1
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Senn KA, Hoskins AA. Mechanisms and regulation of spliceosome-mediated pre-mRNA splicing in Saccharomyces cerevisiae. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1866. [PMID: 38972853 DOI: 10.1002/wrna.1866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/19/2024] [Accepted: 05/28/2024] [Indexed: 07/09/2024]
Abstract
Pre-mRNA splicing, the removal of introns and ligation of flanking exons, is a crucial step in eukaryotic gene expression. The spliceosome, a macromolecular complex made up of five small nuclear RNAs (snRNAs) and dozens of proteins, assembles on introns via a complex pathway before catalyzing the two transesterification reactions necessary for splicing. All of these steps have the potential to be highly regulated to ensure correct mRNA isoform production for proper cellular function. While Saccharomyces cerevisiae (yeast) has a limited set of intron-containing genes, many of these genes are highly expressed, resulting in a large number of transcripts in a cell being spliced. As a result, splicing regulation is of critical importance for yeast. Just as in humans, yeast splicing can be influenced by protein components of the splicing machinery, structures and properties of the pre-mRNA itself, or by the action of trans-acting factors. It is likely that further analysis of the mechanisms and pathways of splicing regulation in yeast can reveal general principles applicable to other eukaryotes. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Katherine Anne Senn
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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He F, Jacobson A. Eukaryotic mRNA decapping factors: molecular mechanisms and activity. FEBS J 2023; 290:5057-5085. [PMID: 36098474 PMCID: PMC10008757 DOI: 10.1111/febs.16626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/11/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022]
Abstract
Decapping is the enzymatic removal of 5' cap structures from mRNAs in eukaryotic cells. Cap structures normally enhance mRNA translation and stability, and their excision commits an mRNA to complete 5'-3' exoribonucleolytic digestion and generally ends the physical and functional cellular presence of the mRNA. Decapping plays a pivotal role in eukaryotic cytoplasmic mRNA turnover and is a critical and highly regulated event in multiple 5'-3' mRNA decay pathways, including general 5'-3' decay, nonsense-mediated mRNA decay (NMD), AU-rich element-mediated mRNA decay, microRNA-mediated gene silencing, and targeted transcript-specific mRNA decay. In the yeast Saccharomyces cerevisiae, mRNA decapping is carried out by a single Dcp1-Dcp2 decapping enzyme in concert with the accessory activities of specific regulators commonly known as decapping activators or enhancers. These regulatory proteins include the general decapping activators Edc1, 2, and 3, Dhh1, Scd6, Pat1, and the Lsm1-7 complex, as well as the NMD-specific factors, Upf1, 2, and 3. Here, we focus on in vivo mRNA decapping regulation in yeast. We summarize recently uncovered molecular mechanisms that control selective targeting of the yeast decapping enzyme and discuss new roles for specific decapping activators in controlling decapping enzyme targeting, assembly of target-specific decapping complexes, and the monitoring of mRNA translation. Further, we discuss the kinetic contribution of mRNA decapping for overall decay of different substrate mRNAs and highlight experimental evidence pointing to the functional coordination and physical coupling between events in mRNA deadenylation, decapping, and 5'-3' exoribonucleolytic decay.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
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3
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He F, Wu C, Jacobson A. Dcp2 C-terminal cis-binding elements control selective targeting of the decapping enzyme by forming distinct decapping complexes. eLife 2022; 11:74410. [PMID: 35604319 PMCID: PMC9170289 DOI: 10.7554/elife.74410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 05/22/2022] [Indexed: 11/13/2022] Open
Abstract
