1
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Wood KA, Rowlands CF, Qureshi WMS, Thomas HB, Buczek WA, Briggs TA, Hubbard SJ, Hentges KE, Newman WG, O’Keefe RT. Disease modeling of core pre-mRNA splicing factor haploinsufficiency. Hum Mol Genet 2019; 28:3704-3723. [PMID: 31304552 PMCID: PMC6935387 DOI: 10.1093/hmg/ddz169] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/04/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022] Open
Abstract
The craniofacial disorder mandibulofacial dysostosis Guion-Almeida type is caused by haploinsufficiency of the U5 snRNP gene EFTUD2/SNU114. However, it is unclear how reduced expression of this core pre-mRNA splicing factor leads to craniofacial defects. Here we use a CRISPR-Cas9 nickase strategy to generate a human EFTUD2-knockdown cell line and show that reduced expression of EFTUD2 leads to diminished proliferative ability of these cells, increased sensitivity to endoplasmic reticulum (ER) stress and the mis-expression of several genes involved in the ER stress response. RNA-Seq analysis of the EFTUD2-knockdown cell line revealed transcriptome-wide changes in gene expression, with an enrichment for genes associated with processes involved in craniofacial development. Additionally, our RNA-Seq data identified widespread mis-splicing in EFTUD2-knockdown cells. Analysis of the functional and physical characteristics of mis-spliced pre-mRNAs highlighted conserved properties, including length and splice site strengths, of retained introns and skipped exons in our disease model. We also identified enriched processes associated with the affected genes, including cell death, cell and organ morphology and embryonic development. Together, these data support a model in which EFTUD2 haploinsufficiency leads to the mis-splicing of a distinct subset of pre-mRNAs with a widespread effect on gene expression, including altering the expression of ER stress response genes and genes involved in the development of the craniofacial region. The increased burden of unfolded proteins in the ER resulting from mis-splicing would exceed the capacity of the defective ER stress response, inducing apoptosis in cranial neural crest cells that would result in craniofacial abnormalities during development.
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Affiliation(s)
- Katherine A Wood
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
- Center for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, St. Mary’s Hospital, The University of Manchester, Manchester Academic Health Science Centre Manchester, M13 9PT, UK
| | - Charlie F Rowlands
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
- Center for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, St. Mary’s Hospital, The University of Manchester, Manchester Academic Health Science Centre Manchester, M13 9PT, UK
| | - Wasay Mohiuddin Shaikh Qureshi
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - Huw B Thomas
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - Weronika A Buczek
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - Tracy A Briggs
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
- Center for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, St. Mary’s Hospital, The University of Manchester, Manchester Academic Health Science Centre Manchester, M13 9PT, UK
| | - Simon J Hubbard
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - Kathryn E Hentges
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
- Center for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, St. Mary’s Hospital, The University of Manchester, Manchester Academic Health Science Centre Manchester, M13 9PT, UK
| | - Raymond T O’Keefe
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
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2
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Baird TD, Cheng KCC, Chen YC, Buehler E, Martin SE, Inglese J, Hogg JR. ICE1 promotes the link between splicing and nonsense-mediated mRNA decay. eLife 2018. [PMID: 29528287 PMCID: PMC5896957 DOI: 10.7554/elife.33178] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The nonsense-mediated mRNA decay (NMD) pathway detects aberrant transcripts containing premature termination codons (PTCs) and regulates expression of 5–10% of non-aberrant human mRNAs. To date, most proteins involved in NMD have been identified by genetic screens in model organisms; however, the increased complexity of gene expression regulation in human cells suggests that additional proteins may participate in the human NMD pathway. To identify proteins required for NMD, we performed a genome-wide RNAi screen against >21,000 genes. Canonical members of the NMD pathway were highly enriched as top hits in the siRNA screen, along with numerous candidate NMD