1
|
Peng Y, Gavis ER. The Drosophila hnRNP F/H homolog Glorund recruits dFMRP to inhibit nanos translation elongation. Nucleic Acids Res 2022; 50:7067-7083. [PMID: 35699205 PMCID: PMC9262583 DOI: 10.1093/nar/gkac500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
Translational control of maternal mRNAs generates spatial and temporal patterns of protein expression necessary to begin animal development. Translational repression of unlocalized nanos (nos) mRNA in late-stage Drosophila oocytes by the hnRNP F/H homolog, Glorund (Glo), is important for embryonic body patterning. While previous work has suggested that repression occurs at both the translation initiation and elongation phases, the molecular mechanism by which Glo regulates nos translation remains elusive. Here, we have identified the Drosophila fragile X mental retardation protein, dFMRP, as a Glo interaction partner with links to the translational machinery. Using an oocyte-based in vitro translation system, we confirmed that Glo regulates both initiation and elongation of a nos translational reporter and showed that dFMRP specifically represses translation elongation and promotes ribosome stalling. Furthermore, we combined mutational analysis and in vivo and in vitro binding assays to show that Glo's qRRM2 domain specifically and directly interacts with dFMRP. Our findings suggest that Glo regulates nos translation elongation by recruiting dFMRP and that Glo's RNA-binding domains can also function as protein-protein interaction interfaces critical for its regulatory functions. Additionally, they reveal a mechanism for targeting dFMRP to specific transcripts.
Collapse
Affiliation(s)
- Yingshi Peng
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | |
Collapse
|
2
|
Ishizawa M, Hashimoto K, Ohtani M, Sano R, Kurihara Y, Kusano H, Demura T, Matsui M, Sato-Nara K. Inhibition of Pre-mRNA Splicing Promotes Root Hair Development in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2019; 60:1974-1985. [PMID: 31368506 DOI: 10.1093/pcp/pcz150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
Root hairs protruding from epidermal cells increase the surface area for water absorption and nutrient uptake. Various environmental factors including light, oxygen concentration, carbon dioxide concentration, calcium and mycorrhizal associations promote root hair formation in Arabidopsis thaliana. Light regulates the expression of a large number of genes at the transcriptional and post-transcriptional levels; however, there is little information linking the light response to root hair development. In this study, we describe a novel mutant, light-sensitive root-hair development 1 (lrh1), that displays enhanced root hair development in response to light. Hypocotyl and root elongation was inhibited in the lrh1 mutant, which had a late flowering phenotype. We identified the gene encoding the p14 protein, a putative component of the splicing factor 3b complex essential for pre-mRNA splicing, as being responsible for the lrh1 phenotype. Indeed, regulation of alternative splicing was affected in lrh1 mutants and treatment with a splicing inhibitor mimicked the lrh1 phenotype. Genome-wide alterations in pre-mRNA splicing patterns including differential splicing events of light signaling- and circadian clock-related genes were found in lrh1 as well as a difference in transcriptional regulation of multiple genes including upregulation of essential genes for root hair development. These results suggest that pre-mRNA splicing is the key mechanism regulating root hair development in response to light signals.