A single Dcp1-Dcp2 decapping enzyme targets diverse classes of yeast mRNAs for decapping-dependent 5' to 3' decay, but the molecular mechanisms controlling mRNA selectivity by the enzyme remain elusive. Through extensive genetic analyses we reveal that Dcp2 C-terminal domain cis-regulatory elements control decapping enzyme target specificity by orchestrating formation of distinct decapping complexes. Two Upf1-binding motifs direct the decapping enzyme to NMD substrates, a single Edc3-binding motif targets both Edc3 and Dhh1 substrates, and Pat1-binding leucine-rich motifs target Edc3 and Dhh1 substrates under selective conditions. Although it functions as a unique targeting component of specific complexes, Edc3 is a common component of multiple complexes. Scd6 and Xrn1 also have specific binding sites on Dcp2, allowing them to be directly recruited to decapping complexes. Collectively, our results demonstrate that Upf1, Edc3, Scd6, and Pat1 function as regulatory subunits of the holo-decapping enzyme, controlling both its substrate specificity and enzymatic activation.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Chan Wu
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, United States
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4
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Abstract
The 5'-terminal cap is a fundamental determinant of eukaryotic gene expression which facilitates cap-dependent translation and protects mRNAs from exonucleolytic degradation. Enzyme-directed hydrolysis of the cap (decapping) decisively affects mRNA expression and turnover, and is a heavily regulated event. Following the identification of the decapping holoenzyme (Dcp1/2) over two decades ago, numerous studies revealed the complexity of decapping regulation across species and cell types. A conserved set of Dcp1/2-associated proteins, implicated in decapping activation and molecular scaffolding, were identified through genetic and molecular interaction studies, and yet their exact mechanisms of action are only emerging. In this review, we discuss the prevailing models on the roles and assembly of decapping co-factors, with considerations of conservation across species and comparison across physiological contexts. We next discuss the functional convergences of decapping machineries with other RNA-protein complexes in cytoplasmic P bodies and compare current views on their impact on mRNA stability and translation. Lastly, we review the current models of decapping activation and highlight important gaps in our current understanding.
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Affiliation(s)
- Elva Vidya
- Goodman Cancer Institute, McGill University, Montréal, QC, Canada
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Thomas F. Duchaine
- Goodman Cancer Institute, McGill University, Montréal, QC, Canada
- Department of Biochemistry, McGill University, Montréal, QC, Canada
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5
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Bearss JJ, Padi SKR, Singh N, Cardo‐Vila M, Song JH, Mouneimne G, Fernandes N, Li Y, Harter MR, Gard JMC, Cress AE, Peti W, Nelson ADL, Buchan JR, Kraft AS, Okumura K. EDC3 phosphorylation regulates growth and invasion through controlling P-body formation and dynamics. EMBO Rep 2021; 22:e50835. [PMID: 33586867 PMCID: PMC8025014 DOI: 10.15252/embr.202050835] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/20/2020] [Accepted: 01/13/2021] [Indexed: 12/18/2022] Open
Abstract
Regulation of mRNA stability and translation plays a critical role in determining protein abundance within cells. Processing bodies (P-bodies) are critical regulators of these processes. Here, we report that the Pim1 and 3 protein kinases bind to the P-body protein enhancer of mRNA decapping 3 (EDC3) and phosphorylate EDC3 on serine (S)161, thereby modifying P-body assembly. EDC3 phosphorylation is highly elevated in many tumor types, is reduced upon treatment of cells with kinase inhibitors, and blocks the localization of EDC3 to P-bodies. Prostate cancer cells harboring an EDC3 S161A mutation show markedly decreased growth, migration, and invasion in tissue culture and in xenograft models. Consistent with these phenotypic changes, the expression of integrin β1 and α6 mRNA and protein is reduced in these mutated cells. These results demonstrate that EDC3 phosphorylation regulates multiple cancer-relevant functions and suggest that modulation of P-body activity may represent a new paradigm for cancer treatment.
