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Graber JH, Hoskinson D, Liu H, Kaczmarek Michaels K, Benson PS, Maki NJ, Wilson CL, McGrath C, Puleo F, Pearson E, Kuehner JN, Moore C. Mutations in yeast Pcf11, a conserved protein essential for mRNA 3' end processing and transcription termination, elicit the Environmental Stress Response. Genetics 2024; 226:iyad199. [PMID: 37967370 PMCID: PMC10847720 DOI: 10.1093/genetics/iyad199] [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: 07/11/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023] Open
Abstract
The Pcf11 protein is an essential subunit of the large complex that cleaves and polyadenylates eukaryotic mRNA precursor. It has also been functionally linked to gene-looping, termination of RNA Polymerase II (Pol II) transcripts, and mRNA export. We have examined a poorly characterized but conserved domain (amino acids 142-225) of the Saccharomyces cerevisiae Pcf11 and found that while it is not needed for mRNA 3' end processing or termination downstream of the poly(A) sites of protein-coding genes, its presence improves the interaction with Pol II and the use of transcription terminators near gene promoters. Analysis of genome-wide Pol II occupancy in cells with Pcf11 missing this region, as well as Pcf11 mutated in the Pol II CTD Interacting Domain, indicates that systematic changes in mRNA expression are mediated primarily at the level of transcription. Global expression analysis also shows that a general stress response, involving both activation and suppression of specific gene sets known to be regulated in response to a wide variety of stresses, is induced in the two pcf11 mutants, even though cells are grown in optimal conditions. The mutants also cause an unbalanced expression of cell wall-related genes that does not activate the Cell Wall Integrity pathway but is associated with strong caffeine sensitivity. Based on these findings, we propose that Pcf11 can modulate the expression level of specific functional groups of genes in ways that do not involve its well-characterized role in mRNA 3' end processing.
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Affiliation(s)
- Joel H Graber
- Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Derick Hoskinson
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Huiyun Liu
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Katarzyna Kaczmarek Michaels
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Peter S Benson
- Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Nathaniel J Maki
- Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA
| | | | - Caleb McGrath
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Franco Puleo
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Erika Pearson
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Jason N Kuehner
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Claire Moore
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
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2
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Rodríguez‐Molina JB, Turtola M. Birth of a poly(A) tail: mechanisms and control of mRNA polyadenylation. FEBS Open Bio 2023; 13:1140-1153. [PMID: 36416579 PMCID: PMC10315857 DOI: 10.1002/2211-5463.13528] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022] Open
Abstract
During their synthesis in the cell nucleus, most eukaryotic mRNAs undergo a two-step 3'-end processing reaction in which the pre-mRNA is cleaved and released from the transcribing RNA polymerase II and a polyadenosine (poly(A)) tail is added to the newly formed 3'-end. These biochemical reactions might appear simple at first sight (endonucleolytic RNA cleavage and synthesis of a homopolymeric tail), but their catalysis requires a multi-faceted enzymatic machinery, the cleavage and polyadenylation complex (CPAC), which is composed of more than 20 individual protein subunits. The activity of CPAC is further orchestrated by Poly(A) Binding Proteins (PABPs), which decorate the poly(A) tail during its synthesis and guide the mRNA through subsequent gene expression steps. Here, we review the structure, molecular mechanism, and regulation of eukaryotic mRNA 3'-end processing machineries with a focus on the polyadenylation step. We concentrate on the CPAC and PABPs from mammals and the budding yeast, Saccharomyces cerevisiae, because these systems are the best-characterized at present. Comparison of their functions provides valuable insights into the principles of mRNA 3'-end processing.
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Affiliation(s)
| | - Matti Turtola
- Department of Life TechnologiesUniversity of TurkuFinland
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3
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Nuclear mRNA Export and Aging. Int J Mol Sci 2022; 23:ijms23105451. [PMID: 35628261 PMCID: PMC9142925 DOI: 10.3390/ijms23105451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
The relationship between transcription and aging is one that has been studied intensively and experimentally with diverse attempts. However, the impact of the nuclear mRNA export on the aging process following its transcription is still poorly understood, although the nuclear events after transcription are coupled closely with the transcription pathway because the essential factors required for mRNA transport, namely TREX, TREX-2, and nuclear pore complex (NPC), physically and functionally interact with various transcription factors, including the activator/repressor and pre-mRNA processing factors. Dysregulation of the mediating factors for mRNA export from the nucleus generally leads to the aberrant accumulation of nuclear mRNA and further impairment in the vegetative growth and normal lifespan and the pathogenesis of neurodegenerative diseases. The optimal stoichiometry and density of NPC are destroyed during the process of cellular aging, and their damage triggers a defect of function in the nuclear permeability barrier. This review describes recent findings regarding the role of the nuclear mRNA export in cellular aging and age-related neurodegenerative disorders.
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4
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Turtola M, Manav MC, Kumar A, Tudek A, Mroczek S, Krawczyk PS, Dziembowski A, Schmid M, Passmore LA, Casañal A, Jensen TH. Three-layered control of mRNA poly(A) tail synthesis in Saccharomyces cerevisiae. Genes Dev 2021; 35:1290-1303. [PMID: 34385261 PMCID: PMC8415320 DOI: 10.1101/gad.348634.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/15/2021] [Indexed: 12/13/2022]
Abstract
Biogenesis of most eukaryotic mRNAs involves the addition of an untemplated polyadenosine (pA) tail by the cleavage and polyadenylation machinery. The pA tail, and its exact length, impacts mRNA stability, nuclear export, and translation. To define how polyadenylation is controlled in S. cerevisiae, we have used an in vivo assay capable of assessing nuclear pA tail synthesis, analyzed tail length distributions by direct RNA sequencing, and reconstituted polyadenylation reactions with purified components. This revealed three control mechanisms for pA tail length. First, we found that the pA binding protein (PABP) Nab2p is the primary regulator of pA tail length. Second, when Nab2p is limiting, the nuclear pool of Pab1p, the second major PABP in yeast, controls the process. Third, when both PABPs are absent, the cleavage and polyadenylation factor (CPF) limits pA tail synthesis. Thus, Pab1p and CPF provide fail-safe mechanisms to a primary Nab2p-dependent pathway, thereby preventing uncontrolled polyadenylation and allowing mRNA export and translation.
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Affiliation(s)
- Matti Turtola
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - M Cemre Manav
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Ananthanarayanan Kumar
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Agnieszka Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Seweryn Mroczek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Paweł S Krawczyk
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Lori A Passmore
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Ana Casañal
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
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5
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Pardamean CI, Wu TT. Inhibition of Host Gene Expression by KSHV: Sabotaging mRNA Stability and Nuclear Export. Front Cell Infect Microbiol 2021; 11:648055. [PMID: 33898329 PMCID: PMC8062738 DOI: 10.3389/fcimb.2021.648055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/19/2021] [Indexed: 12/25/2022] Open
Abstract
Viruses are known for their ability to alter host gene expression. Kaposi sarcoma-associated herpesvirus has two proteins that obstruct host gene expression. KSHV SOX, encoded by the open reading frame 37 (ORF37), induces a widespread cytoplasmic mRNA degradation and a block on mRNA nuclear export. The other KSHV protein, encoded by the open reading frame 10 (ORF10), was recently identified to inhibit host gene expression through its direct function on the cellular mRNA export pathway. In this review, we summarize the studies on both SOX and ORF10 in efforts to elucidate their mechanisms. We also discuss how the findings based on a closely related rodent virus, murine gammaherpesvirus-68 (MHV-68), complement the KSHV findings to decipher the role of these two proteins in viral pathogenesis.
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Affiliation(s)
- Carissa Ikka Pardamean
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, United States
| | - Ting-Ting Wu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, United States
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6
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Vasianovich Y, Bajon E, Wellinger RJ. Telomerase biogenesis requires a novel Mex67 function and a cytoplasmic association with the Sm 7 complex. eLife 2020; 9:60000. [PMID: 33095156 PMCID: PMC7644208 DOI: 10.7554/elife.60000] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/22/2020] [Indexed: 12/15/2022] Open
Abstract
The templating RNA is the core of the telomerase reverse transcriptase. In Saccharomyces cerevisiae, the complex life cycle and maturation of telomerase includes a cytoplasmic stage. However, timing and reason for this cytoplasmic passage are poorly understood. Here, we use inducible RNA tagging experiments to show that immediately after transcription, newly synthesized telomerase RNAs undergo one round of nucleo-cytoplasmic shuttling. Their export depends entirely on Crm1/Xpo1, whereas re-import is mediated by Kap122 plus redundant, kinetically less efficient import pathways. Strikingly, Mex67 is essential to stabilize newly transcribed RNA before Xpo1-mediated nuclear export. The results further show that the Sm7 complex associates with and stabilizes the telomerase RNA in the cytoplasm and promotes its nuclear re-import. Remarkably, after this cytoplasmic passage, the nuclear stability of telomerase RNA no longer depends on Mex67. These results underscore the utility of inducible RNA tagging and challenge current models of telomerase maturation.
