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Depletion of the MFAP1/SPP381 Splicing Factor Causes R-Loop-Independent Genome Instability. Cell Rep 2020; 28:1551-1563.e7. [PMID: 31390568 PMCID: PMC6693559 DOI: 10.1016/j.celrep.2019.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 03/18/2019] [Accepted: 07/01/2019] [Indexed: 01/19/2023] Open
Abstract
THO/TREX is a conserved complex with a role in messenger ribonucleoprotein biogenesis that links gene expression and genome instability. Here, we show that human THO interacts with MFAP1 (microfibrillar-associated protein 1), a spliceosome-associated factor. Interestingly, MFAP1 depletion impairs cell proliferation and genome integrity, increasing γH2AX foci and DNA breaks. This phenotype is not dependent on either transcription or RNA-DNA hybrids. Mutations in the yeast orthologous gene SPP381 cause similar transcription-independent genome instability, supporting a conserved role. MFAP1 depletion has a wide effect on splicing and gene expression in human cells, determined by transcriptome analyses. MFAP1 depletion affects a number of DNA damage response (DDR) genes, which supports an indirect role of MFAP1 on genome integrity. Our work defines a functional interaction between THO and RNA processing and argues that splicing factors may contribute to genome integrity indirectly by regulating the expression of DDR genes rather than by a direct role.
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Kumar P, Kundu D, Mondal AK, Nain V, Puria R. Inhibition of TOR signalling in lea1 mutant induces apoptosis in Saccharomyces cerevisiae. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-018-1422-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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de Almeida RA, O'Keefe RT. The NineTeen Complex (NTC) and NTC-associated proteins as targets for spliceosomal ATPase action during pre-mRNA splicing. RNA Biol 2015; 12:109-14. [PMID: 25654271 PMCID: PMC4615276 DOI: 10.1080/15476286.2015.1008926] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Pre-mRNA splicing is an essential step in gene expression that removes intron sequences efficiently and accurately to produce a mature mRNA for translation. It is the large and dynamic RNA-protein complex called the spliceosome that catalyzes intron removal. To carry out splicing the spliceosome not only needs to assemble correctly with the pre-mRNA but the spliceosome requires extensive remodelling of its RNA and protein components to execute the 2 steps of intron removal. Spliceosome remodelling is achieved through the action of ATPases that target both RNA and proteins to produce spliceosome conformations competent for each step of spliceosome activation, catalysis and disassembly. An increasing amount of research has pointed to the spliceosome associated NineTeen Complex (NTC) of proteins as targets for the action of a number of the spliceosomal ATPases during spliceosome remodelling. In this point-of-view article we present the latest findings on the changes in the NTC that occur following ATPase action that are required for spliceosome activation, catalysis and disassembly. We proposed that the NTC is one of the main targets of ATPase action during spliceosome remodelling required for pre-mRNA splicing.
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Martínez-Lumbreras S, Taverniti V, Zorrilla S, Séraphin B, Pérez-Cañadillas JM. Gbp2 interacts with THO/TREX through a novel type of RRM domain. Nucleic Acids Res 2015; 44:437-48. [PMID: 26602689 PMCID: PMC4705658 DOI: 10.1093/nar/gkv1303] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 11/07/2015] [Indexed: 12/11/2022] Open
Abstract
Metazoan SR and SR-like proteins are important regulatory factors in RNA splicing, export, translation and RNA decay. We determined the NMR structures and nucleic acid interaction modes of Gbp2 and Hrb1, two paralogous budding yeast proteins with similarities to mammalian SR proteins. Gbp2 RRM1 and RRM2 recognise preferentially RNAs containing the core motif GGUG. Sequence selectivity resides in a non-canonical interface in RRM2 that is highly related to the SRSF1 pseudoRRM. The atypical Gbp2/Hrb1 C-terminal RRM domains (RRM3) do not interact with RNA/DNA, likely because of their novel N-terminal extensions that block the canonical RNA binding interface. Instead, we discovered that RRM3 is crucial for interaction with the THO/TREX complex and identified key residues essential for this interaction. Moreover, Gbp2 interacts genetically with Tho2 as the double deletion shows a synthetic phenotype and preventing Gbp2 interaction with the THO/TREX complex partly supresses gene expression defect associated with inactivation of the latter complex. These findings provide structural and functional insights into the contribution of SR-like proteins in the post-transcriptional control of gene expression.