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Affiliation(s)
| | - Sathish KR Padi
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
- Department of Molecular Biology and BiophysicsUConn Health CenterFarmingtonCTUSA
| | - Neha Singh
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
| | - Marina Cardo‐Vila
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
- Department of Otolaryngology‐Head and Neck SurgeryUniversity of ArizonaTucsonAZUSA
| | - Jin H Song
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
- Department of Cellular and Molecular MedicineUniversity of ArizonaTucsonAZUSA
| | - Ghassan Mouneimne
- Department of Cellular and Molecular MedicineUniversity of ArizonaTucsonAZUSA
| | - Nikita Fernandes
- Department of Molecular and Cellular BiologyUniversity of ArizonaTucsonAZUSA
| | - Yang Li
- Department of Molecular Biology and BiophysicsUConn Health CenterFarmingtonCTUSA
- Department of Chemistry and BiochemistryUniversity of ArizonaTucsonAZUSA
| | - Matthew R Harter
- Department of Chemistry and BiochemistryUniversity of ArizonaTucsonAZUSA
| | - Jaime MC Gard
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
| | - Anne E Cress
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
- Department of Cellular and Molecular MedicineUniversity of ArizonaTucsonAZUSA
| | - Wolfgang Peti
- Department of Molecular Biology and BiophysicsUConn Health CenterFarmingtonCTUSA
- Department of Chemistry and BiochemistryUniversity of ArizonaTucsonAZUSA
| | | | - J Ross Buchan
- Department of Molecular and Cellular BiologyUniversity of ArizonaTucsonAZUSA
| | - Andrew S Kraft
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
- Department of MedicineUniversity of ArizonaTucsonAZUSA
| | - Koichi Okumura
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
- Department of PhysiologyUniversity of ArizonaTucsonAZUSA
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6
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Charenton C, Gaudon-Plesse C, Back R, Ulryck N, Cosson L, Séraphin B, Graille M. Pby1 is a direct partner of the Dcp2 decapping enzyme. Nucleic Acids Res 2020; 48:6353-6366. [PMID: 32396195 PMCID: PMC7293026 DOI: 10.1093/nar/gkaa337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/17/2020] [Accepted: 04/23/2020] [Indexed: 12/27/2022] Open
Abstract
Most eukaryotic mRNAs harbor a characteristic 5′ m7GpppN cap that promotes pre-mRNA splicing, mRNA nucleocytoplasmic transport and translation while also protecting mRNAs from exonucleolytic attacks. mRNA caps are eliminated by Dcp2 during mRNA decay, allowing 5′-3′ exonucleases to degrade mRNA bodies. However, the Dcp2 decapping enzyme is poorly active on its own and requires binding to stable or transient protein partners to sever the cap of target mRNAs. Here, we analyse the role of one of these partners, the yeast Pby1 factor, which is known to co-localize into P-bodies together with decapping factors. We report that Pby1 uses its C-terminal domain to directly bind to the decapping enzyme. We solved the structure of this Pby1 domain alone and bound to the Dcp1–Dcp2–Edc3 decapping complex. Structure-based mutant analyses reveal that Pby1 binding to the decapping enzyme is required for its recruitment into P-bodies. Moreover, Pby1 binding to the decapping enzyme stimulates growth in conditions in which decapping activation is compromised. Our results point towards a direct connection of Pby1 with decapping and P-body formation, both stemming from its interaction with the Dcp1–Dcp2 holoenzyme.
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Affiliation(s)
- Clément Charenton
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Claudine Gaudon-Plesse
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Régis Back
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Nathalie Ulryck
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Loreline Cosson
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
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7
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Charenton C, Graille M. mRNA decapping: finding the right structures. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0164. [PMID: 30397101 DOI: 10.1098/rstb.2018.0164] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2018] [Indexed: 12/14/2022] Open
Abstract
In eukaryotes, the elimination of the m7GpppN mRNA cap, a process known as decapping, is a critical, largely irreversible and highly regulated step of mRNA decay that withdraws the targeted mRNAs from the pool of translatable templates. The decapping reaction is catalysed by a multi-protein complex formed by the Dcp2 catalytic subunit and its Dcp1 cofactor, a holoenzyme that is poorly active on its own and needs several accessory proteins (Lsm1-7 complex, Pat1, Edc1-2, Edc3 and/or EDC4) to be fully efficient. Here, we discuss the several crystal structures of Dcp2 domains bound to various partners (proteins or small molecules) determined in the last couple of years that have considerably improved our current understanding of how Dcp2, assisted by its various activators, is recruited to its mRNA targets and adopts its active conformation upon substrate recognition. We also describe how, over the years, elegant integrative structural biology approaches combined to biochemistry and genetics led to the identification of the correct structure of the active Dcp1-Dcp2 holoenzyme among the many available conformations trapped by X-ray crystallography.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Clément Charenton
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