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Affiliation(s)
- Yulia Vasianovich
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Emmanuel Bajon
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
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7
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Gales JP, Kubina J, Geldreich A, Dimitrova M. Strength in Diversity: Nuclear Export of Viral RNAs. Viruses 2020; 12:E1014. [PMID: 32932882 PMCID: PMC7551171 DOI: 10.3390/v12091014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
The nuclear export of cellular mRNAs is a complex process that requires the orchestrated participation of many proteins that are recruited during the early steps of mRNA synthesis and processing. This strategy allows the cell to guarantee the conformity of the messengers accessing the cytoplasm and the translation machinery. Most transcripts are exported by the exportin dimer Nuclear RNA export factor 1 (NXF1)-NTF2-related export protein 1 (NXT1) and the transcription-export complex 1 (TREX1). Some mRNAs that do not possess all the common messenger characteristics use either variants of the NXF1-NXT1 pathway or CRM1, a different exportin. Viruses whose mRNAs are synthesized in the nucleus (retroviruses, the vast majority of DNA viruses, and influenza viruses) exploit both these cellular export pathways. Viral mRNAs hijack the cellular export machinery via complex secondary structures recognized by cellular export factors and/or viral adapter proteins. This way, the viral transcripts succeed in escaping the host surveillance system and are efficiently exported for translation, allowing the infectious cycle to proceed. This review gives an overview of the cellular mRNA nuclear export mechanisms and presents detailed insights into the most important strategies that viruses use to export the different forms of their RNAs from the nucleus to the cytoplasm.
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Affiliation(s)
- Jón Pol Gales
- Institut de Biologie Moléculaire des Plantes, The French National Center for Scientific Research (CNRS) UPR2357, Université de Strasbourg, F-67084 Strasbourg, France; (J.P.G.); (J.K.); (A.G.)
| | - Julie Kubina
- Institut de Biologie Moléculaire des Plantes, The French National Center for Scientific Research (CNRS) UPR2357, Université de Strasbourg, F-67084 Strasbourg, France; (J.P.G.); (J.K.); (A.G.)
- SVQV UMR-A 1131, INRAE, Université de Strasbourg, F-68000 Colmar, France
| | - Angèle Geldreich
- Institut de Biologie Moléculaire des Plantes, The French National Center for Scientific Research (CNRS) UPR2357, Université de Strasbourg, F-67084 Strasbourg, France; (J.P.G.); (J.K.); (A.G.)
| | - Maria Dimitrova
- Institut de Biologie Moléculaire des Plantes, The French National Center for Scientific Research (CNRS) UPR2357, Université de Strasbourg, F-67084 Strasbourg, France; (J.P.G.); (J.K.); (A.G.)
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8
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Viphakone N, Sudbery I, Griffith L, Heath CG, Sims D, Wilson SA. Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome. Mol Cell 2019; 75:310-323.e8. [PMID: 31104896 PMCID: PMC6675937 DOI: 10.1016/j.molcel.2019.04.034] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 02/25/2019] [Accepted: 04/29/2019] [Indexed: 11/29/2022]
Abstract
During gene expression, RNA export factors are mainly known for driving nucleo-cytoplasmic transport. While early studies suggested that the exon junction complex (EJC) provides a binding platform for them, subsequent work proposed that they are only recruited by the cap binding complex to the 5′ end of RNAs, as part of TREX. Using iCLIP, we show that the export receptor Nxf1 and two TREX subunits, Alyref and Chtop, are recruited to the whole mRNA co-transcriptionally via splicing but before 3′ end processing. Consequently, Alyref alters splicing decisions and Chtop regulates alternative polyadenylation. Alyref is recruited to the 5′ end of RNAs by CBC, and our data reveal subsequent binding to RNAs near EJCs. We demonstrate that eIF4A3 stimulates Alyref deposition not only on spliced RNAs close to EJC sites but also on single-exon transcripts. Our study reveals mechanistic insights into the co-transcriptional recruitment of mRNA export factors and how this shapes the human transcriptome. 5′ cap binding complex CBC acts as a transient landing pad for Alyref Alyref is deposited upstream of the exon-exon junction next to the EJC Alyref can be deposited on introns and regulate splicing Chtop is mainly deposited on 3′ UTRs and influences poly(A) site choices
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Affiliation(s)
- Nicolas Viphakone
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
| | - Ian Sudbery
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Llywelyn Griffith
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Catherine G Heath
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - David Sims
- MRC Computational Genomics Analysis and Training Programme (CGAT), MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS UK
| | - Stuart A Wilson
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
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9
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Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination. Genetics 2019; 212:153-174. [PMID: 30902808 DOI: 10.1534/genetics.119.302058] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/19/2019] [Indexed: 11/18/2022] Open
Abstract
RNA helicases are a class of enzymes that unwind RNA duplexes in vitro but whose cellular functions are largely enigmatic. Here, we provide evidence that the DEAD-box protein Dbp2 remodels RNA-protein complex (RNP) structure to facilitate efficient termination of transcription in Saccharomyces cerevisiae via the Nrd1-Nab3-Sen1 (NNS) complex. First, we find that loss of DBP2 results in RNA polymerase II accumulation at the 3' ends of small nucleolar RNAs and a subset of mRNAs. In addition, Dbp2 associates with RNA sequence motifs and regions bound by Nrd1 and can promote its recruitment to NNS-targeted regions. Using Structure-seq, we find altered RNA/RNP structures in dbp2∆ cells that correlate with inefficient termination. We also show a positive correlation between the stability of structures in the 3' ends and a requirement for Dbp2 in termination. Taken together, these studies provide a role for RNA remodeling by Dbp2 and further suggests a mechanism whereby RNA structure is exploited for gene regulation.
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10
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Abstract
In eukaryotes, the separation of translation from transcription by the nuclear envelope enables mRNA modifications such as capping, splicing, and polyadenylation. These modifications are mediated by a spectrum of ribonuclear proteins that associate with preRNA transcripts, coordinating the different steps and coupling them to nuclear export, ensuring that only mature transcripts reach the cytoplasmic translation machinery. Although the components of this machinery have been identified and considerable functional insight has been achieved, a number of questions remain outstanding about mRNA nuclear export and how it is integrated into the nuclear phase of the gene expression pathway. Nuclear export factors mediate mRNA transit through nuclear pores to the cytoplasm, after which these factors are removed from the mRNA, preventing transcripts from returning to the nucleus. However, as outlined in this review, several aspects of the mechanism by which transport factor binding and release are mediated remain unclear, as are the roles of accessory nuclear components in these processes. Moreover, the mechanisms by which completion of mRNA splicing and polyadenylation are recognized, together with how they are coordinated with nuclear export, also remain only partially characterized. One attractive hypothesis is that dissociating poly(A) polymerase from the cleavage and polyadenylation machinery could signal completion of mRNA maturation and thereby provide a mechanism for initiating nuclear export. The impressive array of genetic, molecular, cellular, and structural data that has been generated about these systems now provides many of the tools needed to define the precise mechanisms involved in these processes and how they are integrated.