Collapse
Affiliation(s)
- Miku Ishizawa
- Department of Chemistry, Biology, and Environmental Science, Graduate School of Humanities and Sciences, Nara Women's University, Kitauoya-nishimachi, Nara, Japan
| | - Kayo Hashimoto
- Department of Chemistry, Biology, and Environmental Science, Graduate School of Humanities and Sciences, Nara Women's University, Kitauoya-nishimachi, Nara, Japan
| | - Misato Ohtani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Ryosuke Sano
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, Japan
| | - Yukio Kurihara
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Tsurumi-ku Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Hiroaki Kusano
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
| | - Taku Demura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, Japan
| | - Minami Matsui
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Tsurumi-ku Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Kumi Sato-Nara
- Department of Chemistry, Biology, and Environmental Science, Graduate School of Humanities and Sciences, Nara Women's University, Kitauoya-nishimachi, Nara, Japan
- Research Group of Biological Sciences, Division of Natural Sciences, Nara Women's University, Kitauoya-nishimachi, Nara, Japan
| |
Collapse
|
3
|
Kuwasako K, Nameki N, Tsuda K, Takahashi M, Sato A, Tochio N, Inoue M, Terada T, Kigawa T, Kobayashi N, Shirouzu M, Ito T, Sakamoto T, Wakamatsu K, Güntert P, Takahashi S, Yokoyama S, Muto Y. Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment. Protein Sci 2016; 26:280-291. [PMID: 27862552 PMCID: PMC5275738 DOI: 10.1002/pro.3080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 01/17/2023]
Abstract
The spliceosomal protein SF3b49, a component of the splicing factor 3b (SF3b) protein complex in the U2 small nuclear ribonucleoprotein, contains two RNA recognition motif (RRM) domains. In yeast, the first RRM domain (RRM1) of Hsh49 protein (yeast orthologue of human SF3b49) reportedly interacts with another component, Cus1 protein (orthologue of human SF3b145). Here, we solved the solution structure of the RRM1 of human SF3b49 and examined its mode of interaction with a fragment of human SF3b145 using NMR methods. Chemical shift mapping showed that the SF3b145 fragment spanning residues 598–631 interacts with SF3b49 RRM1, which adopts a canonical RRM fold with a topology of β1‐α1‐β2‐β3‐α2‐β4. Furthermore, a docking model based on NOESY measurements suggests that residues 607–616 of the SF3b145 fragment adopt a helical structure that binds to RRM1 predominantly via α1, consequently exhibiting a helix–helix interaction in almost antiparallel. This mode of interaction was confirmed by a mutational analysis using GST pull‐down assays. Comparison with structures of all RRM domains when complexed with a peptide found that this helix–helix interaction is unique to SF3b49 RRM1. Additionally, all amino acid residues involved in the interaction are well conserved among eukaryotes, suggesting evolutionary conservation of this interaction mode between SF3b49 RRM1 and SF3b145. PDB Code(s): 5GVQ
Collapse
Affiliation(s)
- Kanako Kuwasako
- Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo, Tokyo, 202-8585, Japan.,RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Nobukazu Nameki
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Kengo Tsuda
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mari Takahashi
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Atsuko Sato
- Department of Chemical & Biological Sciences, Japan Women's University, Mejirodai, Bunkyo, Tokyo, 112-8681, Japan
| | - Naoya Tochio
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Makoto Inoue
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takaho Terada
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takanori Kigawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Naohiro Kobayashi
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takuhiro Ito
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan
| | - Kaori Wakamatsu
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Peter Güntert
- Tatsuo Miyazawa Memorial Program, RIKEN Genomic Sciences Center, Yokohama, 230-0045, Japan.,Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt, Max-von-Laue-Str, Frankfurt am Main, 60438, Germany
| | - Seizo Takahashi
- Department of Chemical & Biological Sciences, Japan Women's University, Mejirodai, Bunkyo, Tokyo, 112-8681, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yutaka Muto
- Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo, Tokyo, 202-8585, Japan.,RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| |
Collapse
|
4
|
Rakesh R, Joseph AP, Bhaskara RM, Srinivasan N. Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps. RNA Biol 2016; 13:1025-1040. [PMID: 27618338 DOI: 10.1080/15476286.2016.1218590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Pre-mRNA splicing in eukaryotes is performed by the spliceosome, a highly complex macromolecular machine. SF3b is a multi-protein complex which recognizes the branch point adenosine of pre-mRNA as part of a larger U2 snRNP or U11/U12 di-snRNP in the dynamic spliceosome machinery. Although a cryo-EM map is available for human SF3b complex, the structure and relative spatial arrangement of all components in the complex are not yet known. We have recognized folds of domains in various proteins in the assembly and generated comparative models. Using an integrative approach involving structural and other experimental data, guided by the available cryo-EM density map, we deciphered a pseudo-atomic model of the closed form of SF3b which is found to be a "fuzzy complex" with highly flexible components and multiplicity of folds. Further, the model provides structural information for 5 proteins (SF3b10, SF3b155, SF3b145, SF3b130 and SF3b14b) and localization information for 4 proteins (SF3b10, SF3b145, SF3b130 and SF3b14b) in the assembly for the first time. Integration of this model with the available U11/U12 di-snRNP cryo-EM map enabled elucidation of an open form. This now provides new insights on the mechanistic features involved in the transition between closed and open forms pivoted by a hinge region in the SF3b155 protein that also harbors cancer causing mutations. Moreover, the open form guided model of the 5' end of U12 snRNA, which includes the branch point duplex, shows that the architecture of SF3b acts as a scaffold for U12 snRNA: pre-mRNA branch point duplex formation with potential implications for branch point adenosine recognition fidelity.
