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The Role of Hsp90-R2TP in Macromolecular Complex Assembly and Stabilization. Biomolecules 2022; 12:biom12081045. [PMID: 36008939 PMCID: PMC9406135 DOI: 10.3390/biom12081045] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 01/27/2023] Open
Abstract
Hsp90 is a ubiquitous molecular chaperone involved in many cell signaling pathways, and its interactions with specific chaperones and cochaperones determines which client proteins to fold. Hsp90 has been shown to be involved in the promotion and maintenance of proper protein complex assembly either alone or in association with other chaperones such as the R2TP chaperone complex. Hsp90-R2TP acts through several mechanisms, such as by controlling the transcription of protein complex subunits, stabilizing protein subcomplexes before their incorporation into the entire complex, and by recruiting adaptors that facilitate complex assembly. Despite its many roles in protein complex assembly, detailed mechanisms of how Hsp90-R2TP assembles protein complexes have yet to be determined, with most findings restricted to proteomic analyses and in vitro interactions. This review will discuss our current understanding of the function of Hsp90-R2TP in the assembly, stabilization, and activity of the following seven classes of protein complexes: L7Ae snoRNPs, spliceosome snRNPs, RNA polymerases, PIKKs, MRN, TSC, and axonemal dynein arms.
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2
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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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3
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Caton EA, Kelly EK, Kamalampeta R, Kothe U. Efficient RNA pseudouridylation by eukaryotic H/ACA ribonucleoproteins requires high affinity binding and correct positioning of guide RNA. Nucleic Acids Res 2018; 46:905-916. [PMID: 29177505 PMCID: PMC5778458 DOI: 10.1093/nar/gkx1167] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/31/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022] Open
Abstract
H/ACA ribonucleoproteins (H/ACA RNPs) are responsible for introducing many pseudouridines into RNAs, but are also involved in other cellular functions. Utilizing a purified and reconstituted yeast H/ACA RNP system that is active in pseudouridine formation under physiological conditions, we describe here the quantitative characterization of H/ACA RNP formation and function. This analysis reveals a surprisingly tight interaction of H/ACA guide RNA with the Cbf5p-Nop10p-Gar1p trimeric protein complex whereas Nhp2p binds comparably weakly to H/ACA guide RNA. Substrate RNA is bound to H/ACA RNPs with nanomolar affinity which correlates with the GC content in the guide-substrate RNA base pairing. Both Nhp2p and the conserved Box ACA element in guide RNA are required for efficient pseudouridine formation, but not for guide RNA or substrate RNA binding. These results suggest that Nhp2p and the Box ACA motif indirectly facilitate loading of the substrate RNA in the catalytic site of Cbf5p by correctly positioning the upper and lower parts of the H/ACA guide RNA on the H/ACA proteins. In summary, this study provides detailed insight into the molecular mechanism of H/ACA RNPs.
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Affiliation(s)
- Evan A Caton
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Erin K Kelly
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Rajashekhar Kamalampeta
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Ute Kothe
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
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4
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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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5
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Espinar-Marchena FJ, Babiano R, Cruz J. Placeholder factors in ribosome biogenesis: please, pave my way. MICROBIAL CELL 2017; 4:144-168. [PMID: 28685141 PMCID: PMC5425277 DOI: 10.15698/mic2017.05.572] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The synthesis of cytoplasmic eukaryotic ribosomes is an extraordinarily energy-demanding cellular activity that occurs progressively from the nucleolus to the cytoplasm. In the nucleolus, precursor rRNAs associate with a myriad of trans-acting factors and some ribosomal proteins to form pre-ribosomal particles. These factors include snoRNPs, nucleases, ATPases, GTPases, RNA helicases, and a vast list of proteins with no predicted enzymatic activity. Their coordinate activity orchestrates in a spatiotemporal manner the modification and processing of precursor rRNAs, the rearrangement reactions required for the formation of productive RNA folding intermediates, the ordered assembly of the ribosomal proteins, and the export of pre-ribosomal particles to the cytoplasm; thus, providing speed, directionality and accuracy to the overall process of formation of translation-competent ribosomes. Here, we review a particular class of trans-acting factors known as "placeholders". Placeholder factors temporarily bind selected ribosomal sites until these have achieved a structural context that is appropriate for exchanging the placeholder with another site-specific binding factor. By this strategy, placeholders sterically prevent premature recruitment of subsequently binding factors, premature formation of structures, avoid possible folding traps, and act as molecular clocks that supervise the correct progression of pre-ribosomal particles into functional ribosomal subunits. We summarize the current understanding of those factors that delay the assembly of distinct ribosomal proteins or subsequently bind key sites in pre-ribosomal particles. We also discuss recurrent examples of RNA-protein and protein-protein mimicry between rRNAs and/or factors, which have clear functional implications for the ribosome biogenesis pathway.