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Affiliation(s)
- Santiago Martínez-Lumbreras
- Department of Biological Physical Chemistry, Instituto de Química-Física 'Rocasolano', CSIC, Serrano-119, 28006 Madrid, Spain
| | - Valerio Taverniti
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGMBC), Centre National de Recherche Scientifique (CNRS) UMR 7104/Institut National de Santé et de Recherche Médicale (INSERM) U964/Université de Strasbourg, 67404 Illkirch, France
| | - Silvia Zorrilla
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Bertrand Séraphin
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGMBC), Centre National de Recherche Scientifique (CNRS) UMR 7104/Institut National de Santé et de Recherche Médicale (INSERM) U964/Université de Strasbourg, 67404 Illkirch, France
| | - José Manuel Pérez-Cañadillas
- Department of Biological Physical Chemistry, Instituto de Química-Física 'Rocasolano', CSIC, Serrano-119, 28006 Madrid, Spain
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Tripsianes K, Friberg A, Barrandon C, Brooks M, van Tilbeurgh H, Seraphin B, Sattler M. A novel protein-protein interaction in the RES (REtention and Splicing) complex. J Biol Chem 2014; 289:28640-50. [PMID: 25160624 PMCID: PMC4192513 DOI: 10.1074/jbc.m114.592311] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The retention and splicing (RES) complex is a conserved spliceosome-associated module that was shown to enhance splicing of a subset of transcripts and promote the nuclear retention of unspliced pre-mRNAs in yeast. The heterotrimeric RES complex is organized around the Snu17p protein that binds to both the Bud13p and Pml1p subunits. Snu17p exhibits an RRM domain that resembles a U2AF homology motif (UHM) and Bud13p harbors a Trp residue reminiscent of an UHM-ligand motif (ULM). It has therefore been proposed that the interaction between Snu17p and Bud13p resembles canonical UHM-ULM complexes. Here, we have used biochemical and NMR structural analysis to characterize the structure of the yeast Snu17p-Bud13p complex. Unlike known UHMs that sequester the Trp residue of the ULM ligand in a hydrophobic pocket, Snu17p and Bud13p utilize a large interaction surface formed around the two helices of the Snu17p domain. In total 18 residues of the Bud13p ligand wrap around the Snu17p helical surface in an U-turn-like arrangement. The invariant Trp232 in Bud13p is located in the center of the turn, and contacts surface residues of Snu17p. The structural data are supported by mutational analysis and indicate that Snu17p provides an extended binding surface with Bud13p that is notably distinct from canonical UHM-ULM interactions. Our data highlight structural diversity in RRM-protein interactions, analogous to the one seen for nucleic acid interactions.
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Affiliation(s)
- Konstantinos Tripsianes
- From the Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic,
| | - Anders Friberg
- the Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, the Center for Integrated Protein Science Munich and Chair of Biomolecular NMR, TU München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Charlotte Barrandon
- the Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette, France
| | - Mark Brooks
- the University Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, F-91405 Orsay, France, and
| | - Herman van Tilbeurgh
- the University Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, F-91405 Orsay, France, and
| | - Bertrand Seraphin
- the Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette, France, the Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de Recherche Scientifique (CNRS) UMR 7104, Institut National de Santé et de Recherche Médicale (INSERM) U964, Université de Strasbourg, 67404 Illkirch, France
| | - Michael Sattler
- the Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, the Center for Integrated Protein Science Munich and Chair of Biomolecular NMR, TU München, Lichtenbergstr. 4, 85747 Garching, Germany,
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Sorenson MR, Stevens SW. Rapid identification of mRNA processing defects with a novel single-cell yeast reporter. RNA (NEW YORK, N.Y.) 2014; 20:732-45. [PMID: 24671766 PMCID: PMC3988574 DOI: 10.1261/rna.042663.113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
It has become increasingly evident that gene expression processes in eukaryotes involve communication and coordination between many complex, independent macromolecular machines. To query these processes and to explore the potential relationships between them in the budding yeast Saccharomyces cerevisiae, we designed a versatile reporter using multicolor high-throughput flow cytometry. Due to its design, this single reporter exhibits a distinctive signature for many defects in gene expression including transcription, histone modification, pre-mRNA splicing, mRNA export, nonsense-mediated decay, and mRNA degradation. Analysis of the reporter in 4967 nonessential yeast genes revealed striking phenotypic overlaps between chromatin remodeling, histone modification, and pre-mRNA splicing. Additionally, we developed a copper-inducible reporter, with which we demonstrate that 5-fluorouracil mimics the mRNA decay phenotype of cells lacking the 3'-5' exonuclease Rrp6p. Our reporter is capable of performing high-throughput, rapid, and large-scale screens to identify and characterize genetic and chemical perturbations of the major eukaryotic gene expression processes.
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Affiliation(s)
| | - Scott W. Stevens
- Department of Molecular Biosciences
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
- Corresponding authorE-mail
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