| | - Marc Graille
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
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8
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Gavaldá S, Santos-Pereira JM, García-Rubio ML, Luna R, Aguilera A. Excess of Yra1 RNA-Binding Factor Causes Transcription-Dependent Genome Instability, Replication Impairment and Telomere Shortening. PLoS Genet 2016; 12:e1005966. [PMID: 27035147 PMCID: PMC4818039 DOI: 10.1371/journal.pgen.1005966] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 03/09/2016] [Indexed: 11/19/2022] Open
Abstract
Yra1 is an essential nuclear factor of the evolutionarily conserved family of hnRNP-like export factors that when overexpressed impairs mRNA export and cell growth. To investigate further the relevance of proper Yra1 stoichiometry in the cell, we overexpressed Yra1 by transforming yeast cells with YRA1 intron-less constructs and analyzed its effect on gene expression and genome integrity. We found that YRA1 overexpression induces DNA damage and leads to a transcription-associated hyperrecombination phenotype that is mediated by RNA:DNA hybrids. In addition, it confers a genome-wide replication retardation as seen by reduced BrdU incorporation and accumulation of the Rrm3 helicase. In addition, YRA1 overexpression causes a cell senescence-like phenotype and telomere shortening. ChIP-chip analysis shows that overexpressed Yra1 is loaded to transcribed chromatin along the genome and to Y’ telomeric regions, where Rrm3 is also accumulated, suggesting an impairment of telomere replication. Our work not only demonstrates that a proper stoichiometry of the Yra1 mRNA binding and export factor is required to maintain genome integrity and telomere homeostasis, but suggests that the cellular imbalance between transcribed RNA and specific RNA-binding factors may become a major cause of genome instability mediated by co-transcriptional replication impairment. Yra1 is an essential nuclear RNA-binding protein that plays a role in mRNA export in Saccharomyces cerevisiae. The cellular levels of Yra1 are tightly auto-regulated by splicing of an unusual intron in its pre-mRNA, removal of which causes Yra1 overexpression that results in a dominant-negative growth defect and mRNA export defect. We wondered whether or not YRA1 overexpression has an effect on genome integrity that could explain the loss of cell viability. Our analyses reveal that YRA1 overexpression causes DNA damage, confers a hyperrecombination phenotype that depends on transcription and that is mediated by RNA:DNA hybrids. YRA1 overexpression also leads to a cell senescence-like phenotype and telomere shortening. We show by ChIP-chip analysis that Yra1 binds to active chromatin and Y’ telomeric regions when it is overexpressed, in agreement with a possible role of this mRNP factor in the maintenance of telomere integrity. Our data indicate that YRA1 overexpression correlates with replication impairment as inferred by the reduction of BrdU incorporation and the increase of Rrm3 recruitment, a helicase involved in replication fork progression, at transcribed genes and Y’ regions. We conclude that the stoichiometry of specific RNA-binding factors such as Yra1 at telomeres is critical for genome integrity and for preventing transcription-replication conflicts.
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Affiliation(s)
- Sandra Gavaldá
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Seville, Spain
| | - José M. Santos-Pereira
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Seville, Spain
| | - María L. García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Seville, Spain
| | - Rosa Luna
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Seville, Spain
- * E-mail: (AA); (RL)
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Seville, Spain
- * E-mail: (AA); (RL)
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9
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AbuQattam A, Gallego J, Rodríguez-Navarro S. An intronic RNA structure modulates expression of the mRNA biogenesis factor Sus1. RNA (NEW YORK, N.Y.) 2016; 22:75-86. [PMID: 26546116 PMCID: PMC4691836 DOI: 10.1261/rna.054049.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/03/2015] [Indexed: 06/05/2023]
Abstract
Sus1 is a conserved protein involved in chromatin remodeling and mRNA biogenesis. Unlike most yeast genes, the SUS1 pre-mRNA of Saccharomyces cerevisiae contains two introns and is alternatively spliced, retaining one or both introns in response to changes in environmental conditions. SUS1 splicing may allow the cell to control Sus1 expression, but the mechanisms that regulate this process remain unknown. Using in silico analyses together with NMR spectroscopy, gel electrophoresis, and UV thermal denaturation experiments, we show that the downstream intron (I2) of SUS1 forms a weakly stable, 37-nucleotide stem-loop structure containing the branch site near its apical loop and the 3' splice site after the stem terminus. A cellular assay revealed that two of four mutants containing altered I2 structures had significantly impaired SUS1 expression. Semiquantitative RT-PCR experiments indicated that all mutants accumulated unspliced SUS1 pre-mRNA and/or induced distorted levels of fully spliced mRNA relative to wild type. Concomitantly, Sus1 cellular functions in histone H2B deubiquitination and mRNA export were affected in I2 hairpin mutants that inhibited splicing. This work demonstrates that I2 structure is relevant for SUS1 expression, and that this effect is likely exerted through modulation of splicing.