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Affiliation(s)
- Francisco J Espinar-Marchena
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, E-41013, Seville, Spain
| | - Reyes Babiano
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, E-41013, Seville, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, E-41013, Seville, Spain
| | - Jesús Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, E-41013, Seville, Spain
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6
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Structure of GPN-Loop GTPase Npa3 and Implications for RNA Polymerase II Assembly. Mol Cell Biol 2015; 36:820-31. [PMID: 26711263 DOI: 10.1128/mcb.01009-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/21/2015] [Indexed: 11/20/2022] Open
Abstract
Biogenesis of the 12-subunit RNA polymerase II (Pol II) transcription complex requires so-called GPN-loop GTPases, but the function of these enzymes is unknown. Here we report the first crystal structure of a eukaryotic GPN-loop GTPase, the Saccharomyces cerevisiae enzyme Npa3 (a homolog of human GPN1, also called RPAP4, XAB1, and MBDin), and analyze its catalytic mechanism. The enzyme was trapped in a GDP-bound closed conformation and in a novel GTP analog-bound open conformation displaying a conserved hydrophobic pocket distant from the active site. We show that Npa3 has chaperone activity and interacts with hydrophobic peptide regions of Pol II subunits that form interfaces in the assembled Pol II complex. Biochemical results are consistent with a model that the hydrophobic pocket binds peptides and that this can allosterically stimulate GTPase activity and subsequent peptide release. These results suggest that GPN-loop GTPases are assembly chaperones for Pol II and other protein complexes.
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7
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Quinternet M, Rothé B, Barbier M, Bobo C, Saliou JM, Jacquemin C, Back R, Chagot ME, Cianférani S, Meyer P, Branlant C, Charpentier B, Manival X. Structure/Function Analysis of Protein-Protein Interactions Developed by the Yeast Pih1 Platform Protein and Its Partners in Box C/D snoRNP Assembly. J Mol Biol 2015. [PMID: 26210662 DOI: 10.1016/j.jmb.2015.07.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In eukaryotes, nucleotide post-transcriptional modifications in RNAs play an essential role in cell proliferation by contributing to pre-ribosomal RNA processing, ribosome assembly and activity. Box C/D small nucleolar ribonucleoparticles catalyze site-specific 2'-O-methylation of riboses, one of the most prevalent RNA modifications. They contain one guide RNA and four core proteins and their in vivo assembly requires numerous factors including (HUMAN/Yeast) BCD1/Bcd1p, NUFIP1/Rsa1p, ZNHIT3/Hit1p, the R2TP complex composed of protein PIH1D1/Pih1p and RPAP3/Tah1p that bridges the R2TP complex to the HSP90/Hsp82 chaperone and two AAA+ ATPases. We show that Tah1p can stabilize Pih1p in the absence of Hsp82 activity during the stationary phase of growth and consequently that the Tah1p:Pih1p interaction is sufficient for Pih1p stability. This prompted us to establish the solution structure of the Tah1p:Pih1p complex by NMR. The C-terminal tail S93-S111 of Tah1p snakes along Pih1p264-344 folded in a CS domain to form two intermolecular β-sheets and one covering loop. However, a thorough inspection of the NMR and crystal structures revealed structural differences that may be of functional importance. In addition, our NMR and isothermal titration calorimetry data revealed the formation of direct contacts between Pih1p257-344 and the Hsp82MC domain in the presence of Tah1p. By co-expression in Escherichia coli, we demonstrate that Pih1p has two other direct partners, the Rsa1p assembly factor and the Nop58p core protein, and in vivo and in vitro experiments mapped the required binding domains. Our data suggest that these two interactions are mutually exclusive. The implication of this finding for box C/D small nucleolar ribonucleoparticle assembly is discussed.