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Affiliation(s)
- Murray Stewart
- From the MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
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11
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Katahira J, Ishikawa H, Tsujimura K, Kurono S, Hieda M. Human THO coordinates transcription termination and subsequent transcript release from the
HSP70
locus. Genes Cells 2019; 24:272-283. [DOI: 10.1111/gtc.12672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/16/2019] [Accepted: 01/31/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Jun Katahira
- Laboratory of Cellular and Molecular Biology, Department of Veterinary Sciences Osaka Prefecture University Izumisano Osaka Japan
| | - Hiroki Ishikawa
- Laboratory of Cellular and Molecular Biology, Department of Veterinary Sciences Osaka Prefecture University Izumisano Osaka Japan
| | - Kakeru Tsujimura
- Laboratory of Cellular and Molecular Biology, Department of Veterinary Sciences Osaka Prefecture University Izumisano Osaka Japan
| | - Sadamu Kurono
- Graduate School of Medicine and Health Sciences Osaka University Suita Osaka Japan
- Laboratory Chemicals Division Wako Pure Chemical Industries Ltd Osaka Japan
| | - Miki Hieda
- Graduate School of Health Sciences Ehime Prefectural University of Health Sciences Iyo‐gun Ehime Japan
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12
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Diamos AG, Mason HS. Chimeric 3' flanking regions strongly enhance gene expression in plants. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1971-1982. [PMID: 29637682 PMCID: PMC6230951 DOI: 10.1111/pbi.12931] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/07/2018] [Accepted: 03/30/2018] [Indexed: 05/24/2023]
Abstract
Plants represent a promising platform for the highly scalable production of recombinant proteins. Previously, we identified the tobacco extensin terminator lacking its intron as an element that reduced transcript read-through and improved recombinant protein production in a plant-based system. In this study, we systematically compared nonreplicating plant expression vectors containing over 20 commonly used or newly identified terminators from diverse sources. We found that eight gene terminators enhance reporter gene expression significantly more than the commonly used 35S and NOS terminators. The intronless extensin terminator provided a 13.6-fold increase compared with the NOS terminator. Combining terminators in tandem produced large synergistic effects, with many combinations providing a >25-fold increase in expression. Addition of the tobacco Rb7 or TM6 matrix attachment region (MAR) strongly enhanced protein production when added to most terminators, with the Rb7 MAR providing the greatest enhancement. Using deletion analysis, the full activity of the 1193 bp Rb7 MAR was found to require only a 463-bp region at its 3' end. Combined terminators and MAR together provided a >60-fold increase compared with the NOS terminator alone. These combinations were then placed in a replicating geminiviral vector, providing a total of >150-fold enhancement over the original NOS vector, corresponding to an estimated yield of 3-5 g recombinant protein per kg leaf fresh weight or around 50% of the leaf total soluble protein. These results demonstrate the importance of 3' flanking regions in optimizing gene expression and show great potential for 3' flanking regions to improve DNA-based recombinant protein production systems.
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Affiliation(s)
- Andrew G. Diamos
- Center for Immunotherapy, Vaccines and VirotherapyBiodesign Institute at ASU, and School of Life SciencesArizona State UniversityTempeAZUSA
| | - Hugh S. Mason
- Center for Immunotherapy, Vaccines and VirotherapyBiodesign Institute at ASU, and School of Life SciencesArizona State UniversityTempeAZUSA
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13
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Rosenthal SH, Diamos AG, Mason HS. An intronless form of the tobacco extensin gene terminator strongly enhances transient gene expression in plant leaves. PLANT MOLECULAR BIOLOGY 2018; 96:429-443. [PMID: 29429129 DOI: 10.1007/s11103-018-0708-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 02/01/2018] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE We have found interesting features of a plant gene (extensin) 3' flanking region, including extremely efficient polyadenylation which greatly improves transient expression of transgenes when an intron is removed. Its use will greatly benefit studies of gene expression in plants, research in molecular biology, and applications for recombinant proteins. Plants are a promising platform for the production of recombinant proteins. To express high-value proteins in plants efficiently, the optimization of expression cassettes using appropriate regulatory sequences is critical. Here, we characterize the activity of the tobacco extensin (Ext) gene terminator by transient expression in Nicotiana benthamiana, tobacco, and lettuce. Ext is a member of the hydroxyproline-rich glycoprotein (HRGP) superfamily and constitutes the major protein component of cell walls. The present study demonstrates that the Ext terminator with its native intron removed increased transient gene expression up to 13.5-fold compared to previously established terminators. The enhanced transgene expression was correlated with increased mRNA accumulation and reduced levels of read-through transcripts, which could impair gene expression. Analysis of transcript 3'-ends found that the majority of polyadenylated transcripts were cleaved at a YA dinucleotide downstream from a canonical AAUAAA motif and a UG-rich region, both of which were found to be highly conserved among related extensin terminators. Deletion of either of these regions eliminated most of the activity of the terminator. Additionally, a 45 nt polypurine sequence ~ 175 nt upstream from the polyadenylation sites was found to also be necessary for the enhanced expression. We conclude that the use of Ext terminator has great potential to benefit the production of recombinant proteins in plants.
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Affiliation(s)
- Sun Hee Rosenthal
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA
| | - Andrew G Diamos
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA
| | - Hugh S Mason
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA.
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14
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Abstract
TRanscription and EXport (TREX) is a conserved multisubunit complex essential for embryogenesis, organogenesis and cellular differentiation throughout life. By linking transcription, mRNA processing and export together, it exerts a physiologically vital role in the gene expression pathway. In addition, this complex prevents DNA damage and regulates the cell cycle by ensuring optimal gene expression. As the extent of TREX activity in viral infections, amyotrophic lateral sclerosis and cancer emerges, the need for a greater understanding of TREX function becomes evident. A complete elucidation of the composition, function and interactions of the complex will provide the framework for understanding the molecular basis for a variety of diseases. This review details the known composition of TREX, how it is regulated and its cellular functions with an emphasis on mammalian systems.
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15
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Vera M, Biswas J, Senecal A, Singer RH, Park HY. Single-Cell and Single-Molecule Analysis of Gene Expression Regulation. Annu Rev Genet 2017; 50:267-291. [PMID: 27893965 DOI: 10.1146/annurev-genet-120215-034854] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent advancements in single-cell and single-molecule imaging technologies have resolved biological processes in time and space that are fundamental to understanding the regulation of gene expression. Observations of single-molecule events in their cellular context have revealed highly dynamic aspects of transcriptional and post-transcriptional control in eukaryotic cells. This approach can relate transcription with mRNA abundance and lifetimes. Another key aspect of single-cell analysis is the cell-to-cell variability among populations of cells. Definition of heterogeneity has revealed stochastic processes, determined characteristics of under-represented cell types or transitional states, and integrated cellular behaviors in the context of multicellular organisms. In this review, we discuss novel aspects of gene expression of eukaryotic cells and multicellular organisms revealed by the latest advances in single-cell and single-molecule imaging technology.
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Affiliation(s)
- Maria Vera
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , ,
| | - Jeetayu Biswas
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , ,
| | - Adrien Senecal
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , ,
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , , .,Janelia Research Campus of the HHMI, Ashburn, Virginia 20147
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Korea; .,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Korea
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Gudde AEEG, van Kessel IDG, André LM, Wieringa B, Wansink DG. Trinucleotide-repeat expanded and normal DMPK transcripts contain unusually long poly(A) tails despite differential nuclear residence. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:740-749. [PMID: 28435090 DOI: 10.1016/j.bbagrm.2017.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/26/2017] [Accepted: 04/14/2017] [Indexed: 12/29/2022]
Abstract
In yeast and higher eukaryotes nuclear retention of transcripts may serve in control over RNA decay, nucleocytoplasmic transport and premature cytoplasmic appearance of mRNAs. Hyperadenylation of RNA is known to be associated with nuclear retention, but the cause-consequence relationship between hyperadenylation and regulation of RNA nuclear export is still unclear. We compared polyadenylation status between normal and expanded DMPK transcripts in muscle cells and tissues derived from unaffected individuals and patients with myotonic dystrophy type 1 (DM1). DM1 is an autosomal dominant disorder caused by (CTG)n repeat expansion in the DMPK gene. DM1 etiology is characterized by an almost complete block of nuclear export of DMPK transcripts carrying a long (CUG)n repeat, including aberrant sequestration of RNA-binding proteins. We show here by use of cell fractionation, RNA size separation and analysis of poly(A) tail length that a considerable fraction of transcripts from the normal DMPK allele is also retained in the nucleus (~30%). They carry poly(A) tails with an unusually broad length distribution, ranging between a few dozen to >500 adenosine residues. Remarkably, expanded DMPK (CUG)n transcripts from the mutant allele, almost exclusively nuclear, carry equally long poly(A) tails. Our findings thus suggest that nuclear retention may be a common feature of regulation of DMPK RNA expression. The typical forced nuclear residence of expanded DMPK transcripts affects this regulation in tissues of DM1 patients, but not through hyperadenylation.
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Affiliation(s)
- Anke E E G Gudde
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Ingeborg D G van Kessel
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Laurène M André
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Bé Wieringa
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Derick G Wansink
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands.