Collapse
Affiliation(s)
- Ramachandran Rakesh
- a Molecular Biophysics Unit, Indian Institute of Science , Bangalore , India
| | - Agnel Praveen Joseph
- b National Center for Biological Sciences, TIFR, GKVK Campus , Bangalore , India
| | - Ramachandra M Bhaskara
- a Molecular Biophysics Unit, Indian Institute of Science , Bangalore , India.,b National Center for Biological Sciences, TIFR, GKVK Campus , Bangalore , India
| | | |
Collapse
|
5
|
Perea W, Schroeder KT, Bryant AN, Greenbaum NL. Interaction between the Spliceosomal Pre-mRNA Branch Site and U2 snRNP Protein p14. Biochemistry 2016; 55:629-32. [PMID: 26784522 DOI: 10.1021/acs.biochem.5b01036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have probed the molecular basis of recognition between human spliceosomal U2 snRNP protein p14 and RNA targets representing the intron branch site region. Interaction of an RNA duplex representing the branch site helix perturbed at least 10 nuclear magnetic resonance cross-peaks of (15)N-labeled p14. However, similar chemical shift changes were observed upon interaction with a duplex without the bulged branch site residue, suggesting that binding of p14 to RNA is nonspecific and does not recognize the branch site. We propose that the p14-RNA interaction screens charges on the backbone of the branch site during spliceosome assembly.
Collapse
Affiliation(s)
- William Perea
- Department of Chemistry & Biochemistry, Hunter College of the City University of New York , New York, New York 10065, United States.,The Graduate Group in Chemistry, The Graduate Center, City University of New York , New York, New York 10016, United States
| | - Kersten T Schroeder
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Amy N Bryant
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Nancy L Greenbaum
- Department of Chemistry & Biochemistry, Hunter College of the City University of New York , New York, New York 10065, United States.,The Graduate Group in Chemistry, The Graduate Center, City University of New York , New York, New York 10016, United States
| |
Collapse
|
6
|
Wysoczański P, Schneider C, Xiang S, Munari F, Trowitzsch S, Wahl MC, Lührmann R, Becker S, Zweckstetter M. Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex. Nat Struct Mol Biol 2014; 21:911-8. [PMID: 25218446 DOI: 10.1038/nsmb.2889] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 08/15/2014] [Indexed: 02/08/2023]
Abstract
The precursor mRNA (pre-mRNA) retention and splicing (RES) complex is a spliceosomal complex that is present in yeast and humans and is important for RNA splicing and retention of unspliced pre-mRNA. Here, we present the solution NMR structure of the RES core complex from Saccharomyces cerevisiae. Complex formation leads to an intricate folding of three components-Snu17p, Bud13p and Pml1p-that stabilizes the RNA-recognition motif (RRM) fold of Snu17p and increases binding affinity in tertiary interactions between the components by more than 100-fold compared to that in binary interactions. RES interacts with pre-mRNA within the spliceosome, and through the assembly of the RES core complex RNA binding efficiency is increased. The three-dimensional structure of the RES core complex highlights the importance of cooperative folding and binding in the functional organization of the spliceosome.