factors, including the conserved ICE1/KIAA0947 protein. RNAseq studies reveal that depletion of ICE1 globally enhances accumulation and stability of NMD-target mRNAs. Further, our data suggest that ICE1 uses a putative MIF4G domain to interact with exon junction complex (EJC) proteins and promotes the association of the NMD protein UPF3B with the EJC. The DNA in our cells contains the hereditary information that makes each of us unique. Molecules called mRNAs are copies of this information and are used as templates for making proteins. When a strand of incorrectly copied mRNA, or one including errors from the original DNA template, is recognized, our cells destroy the mRNA to prevent it from producing a damaged protein. Organisms from yeast to humans have evolved a mechanism for finding and destroying faulty mRNAs, called mRNA surveillance. Animals are particularly reliant on mRNA surveillance, as their proteins are often made from cutting and pasting together mRNA from different portions of DNA, in a process known as splicing. Despite being a vital process, we still lack a good understanding of how mRNA surveillance works. Now, Baird et al. used human kidney cells that produced an error-containing mRNA that could be tracked. To investigate how efficient RNA surveillance is under different conditions, the levels of individual proteins were reduced one at a time. By tracking the amount of faulty mRNA, it was possible to find out if a single protein plays a role in human mRNA surveillance. If the number of faulty mRNAs is high when a protein is reduced, it suggests that this protein may be involved in mRNA surveillance. Baird et al. screened more than 21,000 proteins, the majority of proteins made in human cells. Many of the proteins that stood out as important in mRNA surveillance were the ones already known to be relevant in yeast and worm cells. But the experiments also identified new proteins that appear to play a role specifically in human RNA surveillance. One of the proteins, ICE1, is essential for the relationship between mRNA splicing and mRNA surveillance. Without ICE1, the mRNA surveillance machinery can no longer find and destroy faulty mRNAs. Nearly one-third of genetic diseases are caused by mutations that result in faulty mRNAs, which can be detected by mRNA surveillance pathways. Depending on the disease, destroying these error-containing mRNAs can either improve or worsen disease symptoms. A better understanding of the factors that control human RNA surveillance could one day help to develop treatments that affect mRNA surveillance to improve disease outcomes.
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Affiliation(s)
- Thomas D Baird
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Ken Chih-Chien Cheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - Yu-Chi Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - Eugen Buehler
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - Scott E Martin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
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3
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Lee HC, Jung SH, Hwang HJ, Kang D, De S, Dudekula DB, Martindale JL, Park B, Park SK, Lee EK, Lee JH, Jeong S, Han K, Park HJ, Ko YG, Gorospe M, Lee JS. WIG1 is crucial for AGO2-mediated ACOT7 mRNA silencing via miRNA-dependent and -independent mechanisms. Nucleic Acids Res 2017; 45:6894-6910. [PMID: 28472401 PMCID: PMC5499809 DOI: 10.1093/nar/gkx307] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 04/28/2017] [Indexed: 12/14/2022] Open
Abstract
RNA-binding proteins (RBPs) are involved in mRNA splicing, maturation, transport, translation, storage and turnover. Here, we identified ACOT7 mRNA as a novel target of human WIG1. ACOT7 mRNA decay was triggered by the microRNA miR-9 in a WIG1-dependent manner via classic recruitment of Argonaute 2 (AGO2). Interestingly, AGO2 was also recruited to ACOT7 mRNA in a WIG1-dependent manner in the absence of miR-9, which indicates an alternative model whereby WIG1 controls AGO2-mediated gene silencing. The WIG1–AGO2 complex attenuated translation initiation via an interaction with translation initiation factor 5B (eIF5B). These results were confirmed using a WIG1 tethering system based on the MS2 bacteriophage coat protein and a reporter construct containing an MS2-binding site, and by immunoprecipitation of WIG1 and detection of WIG1-associated proteins using liquid chromatography-tandem mass spectrometry. We also identified WIG1-binding motifs using photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation analyses. Altogether, our data indicate that WIG1 governs the miRNA-dependent and the miRNA-independent recruitment of AGO2 to lower the stability of and suppress the translation of ACOT7 mRNA.