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17
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Eshleman N, Liu G, McGrath K, Parker R, Buchan JR. Defects in THO/TREX-2 function cause accumulation of novel cytoplasmic mRNP granules that can be cleared by autophagy. RNA (NEW YORK, N.Y.) 2016; 22:1200-14. [PMID: 27251550 PMCID: PMC4931113 DOI: 10.1261/rna.057224.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 05/09/2016] [Indexed: 05/08/2023]
Abstract
The nuclear THO and TREX-2 complexes are implicated in several steps of nuclear mRNP biogenesis, including transcription, 3' end processing and export. In a recent genomic microscopy screen in Saccharomyces cerevisiae for mutants with constitutive stress granules, we identified that absence of THO and TREX-2 complex subunits leads to the accumulation of Pab1-GFP in cytoplasmic foci. We now show that these THO/TREX-2 mutant induced foci ("TT foci") are not stress granules but instead are a mRNP granule containing poly(A)(+) mRNA, some mRNP components also found in stress granules, as well several proteins involved in mRNA 3' end processing and export not normally seen in stress granules. In addition, TT foci are resistant to cycloheximide-induced disassembly, suggesting the presence of mRNPs impaired for entry into translation. THO mutants also exhibit defects in normal stress granule assembly. Finally, our data also suggest that TT foci are targeted by autophagy. These observations argue that defects in nuclear THO and TREX-2 complexes can affect cytoplasmic mRNP function by producing aberrant mRNPs that are exported to cytosol, where they accumulate in TT foci and ultimately can be cleared by autophagy. This identifies a novel mechanism of quality control for aberrant mRNPs assembled in the nucleus.
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Affiliation(s)
- Nichole Eshleman
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Guangbo Liu
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Kaitlyn McGrath
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado 80303, USA
| | - J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
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18
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Musser SM, Grünwald D. Deciphering the Structure and Function of Nuclear Pores Using Single-Molecule Fluorescence Approaches. J Mol Biol 2016; 428:2091-119. [PMID: 26944195 DOI: 10.1016/j.jmb.2016.02.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/05/2016] [Accepted: 02/17/2016] [Indexed: 01/06/2023]
Abstract
Due to its central role in macromolecular trafficking and nucleocytoplasmic information transfer, the nuclear pore complex (NPC) has been studied in great detail using a wide spectrum of methods. Consequently, many aspects of its architecture, general function, and role in the life cycle of a cell are well understood. Over the last decade, fluorescence microscopy methods have enabled the real-time visualization of single molecules interacting with and transiting through the NPC, allowing novel questions to be examined with nanometer precision. While initial single-molecule studies focused primarily on import pathways using permeabilized cells, it has recently proven feasible to investigate the export of mRNAs in living cells. Single-molecule assays can address questions that are difficult or impossible to answer by other means, yet the complexity of nucleocytoplasmic transport requires that interpretation be based on a firm genetic, biochemical, and structural foundation. Moreover, conceptually simple single-molecule experiments remain technically challenging, particularly with regard to signal intensity, signal-to-noise ratio, and the analysis of noise, stochasticity, and precision. We discuss nuclear transport issues recently addressed by single-molecule microscopy, evaluate the limits of existing assays and data, and identify open questions for future studies. We expect that single-molecule fluorescence approaches will continue to be applied to outstanding nucleocytoplasmic transport questions, and that the approaches developed for NPC studies are extendable to additional complex systems and pathways within cells.
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Affiliation(s)
- Siegfried M Musser
- Department of Molecular and Cellular Medicine, College of Medicine, The Texas A&M Health Science Center, 1114 TAMU, College Station, TX 77843, USA.
| | - David Grünwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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19
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Tran EJ, King MC, Corbett AH. Macromolecular transport between the nucleus and the cytoplasm: Advances in mechanism and emerging links to disease. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1843:2784-2795. [PMID: 25116306 PMCID: PMC4161953 DOI: 10.1016/j.bbamcr.2014.08.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/01/2014] [Accepted: 08/02/2014] [Indexed: 01/08/2023]
Abstract
Transport of macromolecules between the cytoplasm and the nucleus is critical for the function of all eukaryotic cells. Large macromolecular channels termed nuclear pore complexes that span the nuclear envelope mediate the bidirectional transport of cargoes between the nucleus and cytoplasm. However, the influence of macromolecular trafficking extends past the nuclear pore complex to transcription and RNA processing within the nucleus and signaling pathways that reach into the cytoplasm and beyond. At the Mechanisms of Nuclear Transport biennial meeting held from October 18 to 23, 2013 in Woods Hole, MA, researchers in the field met to report on their recent findings. The work presented highlighted significant advances in understanding nucleocytoplasmic trafficking including how transport receptors and cargoes pass through the nuclear pore complex, the many signaling pathways that impinge on transport pathways, interplay between the nuclear envelope, nuclear pore complexes, and transport pathways, and numerous links between transport pathways and human disease. The goal of this review is to highlight newly emerging themes in nuclear transport and underscore the major questions that are likely to be the focus of future research in the field.
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Affiliation(s)
- Elizabeth J Tran
- Department of Biochemistry, Purdue University, 175 S. University Street, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West Lafayette, IN 47907, USA.
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, 4117 Rollins Research Center, 1510 Clifton Road, NE, Atlanta, GA 30322, USA.
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20
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Björk P, Wieslander L. Mechanisms of mRNA export. Semin Cell Dev Biol 2014; 32:47-54. [PMID: 24813364 DOI: 10.1016/j.semcdb.2014.04.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/17/2014] [Indexed: 02/02/2023]
Abstract
Release of properly processed and assembled mRNPs from the actively transcribing genes, movement of the mRNPs through the interchromatin and interaction with the Nuclear Pore Complexes, leading to cytoplasmic export, are essential steps of eukaryotic gene expression. Here, we review these intranuclear gene expression steps.
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Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden.
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21
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Charlesworth A, Meijer HA, de Moor CH. Specificity factors in cytoplasmic polyadenylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 4:437-61. [PMID: 23776146 PMCID: PMC3736149 DOI: 10.1002/wrna.1171] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 12/12/2022]
Abstract
Poly(A) tail elongation after export of an messenger RNA (mRNA) to the cytoplasm is called cytoplasmic polyadenylation. It was first discovered in oocytes and embryos, where it has roles in meiosis and development. In recent years, however, has been implicated in many other processes, including synaptic plasticity and mitosis. This review aims to introduce cytoplasmic polyadenylation with an emphasis on the factors and elements mediating this process for different mRNAs and in different animal species. We will discuss the RNA sequence elements mediating cytoplasmic polyadenylation in the 3' untranslated regions of mRNAs, including the CPE, MBE, TCS, eCPE, and C-CPE. In addition to describing the role of general polyadenylation factors, we discuss the specific RNA binding protein families associated with cytoplasmic polyadenylation elements, including CPEB (CPEB1, CPEB2, CPEB3, and CPEB4), Pumilio (PUM2), Musashi (MSI1, MSI2), zygote arrest (ZAR2), ELAV like proteins (ELAVL1, HuR), poly(C) binding proteins (PCBP2, αCP2, hnRNP-E2), and Bicaudal C (BICC1). Some emerging themes in cytoplasmic polyadenylation will be highlighted. To facilitate understanding for those working in different organisms and fields, particularly those who are analyzing high throughput data, HUGO gene nomenclature for the human orthologs is used throughout. Where human orthologs have not been clearly identified, reference is made to protein families identified in man.
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Affiliation(s)
- Amanda Charlesworth
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
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22
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The human nuclear poly(a)-binding protein promotes RNA hyperadenylation and decay. PLoS Genet 2013; 9:e1003893. [PMID: 24146636 PMCID: PMC3798265 DOI: 10.1371/journal.pgen.1003893] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 09/05/2013] [Indexed: 12/05/2022] Open
Abstract
Control of nuclear RNA stability is essential for proper gene expression, but the mechanisms governing RNA degradation in mammalian nuclei are poorly defined. In this study, we uncover a mammalian RNA decay pathway that depends on the nuclear poly(A)-binding protein (PABPN1), the poly(A) polymerases (PAPs), PAPα and PAPγ, and the exosome subunits RRP6 and DIS3. Using a targeted knockdown approach and nuclear RNA reporters, we show that PABPN1 and PAPα, redundantly with PAPγ, generate hyperadenylated decay substrates that are recognized by the exosome and degraded. Poly(A) tail extension appears to be necessary for decay, as cordycepin treatment or point mutations in the PAP-stimulating domain of PABPN1 leads to the accumulation of stable transcripts with shorter poly(A) tails than controls. Mechanistically, these data suggest that PABPN1-dependent promotion of PAP activity can stimulate nuclear RNA decay. Importantly, efficiently exported RNAs are unaffected by this decay pathway, supporting an mRNA quality control function for this pathway. Finally, analyses of both bulk poly(A) tails and specific endogenous transcripts reveals that a subset of nuclear RNAs are hyperadenylated in a PABPN1-dependent fashion, and this hyperadenylation can be either uncoupled or coupled with decay. Our results highlight a complex relationship between PABPN1, PAPα/γ, and nuclear RNA decay, and we suggest that these activities may play broader roles in the regulation of human gene expression. In eukaryotes, mRNAs include a stretch of adenosine nucleotides at their 3′ end termed the poly(A) tail. In the cytoplasm, the poly(A) tail stimulates translation of the mRNA into protein, and protects the transcript from degradation. Evidence suggests that poly(A) tails may play distinct roles in RNA metabolism in the nucleus, but little is known about these functions and mechanisms. We show here that poly(A) tails can stimulate transcript decay in the nucleus, a function mediated by the ubiquitous nuclear poly(A) binding protein PABPN1. We find that PABPN1 is required for the degradation of a viral nuclear noncoding RNA as well as an inefficiently exported human mRNA. Importantly, the targeting of RNAs to this decay pathway requires the PABPN1 and poly(A) polymerase-dependent extension of the poly(A) tail. Nuclear transcripts with longer poly(A) tails are then selectively degraded by components of the nuclear exosome. These studies elucidate mechanisms that mammalian cells use to ensure proper mRNA “quality control” and may be important to regulate the expression of nuclear noncoding RNAs. Furthermore, our results suggest that the poly(A) tail has diverse and context-specific roles in gene expression.