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Affiliation(s)
- Ali AbuQattam
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain Facultad de Medicina, Universidad Católica de Valencia, Valencia 46001, Spain
| | - José Gallego
- Facultad de Medicina, Universidad Católica de Valencia, Valencia 46001, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
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10
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He F, Jacobson A. Control of mRNA decapping by positive and negative regulatory elements in the Dcp2 C-terminal domain. RNA (NEW YORK, N.Y.) 2015; 21:1633-47. [PMID: 26184073 PMCID: PMC4536323 DOI: 10.1261/rna.052449.115] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 06/08/2015] [Indexed: 05/23/2023]
Abstract
Decapping commits an mRNA to complete degradation and promotes general 5' to 3' decay, nonsense-mediated decay (NMD), and transcript-specific degradation. In Saccharomyces cerevisiae, a single decapping enzyme composed of a regulatory subunit (Dcp1) and a catalytic subunit (Dcp2) targets thousands of distinct substrate mRNAs. However, the mechanisms controlling this enzyme's in vivo activity and substrate specificity remain elusive. Here, using a genetic approach, we show that the large C-terminal domain of Dcp2 includes a set of conserved negative and positive regulatory elements. A single negative element inhibits enzymatic activity and controls the downstream functions of several positive elements. The positive elements recruit the specific decapping activators Edc3, Pat1, and Upf1 to form distinct decapping complexes and control the enzyme's substrate specificity and final activation. Our results reveal unforeseen regulatory mechanisms that control decapping enzyme activity and function in vivo, and define roles for several decapping activators in the regulation of mRNA decapping.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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11
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The C-terminal domain from S. cerevisiae Pat1 displays two conserved regions involved in decapping factor recruitment. PLoS One 2014; 9:e96828. [PMID: 24830408 PMCID: PMC4022514 DOI: 10.1371/journal.pone.0096828] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/11/2014] [Indexed: 12/03/2022] Open
Abstract
Eukaryotic mRNA decay is a highly regulated process allowing cells to rapidly modulate protein production in response to internal and environmental cues. Mature translatable eukaryotic mRNAs are protected from fast and uncontrolled degradation in the cytoplasm by two cis-acting stability determinants: a methylguanosine (m7G) cap and a poly(A) tail at their 5′ and 3′ extremities, respectively. The hydrolysis of the m7G cap structure, known as decapping, is performed by the complex composed of the Dcp2 catalytic subunit and its partner Dcp1. The Dcp1-Dcp2 decapping complex has a low intrinsic activity and requires accessory factors to be fully active. Among these factors, Pat1 is considered to be a central scaffolding protein involved in Dcp2 activation but also in inhibition of translation initiation. Here, we present the structural and functional study of the C-terminal domain from S. cerevisiae Pat1 protein. We have identified two conserved and functionally important regions located at both extremities of the domain. The first region is involved in binding to Lsm1-7 complex. The second patch is specific for fungal proteins and is responsible for Pat1 interaction with Edc3. These observations support the plasticity of the protein interaction network involved in mRNA decay and show that evolution has extended the C-terminal alpha-helical domain from fungal Pat1 proteins to generate a new binding platform for protein partners.