Collapse
Affiliation(s)
- Piotr Wysoczański
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Cornelius Schneider
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - ShengQi Xiang
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Francesca Munari
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Simon Trowitzsch
- 1] Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. [2]
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Markus Zweckstetter
- 1] Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. [2] German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany. [3] Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center, Göttingen, Germany
| |
Collapse
|
7
|
Muto Y, Yokoyama S. Structural insight into RNA recognition motifs: versatile molecular Lego building blocks for biological systems. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:229-46. [PMID: 22278943 DOI: 10.1002/wrna.1107] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
'RNA recognition motifs (RRMs)' are common domain-folds composed of 80-90 amino-acid residues in eukaryotes, and have been identified in many cellular proteins. At first they were known as RNA binding domains. Through discoveries over the past 20 years, however, the RRMs have been shown to exhibit versatile molecular recognition activities and to behave as molecular Lego building blocks to construct biological systems. Novel RNA/protein recognition modes by RRMs are being identified, and more information about the molecular recognition by RRMs is becoming available. These RNA/protein recognition modes are strongly correlated with their biological significance. In this review, we would like to survey the recent progress on these versatile molecular recognition modules.
Collapse
Affiliation(s)
- Yutaka Muto
- Systems and Structural Biology Center, RIKEN, Tsurumi, Japan.
| | | |
Collapse
|
8
|
Schellenberg MJ, Dul EL, MacMillan AM. Structural model of the p14/SF3b155 · branch duplex complex. RNA (NEW YORK, N.Y.) 2011; 17:155-65. [PMID: 21062891 PMCID: PMC3004057 DOI: 10.1261/rna.2224411] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 10/01/2010] [Indexed: 05/30/2023]
Abstract
Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14 · bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein-RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14 · duplex interaction must be disrupted before the first step of splicing.
Collapse
Affiliation(s)
- Matthew J Schellenberg
- Department of Biochemistry, School of Molecular and Systems Medicine, University of Alberta, Edmonton, Alberta, Canada
| | | | | |
Collapse
|
9
|
Roybal GA, Jurica MS. Spliceostatin A inhibits spliceosome assembly subsequent to prespliceosome formation. Nucleic Acids Res 2010; 38:6664-72. [PMID: 20529876 PMCID: PMC2965229 DOI: 10.1093/nar/gkq494] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Pre-mRNA splicing is catalyzed by the large ribonucleoprotein spliceosome. Spliceosome assembly is a highly dynamic process in which the complex transitions through a number of intermediates. Recently, the potent anti-tumor compound Spliceostatin A (SSA) was shown to inhibit splicing and to interact with an essential component of the spliceosome, SF3b. However, it was unclear whether SSA directly impacts the spliceosome and, if so, by what mechanism, which limits interpretation of the drugs influence on splicing. Here, we report that SSA inhibits pre-mRNA splicing by interfering with the spliceosome subsequent to U2 snRNP addition. We demonstrate that SSA inhibition of spliceosome assembly requires ATP, key pre-mRNA splicing sequences and intact U1 and U2 snRNAs. Furthermore all five U snRNAs in addition to the SSA molecule associate with pre-mRNA during SSA inhibition. Kinetic analyses reveal that SSA impedes the A to B complex transition. Remarkably, our data imply that, in addition to its established function in early U2 snRNP recruitment, SF3b plays a role in later maturation of spliceosomes. This work establishes SSA as a powerful tool for dissecting the dynamics of spliceosomes in cells. In addition our data will inform the design of synthetic splicing modulator compounds for targeted anti-tumor treatment.