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23
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Kuss SK, Mata MA, Zhang L, Fontoura BMA. Nuclear imprisonment: viral strategies to arrest host mRNA nuclear export. Viruses 2013; 5:1824-49. [PMID: 23872491 PMCID: PMC3738964 DOI: 10.3390/v5071824] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 06/27/2013] [Accepted: 07/11/2013] [Indexed: 12/15/2022] Open
Abstract
Viruses possess many strategies to impair host cellular responses to infection. Nuclear export of host messenger RNAs (mRNA) that encode antiviral factors is critical for antiviral protein production and control of viral infections. Several viruses have evolved sophisticated strategies to inhibit nuclear export of host mRNAs, including targeting mRNA export factors and nucleoporins to compromise their roles in nucleo-cytoplasmic trafficking of cellular mRNA. Here, we present a review of research focused on suppression of host mRNA nuclear export by viruses, including influenza A virus and vesicular stomatitis virus, and the impact of this viral suppression on host antiviral responses.
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Affiliation(s)
- Sharon K Kuss
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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24
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25
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Ma WK, Cloutier SC, Tran EJ. The DEAD-box protein Dbp2 functions with the RNA-binding protein Yra1 to promote mRNP assembly. J Mol Biol 2013; 425:3824-38. [PMID: 23721653 DOI: 10.1016/j.jmb.2013.05.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/01/2013] [Accepted: 05/18/2013] [Indexed: 11/25/2022]
Abstract
Eukaryotic gene expression involves numerous biochemical steps that are dependent on RNA structure and ribonucleoprotein (RNP) complex formation. The DEAD-box class of RNA helicases plays fundamental roles in formation of RNA and RNP structure in every aspect of RNA metabolism. In an effort to explore the diversity of biological roles for DEAD-box proteins, our laboratory recently demonstrated that the DEAD-box protein Dbp2 associates with actively transcribing genes and is required for normal gene expression in Saccharomyces cerevisiae. We now provide evidence that Dbp2 interacts genetically and physically with the mRNA export factor Yra1. In addition, we find that Dbp2 is required for in vivo assembly of mRNA-binding proteins Yra1, Nab2, and Mex67 onto poly(A)+ RNA. Strikingly, we also show that Dbp2 is an efficient RNA helicase in vitro and that Yra1 decreases the efficiency of ATP-dependent duplex unwinding. We provide a model whereby messenger ribonucleoprotein (mRNP) assembly requires Dbp2 unwinding activity and once the mRNP is properly assembled, inhibition by Yra1 prevents further rearrangements. Both Yra1 and Dbp2 are conserved in multicellular eukaryotes, suggesting that this constitutes a broadly conserved mechanism for stepwise assembly of mature mRNPs in the nucleus.
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Affiliation(s)
- Wai Kit Ma
- Department of Biochemistry, Purdue University, BCHM 305, 175 South University Street, West Lafayette, IN 47907-2063, USA; Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 South University Street, West Lafayette, IN 47907-2064, USA
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26
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Langemeier J, Schrom EM, Rabner A, Radtke M, Zychlinski D, Saborowski A, Bohn G, Mandel-Gutfreund Y, Bodem J, Klein C, Bohne J. A complex immunodeficiency is based on U1 snRNP-mediated poly(A) site suppression. EMBO J 2012; 31:4035-44. [PMID: 22968171 DOI: 10.1038/emboj.2012.252] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 08/10/2012] [Indexed: 01/01/2023] Open
Abstract
Biallelic mutations in the untranslated regions (UTRs) of mRNAs are rare causes for monogenetic diseases whose mechanisms remain poorly understood. We investigated a 3'UTR mutation resulting in a complex immunodeficiency syndrome caused by decreased mRNA levels of p14/robld3 by a previously unknown mechanism. Here, we show that the mutation creates a functional 5' splice site (SS) and that its recognition by the spliceosomal component U1 snRNP causes p14 mRNA suppression in the absence of splicing. Histone processing signals are able to rescue p14 expression. Therefore, the mutation interferes only with canonical poly(A)-site 3' end processing. Our data suggest that U1 snRNP inhibits cleavage or poly(A) site recognition. This is the first description of a 3'UTR mutation that creates a functional 5'SS causative of a monogenetic disease. Moreover, our data endorse the recently described role of U1 snRNP in suppression of intronic poly(A) sites, which is here deleterious for p14 mRNA biogenesis.
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Affiliation(s)
- Jörg Langemeier
- Cell and Virus Genetics Group, Institute for Virology, Hannover Medical School, Hannover, Germany
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27
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Schmid M, Jensen TH. Transcription-associated quality control of mRNP. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:158-68. [PMID: 22982197 DOI: 10.1016/j.bbagrm.2012.08.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 08/24/2012] [Accepted: 08/29/2012] [Indexed: 01/06/2023]
Abstract
Although a prime purpose of transcription is to produce RNA, a substantial amount of transcript is nevertheless turned over very early in its lifetime. During transcription RNAs are matured by nucleases from longer precursors and activities are also employed to exert quality control over the RNA synthesis process so as to discard, retain or transcriptionally silence unwanted molecules. In this review we discuss the somewhat paradoxical circumstance that the retention or turnover of RNA is often linked to its synthesis. This occurs via the association of chromatin, or the transcription elongation complex, with RNA degradation (co)factors. Although our main focus is on protein-coding genes, we also discuss mechanisms of transcription-connected turnover of non-protein-coding RNA from where important general principles are derived. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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Affiliation(s)
- Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C., Denmark
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28
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Kallehauge TB, Robert MC, Bertrand E, Jensen TH. Nuclear retention prevents premature cytoplasmic appearance of mRNA. Mol Cell 2012; 48:145-52. [PMID: 22921936 DOI: 10.1016/j.molcel.2012.07.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 07/02/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
Abstract
In S. cerevisiae cells debilitated in mRNA nuclear export, transcripts are retained in nuclear foci ("dots"). The ultimate fate of dot-mRNA has remained elusive. Here, we use single molecule counting microscopy and (35)S-methionine pulse-labeling assays to quantify cytoplasmic HSP104 RNA levels and estimate HSP104 RNA translation status. HSP104 transcripts, retained in dots as a consequence of the mex67-5 mutation, are slowly released over time for cytoplasmic translation. Thus, dot-mRNA retains function. However, forcing its nuclear export, by overexpressing the Sub2p mRNA export factor, does not elevate Hsp104p protein levels but is instead paralleled by growth deficiency. Nuclear export and growth phenotypes are both counteracted by coexpressing the nuclear RNA quality control factor Rrp6p. Thus, prematurely released dot-mRNA is translationally inactive and possibly toxic. Accordingly, nuclear retention of mRNA may serve a precautionary role during stressful situations such as, e.g., decreased mRNA maturation competence.
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Affiliation(s)
- Thomas Beuchert Kallehauge
- Department of Molecular Biology and Genetics, Centre for mRNP Biogenesis and Metabolism, Aarhus University, Aarhus C, Denmark
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29
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Schmid M, Poulsen MB, Olszewski P, Pelechano V, Saguez C, Gupta I, Steinmetz LM, Moore C, Jensen TH. Rrp6p controls mRNA poly(A) tail length and its decoration with poly(A) binding proteins. Mol Cell 2012; 47:267-80. [PMID: 22683267 DOI: 10.1016/j.molcel.2012.05.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 03/30/2012] [Accepted: 05/01/2012] [Indexed: 11/17/2022]
Abstract
Poly(A) (pA) tail binding proteins (PABPs) control mRNA polyadenylation, stability, and translation. In a purified system, S. cerevisiae PABPs, Pab1p and Nab2p, are individually sufficient to provide normal pA tail length. However, it is unknown how this occurs in more complex environments. Here we find that the nuclear exosome subunit Rrp6p counteracts the in vitro and in vivo extension of mature pA tails by the noncanonical pA polymerase Trf4p. Moreover, PABP loading onto nascent pA tails is controlled by Rrp6p; while Pab1p is the major PABP, Nab2p only associates in the absence of Rrp6p. This is because Rrp6p can interact with Nab2p and displace it from pA tails, potentially leading to RNA turnover, as evidenced for certain pre-mRNAs. We suggest that a nuclear mRNP surveillance step involves targeting of Rrp6p by Nab2p-bound pA-tailed RNPs and that pre-mRNA abundance is regulated at this level.
