth and division depending on resource availability, in parallel to the nutrient-activated Tor1 kinase. To define the Rio1 network, we identified its physical interactors, profiled its target genes/transcripts, mapped its chromatin-binding sites and integrated our data with yeast’s protein–protein and protein–DNA interaction catalogs using network computation. We experimentally confirmed network components and localized Rio1 also to mitochondria and vacuoles. Via its network, Rio1 commands protein synthesis (ribosomal gene expression, assembly and activity) and turnover (26S proteasome expression), and impinges on metabolic, energy-production and cell-cycle programs. We find that Rio1 activity is conserved to humans and propose that pathological RIOK1 may fuel promiscuous transcription, ribosome production, chromosomal instability, unrestrained metabolism and proliferation; established contributors to cancer. Our study will advance the understanding of numerous processes, here revealed to depend on Rio1 activity.
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Affiliation(s)
- Maria G Iacovella
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Current address: Proteome Sciences Plc, Hamilton House, Mabledon Place, London, United Kingdom
| | - Omer Basha
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, POB 653, Beer-Sheva 84105, Israel
| | - Luciano Giacò
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Walter Carotenuto
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Cristina Golfieri
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Barnabas Szakal
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Marianna Dal Maschio
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Valentina Infantino
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Galina V Beznoussenko
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Chinnu R Joseph
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Clara Visintin
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Alexander A Mironov
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Rosella Visintin
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Dana Branzei
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Sébastien Ferreira-Cerca
- Lehrstuhl für Biochemie III, Universität Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Esti Yeger-Lotem
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, POB 653, Beer-Sheva 84105, Israel
| | - Peter De Wulf
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
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8
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Lynham J, Houry WA. The Multiple Functions of the PAQosome: An R2TP- and URI1 Prefoldin-Based Chaperone Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1106:37-72. [DOI: 10.1007/978-3-030-00737-9_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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9
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Pontin/Tip49 negatively regulates JNK-mediated cell death in Drosophila. Cell Death Discov 2018; 4:8. [PMID: 30062057 PMCID: PMC6060144 DOI: 10.1038/s41420-018-0074-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 06/12/2018] [Indexed: 01/02/2023] Open
Abstract
Pontin (Pont), also known as Tip49, encodes a member of the AAA+ (ATPases Associated with Diverse Cellular Activities) superfamily and plays pivotal roles in cell proliferation and growth, yet its function in cell death has remained poorly understood. Here we performed a genetic screen for dominant modifiers of Eiger-induced JNK-dependent cell death in Drosophila, and identified Pont as a negative regulator of JNK-mediated cell death. In addition, loss of function of Pont is sufficient to induce cell death and activate the transcription of JNK target gene puc. Furthermore, the epistasis analysis indicates that Pont acts downstream of Hep. Finally, we found that Pont is also required for JNK-mediated thorax development and acts as a negative regulator of JNK phosphorylation. Together, our data suggest that pont encodes a negative component of Egr/JNK signaling pathway in Drosophila through negatively regulating JNK phosphorylation, which provides a novel role of ATPase in Egr-JNK signaling.
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10
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Terns MP, Terns RM. Small nucleolar RNAs: versatile trans-acting molecules of ancient evolutionary origin. Gene Expr 2018; 10:17-39. [PMID: 11868985 PMCID: PMC5977530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The small nucleolar RNAs (snoRNAs) are an abundant class of trans-acting RNAs that function in ribosome biogenesis in the eukaryotic nucleolus. Elegant work has revealed that most known snoRNAs guide modification of pre-ribosomal RNA (pre-rRNA) by base pairing near target sites. Other snoRNAs are involved in cleavage of pre-rRNA by mechanisms that have not yet been detailed. Moreover, our appreciation of the cellular roles of the snoRNAs is expanding with new evidence that snoRNAs also target modification of small nuclear RNAs and messenger RNAs. Many snoRNAs are produced by unorthodox modes of biogenesis including salvage from introns of pre-mRNAs. The recent discovery that homologs of snoRNAs as well as associated proteins exist in the domain Archaea indicates that the RNA-guided RNA modification system is of ancient evolutionary origin. In addition, it has become clear that the RNA component of vertebrate telomerase (an enzyme implicated in cancer and cellular senescence) is related to snoRNAs. During its evolution, vertebrate telomerase RNA appears to have co-opted a snoRNA domain that is essential for the function of telomerase RNA in vivo. The unique properties of snoRNAs are now being harnessed for basic research and therapeutic applications.
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MESH Headings
- Animals
- Base Pairing
- Biological Transport
- Cell Nucleolus/metabolism
- Cell Nucleus/metabolism
- Eukaryotic Cells/metabolism
- Evolution, Molecular
- Methylation
- Prokaryotic Cells/metabolism
- Pseudouridine/metabolism
- RNA/metabolism
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA, Archaeal/genetics
- RNA, Archaeal/physiology
- RNA, Catalytic/metabolism
- RNA, Messenger/metabolism
- RNA, Ribosomal/biosynthesis
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/classification
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA, Small Nucleolar/physiology
- Ribonucleoproteins, Small Nucleolar/metabolism
- Ribosomes/metabolism
- Species Specificity
- Structure-Activity Relationship
- Telomerase/metabolism
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Affiliation(s)
- Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens 30602, USA.
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11
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de Los Santos-Velázquez AI, de Oya IG, Manzano-López J, Monje-Casas F. Late rDNA Condensation Ensures Timely Cdc14 Release and Coordination of Mitotic Exit Signaling with Nucleolar Segregation. Curr Biol 2017; 27:3248-3263.e5. [PMID: 29056450 DOI: 10.1016/j.cub.2017.09.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/16/2017] [Accepted: 09/13/2017] [Indexed: 12/28/2022]
Abstract
The nucleolus plays a pivotal role in multiple key cellular processes. An illustrative example is the regulation of mitotic exit in Saccharomyces cerevisiae through the nucleolar sequestration of the Cdc14 phosphatase. The peculiar structure of the nucleolus, however, has also its drawbacks. The repetitive nature of the rDNA gives rise to cohesion-independent linkages whose resolution in budding yeast requires the Cdc14-dependent inhibition of rRNA transcription, which facilitates condensin accessibility to this locus. Thus, the rDNA condenses and segregates later than most other yeast genomic regions. Here, we show that defective function of a small nucleolar ribonucleoprotein particle (snoRNP) assembly factor facilitates condensin accessibility to the rDNA and induces nucleolar hyper-condensation. Interestingly, this increased compaction of the nucleolus interferes with the proper release of Cdc14 from this organelle. This observation provides an explanation for the delayed rDNA condensation in budding yeast, which is necessary to efficiently coordinate timely Cdc14 release and mitotic exit with nucleolar compaction and segregation.