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Affiliation(s)
- Marc Quinternet
- FR 3209 CNRS-Université de Lorraine, Bioingénierie Moléculaire, Cellulaire et Thérapeutique, Biopôle, Campus Biologie-Santé, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Benjamin Rothé
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Muriel Barbier
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Claude Bobo
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Jean-Michel Saliou
- BioOrganic Mass Spectrometry Laboratory, IPHC-DSA, UMR 7178 Université de Strasbourg-CNRS, 25 rue Becquerel, 67087 Strasbourg, France
| | - Clémence Jacquemin
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Régis Back
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Marie-Eve Chagot
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Sarah Cianférani
- BioOrganic Mass Spectrometry Laboratory, IPHC-DSA, UMR 7178 Université de Strasbourg-CNRS, 25 rue Becquerel, 67087 Strasbourg, France
| | - Philippe Meyer
- Sorbonne Universités, UPMC University Paris 6, CNRS, UMR 8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France.
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8
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Kumalo HM, Bhakat S, Soliman ME. Heat-shock protein 90 (Hsp90) as anticancer target for drug discovery: an ample computational perspective. Chem Biol Drug Des 2015; 86:1131-60. [PMID: 25958815 DOI: 10.1111/cbdd.12582] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There are over 100 different types of cancer, and each is classified based on the type of cell that is initially affected. If left untreated, cancer can result in serious health problems and eventually death. Recently, the paradigm of cancer chemotherapy has evolved to use a combination approach, which involves the use of multiple drugs each of which targets an individual protein. Inhibition of heat-shock protein 90 (Hsp90) is one of the novel key cancer targets. Because of its ability to target several signaling pathways, Hsp90 inhibition emerged as a useful strategy to treat a wide variety of cancers. Molecular modeling approaches and methodologies have become 'close counterparts' to experiments in drug design and discovery workflows. A wide range of molecular modeling approaches have been developed, each of which has different objectives and outcomes. In this review, we provide an up-to-date systematic overview on the different computational models implemented toward the design of Hsp90 inhibitors as anticancer agents. Although this is the main emphasis of this review, different topics such as background and current statistics of cancer, different anticancer targets including Hsp90, and the structure and function of Hsp90 from an experimental perspective, for example, X-ray and NMR, are also addressed in this report. To the best of our knowledge, this review is the first account, which comprehensively outlines various molecular modeling efforts directed toward identification of anticancer drugs targeting Hsp90. We believe that the information, methods, and perspectives highlighted in this report would assist researchers in the discovery of potential anticancer agents.
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Affiliation(s)
- Hezekiel M Kumalo
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Soumendranath Bhakat
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa.,Division of Biophysical Chemistry, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| | - Mahmoud E Soliman
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
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9
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Singh M, Wang Z, Cascio D, Feigon J. Structure and interactions of the CS domain of human H/ACA RNP assembly protein Shq1. J Mol Biol 2015; 427:807-823. [PMID: 25553844 PMCID: PMC4323627 DOI: 10.1016/j.jmb.2014.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/13/2014] [Accepted: 12/16/2014] [Indexed: 12/27/2022]
Abstract
Shq1 is an essential protein involved in the early steps of biogenesis and assembly of H/ACA ribonucleoprotein particles (RNPs). Shq1 binds to dyskerin (Cbf5 in yeast) at an early step of H/ACA RNP assembly and is subsequently displaced by the H/ACA RNA. Shq1 contains an N-terminal CS and a C-terminal Shq1-specific domain (SSD). Dyskerin harbors many mutations associated with dyskeratosis congenita. Structures of yeast Shq1 SSD bound to Cbf5 revealed that only a subset of these mutations is in the SSD binding site, implicating another subset in the putative CS binding site. Here, we present the crystal structure of human Shq1 CS (hCS) and the nuclear magnetic resonance (NMR) and crystal structures of hCS containing a serine substitution for proline 22 that is associated with some prostate cancers. The structure of hCS is similar to yeast Shq1 CS domain (yCS) and consists of two β-sheets that form an immunoglobulin-like β-sandwich fold. The N-terminal affinity tag sequence AHHHHHH associates with a neighboring protein in the crystal lattice to form an extra β-strand. Deletion of this tag was required to get spectra suitable for NMR structure determination, while the tag was required for crystallization. NMR chemical shift perturbation (CSP) experiments with peptides derived from putative CS binding sites on dyskerin and Cbf5 revealed a conserved surface on CS important for Cbf5/dyskerin binding. A HADDOCK (high-ambiguity-driven protein-protein docking) model of a Shq1-Cbf5 complex that defines the position of CS domain in the pre-H/ACA RNP was calculated using the CSP data.