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Affiliation(s)
- Manfred Schmid
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, DK-8000 Aarhus C., Denmark
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30
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Brockmann C, Soucek S, Kuhlmann SI, Mills-Lujan K, Kelly SM, Yang JC, Iglesias N, Stutz F, Corbett AH, Neuhaus D, Stewart M. Structural basis for polyadenosine-RNA binding by Nab2 Zn fingers and its function in mRNA nuclear export. Structure 2012; 20:1007-18. [PMID: 22560733 PMCID: PMC3384006 DOI: 10.1016/j.str.2012.03.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/19/2012] [Accepted: 03/26/2012] [Indexed: 01/19/2023]
Abstract
Polyadenylation regulation and efficient nuclear export of mature mRNPs both require the polyadenosine-RNA-binding protein, Nab2, which contains seven CCCH Zn fingers. We describe here the solution structure of fingers 5-7, which are necessary and sufficient for high-affinity polyadenosine-RNA binding, and identify key residues involved. These Zn fingers form a single structural unit. Structural coherence is lost in the RNA-binding compromised Nab2-C437S mutant, which also suppresses the rat8-2 allele of RNA helicase Dbp5. Structure-guided Nab2 variants indicate that dbp5(rat8-2) suppression is more closely linked to hyperadenylation and suppression of mutant alleles of the nuclear RNA export adaptor, Yra1, than to affinity for polyadenosine-RNA. These results indicate that, in addition to modulating polyA tail length, Nab2 has an unanticipated function associated with generating export-competent mRNPs, and that changes within fingers 5-7 lead to suboptimal assembly of mRNP export complexes that are more easily disassembled by Dbp5 upon reaching the cytoplasm.
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Affiliation(s)
- Christoph Brockmann
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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Vitaliano-Prunier A, Babour A, Hérissant L, Apponi L, Margaritis T, Holstege FCP, Corbett AH, Gwizdek C, Dargemont C. H2B ubiquitylation controls the formation of export-competent mRNP. Mol Cell 2012; 45:132-9. [PMID: 22244335 DOI: 10.1016/j.molcel.2011.12.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 09/15/2011] [Accepted: 11/01/2011] [Indexed: 01/18/2023]
Abstract
Histone H2B ubiquitylation is a transcription-dependent modification that not only regulates nucleosome dynamics but also controls the trimethylation of histone H3 on lysine 4 by promoting ubiquitylation of Swd2, a component of both the histone methyltransferase COMPASS complex and the cleavage and polyadenylation factor(CPF). We show that preventing either H2B ubiquitylation or H2B-dependent modification of Swd2 results in nuclear accumulation of poly(A) RNA due to a defect in the integrity and stability of APT, a subcomplex of the CPF. Ubiquitin-regulated APT complex dynamics is required for the correct recruitment of the mRNA export receptor Mex67 to nuclear mRNPs. While H2B ubiquitylation controls the recruitment of the different Mex67 adaptors to mRNPs, the effect of Swd2 ubiquitylation is restricted to Yra1 and Nab2, which, in turn, controls poly(A) tail length. Modification of H2B thus participates in the crosstalk between cotranscriptional events and assembly of mRNPs linking nuclear processing and mRNA export.
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Affiliation(s)
- Adeline Vitaliano-Prunier
- Institut Jacques Monod, Université Paris Diderot, CNRS, Bâtiment Buffon, 15 rue Hélène Brion, 75205 Paris Cedex 13, France
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Oeffinger M, Zenklusen D. To the pore and through the pore: a story of mRNA export kinetics. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:494-506. [PMID: 22387213 DOI: 10.1016/j.bbagrm.2012.02.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 02/07/2012] [Accepted: 02/09/2012] [Indexed: 12/26/2022]
Abstract
The evolutionary 'decision' to store genetic information away from the place of protein synthesis, in a separate compartment, has forced eukaryotic cells to establish a system to transport mRNAs from the nucleus to the cytoplasm for translation. To ensure export to be fast and efficient, cells have evolved a complex molecular interplay that is tightly regulated. Over the last few decades, many of the individual players in this process have been described, starting with the composition of the nuclear pore complex to proteins that modulate co-transcriptional events required to prepare an mRNP for export to the cytoplasm. How the interplay between all the factors and processes results in the efficient and selective export of mRNAs from the nucleus and how the export process itself is executed within cells, however, is still not fully understood. Recent advances in using proteomic and single molecule microscopy approaches have provided important insights into the process and its kinetics. This review summarizes these recent advances and how they led to the current view on how cells orchestrate the export of mRNAs. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Marlene Oeffinger
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec, Canada.
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33
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Abstract
TREX is a conserved multiprotein complex that is necessary for efficient mRNA export to the cytoplasm. In Saccharomyces cerevisiae, the TREX complex is additionally implicated in RNA quality control pathways, but it is unclear whether this function is conserved in mammalian cells. The Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 protein binds and recruits the TREX component REF/Aly to viral mRNAs. Here, we demonstrate that REF/Aly is recruited to the KSHV noncoding polyadenylated nuclear (PAN) RNA by ORF57. This recruitment correlates with ORF57-mediated stabilization of PAN RNA, suggesting that REF/Aly promotes nuclear RNA stability. Further supporting this idea, tethering REF/Aly to PAN RNA is sufficient to increase the nuclear abundance and half-life of PAN RNA but is not sufficient to promote its export. Interestingly, REF/Aly appears to protect the poly(A) tail from deadenylation, and REF/Aly-stabilized transcripts are further adenylated over time, consistent with previous reports linking poly(A) tail length with nuclear RNA surveillance. These studies show that REF/Aly can stabilize nuclear RNAs independently of their export and support a broader conservation of RNA quality control mechanisms from yeast to humans.
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Abstract
During transcription elongation, RNA polymerase II (Pol II) binds the general elongation factor Spt5. Spt5 contains a repetitive C-terminal region (CTR) that is required for cotranscriptional recruitment of the Paf1 complex (D. L. Lindstrom et al., Mol. Cell. Biol. 23:1368-1378, 2003; Z. Zhang, J. Fu, and D. S. Gilmour, Genes Dev. 19:1572-1580, 2005). Here we report a new role of the Spt5 CTR in the recruitment of 3' RNA-processing factors. Chromatin immunoprecipitation (ChIP) revealed that the Spt5 CTR is required for normal recruitment of pre-mRNA cleavage factor I (CFI) to the 3' ends of Saccharomyces cerevisiae genes. RNA contributes to CFI recruitment, as RNase treatment prior to ChIP further decreases CFI ChIP signals. Genome-wide ChIP profiling detected occupancy peaks of CFI subunits around 100 nucleotides downstream of the polyadenylation (pA) sites of genes. CFI recruitment to this defined region may result from simultaneous binding to the Spt5 CTR, to nascent RNA containing the pA sequence, and to the elongating Pol II isoform that is phosphorylated at serine 2 (S2) residues in its C-terminal domain (CTD). Consistent with this model, the CTR interacts with CFI in vitro but is not required for pA site recognition and transcription termination in vivo.