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Affiliation(s)
- Ana Isabel de Los Santos-Velázquez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC), University of Seville, and University Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - Inés G de Oya
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC), University of Seville, and University Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - Javier Manzano-López
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC), University of Seville, and University Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - Fernando Monje-Casas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Spanish National Research Council (CSIC), University of Seville, and University Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain.
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12
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Rothé B, Manival X, Rolland N, Charron C, Senty-Ségault V, Branlant C, Charpentier B. Implication of the box C/D snoRNP assembly factor Rsa1p in U3 snoRNP assembly. Nucleic Acids Res 2017; 45:7455-7473. [PMID: 28505348 PMCID: PMC5499572 DOI: 10.1093/nar/gkx424] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/02/2017] [Indexed: 01/23/2023] Open
Abstract
The U3 box C/D snoRNA is one key element of 90S pre-ribosome. It contains a 5΄ domain pairing with pre-rRNA and the U3B/C and U3C΄/D motifs for U3 packaging into a unique small nucleolar ribonucleoprotein particle (snoRNP). The RNA-binding protein Snu13/SNU13 nucleates on U3B/C the assembly of box C/D proteins Nop1p/FBL and Nop56p/NOP56, and the U3-specific protein Rrp9p/U3-55K. Snu13p/SNU13 has a much lower affinity for U3C΄/D but nevertheless forms on this motif an RNP with box C/D proteins Nop1p/FBL and Nop58p/NOP58. In this study, we characterized the influence of the RNP assembly protein Rsa1 in the early steps of U3 snoRNP biogenesis in yeast and we propose a refined model of U3 snoRNP biogenesis. While recombinant Snu13p enhances the binding of Rrp9p to U3B/C, we observed that Rsa1p has no effect on this activity but forms with Snu13p and Rrp9p a U3B/C pre-RNP. In contrast, we found that Rsa1p enhances Snu13p binding on U3C΄/D. RNA footprinting experiments indicate that this positive effect most likely occurs by direct contacts of Rsa1p with the U3 snoRNA 5΄ domain. In light of the recent U3 snoRNP cryo-EM structures, our data suggest that Rsa1p has a dual role by also preventing formation of a pre-mature functional U3 RNP.
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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, BP 20199, 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, BP 20199, 54505 Vandœuvre-lès-Nancy, France
| | - Nicolas Rolland
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, BP 20199, 54505 Vandœuvre-lès-Nancy, France
| | - Christophe Charron
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, BP 20199, 54505 Vandœuvre-lès-Nancy, France
| | - Véronique Senty-Ségault
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, BP 20199, 54505 Vandœuvre-lès-Nancy, 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, BP 20199, 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, BP 20199, 54505 Vandœuvre-lès-Nancy, France
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13
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Tian S, Yu G, He H, Zhao Y, Liu P, Marshall AG, Demeler B, Stagg SM, Li H. Pih1p-Tah1p Puts a Lid on Hexameric AAA+ ATPases Rvb1/2p. Structure 2017; 25:1519-1529.e4. [PMID: 28919439 PMCID: PMC6625358 DOI: 10.1016/j.str.2017.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/11/2017] [Accepted: 08/07/2017] [Indexed: 11/21/2022]
Abstract
The Saccharomyces cerevisiae (Sc) R2TP complex affords an Hsp90-mediated and nucleotide-driven chaperone activity to proteins of small ribonucleoprotein particles (snoRNPs). The current lack of structural information on the ScR2TP complex, however, prevents a mechanistic understanding of this biological process. We characterized the structure of the ScR2TP complex made up of two AAA+ ATPases, Rvb1/2p, and two Hsp90 binding proteins, Tah1p and Pih1p, and its interaction with the snoRNP protein Nop58p by a combination of analytical ultracentrifugation, isothermal titration calorimetry, chemical crosslinking, hydrogen-deuterium exchange, and cryoelectron microscopy methods. We find that Pih1p-Tah1p interacts with Rvb1/2p cooperatively through the nucleotide-sensitive domain of Rvb1/2p. Nop58p further binds Pih1p-Tahp1 on top of the dome-shaped R2TP. Consequently, nucleotide binding releases Pih1p-Tah1p from Rvb1/2p, which offers a mechanism for nucleotide-driven binding and release of snoRNP intermediates.
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Affiliation(s)
- Shaoxiong Tian
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Ge Yu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Huan He
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Yu Zhao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Peilu Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Ion Cyclotron Resonance Program, The National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Scott M Stagg
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hong Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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14
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Massenet S, Bertrand E, Verheggen C. Assembly and trafficking of box C/D and H/ACA snoRNPs. RNA Biol 2017; 14:680-692. [PMID: 27715451 PMCID: PMC5519232 DOI: 10.1080/15476286.2016.1243646] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/09/2016] [Accepted: 09/27/2016] [Indexed: 12/23/2022] Open
Abstract
Box C/D and box H/ACA snoRNAs are abundant non-coding RNAs that localize in the nucleolus and mostly function as guides for nucleotide modifications. While a large pool of snoRNAs modifies rRNAs, an increasing number of snoRNAs could also potentially target mRNAs. ScaRNAs belong to a family of specific RNAs that localize in Cajal bodies and that are structurally similar to snoRNAs. Most scaRNAs are involved in snRNA modification, while telomerase RNA, which contains H/ACA motifs, functions in telomeric DNA synthesis. In this review, we describe how box C/D and H/ACA snoRNAs are processed and assembled with core proteins to form functional RNP particles. Their biogenesis involve several transport factors that first direct pre-snoRNPs to Cajal bodies, where some processing steps are believed to take place, and then to nucleoli. Assembly of core proteins involves the HSP90/R2TP chaperone-cochaperone system for both box C/D and H/ACA RNAs, but also several factors specific for each family. These assembly factors chaperone unassembled core proteins, regulate the formation and disassembly of pre-snoRNP intermediates, and control the activity of immature particles. The AAA+ ATPase RUVBL1 and RUVBL2 belong to the R2TP co-chaperones and play essential roles in snoRNP biogenesis, as well as in the formation of other macro-molecular complexes. Despite intensive research, their mechanisms of action are still incompletely understood.