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Affiliation(s)
- Hyung Chul Lee
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Seung Hee Jung
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Hyun Jung Hwang
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Donghee Kang
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Supriyo De
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Dawood B Dudekula
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Byungkyu Park
- Department of Computer Science and Engineering, Inha University, Incheon 22212, Korea
| | - Seung Kuk Park
- Department of Molecular Biology, Dankook University, Yongin 16890, Korea
| | - Eun Kyung Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Jeong-Hwa Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Sunjoo Jeong
- Department of Molecular Biology, Dankook University, Yongin 16890, Korea
| | - Kyungsook Han
- Department of Computer Science and Engineering, Inha University, Incheon 22212, Korea
| | - Heon Joo Park
- Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Department of Microbiology, Inha University College of Medicine, Incheon 22212, Korea
| | - Young-Gyu Ko
- Division of Life Sciences, Korea University, Seoul 02841, Korea
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Jae-Seon Lee
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
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4
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Boehm V, Gerbracht JV, Marx MC, Gehring NH. Interrogating the degradation pathways of unstable mRNAs with XRN1-resistant sequences. Nat Commun 2016; 7:13691. [PMID: 27917860 PMCID: PMC5150221 DOI: 10.1038/ncomms13691] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 10/25/2016] [Indexed: 12/22/2022] Open
Abstract
The turnover of messenger RNAs (mRNAs) is a key regulatory step of gene expression in eukaryotic cells. Due to the complexity of the mammalian degradation machinery, the contribution of decay factors to the directionality of mRNA decay is poorly understood. Here we characterize a molecular tool to interrogate mRNA turnover via the detection of XRN1-resistant decay fragments (xrFrag). Using nonsense-mediated mRNA decay (NMD) as a model pathway, we establish xrFrag analysis as a robust indicator of accelerated 5'-3' mRNA decay. In tethering assays, monitoring xrFrag accumulation allows to distinguish decapping and endocleavage activities from deadenylation. Moreover, xrFrag analysis of mRNA degradation induced by miRNAs, AU-rich elements (AREs) as well as the 3' UTRs of cytokine mRNAs reveals the contribution of 5'-3' decay and endonucleolytic cleavage. Our work uncovers formerly unrecognized modes of mRNA turnover and establishes xrFrag as a powerful tool for RNA decay analyses.
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Affiliation(s)
- Volker Boehm
- Institute for Genetics, Department of Biology, University of Cologne, Zuelpicher Straße 47a, 50674 Cologne, Germany
| | - Jennifer V Gerbracht
- Institute for Genetics, Department of Biology, University of Cologne, Zuelpicher Straße 47a, 50674 Cologne, Germany
| | - Marie-Charlotte Marx
- Institute for Genetics, Department of Biology, University of Cologne, Zuelpicher Straße 47a, 50674 Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, Department of Biology, University of Cologne, Zuelpicher Straße 47a, 50674 Cologne, Germany
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5
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Bhuvanagiri M, Lewis J, Putzker K, Becker JP, Leicht S, Krijgsveld J, Batra R, Turnwald B, Jovanovic B, Hauer C, Sieber J, Hentze MW, Kulozik AE. 5-azacytidine inhibits nonsense-mediated decay in a MYC-dependent fashion. EMBO Mol Med 2015; 6:1593-609. [PMID: 25319547 PMCID: PMC4287977 DOI: 10.15252/emmm.201404461] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Nonsense-mediated RNA decay (NMD) is an RNA-based quality control mechanism that eliminates
transcripts bearing premature translation termination codons (PTC). Approximately, one-third of all
inherited disorders and some forms of cancer are caused by nonsense or frame shift mutations that
introduce PTCs, and NMD can modulate the clinical phenotype of these diseases. 5-azacytidine is an
analogue of the naturally occurring pyrimidine nucleoside cytidine, which is approved for the
treatment of myelodysplastic syndrome and myeloid leukemia. Here, we reveal that 5-azacytidine
inhibits NMD in a dose-dependent fashion specifically upregulating the expression of both
PTC-containing mutant and cellular NMD targets. Moreover, this activity of 5-azacytidine depends on
the induction of MYC expression, thus providing a link between the effect of this drug and one of
the key cellular pathways that are known to affect NMD activity. Furthermore, the effective
concentration of 5-azacytidine in cells corresponds to drug levels used in patients, qualifying
5-azacytidine as a candidate drug that could potentially be repurposed for the treatment of
Mendelian and acquired genetic diseases that are caused by PTC mutations.