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Babour A, Dargemont C, Stutz F. Ubiquitin and assembly of export competent mRNP. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:521-30. [PMID: 22240387 DOI: 10.1016/j.bbagrm.2011.12.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 12/20/2011] [Accepted: 12/22/2011] [Indexed: 11/24/2022]
Abstract
The production of mature and export competent mRNP (mRNA ribonucleoprotein) complexes depends on a series of highly coordinated processing reactions. RNA polymerase II (RNAPII) plays a central role in this process by mediating the sequential recruitment of mRNA maturation and export factors to transcribing genes, thereby establishing a strong functional link between transcription and export through nuclear pore complexes (NPC). Growing evidence indicates that post-translational modifications participate in the dynamic association of processing and export factors with mRNAs ensuring that the transitions and rearrangements undergone by the mRNP occur at the right time and place. This review mainly focuses on the role of ubiquitin conjugation in controlling mRNP assembly and quality control from transcription down to export through the NPC. It emphasizes the central role of ubiquitylation in organizing the chronology of events along this highly dynamic pathway. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Anna Babour
- Institut Jacques Monod, Université Paris Diderot, CNRS, Bâtiment Buffon, 15 rue Hélène Brion, 75205 Paris Cedex 13, France
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36
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Luna R, Rondón AG, Aguilera A. New clues to understand the role of THO and other functionally related factors in mRNP biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:514-20. [PMID: 22207203 DOI: 10.1016/j.bbagrm.2011.11.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 11/24/2011] [Accepted: 11/29/2011] [Indexed: 02/02/2023]
Abstract
Coupling of transcription with mRNA processing and export has been shown to be relevant to efficient gene expression. A number of studies have determined that THO/TREX, a nuclear protein complex conserved from yeast to humans, plays an important role in mRNP biogenesis connecting transcription elongation, mRNA export and preventing genetic instability. Recent data indicates that THO could be relevant to different mRNA processing steps, including the 3'-end formation, transcript release and export. Novel connections of THO to proteins related to the splicing machinery, provide new views about possible functions of THO in mRNP biogenesis. In this review, we summarize the previous and new results concerning the impact of THO in transcription and its biological implications, with a special emphasis on the relationship with THSC/TREX-2 and other functionally related factors involved in mRNA biogenesis and export. The emerging picture presents THO as a dynamic complex interacting with the nascent RNA and with different factors connecting nuclear functions necessary for mRNP biogenesis with genome integrity, cellular homeostasis and development. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Rosa Luna
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC, Av Américo Vespucio s/n, 41092 Sevilla, Spain. rlvarp@is/es
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37
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Katahira J. mRNA export and the TREX complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:507-13. [PMID: 22178508 DOI: 10.1016/j.bbagrm.2011.12.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 11/29/2011] [Accepted: 12/01/2011] [Indexed: 02/08/2023]
Abstract
Over the past few decades, we have learned that eukaryotes have evolved sophisticated means to coordinate the nuclear export of mRNAs with different steps of gene expression. This functional orchestration is important for the maintenance of the efficiency and fidelity of gene expression processes. The TREX (TRanscription-EXport) complex is an evolutionarily conserved multiprotein complex that plays a major role in the functional coupling of different steps during mRNA biogenesis, including mRNA transcription, processing, decay, and nuclear export. Furthermore, recent gene knockout studies in mice have revealed that the metazoan TREX complex is required for cell differentiation and development, likely because this complex regulates the expression of key genes. These newly identified roles for the TREX complex suggest the existence of a relationship between mRNA nuclear biogenesis and more complex cellular processes. This review describes the functional roles of the TREX complex in gene expression and the nuclear export of mRNAs. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Jun Katahira
- Biomolecular Networks Laboratories, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka, Suita, Osaka, Japan.
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38
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Nucleophosmin deposition during mRNA 3' end processing influences poly(A) tail length. EMBO J 2011; 30:3994-4005. [PMID: 21822216 DOI: 10.1038/emboj.2011.272] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 07/04/2011] [Indexed: 12/12/2022] Open
Abstract
During polyadenylation, the multi-functional protein nucleophosmin (NPM1) is deposited onto all cellular mRNAs analysed to date. Premature termination of poly(A) tail synthesis in the presence of cordycepin abrogates deposition of the protein onto the mRNA, indicating natural termination of poly(A) addition is required for NPM1 binding. NPM1 appears to be a bona fide member of the complex involved in 3' end processing as it is associated with the AAUAAA-binding CPSF factor and can be co-immunoprecipitated with other polyadenylation factors. Furthermore, reduction in the levels of NPM1 results in hyperadenylation of mRNAs, consistent with alterations in poly(A) tail chain termination. Finally, knockdown of NPM1 results in retention of poly(A)(+) RNAs in the cell nucleus, indicating that NPM1 influences mRNA export. Collectively, these data suggest that NPM1 has an important role in poly(A) tail length determination and may help network 3' end processing with other aspects of nuclear mRNA maturation.
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39
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Abstract
The cell nucleus is an intricate organelle that coordinates multiple activities that are associated with DNA replication and gene expression. In all eukaryotes, it stores the genetic information and the machineries that control the production of mature and export-competent messenger ribonucleoproteins (mRNPs), a multistep process that is regulated in a spatial and temporal manner. Recent studies suggest that post-translational modifications play a part in coordinating the co-transcriptional assembly, remodelling and export of mRNP complexes through nuclear pores, adding a new level of regulation to the process of gene expression.
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40
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Abstract
Messenger RNAs undergo 5' capping, splicing, 3'-end processing, and export before translation in the cytoplasm. It has become clear that these mRNA processing events are tightly coupled and have a profound effect on the fate of the resulting transcript. This processing is represented by modifications of the pre-mRNA and loading of various protein factors. The sum of protein factors that stay with the mRNA as a result of processing is modified over the life of the transcript, conferring significant regulation to its expression.
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Affiliation(s)
- Sami Hocine
- Department for Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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41
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Chan S, Choi EA, Shi Y. Pre-mRNA 3'-end processing complex assembly and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:321-35. [PMID: 21957020 DOI: 10.1002/wrna.54] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The 3'-ends of almost all eukaryotic mRNAs are formed in a two-step process, an endonucleolytic cleavage followed by polyadenylation (the addition of a poly-adenosine or poly(A) tail). These reactions take place in the pre-mRNA 3' processing complex, a macromolecular machinery that consists of more than 20 proteins. A general framework for how the pre-mRNA 3' processing complex assembles and functions has emerged from extensive studies over the past several decades using biochemical, genetic, computational, and structural approaches. In this article, we review what we have learned about this important cellular machine and discuss the remaining questions and future challenges.
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Affiliation(s)
- Serena Chan
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, USA
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42
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Gene-specific RNA polymerase II phosphorylation and the CTD code. Nat Struct Mol Biol 2010; 17:1279-86. [PMID: 20835241 PMCID: PMC3048030 DOI: 10.1038/nsmb.1913] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 08/20/2010] [Indexed: 12/21/2022]
Abstract
Dynamic phosphorylation of the RNA polymerase II CTD repeats (YS2PTS5PS7) is coupled to transcription and may act as a “code” that controls mRNA synthesis and processing. To examine the "code" in budding yeast, we mapped genome-wide CTD S2, 5 and 7 phosphorylations (PO4) and compared them with the CTD-associated termination factors, Nrd1 and Pcf11. CTD-PO4 dynamics are not scaled to the size of the gene. At 5’ ends, the onset of S2-PO4 is delayed by about 450 bases relative to S5-PO4, regardless of gene length. Phospho-CTD dynamics are gene-specific, with high S5/7-PO4 at the 5' end being characteristic of well-expressed genes with nucleosome-occupied promoters. Furthermore, the CTD kinases Kin28 and Ctk1 profoundly affect pol II distribution along genes in a highly gene-specific way. The "code" is therefore written differently on different genes, probably under the control of promoters. S7-PO4 is enriched on introns and at sites of Nrd1 accumulation suggesting that this modification may function in splicing and Nrd1 recruitment. Nrd1 and Pcf11 frequently co-localized, suggesting functional overlap between these terminators. Surprisingly, Pcf11 is also recruited to centromeres and pol III transcribed genes.
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43
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The mitogen-activated protein kinase Slt2 regulates nuclear retention of non-heat shock mRNAs during heat shock-induced stress. Mol Cell Biol 2010; 30:5168-79. [PMID: 20823268 DOI: 10.1128/mcb.00735-10] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cellular adaptation to environmental stress conditions requires rapid and specific changes in gene expression. During heat shock, most polyadenylated mRNAs are retained in the nucleus, whereas the export of heat shock-induced mRNAs is allowed. Although essential mRNA export factors are known, the precise mechanism for regulating transport is not fully understood. Here we find that during heat shock in Saccharomyces cerevisiae, the mRNA-binding protein Nab2 is phosphorylated on threonine 178 and serine 180 by the mitogen-activated protein (MAP) kinase Slt2/Mpk1. Slt2 is required for nuclear poly(A(+)) mRNA accumulation upon heat shock, and thermotolerance is decreased in a nup42 nab2-T178A/S180A mutant. Coincident with phosphorylation, Nab2 and Yra1 colocalize in nuclear foci with Mlp1, a protein involved in mRNA retention. Nab2 nuclear focus formation and Nab2 phosphorylation are independent, suggesting that heat shock induces multiple cellular alterations that impinge upon transport efficiency. Under normal conditions, we find that the mRNA export receptor Mex67 and Nab2 directly interact. However, upon heat shock stress, Mex67 does not localize to the Mlp1 nuclear foci, and its association with Nab2 complexes is reduced. These results reveal a novel mechanism by which the MAP kinase Slt2 and Mlp1 control mRNA export factors during heat shock stress.