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Affiliation(s)
- Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS, 9 Avenue de la forêt de Haye, 54505 Vandoeuvre-les-Nancy Cedex, France, Université de Lorraine, Campus Biologie –Santé, CS 50184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France, Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Céline Verheggen
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France, Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
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15
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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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16
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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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17
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Abstract
In this review, Schmidt and Cech cover human telomerase biogenesis, trafficking, and activation, comparing key aspects with the analogous events in other species. Telomerase is the ribonucleoprotein enzyme that catalyzes the extension of telomeric DNA in eukaryotes. Recent work has begun to reveal key aspects of the assembly of the human telomerase complex, its intracellular trafficking involving Cajal bodies, and its recruitment to telomeres. Once telomerase has been recruited to the telomere, it appears to undergo a separate activation step, which may include an increase in its repeat addition processivity. This review covers human telomerase biogenesis, trafficking, and activation, comparing key aspects with the analogous events in other species.
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Affiliation(s)
- Jens C Schmidt
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Thomas R Cech
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, USA
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18
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Bizarro J, Dodré M, Huttin A, Charpentier B, Schlotter F, Branlant C, Verheggen C, Massenet S, Bertrand E. NUFIP and the HSP90/R2TP chaperone bind the SMN complex and facilitate assembly of U4-specific proteins. Nucleic Acids Res 2015; 43:8973-89. [PMID: 26275778 PMCID: PMC4605303 DOI: 10.1093/nar/gkv809] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/27/2015] [Indexed: 12/17/2022] Open
Abstract
The Sm proteins are loaded on snRNAs by the SMN complex, but how snRNP-specific proteins are assembled remains poorly characterized. U4 snRNP and box C/D snoRNPs have structural similarities. They both contain the 15.5K and proteins with NOP domains (PRP31 for U4, NOP56/58 for snoRNPs). Biogenesis of box C/D snoRNPs involves NUFIP and the HSP90/R2TP chaperone system and here, we explore the function of this machinery in U4 RNP assembly. We show that yeast Prp31 interacts with several components of the NUFIP/R2TP machinery, and that these interactions are separable from each other. In human cells, PRP31 mutants that fail to stably associate with U4 snRNA still interact with components of the NUFIP/R2TP system, indicating that these interactions precede binding of PRP31 to U4 snRNA. Knock-down of NUFIP leads to mislocalization of PRP31 and decreased association with U4. Moreover, NUFIP is associated with the SMN complex through direct interactions with Gemin3 and Gemin6. Altogether, our data suggest a model in which the NUFIP/R2TP system is connected with the SMN complex and facilitates assembly of U4 snRNP-specific proteins.
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Affiliation(s)
- Jonathan Bizarro
- Equipe labélisée Ligue contre le Cancer, Institut de Génétique Moléculaire de Montpellier, IGMM-UMR 5535 du CNRS-Université de Montpellier, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - Maxime Dodré
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Alexandra Huttin
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Florence Schlotter
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Céline Verheggen
- Equipe labélisée Ligue contre le Cancer, Institut de Génétique Moléculaire de Montpellier, IGMM-UMR 5535 du CNRS-Université de Montpellier, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Edouard Bertrand
- Equipe labélisée Ligue contre le Cancer, Institut de Génétique Moléculaire de Montpellier, IGMM-UMR 5535 du CNRS-Université de Montpellier, 1919, route de Mende, 34293 Montpellier Cedex 5, France
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19
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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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20
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Lakomek K, Stoehr G, Tosi A, Schmailzl M, Hopfner KP. Structural basis for dodecameric assembly states and conformational plasticity of the full-length AAA+ ATPases Rvb1 · Rvb2. Structure 2015; 23:483-495. [PMID: 25661652 DOI: 10.1016/j.str.2014.12.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/14/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
Abstract
As building blocks of diverse macromolecular complexes, the AAA+ ATPases Rvb1 and Rvb2 are crucial for many cellular activities including cancer-related processes. Their oligomeric structure and function remain unclear. We report the crystal structures of full-length heteromeric Rvb1·Rvb2 complexes in distinct nucleotide binding states. Chaetomium thermophilum Rvb1·Rvb2 assemble into hexameric rings of alternating molecules and into stable dodecamers. Intriguingly, the characteristic oligonucleotide-binding (OB) fold domains (DIIs) of Rvb1 and Rvb2 occupy unequal places relative to the compact AAA+ core ring. While Rvb1's DII forms contacts between hexamers, Rvb2's DII is rotated 100° outward, occupying lateral positions. ATP was retained bound to Rvb1 but not Rvb2 throughout purification, suggesting nonconcerted ATPase activities and nucleotide binding. Significant conformational differences between nucleotide-free and ATP-/ADP-bound states in the crystal structures and in solution suggest that the functional role of Rvb1·Rvb2 is mediated by highly interconnected structural switches. Our structures provide an atomic framework for dodecameric states and Rvb1·Rvb2's conformational plasticity.
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Affiliation(s)
- Kristina Lakomek
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Gabriele Stoehr
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Alessandro Tosi
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Monika Schmailzl
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Karl-Peter Hopfner
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians University Munich, 81377 Munich, Germany; Center for Integrated Protein Sciences, Ludwig-Maximilians University Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
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21
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Kakihara Y, Saeki M. The R2TP chaperone complex: its involvement in snoRNP assembly and tumorigenesis. Biomol Concepts 2014; 5:513-20. [DOI: 10.1515/bmc-2014-0028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/11/2014] [Indexed: 01/07/2023] Open
Abstract
AbstractR2TP was originally identified in yeast Saccharomyces cerevisiae as Hsp90 interacting complex, and is composed of four different proteins: Rvb1, Rvb2, Tah1, and Pih1. This complex is well-conserved in eukaryotes, and is involved in many cellular processes such as snoRNP biogenesis, RNA polymerase assembly, PIKK signaling, and apoptosis. An increasing number of research related to R2TP suggests a linkage of its function with tumorigenesis. In this review, we provide an overview of several recent studies on R2TP that are related to cell proliferation and carcinogenesis, and propose a possible role of R2TP in tumorigenesis through regulating snoRNA/snoRNP biogenesis.