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Affiliation(s)
- Mahavir Singh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Zhonghua Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- University of California Los Angeles-Department of Energy (UCLA-DOE) Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; University of California Los Angeles-Department of Energy (UCLA-DOE) Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.
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10
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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: 92] [Impact Index Per Article: 9.2] [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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11
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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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Walbott H, Machado-Pinilla R, Liger D, Blaud M, Réty S, Grozdanov PN, Godin K, van Tilbeurgh H, Varani G, Meier UT, Leulliot N. The H/ACA RNP assembly factor SHQ1 functions as an RNA mimic. Genes Dev 2011; 25:2398-408. [PMID: 22085966 DOI: 10.1101/gad.176834.111] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
SHQ1 is an essential assembly factor for H/ACA ribonucleoproteins (RNPs) required for ribosome biogenesis, pre-mRNA splicing, and telomere maintenance. SHQ1 binds dyskerin/NAP57, the catalytic subunit of human H/ACA RNPs, and this interaction is modulated by mutations causing X-linked dyskeratosis congenita. We report the crystal structure of the C-terminal domain of yeast SHQ1, Shq1p, and its complex with yeast dyskerin/NAP57, Cbf5p, lacking its catalytic domain. The C-terminal domain of Shq1p interacts with the RNA-binding domain of Cbf5p and, through structural mimicry, uses the RNA-protein-binding sites to achieve a specific protein-protein interface. We propose that Shq1p operates as a Cbf5p chaperone during RNP assembly by acting as an RNA placeholder, thereby preventing Cbf5p from nonspecific RNA binding before association with an H/ACA RNA and the other core RNP proteins.
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Affiliation(s)
- Hélène Walbott
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université de Paris-Sud, Orsay Cedex, France
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Bratkovič T, Rogelj B. Biology and applications of small nucleolar RNAs. Cell Mol Life Sci 2011; 68:3843-51. [PMID: 21748470 PMCID: PMC11114935 DOI: 10.1007/s00018-011-0762-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 06/20/2011] [Accepted: 06/21/2011] [Indexed: 10/18/2022]
Abstract
Small nucleolar RNAs (snoRNAs) constitute a group of non-coding RNAs principally involved in posttranscriptional modification of ubiquitously expressed ribosomal and small nuclear RNAs. However, a number of tissue-specific snoRNAs have recently been identified that apparently do not target conventional substrates and are presumed to guide processing of primary transcripts of protein-coding genes, potentially expanding the diapason of regulatory RNAs that control translation of mRNA to proteins. Here, we review biogenesis of snoRNAs and redefine their function in light of recent exciting discoveries. We also discuss the potential of recombinant snoRNAs to be used in modulation of gene expression.
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Affiliation(s)
- Tomaž Bratkovič
- Department of Pharmaceutical Biology, University of Ljubljana, Slovenia.
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Li S, Duan J, Li D, Ma S, Ye K. Structure of the Shq1-Cbf5-Nop10-Gar1 complex and implications for H/ACA RNP biogenesis and dyskeratosis congenita. EMBO J 2011; 30:5010-20. [PMID: 22117216 DOI: 10.1038/emboj.2011.427] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 11/07/2011] [Indexed: 12/22/2022] Open
Abstract
Shq1 is a conserved protein required for the biogenesis of eukaryotic H/ACA ribonucleoproteins (RNPs), including human telomerase. We report the structure of the Shq1-specific domain alone and in complex with H/ACA RNP proteins Cbf5, Nop10 and Gar1. The Shq1-specific domain adopts a novel helical fold and primarily contacts the PUA domain and the otherwise disordered C-terminal extension (CTE) of Cbf5. The structure shows that dyskeratosis congenita mutations found in the CTE of human Cbf5 likely interfere with Shq1 binding. However, most mutations in the PUA domain are not located at the Shq1-binding surface and also have little effect on the yeast Cbf5-Shq1 interaction. Shq1 binds Cbf5 independently of the H/ACA RNP proteins Nop10, Gar1 and Nhp2 and the assembly factor Naf1, but shares an overlapping binding surface with H/ACA RNA. Shq1 point mutations that disrupt Cbf5 interaction suppress yeast growth particularly at elevated temperatures. Our results suggest that Shq1 functions as an assembly chaperone that protects the Cbf5 protein complexes from non-specific RNA binding and aggregation before assembly of H/ACA RNA.