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Affiliation(s)
- Madhuri Bhuvanagiri
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany European Molecular Biology Laboratory, Heidelberg, Germany
| | - Joe Lewis
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Jonas P Becker
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Stefan Leicht
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Richa Batra
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Brad Turnwald
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Bogdan Jovanovic
- Centre for Molecular Biology of the University of HeidelbergUniversity of Heidelberg, Heidelberg, Germany
| | - Christian Hauer
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jana Sieber
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
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6
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Shi M, Zhang H, Wang L, Zhu C, Sheng K, Du Y, Wang K, Dias A, Chen S, Whitman M, Wang E, Reed R, Cheng H. Premature Termination Codons Are Recognized in the Nucleus in A Reading-Frame Dependent Manner. Cell Discov 2015; 1. [PMID: 26491543 PMCID: PMC4610414 DOI: 10.1038/celldisc.2015.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
mRNAs containing premature termination codons (PTCs) are known to be degraded via nonsense-mediated mRNA decay (NMD). Unexpectedly, we found that mRNAs containing any type of PTC (UAA, UAG, UGA) are detained in the nucleus whereas their wild-type counterparts are rapidly exported. This retention is strictly reading-frame dependent. Strikingly, our data indicate that translating ribosomes in the nucleus proofread the frame and detect the PTCs in the nucleus. Moreover, the shuttling NMD protein Upf1 specifically associates with PTC+ mRNA in the nucleus and is required for nuclear retention of PTC+ mRNA. Together, our data lead to a working model that PTCs are recognized in the nucleus by translating ribosomes, resulting in recruitment of Upf1, which in turn functions in nuclear retention of PTC+ mRNA. Nuclear PTC recognition adds a new layer of proofreading for mRNA and may be vital for ensuring the extraordinary fidelity required for protein production.
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Affiliation(s)
- Min Shi
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Heng Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lantian Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Changlan Zhu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ke Sheng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanhua Du
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ke Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Anusha Dias
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Enduo Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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7
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Garcia D, Garcia S, Voinnet O. Nonsense-mediated decay serves as a general viral restriction mechanism in plants. Cell Host Microbe 2014; 16:391-402. [PMID: 25155460 PMCID: PMC7185767 DOI: 10.1016/j.chom.2014.08.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/16/2014] [Accepted: 07/14/2014] [Indexed: 11/17/2022]
Abstract
(+)strand RNA viruses have to overcome various points of restriction in the host to establish successful infection. In plants, this includes RNA silencing. To uncover additional bottlenecks to RNA virus infection, we genetically attenuated the impact of RNA silencing on transgenically expressed Potato virus X (PVX), a (+)strand RNA virus that replicates in Arabidopsis. A genetic screen in this sensitized background uncovered how nonsense-mediated decay (NMD), a host RNA quality control mechanism, recognizes and eliminates PVX RNAs with internal termination codons and long 3′ UTRs. NMD also operates in natural infection contexts, and while some viruses have evolved genome expression strategies to overcome this process altogether, the virulence of NMD-activating viruses entails their ability to directly suppress NMD or to promote an NMD-unfavorable cellular state. These principles of induction, evasion, and suppression define NMD as a general viral restriction mechanism in plants that also likely operates in animals. A sensitized genetic screen for modifiers of (+)strand RNA virus accumulation in Arabidopsis The host nonsense-mediated decay (NMD) pathway restricts PVX during natural infection NMD targets viral RNAs containing internal termination codons and long 3′ UTRs Some viruses have evolved to evade NMD altogether, while others may suppress NMD actively
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Affiliation(s)
- Damien Garcia
- Institut de Biologie Moléculaire des Plantes (IBMP), Centre National de la Recherche Scientifique, UPR 2357, 67084 Strasbourg, France.
| | - Shahinez Garcia
- Institut de Biologie Moléculaire des Plantes (IBMP), Centre National de la Recherche Scientifique, UPR 2357, 67084 Strasbourg, France
| | - Olivier Voinnet
- Institut de Biologie Moléculaire des Plantes (IBMP), Centre National de la Recherche Scientifique, UPR 2357, 67084 Strasbourg, France; Swiss Federal Institute of Technology Zurich, Department of Biology, Universitätstrasse 2, 8092 Zürich, Switzerland.
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8
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Abstract
The 7mG (7-methylguanosine cap) formed on mRNA is fundamental to eukaryotic gene expression. Protein complexes recruited to 7mG mediate key processing events throughout the lifetime of the transcript. One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation. Gene expression can be regulated by signalling pathways which influence CBC function. The aim of the present review is to discuss the mechanisms by which CBC mediates and co-ordinates multiple gene expression events.
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9
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Gonatopoulos-Pournatzis T, Cowling VH. Cap-binding complex (CBC). Biochem J 2014. [PMID: 24354960 DOI: 10.1042/bj2013121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The 7mG (7-methylguanosine cap) formed on mRNA is fundamental to eukaryotic gene expression. Protein complexes recruited to 7mG mediate key processing events throughout the lifetime of the transcript. One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation. Gene expression can be regulated by signalling pathways which influence CBC function. The aim of the present review is to discuss the mechanisms by which CBC mediates and co-ordinates multiple gene expression events.