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Affiliation(s)
- Yoshito Kakihara
- 1Division of Dental Pharmacology, Department of Dentistry, Niigata University, 2-5274 Gakkocho-dori, Chuo-ku, Niigata, 951-8514, Japan
| | - Makio Saeki
- 1Division of Dental Pharmacology, Department of Dentistry, Niigata University, 2-5274 Gakkocho-dori, Chuo-ku, Niigata, 951-8514, Japan
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22
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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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23
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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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24
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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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25
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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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26
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Nallar SC, Kalvakolanu DV. Regulation of snoRNAs in cancer: close encounters with interferon. J Interferon Cytokine Res 2013; 33:189-98. [PMID: 23570385 DOI: 10.1089/jir.2012.0106] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The interferon (IFN) family of cytokines regulates many cellular processes, such as transcription, translation, post-translational modifications, and protein degradation. IFNs induce growth inhibition and/or cell death, depending on the cell type, by employing different proteins. This review describes a novel growth-suppressive pathway employed by IFNs that affects rRNA levels. Maturation of rRNA involves numerous noncoding small regulatory RNA-guided processes. These regulatory RNAs, called small nucleolar RNA (snoRNAs), function as a ribonucleoprotein particle (RNP) in the nucleolus. The biogenesis of snoRNPs is dependent on core protein and assembly factors. Our laboratory recently isolated a growth-suppressive protein gene associated with retinoid-IFN-induced mortality (GRIM)-1 using a genetic screen. IFN-inducible GRIM-1 (SHQ1) is an assembly factor that controls one arm of the snoRNP machinery. GRIM-1 inhibits sno/scaRNP formation to induce growth suppression via reduction in mature rRNA levels. Loss of GRIM-1 observed in certain cancers implicates it to be a novel tumor suppressor. Certain snoRNAs have been reported to act as either oncogenes or tumor suppressors in vitro. Recent studies have shown that certain sno/scaRNAs are further processed into micro RNA-like molecules to control translation of protein-coding RNAs. We present a model as to how these small regulatory RNAs influence cell growth and a potential role for GRIM-1 in this process.
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Affiliation(s)
- Shreeram C Nallar
- Department of Microbiology & Immunology, Greenebaum Cancer Center, University of Maryland School of Medicine , Baltimore, MD 21201, USA
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27
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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: 10] [Impact Index Per Article: 0.9] [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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28
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Reptin/Ruvbl2 is a Lrrc6/Seahorse interactor essential for cilia motility. Proc Natl Acad Sci U S A 2013; 110:12697-702. [PMID: 23858445 DOI: 10.1073/pnas.1300968110] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is an autosomal recessive disease caused by defective cilia motility. The identified PCD genes account for about half of PCD incidences and the underlying mechanisms remain poorly understood. We demonstrate that Reptin/Ruvbl2, a protein known to be involved in epigenetic and transcriptional regulation, is essential for cilia motility in zebrafish. We further show that Reptin directly interacts with the PCD protein Lrrc6/Seahorse and this interaction is critical for the in vivo function of Lrrc6/Seahorse in zebrafish. Moreover, whereas the expression levels of multiple dynein arm components remain unchanged or become elevated, the density of axonemal dynein arms is reduced in reptin(hi2394) mutants. Furthermore, Reptin is highly enriched in the cytosol and colocalizes with Lrrc6/Seahorse. Combined, these results suggest that the Reptin-Lrrc6/Seahorse complex is involved in dynein arm formation. We also show that although the DNA damage response is induced in reptin(hi2394) mutants, it remains unchanged in cilia biogenesis mutants and lrrc6/seahorse mutants, suggesting that increased DNA damage response is not intrinsic to ciliary defects and that in vertebrate development, Reptin functions in multiple processes, both cilia specific and cilia independent.
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29
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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: 72] [Impact Index Per Article: 6.5] [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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30
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Schubert T, Längst G. Changes in higher order structures of chromatin by RNP complexes. RNA Biol 2013; 10:175-9. [PMID: 23353578 DOI: 10.4161/rna.23175] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
More than four decades ago, it was shown that RNA stably associates with chromatin. These studies indicated that chromatin-associated RNAs (caRNA) might be involved in the organization of chromatin structure. However, it is only recently that pools of chromatin-associated RNAs were characterized and functional studies were initiated. In Drosophila cells, an RNP complex consisting of snoRNAs and Decondensation factor 31 (Df31) is stably tethered to chromatin, mediated by the RNA- and histone-binding activities of Df31. Biochemical and functional characterizations suggest a structural role of this complex in chromatin organization. The binding of the Df31-snoRNA complex to chromatin results in the opening and the maintenance of accessible higher order structures of chromatin. We suggest that different classes of chromatin-associated RNPs are required for the targeted opening of higher order structures of chromatin, enabling the activation of DNA-dependent processes such as transcription.
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Affiliation(s)
- Thomas Schubert
- Institut für Biochemie III, Universität Regensburg, Regensburg, Germany
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31
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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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32
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Grigoletto A, Neaud V, Allain-Courtois N, Lestienne P, Rosenbaum J. The ATPase activity of reptin is required for its effects on tumor cell growth and viability in hepatocellular carcinoma. Mol Cancer Res 2012; 11:133-9. [PMID: 23233483 DOI: 10.1158/1541-7786.mcr-12-0455] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Reptin is overexpressed in most human hepatocellular carcinomas. Reptin is involved in chromatin remodeling, transcription regulation, or supramolecular complexes assembly. Its silencing leads to growth arrest and apoptosis in cultured hepatocellular carcinoma cells and stops hepatocellular carcinoma progression in xenografts. Reptin has an ATPase activity linked to Walker A and B domains. It is unclear whether every Reptin function depends on its ATPase activity. Here, we expressed Walker B ATPase-dead mutants (D299N or E300G) in hepatocellular carcinoma cells in the presence of endogenous Reptin. Then, we silenced endogenous Reptin and substituted it with siRNA-resistant wild-type (WT) or Flag-Reptin mutants. There was a significant decrease in cell growth when expressing either mutant in the presence of endogenous Reptin, revealing a dominant negative effect of the ATPase dead mutants on hepatocellular carcinoma cell growth. Substitution of endogenous Reptin by WT Flag-Reptin rescued cell growth of HuH7. On the other hand, substitution by Flag-Reptin D299N or E300G led to cell growth arrest. Similar results were seen with Hep3B cells. Reptin silencing in HuH7 cells led to an increased apoptotic cell death, which was prevented by WT Flag-Reptin but not by the D299N mutant. These data show that Reptin functions relevant for cancer are dependent on its ATPase activity, and suggest that antagonists of Reptin ATPase activity may be useful as anticancer agents.