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12
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He F, Li C, Roy B, Jacobson A. Yeast Edc3 targets RPS28B mRNA for decapping by binding to a 3' untranslated region decay-inducing regulatory element. Mol Cell Biol 2014; 34:1438-51. [PMID: 24492965 PMCID: PMC3993580 DOI: 10.1128/mcb.01584-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 12/31/2013] [Accepted: 01/30/2014] [Indexed: 11/20/2022] Open
Abstract
mRNA decapping commits a transcript to complete turnover in eukaryotic cells. In yeast, general mRNA decapping requires the Dcp1/Dcp2 decapping enzyme and a set of decapping activators, including Pat1, Dhh1, Edc3, and the Lsm1-7 complex. The exact function and mode of action of each of these decapping activators in mRNA decapping largely remain elusive. Here, we analyzed the role of Edc3 in the decay of yeast RPS28B mRNA, a pathway triggered by a negative-feedback autoregulatory mechanism. We show that Edc3-mediated RPS28B mRNA decay requires either of two orthologous proteins, Rps28a and Rps28b, expressed from the RPS28A and RPS28B genes, respectively. Contrary to a generally accepted model, we found that Rps28b does not bind to the 3'-untranslated region (UTR) regulatory element in RPS28B mRNA. Instead, Edc3 is directly involved in binding the element, and Rps28b binds Edc3 and regulates its activity. Decay of RPS28B mRNA requires the Lsm and YjeF-N domains of Edc3, but surprisingly, decay of YRA1 pre-mRNA, the only other known substrate of Edc3, requires only the Lsm domain. Collectively, our experiments reveal a new role for Edc3 in mRNA substrate recognition and suggest that this activity is subject to intricate regulation by additional factors, including the Rps28 ribosomal protein.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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13
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Jonas S, Izaurralde E. The role of disordered protein regions in the assembly of decapping complexes and RNP granules. Genes Dev 2014; 27:2628-41. [PMID: 24352420 PMCID: PMC3877753 DOI: 10.1101/gad.227843.113] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Removal of the 5′ cap structure is a critical step in mRNA turnover, yet key questions regarding the assembly and regulation of decapping complexes remain unanswered. This review provides comprehensive insight into the structural and biochemical properties of decapping factors. Jonas and Izaurralde highlight the plasticity of the decapping network and cover recent advances that reveal how short linear motifs (SliMs) in disordered regions help maintain interactions between decapping network members. The removal of the 5′ cap structure by the decapping enzyme DCP2 inhibits translation and generally commits the mRNA to irreversible 5′-to-3′ exonucleolytic degradation by XRN1. DCP2 catalytic activity is stimulated by DCP1, and these proteins form the conserved core of the decapping complex. Additional decapping factors orchestrate the recruitment and activity of this complex in vivo. These factors include enhancer of decapping 3 (EDC3), EDC4, like Sm14A (LSm14A), Pat, the LSm1–7 complex, and the RNA helicase DDX6. Decapping factors are often modular and feature folded domains flanked or connected by low-complexity disordered regions. Recent studies have made important advances in understanding how these disordered regions contribute to the assembly of decapping complexes and promote phase transitions that drive RNP granule formation. These studies have also revealed that the decapping network is governed by interactions mediated by short linear motifs (SLiMs) in these disordered regions. Consequently, the network has rapidly evolved, and although decapping factors are conserved, individual interactions between orthologs have been rewired during evolution. The plasticity of the network facilitates the acquisition of additional subunits or domains in pre-existing subunits, enhances opportunities for regulating mRNA degradation, and eventually leads to the emergence of novel functions.
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Affiliation(s)
- Stefanie Jonas
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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14
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Intra- and intermolecular regulatory interactions in Upf1, the RNA helicase central to nonsense-mediated mRNA decay in yeast. Mol Cell Biol 2013; 33:4672-84. [PMID: 24100012 DOI: 10.1128/mcb.01136-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA helicases are involved in almost every aspect of RNA metabolism, yet very little is known about the regulation of this class of enzymes. In Saccharomyces cerevisiae, the stability and translational fidelity of nonsense-containing mRNAs are controlled by the group I RNA helicase Upf1 and the proteins it interacts with, Upf2 and Upf3. Combining the yeast two-hybrid system with genetic analysis, we show here that the cysteine- and histidine-rich (CH) domain and the RNA helicase domain of yeast Upf1 can engage in two new types of molecular interactions: an intramolecular interaction between these two domains and self-association of each of these domains. Multiple observations indicate that these molecular interactions are crucial for Upf1 regulation. First, coexpression of the CH domain and the RNA helicase domain in trans can reconstitute Upf1 function in both promoting nonsense-mediated mRNA decay (NMD) and preventing nonsense suppression. Second, mutations that disrupt Upf1 intramolecular interaction cause loss of Upf1 function. These mutations weaken Upf2 interaction and, surprisingly, promote Upf1 self-association. Third, the genetic defects resulting from deficiency in Upf1 intramolecular interaction or RNA binding are suppressed by expression of Upf2. Collectively, these data reveal a set of sequential molecular interactions and their roles in regulating Upf1 function during activation of NMD and suggest that cis intramolecular interaction and trans self-association may be general mechanisms for regulation of RNA helicase functions.