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Affiliation(s)
- Shuang Li
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
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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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Hofmann ER, Nallar SC, Lin L, D'Cunha J, Lindner DJ, Weihua X, Kalvakolanu DV. Identification and characterization of GRIM-1, a cell-death-associated gene product. J Cell Sci 2010; 123:2781-91. [PMID: 20663920 PMCID: PMC2915880 DOI: 10.1242/jcs.070250] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2010] [Indexed: 12/27/2022] Open
Abstract
Using a genome-wide technical knockout, we isolated a newly identified set of GRIM (genes associated with retinoid-interferon-induced mortality) genes; GRIM genes mediate IFN- and retinoic-acid (RA)-induced cell death. Here, we describe the isolation and characterization of one such gene, GRIM-1. Three proteins, with identical C-termini, were produced from the GRIM-1 open reading frame when this gene was transcribed and translated in vitro. These protein isoforms, designated GRIM-1alpha, GRIM-1beta and GRIM-1gamma, differentially suppressed growth via apoptosis in various cell lines. We also show that a caspase-dependent mechanism generates the proapoptotic GRIM-1 isoforms. Lastly, GRIM-1 isoforms differentially blocked maturation of 18S ribosomal RNA, consistent with their respective growth-suppressive ability. Together, these studies identified a novel protein involved in growth suppression and cell death.
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Affiliation(s)
- Edward R. Hofmann
- Greenebaum Cancer Center, Department of Microbiology and Immunology, Molecular and Cellular Cancer Biology Track, GPILS, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Shreeram C. Nallar
- Greenebaum Cancer Center, Department of Microbiology and Immunology, Molecular and Cellular Cancer Biology Track, GPILS, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Limei Lin
- Greenebaum Cancer Center, Department of Microbiology and Immunology, Molecular and Cellular Cancer Biology Track, GPILS, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jonathan D'Cunha
- Greenebaum Cancer Center, Department of Microbiology and Immunology, Molecular and Cellular Cancer Biology Track, GPILS, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Daniel J. Lindner
- Taussig Cancer Center, Lerner Research Institute, Cleveland, OH 44195, USA
| | - Xiao Weihua
- Hefei National Laboratory of Physical Sciences at Microscale, University of Science and Technology, Hefei, Anhui 230027, China
| | - Dhananjaya V. Kalvakolanu
- Greenebaum Cancer Center, Department of Microbiology and Immunology, Molecular and Cellular Cancer Biology Track, GPILS, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Kiss T, Fayet-Lebaron E, Jády BE. Box H/ACA small ribonucleoproteins. Mol Cell 2010; 37:597-606. [PMID: 20227365 DOI: 10.1016/j.molcel.2010.01.032] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 01/06/2010] [Accepted: 01/12/2010] [Indexed: 11/25/2022]
Abstract
Box H/ACA RNAs represent an abundant, evolutionarily conserved class of small noncoding RNAs. All H/ACA RNAs associate with a common set of proteins, and they function as ribonucleoprotein (RNP) enzymes mainly in the site-specific pseudouridylation of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). Some H/ACA RNPs function in the nucleolytic processing of precursor rRNA (pre-rRNA) and synthesis of telomeric DNA. Thus, H/ACA RNPs are essential for three fundamental cellular processes: protein synthesis, mRNA splicing, and maintenance of genome integrity. Recently, great progress has been made toward understanding of the biogenesis, intracellular trafficking, structure, and function of H/ACA RNPs.
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Affiliation(s)
- Tamás Kiss
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, IFR109 CNRS, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse Cedex 9, France.
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