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Affiliation(s)
- Aude Grigoletto
- INSERM U1053, Université Bordeaux Segalen, 146 rue Léo Saignat, 33076 Bordeaux cedex, France
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33
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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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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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Schubert T, Pusch MC, Diermeier S, Benes V, Kremmer E, Imhof A, Längst G. Df31 protein and snoRNAs maintain accessible higher-order structures of chromatin. Mol Cell 2012; 48:434-44. [PMID: 23022379 DOI: 10.1016/j.molcel.2012.08.021] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 07/02/2012] [Accepted: 08/07/2012] [Indexed: 12/13/2022]
Abstract
Packaging of DNA into nucleosomes and the formation of higher-order chromatin structures determine DNA accessibility and activity of genome domains. We identified an RNA-dependent mechanism maintaining the open chromatin structure within euchromatic regions in Drosophila cells. The mechanism of reversible chromatin opening, reconstituted in vitro, depends on the Drosophila decondensation factor 31 (Df31) that specifically binds to RNA and localizes to euchromatic regions. Df31 is capable to tether a heterogeneous pool of short, single-stranded RNAs to chromatin. This class of chromatin-associated RNA (caRNA) is stably linked to chromatin and is largely composed of snoRNAs, which are preferentially bound by Df31. We suggest that the Df31-mediated linkage of snoRNAs and chromatin, forms a RNA-chromatin network resulting in the establishment of open chromatin domains. Analysis of caRNAs in human cells also reveals a strong enrichment of snoRNAs, implying a conserved role for these molecules in higher-order structures of chromatin.
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Affiliation(s)
- Thomas Schubert
- Institut für Biochemie III, Universität Regensburg, Universitätsstrasse 31. 93053 Regensburg, Germany
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Novel RuvB nuclear ATPase is specific to intraerythrocytic mitosis during schizogony of Plasmodium falciparum. Mol Biochem Parasitol 2012; 185:58-65. [DOI: 10.1016/j.molbiopara.2012.06.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 06/01/2012] [Accepted: 06/06/2012] [Indexed: 12/17/2022]
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First identification of small-molecule inhibitors of Pontin by combining virtual screening and enzymatic assay. Biochem J 2012; 443:549-59. [PMID: 22273052 DOI: 10.1042/bj20111779] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The human protein Pontin, which belongs to the AAA+ (ATPases associated with various cellular activities) family, is overexpressed in several cancers and its silencing in vitro leads to tumour cell growth arrest and apoptosis, making it a good target for cancer therapy. In particular, high levels of expression were found in hepatic tumours for which the therapeutic arsenal is rather limited. The three-dimensional structure of Pontin has been resolved previously, revealing a hexameric assembly with one ADP molecule co-crystallized in each subunit. Using Vina, DrugScore and Xscore, structure-based virtual screening of 2200 commercial molecules was conducted into the ATP-binding site formed by a dimer of Pontin in order to prioritize the best candidates. Complementary to the in silico screening, a versatile and sensitive colorimetric assay was set up to measure the disruption of the ATPase activity of Pontin. This assay allowed the determination of inhibition curves for more than 20 top-scoring compounds, resulting in the identification of four ligands presenting an inhibition constant in the micromolar concentration range. Three of them inhibited tumour cell proliferation. The association of virtual screening and experimental assay thus proved successful for the discovery of the first small-molecule inhibitors of Pontin.
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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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Kakihara Y, Houry WA. The R2TP complex: Discovery and functions. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:101-7. [DOI: 10.1016/j.bbamcr.2011.08.016] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 08/30/2011] [Accepted: 08/30/2011] [Indexed: 10/17/2022]
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40
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Franzosa EA, Albanèse V, Frydman J, Xia Y, McClellan AJ. Heterozygous yeast deletion collection screens reveal essential targets of Hsp90. PLoS One 2011; 6:e28211. [PMID: 22140548 PMCID: PMC3227642 DOI: 10.1371/journal.pone.0028211] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 11/03/2011] [Indexed: 02/01/2023] Open
Abstract
Hsp90 is an essential eukaryotic chaperone with a role in folding specific “client” proteins such as kinases and hormone receptors. Previously performed homozygous diploid yeast deletion collection screens uncovered broad requirements for Hsp90 in cellular transport and cell cycle progression. These screens also revealed that the requisite cellular functions of Hsp90 change with growth temperature. We present here for the first time the results of heterozygous deletion collection screens conducted at the hypothermic stress temperature of 15°C. Extensive bioinformatic analyses were performed on the resulting data in combination with data from homozygous and heterozygous screens previously conducted at normal (30°C) and hyperthermic stress (37°C) growth temperatures. Our resulting meta-analysis uncovered extensive connections between Hsp90 and (1) general transcription, (2) ribosome biogenesis and (3) GTP binding proteins. Predictions from bioinformatic analyses were tested experimentally, supporting a role for Hsp90 in ribosome stability. Importantly, the integrated analysis of the 15°C heterozygous deletion pool screen with previously conducted 30°C and 37°C screens allows for essential genetic targets of Hsp90 to emerge. Altogether, these novel contributions enable a more complete picture of essential Hsp90 functions.