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15
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Roy B, Jacobson A. The intimate relationships of mRNA decay and translation. Trends Genet 2013; 29:691-9. [PMID: 24091060 DOI: 10.1016/j.tig.2013.09.002] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 08/21/2013] [Accepted: 09/03/2013] [Indexed: 11/18/2022]
Abstract
The decay rate of an mRNA and the efficiency with which it is translated are key determinants of eukaryotic gene expression. Although it was once thought that mRNA stability and translational efficiency were directly linked, the interrelationships between the two processes are considerably more complex. The decay of individual mRNAs can be triggered or antagonized by translational impairment, and alterations in the half-life of certain mRNAs can even alter translational fidelity. In this review we consider whether mRNA translation and turnover are distinct or overlapping phases of an mRNA life cycle, and then address some of the many ways in which the two processes influence each other in eukaryotic cells.
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Affiliation(s)
- Bijoyita Roy
- Department of Microbiology and Physiological Systems, Albert Sherman Center, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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16
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Kolesnikova O, Back R, Graille M, Séraphin B. Identification of the Rps28 binding motif from yeast Edc3 involved in the autoregulatory feedback loop controlling RPS28B mRNA decay. Nucleic Acids Res 2013; 41:9514-23. [PMID: 23956223 PMCID: PMC3814365 DOI: 10.1093/nar/gkt607] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, the Edc3 protein was previously reported to participate in the auto-regulatory feedback loop controlling the level of the RPS28B messenger RNA (mRNA). We show here that Edc3 binds directly and tightly to the globular core of Rps28 ribosomal protein. This binding occurs through a motif that is present exclusively in Edc3 proteins from yeast belonging to the Saccharomycetaceae phylum. Functional analyses indicate that the ability of Edc3 to interact with Rps28 is not required for its general function and for its role in the regulation of the YRA1 pre-mRNA decay. In contrast, this interaction appears to be exclusively required for the auto-regulatory mechanism controlling the RPS28B mRNA decay. These observations suggest a plausible model for the evolutionary appearance of a Rps28 binding motif in Edc3.
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Affiliation(s)
- Olga Kolesnikova
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé et de la Recherche Médicale (INSERM) U964/Université de Strasbourg, 67404 Illkirch, France, Ecole Polytechnique, Laboratoire de Biochimie, CNRS UMR7654, 91128 Palaiseau Cedex, France and Institut de Biochimie et Biophysique Moléculaire et Cellulaire (IBBMC), CNRS, UMR8619, Bat 430, Université Paris Sud, 91405 Orsay Cedex, France
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17
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Balagopal V, Fluch L, Nissan T. Ways and means of eukaryotic mRNA decay. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:593-603. [DOI: 10.1016/j.bbagrm.2012.01.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 12/29/2011] [Accepted: 01/03/2012] [Indexed: 10/14/2022]
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18
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Cuenca-Bono B, García-Molinero V, Pascual-García P, Dopazo H, Llopis A, Vilardell J, Rodríguez-Navarro S. SUS1 introns are required for efficient mRNA nuclear export in yeast. Nucleic Acids Res 2011; 39:8599-611. [PMID: 21749979 PMCID: PMC3201862 DOI: 10.1093/nar/gkr496] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Efficient coupling between mRNA synthesis and export is essential for gene expression. Sus1/ENY2, a component of the SAGA and TREX-2 complexes, is involved in both transcription and mRNA export. While most yeast genes lack introns, we previously reported that yeast SUS1 bears two. Here we show that this feature is evolutionarily conserved and critical for Sus1 function. We determine that while SUS1 splicing is inefficient, it responds to cellular conditions, and intronic mutations either promoting or blocking splicing lead to defects in mRNA export and cell growth. Consistent with this, we find that an intron-less SUS1 only partially rescues sus1Δ phenotypes. Remarkably, splicing of each SUS1 intron is also affected by the presence of the other and by SUS1 exonic sequences. Moreover, by following SUS1 RNA and protein levels we establish that nonsense-mediated decay (NMD) pathway and the splicing factor Mud2 both play a role in SUS1 expression. Our data (and those of the accompanying work by Hossain et al.) provide evidence of the involvement of splicing, translation, and decay in the regulation of early events in mRNP biogenesis; and imply the additional requirement for a balance in splicing isoforms from a single gene.
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Affiliation(s)
- Bernardo Cuenca-Bono
- Centro de Investigación Príncipe Felipe, Gene Expression coupled to RNA Transport Laboratory, Av Saler 16. E-46012, Valencia, Spain
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19
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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