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44
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Nuclear import of cytoplasmic poly(A) binding protein restricts gene expression via hyperadenylation and nuclear retention of mRNA. Mol Cell Biol 2010; 30:4996-5008. [PMID: 20823266 DOI: 10.1128/mcb.00600-10] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Poly(A) tail length is emerging as an important marker of mRNA fate, where deviations from the canonical length can signal degradation or nuclear retention of transcripts. Pathways regulating polyadenylation thus have the potential to broadly influence gene expression. Here we demonstrate that accumulation of cytoplasmic poly(A) binding protein (PABPC) in the nucleus, which can occur during viral infection or other forms of cellular stress, causes mRNA hyperadenylation and nuclear accumulation of poly(A) RNA. This inhibits gene expression but does not affect mRNA stability. Unexpectedly, PABPC-induced hyperadenylation can occur independently of mRNA 3'-end processing yet requires the canonical mRNA poly(A) polymerase II. We find that nuclear PABPC-induced hyperadenylation is triggered by multiple divergent viral factors, suggesting that altering the subcellular localization of PABPC may be a commonly used mechanism to regulate cellular gene expression in a polyadenylation-linked manner.
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45
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Nuclear export of mRNA. Trends Biochem Sci 2010; 35:609-17. [PMID: 20719516 DOI: 10.1016/j.tibs.2010.07.001] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 07/05/2010] [Accepted: 07/07/2010] [Indexed: 01/19/2023]
Abstract
The nuclear export of mRNA, in which Mex67-Mtr2 mediates movement of mature transcripts through nuclear pores, represents the culmination of the nuclear portion of the gene expression pathway. Nuclear export is closely integrated with transcription and processing, and is based on forming a messenger ribonucleoprotein (mRNP) export complex in the nucleus that is able to diffuse back and forth through the pores. Directionality is imposed by remodelling of the mRNP in the cytoplasm, thereby removing key transport-related proteins and preventing its return to the nucleus. The nuclear and cytoplasmic steps of this pathway, in which Mex67-Mtr2 and Nab2 are added and removed, are crucial, and both involve remodelling of the mRNP, which is mediated by DEAD-box helicases together with adaptor and accessory proteins. Recent structural and cell biology results provide key information that should enable development of a detailed understanding of this central cellular process at a molecular level.
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46
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Leeper TC, Qu X, Lu C, Moore C, Varani G. Novel protein-protein contacts facilitate mRNA 3'-processing signal recognition by Rna15 and Hrp1. J Mol Biol 2010; 401:334-49. [PMID: 20600122 DOI: 10.1016/j.jmb.2010.06.032] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 06/10/2010] [Accepted: 06/10/2010] [Indexed: 12/22/2022]
Abstract
Precise 3'-end processing of mRNA is essential for correct gene expression, yet in yeast, 3'-processing signals consist of multiple ambiguous sequence elements. Two neighboring elements upstream of the cleavage site are particularly important for the accuracy (positioning element) and efficiency (efficiency element) of 3'-processing and are recognized by the RNA-binding proteins Rna15 and Hrp1, respectively. In vivo, these interactions are strengthened by the scaffolding protein Rna14 that stabilizes their association. The NMR structure of the 34 -kDa ternary complex of the RNA recognition motif (RRM) domains of Hrp1 and Rna15 bound to this pair of RNA elements was determined by residual dipolar coupling and paramagnetic relaxation experiments. It reveals how each of the proteins binds to RNA and introduces a novel class of protein-protein contact in regions of previously unknown function. These interdomain contacts had previously been overlooked in other multi-RRM structures, although a careful analysis suggests that they may be frequently present. Mutations in the regions of these contacts disrupt 3'-end processing, suggesting that they may structurally organize the ribonucleoprotein complexes responsible for RNA processing.
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Affiliation(s)
- Thomas C Leeper
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA.
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47
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The interface between transcription and mRNP export: from THO to THSC/TREX-2. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:533-8. [PMID: 20601280 DOI: 10.1016/j.bbagrm.2010.06.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 06/10/2010] [Accepted: 06/14/2010] [Indexed: 11/20/2022]
Abstract
Eukaryotic gene expression is a multilayer process covering transcription to post-translational protein modifications. As the nascent pre-mRNA emerges from the RNA polymerase II (RNAPII), it is packed in a messenger ribonucleoparticle (mRNP) whose optimal configuration is critical for the normal pre-mRNA processing and mRNA export, mRNA integrity as well as for transcription elongation efficiency. The interplay between transcription and mRNP formation feeds forward and backward and involves a number of conserved factors, from THO to THSC/TREX-2, which in addition have a unique impact on transcription-dependent genome instability. Here we review our actual knowledge of the role that these factors play at the interface between transcription and mRNA export in the model organism Saccharomyces cerevisiae.
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48
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Dieppois G, Stutz F. Connecting the transcription site to the nuclear pore: a multi-tether process that regulates gene expression. J Cell Sci 2010; 123:1989-99. [DOI: 10.1242/jcs.053694] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It is now well established that the position of a gene within the nucleus can influence the level of its activity. So far, special emphasis has been placed on the nuclear envelope (NE) as a transcriptionally silent nuclear sub-domain. Recent work, however, indicates that peripheral localization is not always associated with repression, but rather fulfills a dual function in gene expression. In particular, in the yeast Saccharomyces cerevisiae, a large number of highly expressed genes and activated inducible genes preferentially associate with nuclear pore complexes (NPCs), a process that is mediated by transient interactions between the transcribed locus and the NPC. Recent studies aimed at unraveling the molecular basis of this mechanism have revealed that maintenance of genes at the NPC involves multiple tethers at different steps of gene expression. These observations are consistent with tight interconnections between transcription, mRNA processing and export into the cytoplasm, and highlight a role for the NPC in promoting and orchestrating the gene expression process. In this Commentary, we discuss the factors involved in active gene anchoring to the NPC and the diverse emerging roles of the NPC environment in promoting gene expression, focusing on yeast as a model organism.
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Affiliation(s)
- Guennaëlle Dieppois
- Department of Cell Biology and Frontiers in Genetics, University of Geneva, Sciences III, 30 Quai E. Ansermet, Geneva 4, 1211, Switzerland
| | - Françoise Stutz
- Department of Cell Biology and Frontiers in Genetics, University of Geneva, Sciences III, 30 Quai E. Ansermet, Geneva 4, 1211, Switzerland
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49
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Kaposi's sarcoma-associated herpesvirus ORF57 protein binds and protects a nuclear noncoding RNA from cellular RNA decay pathways. PLoS Pathog 2010; 6:e1000799. [PMID: 20221435 PMCID: PMC2832700 DOI: 10.1371/journal.ppat.1000799] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Accepted: 01/28/2010] [Indexed: 02/07/2023] Open
Abstract
The control of RNA stability is a key determinant in cellular gene expression. The stability of any transcript is modulated through the activity of cis- or trans-acting regulatory factors as well as cellular quality control systems that ensure the integrity of a transcript. As a result, invading viral pathogens must be able to subvert cellular RNA decay pathways capable of destroying viral transcripts. Here we report that the Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 protein binds to a unique KSHV polyadenylated nuclear RNA, called PAN RNA, and protects it from degradation by cellular factors. ORF57 increases PAN RNA levels and its effects are greatest on unstable alleles of PAN RNA. Kinetic analysis of transcription pulse assays shows that ORF57 protects PAN RNA from a rapid cellular RNA decay process, but ORF57 has little effect on transcription or PAN RNA localization based on chromatin immunoprecipitation and in situ hybridization experiments, respectively. Using a UV cross-linking technique, we further demonstrate that ORF57 binds PAN RNA directly in living cells and we show that binding correlates with function. In addition, we define an ORF57-responsive element (ORE) that is necessary for ORF57 binding to PAN RNA and sufficient to confer ORF57-response to a heterologous intronless beta-globin mRNA, but not its spliced counterparts. We conclude that ORF57 binds to viral transcripts in the nucleus and protects them from a cellular RNA decay pathway. We propose that KSHV ORF57 protein functions to enhance the nuclear stability of intronless viral transcripts by protecting them from a cellular RNA quality control pathway.
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50
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Butler JS, Mitchell P. Rrp6, Rrp47 and Cofactors of the Nuclear Exosome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 702:91-104. [DOI: 10.1007/978-1-4419-7841-7_8] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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