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Affiliation(s)
- Eric A. Franzosa
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Véronique Albanèse
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Yu Xia
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Chemistry, Boston University, Boston, Massachusetts, United States of America
| | - Amie J. McClellan
- Division of Natural Sciences and Mathematics, Bennington College, Bennington, Vermont, United States of America
- * E-mail:
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Joardar A, Malliahgari SR, Skariah G, Gupta R. 2'-O-methylation of the wobble residue of elongator pre-tRNA(Met) in Haloferax volcanii is guided by a box C/D RNA containing unique features. RNA Biol 2011; 8:782-91. [PMID: 21654217 PMCID: PMC3256356 DOI: 10.4161/rna.8.5.16015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 02/16/2011] [Accepted: 03/29/2011] [Indexed: 11/19/2022] Open
Abstract
The wobble residue C34 of Haloferax volcanii elongator tRNA(Met) is 2'-O-methylated. Neither a protein enzyme nor a guide RNA for this modification has been described. In this study, we show that this methylation is guided by a box C/D RNA targeting the intron-containing precursor of the tRNA. This guide RNA is starkly different from its homologs. This unique RNA of approximately 75 bases, named sR-tMet, is encoded in the genomes of H. volcanii and several other haloarchaea. A unique feature of sR-tMet is that the mature RNA in H. volcanii is substantially larger than its predicted size, whereas those in other haloarchaea are as predicted. While the 5'-ends of all tested haloarchaeal sR-tMets are equivalent, H. volcanii sR-tMet possesses an additional 51-base extension at its 3' end. This extension is present in the precursor but not in the mature sR-tMet of Halobacterium sp., suggesting differential 3'-end processing of sR-tMet in these two closely related organisms. Archaeal box C/D RNAs mostly contain a K-loop at the C'/D' motif. Another unique feature of sR-tMet is that its C'/D' motif lacks either a conventional K-turn or a K-loop. Instead, it contains two tandem, sheared G•A base pairs and a pyrimidine-pyrimidine pair in the non-canonical stem; the latter may form an alternative K-turn. Gel shift assays indicate that the L7Ae protein can form a stable complex with this unusual C'/D' motif, suggesting a novel RNA structure for L7Ae interaction.
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Affiliation(s)
- Archi Joardar
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, IL, USA
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42
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Grigoletto A, Lestienne P, Rosenbaum J. The multifaceted proteins Reptin and Pontin as major players in cancer. Biochim Biophys Acta Rev Cancer 2011; 1815:147-57. [DOI: 10.1016/j.bbcan.2010.11.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 11/17/2010] [Accepted: 11/17/2010] [Indexed: 01/29/2023]
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Boulon S, Pradet-Balade B, Verheggen C, Molle D, Boireau S, Georgieva M, Azzag K, Robert MC, Ahmad Y, Neel H, Lamond AI, Bertrand E. HSP90 and its R2TP/Prefoldin-like cochaperone are involved in the cytoplasmic assembly of RNA polymerase II. Mol Cell 2010; 39:912-924. [PMID: 20864038 DOI: 10.1016/j.molcel.2010.08.023] [Citation(s) in RCA: 216] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 05/12/2010] [Accepted: 06/16/2010] [Indexed: 01/09/2023]
Abstract
RNA polymerases are key multisubunit cellular enzymes. Microscopy studies indicated that RNA polymerase I assembles near its promoter. However, the mechanism by which RNA polymerase II is assembled from its 12 subunits remains unclear. We show here that RNA polymerase II subunits Rpb1 and Rpb3 accumulate in the cytoplasm when assembly is prevented and that nuclear import of Rpb1 requires the presence of all subunits. Using MS-based quantitative proteomics, we characterized assembly intermediates. These included a cytoplasmic complex containing subunits Rpb1 and Rpb8 associated with the HSP90 cochaperone hSpagh (RPAP3) and the R2TP/Prefoldin-like complex. Remarkably, HSP90 activity stabilized incompletely assembled Rpb1 in the cytoplasm. Our data indicate that RNA polymerase II is built in the cytoplasm and reveal quality-control mechanisms that link HSP90 to the nuclear import of fully assembled enzymes. hSpagh also bound the free RPA194 subunit of RNA polymerase I, suggesting a general role in assembling RNA polymerases.
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Affiliation(s)
- Séverine Boulon
- Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
| | - Bérengère Pradet-Balade
- Institut de Génétique Moléculaire de Montpellier - UMR 5535 CNRS, Université Montpellier 2, 34293 Montpellier Cedex 5, France.,Université Montpellier 2, 34095 Montpellier Cedex 5, France.,Université Montpellier 1, 34060 Montpellier Cedex 2, France
| | - Céline Verheggen
- Institut de Génétique Moléculaire de Montpellier - UMR 5535 CNRS, Université Montpellier 2, 34293 Montpellier Cedex 5, France.,Université Montpellier 2, 34095 Montpellier Cedex 5, France.,Université Montpellier 1, 34060 Montpellier Cedex 2, France
| | - Dorothée Molle
- Institut de Génétique Moléculaire de Montpellier - UMR 5535 CNRS, Université Montpellier 2, 34293 Montpellier Cedex 5, France.,Université Montpellier 2, 34095 Montpellier Cedex 5, France.,Université Montpellier 1, 34060 Montpellier Cedex 2, France
| | - Stéphanie Boireau
- Institut de Génétique Moléculaire de Montpellier - UMR 5535 CNRS, Université Montpellier 2, 34293 Montpellier Cedex 5, France.,Université Montpellier 2, 34095 Montpellier Cedex 5, France.,Université Montpellier 1, 34060 Montpellier Cedex 2, France
| | - Marya Georgieva
- Institut de Génétique Moléculaire de Montpellier - UMR 5535 CNRS, Université Montpellier 2, 34293 Montpellier Cedex 5, France.,Université Montpellier 2, 34095 Montpellier Cedex 5, France.,Université Montpellier 1, 34060 Montpellier Cedex 2, France
| | - Karim Azzag
- Institut de Génétique Moléculaire de Montpellier - UMR 5535 CNRS, Université Montpellier 2, 34293 Montpellier Cedex 5, France.,Université Montpellier 2, 34095 Montpellier Cedex 5, France.,Université Montpellier 1, 34060 Montpellier Cedex 2, France
| | - Marie-Cécile Robert
- Institut de Génétique Moléculaire de Montpellier - UMR 5535 CNRS, Université Montpellier 2, 34293 Montpellier Cedex 5, France.,Université Montpellier 2, 34095 Montpellier Cedex 5, France.,Université Montpellier 1, 34060 Montpellier Cedex 2, France
| | - Yasmeen Ahmad
- Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
| | - Henry Neel
- Institut de Génétique Moléculaire de Montpellier - UMR 5535 CNRS, Université Montpellier 2, 34293 Montpellier Cedex 5, France.,Université Montpellier 2, 34095 Montpellier Cedex 5, France
| | - Angus I Lamond
- Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier - UMR 5535 CNRS, Université Montpellier 2, 34293 Montpellier Cedex 5, France.,Université Montpellier 2, 34095 Montpellier Cedex 5, France.,Université Montpellier 1, 34060 Montpellier Cedex 2, France
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44
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Abstract
Small nucleolar and Cajal body ribonucleoprotein particles (RNPs) are required for the maturation of ribosomes and spliceosomes. They consist of small nucleolar RNA or Cajal body RNA combined with partner proteins and represent the most complex RNA modification enzymes. Recent advances in structure and function studies have revealed detailed information regarding ribonucleoprotein assembly and substrate binding. These enzymes form intertwined RNA-protein assemblies that facilitate reversible binding of the large ribosomal RNA or small nuclear RNA. These revelations explain the specificity among the components in enzyme assembly and substrate modification. The multiple conformations of individual components and those of complete RNPs suggest a dynamic assembly process and justify the requirement of many assembly factors in vivo.