Collapse
Affiliation(s)
- Gabriel A Roybal
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
| | | |
Collapse
|
10
|
Sperling J, Azubel M, Sperling R. Structure and function of the Pre-mRNA splicing machine. Structure 2009; 16:1605-15. [PMID: 19000813 DOI: 10.1016/j.str.2008.08.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 08/22/2008] [Accepted: 08/27/2008] [Indexed: 12/14/2022]
Abstract
Most eukaryotic pre-mRNAs contain non-coding sequences (introns) that must be removed in order to accurately place the coding sequences (exons) in the correct reading frame. This critical regulatory pre-mRNA splicing event is fundamental in development and cancer. It occurs within a mega-Dalton multicomponent machine composed of RNA and proteins, which undergoes dynamic changes in RNA-RNA, RNA-protein, and protein-protein interactions during the splicing reaction. Recent years have seen progress in functional and structural analyses of the splicing machine and its subcomponents, and this review is focused on structural aspects of the pre-mRNA splicing machine and their mechanistic implications on the splicing of multi-intronic pre-mRNAs. It brings together, in a comparative manner, structural information on spliceosomes and their intermediates in the stepwise assembly process in vitro, and on the preformed supraspliceosomes, which are isolated from living cell nuclei, with a view of portraying a consistent picture.
Collapse
Affiliation(s)
- Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | |
Collapse
|
11
|
Ohnishi S, Pääkkönen K, Koshiba S, Tochio N, Sato M, Kobayashi N, Harada T, Watanabe S, Muto Y, Güntert P, Tanaka A, Kigawa T, Yokoyama S. Solution structure of the GUCT domain from human RNA helicase II/Guβ reveals the RRM fold, but implausible RNA interactions. Proteins 2009; 74:133-44. [DOI: 10.1002/prot.22138] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
12
|
Cléry A, Blatter M, Allain FHT. RNA recognition motifs: boring? Not quite. Curr Opin Struct Biol 2008; 18:290-8. [PMID: 18515081 DOI: 10.1016/j.sbi.2008.04.002] [Citation(s) in RCA: 455] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Accepted: 04/09/2008] [Indexed: 01/10/2023]
Abstract
The RNA recognition motif (RRM) is one of the most abundant protein domains in eukaryotes. While the structure of this domain is well characterized by the packing of two alpha-helices on a four-stranded beta-sheet, the mode of protein and RNA recognition by RRMs is not clear owing to the high variability of these interactions. Here we report recent structural data on RRM-RNA and RRM-protein interactions showing the ability of this domain to modulate its binding affinity and specificity using each of its constitutive elements (beta-strands, loops, alpha-helices). The extreme structural versatility of the RRM interactions explains why RRM-containing proteins have so diverse biological functions.
Collapse
Affiliation(s)
- Antoine Cléry
- Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
| | | | | |
Collapse
|
13
|
Jurica MS. Detailed close-ups and the big picture of spliceosomes. Curr Opin Struct Biol 2008; 18:315-20. [PMID: 18550358 DOI: 10.1016/j.sbi.2008.05.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 05/08/2008] [Accepted: 05/13/2008] [Indexed: 02/04/2023]
Abstract
The spliceosome is the huge macromolecular assembly responsible for the removal of introns from pre-mRNA transcripts. The size and complexity of this dynamic cellular machine dictate that structural analysis of the spliceosome is best served by a combination of techniques. Electron microscopy is providing a more global, albeit less detailed, view of spliceosome assemblies. X-ray crystallographers and NMR spectroscopists are steadily reporting more atomic resolution structures of individual spliceosome components and fragments. Increasingly, structures of these individual pieces in complex with binding partners are yielding insights into the interfaces that hold the entire spliceosome assembly together. Although the information arising from the various structural studies of splicing machinery has not yet fully converged into a complete model, we can expect that a detailed understanding of spliceosome structure will arise at the juncture of structural and computational modeling methods.
Collapse
Affiliation(s)
- Melissa S Jurica
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, CA 95064, United States.
| |
Collapse
|