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45
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Cloutier P, Coulombe B. New insights into the biogenesis of nuclear RNA polymerases? Biochem Cell Biol 2010; 88:211-21. [PMID: 20453924 DOI: 10.1139/o09-173] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
More than 30 years of research on nuclear RNA polymerases (RNAP I, II, and III) has uncovered numerous factors that regulate the activity of these enzymes during the transcription reaction. However, very little is known about the machinery that regulates the fate of RNAPs before or after transcription. In particular, the mechanisms of biogenesis of the 3 nuclear RNAPs, which comprise both common and specific subunits, remains mostly uncharacterized and the proteins involved are yet to be discovered. Using protein affinity purification coupled to mass spectrometry (AP-MS), we recently unraveled a high-density interaction network formed by nuclear RNAP subunits from the soluble fraction of human cell extracts. Validation of the dataset using a machine learning approach trained to minimize the rate of false positives and false negatives yielded a high-confidence dataset and uncovered novel interactors that regulate the RNAP II transcription machinery, including a set of proteins we named the RNAP II-associated proteins (RPAPs). One of the RPAPs, RPAP3, is part of an 11-subunit complex we termed the RPAP3/R2TP/prefoldin-like complex. Here, we review the literature on the subunits of this complex, which points to a role in nuclear RNAP biogenesis.
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Affiliation(s)
- Philippe Cloutier
- Laboratory of Gene Transcription and Proteomics, Institut de recherches cliniques de Montreal, 110 avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada
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46
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Papin C, Humbert O, Kalashnikova A, Eckert K, Morera S, Käs E, Grigoriev M. 3′- to 5′ DNA unwinding by TIP49b proteins. FEBS J 2010. [DOI: 10.1111/j.1742-4658.2010.07687.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Cheung KLY, Huen J, Houry WA, Ortega J. Comparison of the multiple oligomeric structures observed for the Rvb1 and Rvb2 proteins. Biochem Cell Biol 2010; 88:77-88. [PMID: 20130681 DOI: 10.1139/o09-159] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The Rvb1 and Rvb2 proteins are 2 members of the AAA+ family, involved in roles as diverse as chromatin remodeling, transcription, small nucleolar RNA maturation, cellular transformation, signaling of apoptosis and mitosis. These proteins are capable of playing a role in such diverse cellular activities because they are components of different macromolecular assemblies. In the last few years, there has been a number of groups reporting on the structure of purified Rvbs. The reported results have been rather controversial, because there are significant differences observed among the published structures in spite of the high degree of homology among these proteins. Surprisingly, contradictions are observed not only between structures representing the Rvb proteins from different species, but also between protein structures from the same species. This review describes the available Rvb structures from different species and also makes a comparative analysis of them. Finally, we identify some aspects of these structural studies worth pursuing in additional investigations to ensure that the reported structures reflect physiologically relevant conformations of the Rvb1-Rvb2 complex.
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Affiliation(s)
- Kevin L Y Cheung
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON, L8N3Z5, Canada
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48
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Izumi N, Yamashita A, Iwamatsu A, Kurata R, Nakamura H, Saari B, Hirano H, Anderson P, Ohno S. AAA+ proteins RUVBL1 and RUVBL2 coordinate PIKK activity and function in nonsense-mediated mRNA decay. Sci Signal 2010; 3:ra27. [PMID: 20371770 DOI: 10.1126/scisignal.2000468] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Phosphatidylinositol 3-kinase-related protein kinase (PIKK) family proteins play essential roles in DNA-based and RNA-based processes, such as the response to DNA damage, messenger RNA (mRNA) quality control, transcription, and translation, where they contribute to the maintenance of genome integrity and accurate gene expression. The adenosine triphosphatases associated with diverse cellular activities (AAA+) family proteins RuvB-like 1 (RUVBL1) and RUVBL2 are involved in various cellular processes, including transcription, RNA modification, DNA repair, and telomere maintenance. We show that RUVBL1 and RUVBL2 associate with each PIKK family member. We also show that RUVBL1 and RUVBL2 control PIKK abundance at least at the mRNA level. Knockdown of RUVBL1 or RUVBL2 decreased PIKK abundance and impaired PIKK-mediated signaling. Analysis of SMG-1, a PIKK family member involved in nonsense-mediated mRNA decay (NMD), revealed an essential role for RUVBL1 and RUVBL2 in NMD. RUVBL1 and RUVBL2 associated with SMG-1 and the messenger ribonucleoproteins in the cytoplasm and promoted the formation of mRNA surveillance complexes during NMD. Thus, RUVBL1 and RUVBL2 regulate PIKK functions on two different levels: They control the abundance of PIKKs, and they stimulate the formation of PIKK-containing molecular complexes, such as those involved in NMD.
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Affiliation(s)
- Natsuko Izumi
- Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama, Japan
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49
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Huen J, Kakihara Y, Ugwu F, Cheung KLY, Ortega J, Houry WA. Rvb1–Rvb2: essential ATP-dependent helicases for critical complexesThis paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process. Biochem Cell Biol 2010; 88:29-40. [DOI: 10.1139/o09-122] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Rvb1 and Rvb2 are highly conserved, essential AAA+ helicases found in a wide range of eukaryotes. The versatility of these helicases and their central role in the biology of the cell is evident from their involvement in a wide array of critical cellular complexes. Rvb1 and Rvb2 are components of the chromatin-remodeling complexes INO80, Swr-C, and BAF. They are also members of the histone acetyltransferase Tip60 complex, and the recently identified R2TP complex present in Saccharomyces cerevisiae and Homo sapiens; a complex that is involved in small nucleolar ribonucleoprotein (snoRNP) assembly. Furthermore, in humans, Rvb1 and Rvb2 have been identified in the URI prefoldin-like complex. In Drosophila, the Polycomb Repressive complex 1 contains Rvb2, but not Rvb1, and the Brahma complex contains Rvb1 and not Rvb2. Both of these complexes are involved in the regulation of growth and development genes in Drosophila. Rvbs are therefore crucial factors in various cellular processes. Their importance in chromatin remodeling, transcription regulation, DNA damage repair, telomerase assembly, mitotic spindle formation, and snoRNP biogenesis is discussed in this review.
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Affiliation(s)
- Jennifer Huen
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Yoshito Kakihara
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Francisca Ugwu
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Kevin L. Y. Cheung
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Joaquin Ortega
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
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50
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Haurie V, Ménard L, Nicou A, Touriol C, Metzler P, Fernandez J, Taras D, Lestienne P, Balabaud C, Bioulac-Sage P, Prats H, Zucman-Rossi J, Rosenbaum J. Adenosine triphosphatase pontin is overexpressed in hepatocellular carcinoma and coregulated with reptin through a new posttranslational mechanism. Hepatology 2009; 50:1871-83. [PMID: 19877184 PMCID: PMC2927003 DOI: 10.1002/hep.23215] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
UNLABELLED Reptin and Pontin are related ATPases associated with stoichiometric amounts in several complexes involved in chromatin remodeling, transcriptional regulation, and telomerase activity. We found that Reptin was up-regulated in hepatocellular carcinoma (HCC) and that down-regulation of Reptin led to growth arrest. We show here that Pontin messenger RNA (mRNA) is also up-regulated in human HCC 3.9-fold as compared to nontumor liver (P = 0.0004). Pontin expression was a strong independent factor of poor prognosis in a multivariate analysis. As for Reptin, depletion of Pontin in HuH7 cells with small interfering RNAs (siRNAs) led to growth arrest. Remarkably, Pontin depletion led to down-regulation of Reptin as shown with western blot, and vice versa. Whereas siRNAs induced a decrease of their cognate mRNA targets, they did not affect the transcripts of the partner protein. Translation of Pontin or Reptin was not altered when the partner protein was silenced. However, pulse-chase experiments demonstrated that newly synthesized Pontin or Reptin stability was reduced in Reptin- or Pontin-depleted cells, respectively. This phenomenon was reversed upon inhibition of proteasome or ubiquitin-activating enzyme (E1). In addition, proteasome inhibition could partly restore Pontin steady-state levels in Reptin-depleted cells, as shown by western blot. This restoration was not observed when cells were also treated with cycloheximide, thus confirming that proteasomal degradation in this setting was restricted to newly synthesized Pontin. CONCLUSION Reptin and Pontin protein levels are strictly controlled by a posttranslational mechanism involving proteasomal degradation of newly synthesized proteins. These data demonstrate a tight regulatory and reciprocal interaction between Reptin and Pontin, which may in turn lead to the maintenance of their 1:1 stoichiometry.
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Affiliation(s)
- Valérie Haurie
- Fibrose hépatique et cancer du foie
INSERM : U889Université Victor Segalen - Bordeaux IIIFR66146 rue léo saignat, 33076 Bordeaux Cedex,FR
| | - Ludovic Ménard
- Fibrose hépatique et cancer du foie
INSERM : U889Université Victor Segalen - Bordeaux IIIFR66146 rue léo saignat, 33076 Bordeaux Cedex,FR
| | - Alexandra Nicou
- Fibrose hépatique et cancer du foie
INSERM : U889Université Victor Segalen - Bordeaux IIIFR66146 rue léo saignat, 33076 Bordeaux Cedex,FR
| | - Christian Touriol
- I2MR, Institut de médecine moléculaire de Rangueil
INSERM : U858IFR31IFR150Université Paul Sabatier - Toulouse IIIInstitut Louis Bugnard 1, avenue Jean Poulhes BP 84225 31432 TOULOUSE CEDEX 4,FR
| | - Philippe Metzler
- Fibrose hépatique et cancer du foie
INSERM : U889Université Victor Segalen - Bordeaux IIIFR66146 rue léo saignat, 33076 Bordeaux Cedex,FR
| | - Jérémy Fernandez
- Fibrose hépatique et cancer du foie
INSERM : U889Université Victor Segalen - Bordeaux IIIFR66146 rue léo saignat, 33076 Bordeaux Cedex,FR
| | - Danièle Taras
- Fibrose hépatique et cancer du foie
INSERM : U889Université Victor Segalen - Bordeaux IIIFR66146 rue léo saignat, 33076 Bordeaux Cedex,FR
| | - Patrick Lestienne
- Fibrose hépatique et cancer du foie
INSERM : U889Université Victor Segalen - Bordeaux IIIFR66146 rue léo saignat, 33076 Bordeaux Cedex,FR
| | - Charles Balabaud
- Fibrose hépatique et cancer du foie
INSERM : U889Université Victor Segalen - Bordeaux IIIFR66146 rue léo saignat, 33076 Bordeaux Cedex,FR,Service d'hépato-gastroentérologie
CHU BordeauxFR
| | - Paulette Bioulac-Sage
- Fibrose hépatique et cancer du foie
INSERM : U889Université Victor Segalen - Bordeaux IIIFR66146 rue léo saignat, 33076 Bordeaux Cedex,FR,Laboratoire d'anatomie pathologique
CHU BordeauxGroupe hospitalier PellegrinFR
| | - Hervé Prats
- I2MR, Institut de médecine moléculaire de Rangueil
INSERM : U858IFR31IFR150Université Paul Sabatier - Toulouse IIIInstitut Louis Bugnard 1, avenue Jean Poulhes BP 84225 31432 TOULOUSE CEDEX 4,FR
| | - Jessica Zucman-Rossi
- Genomique Fonctionnelle des Tumeurs Solides
INSERM : U674Université Paris-Diderot - Paris VIIIFR105Hopital Saint-Louis - IFR 105 PARIS VII 27, Rue Juliette Dodu 75010 PARIS,FR
| | - Jean Rosenbaum
- Fibrose hépatique et cancer du foie
INSERM : U889Université Victor Segalen - Bordeaux IIIFR66146 rue léo saignat, 33076 Bordeaux Cedex,FR,* Correspondence should be adressed to: Jean Rosenbaum
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