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Affiliation(s)
| | - Victoria H Cowling
- *MRC Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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10
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Nonsense-mediated mRNA decay occurs during eIF4F-dependent translation in human cells. Nat Struct Mol Biol 2013; 20:702-9. [PMID: 23665580 DOI: 10.1038/nsmb.2575] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/03/2013] [Indexed: 11/08/2022]
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11
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Abstract
NMD (nonsense-mediated mRNA decay) belongs to the best-studied mRNA surveillance systems of the cell, limiting the synthesis of truncated and potentially harmful proteins on the one hand and playing an initially unexpected role in the regulation of global gene expression on the other hand. In the present review, we briefly discuss the factors involved in NMD, the different models proposed for the recognition of PTCs (premature termination codons), the diverse physiological roles of NMD, the involvement of this surveillance pathway in disease and the current strategies for medical treatment of PTC-related diseases.
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12
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Ivanov P, Anderson P. CBP80 choreographs the NMD two-step. Mol Cell 2010; 39:317-8. [PMID: 20705234 DOI: 10.1016/j.molcel.2010.07.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this issue of Molecular Cell, Hwang et al. (2010) show that the cap-binding protein CBP80 promotes nonsense-mediated decay (NMD) at two steps. In this dual capacity, CBP80 may facilitate essential communication between the premature termination codon (PTC) and the exon-junction complex (EJC) to trigger NMD.
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Affiliation(s)
- Pavel Ivanov
- Department of Medicine, Harvard Medical School, Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA.
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13
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Dang Y, Low WK, Xu J, Gehring NH, Dietz HC, Romo D, Liu JO. Inhibition of nonsense-mediated mRNA decay by the natural product pateamine A through eukaryotic initiation factor 4AIII. J Biol Chem 2009; 284:23613-21. [PMID: 19570977 DOI: 10.1074/jbc.m109.009985] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) in mammalian cells is a key mechanism for the removal of mRNA containing premature stop codons and is mediated by the coordinated function of numerous proteins that dynamically associate with the exon junction complex. The information communicated by these interactions and the functional consequences from a mechanistic perspective, however, are not completely documented. Herein, we report that the natural product pateamine A (PatA) is capable of inhibiting NMD through direct interaction with eIF4AIII, which is independent of its inhibition of translation initiation. Furthermore, we have characterized the mechanisms by which PatA and cycloheximide modulate NMD. Unlike CHX, PatA was found to inhibit NMD by a novel mechanism that is independent of the phosphorylation of Up-frameshift protein 1.
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Affiliation(s)
- Yongjun Dang
- Department of Pharmacology, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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14
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Execution of nonsense-mediated mRNA decay: what defines a substrate? Curr Opin Cell Biol 2009; 21:394-402. [PMID: 19359157 DOI: 10.1016/j.ceb.2009.02.007] [Citation(s) in RCA: 212] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Revised: 02/17/2009] [Accepted: 02/20/2009] [Indexed: 11/23/2022]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway targets mRNAs with premature termination codons as well as a subset of normal mRNAs for rapid decay. Emerging evidence suggests that mRNAs become NMD substrates based on the composition of the mRNP downstream of the translation termination event, which either stimulates or antagonizes recruitment of the NMD machinery. The NMD mRNP subsequently undergoes several remodeling events, which involve hydrolysis of ATP by the NMD factor Upf1 and in metazoans, a phosphorylation/dephosphorylation cycle of Upf1 mediated by Smg proteins. This leads to mRNA decay following translational repression. Recent evidence suggests that in Drosophila and human cells, decay is initiated by the endonuclease Smg6.
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Isken O, Kim YK, Hosoda N, Mayeur GL, Hershey JWB, Maquat LE. Upf1 phosphorylation triggers translational repression during nonsense-mediated mRNA decay. Cell 2008; 133:314-27. [PMID: 18423202 DOI: 10.1016/j.cell.2008.02.030] [Citation(s) in RCA: 229] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2007] [Revised: 11/18/2007] [Accepted: 02/04/2008] [Indexed: 11/18/2022]
Abstract
In mammalian cells, nonsense-mediated mRNA decay (NMD) generally requires that translation terminates sufficiently upstream of a post-splicing exon junction complex (EJC) during a pioneer round of translation. The subsequent binding of Upf1 to the EJC triggers Upf1 phosphorylation. We provide evidence that phospho-Upf1 functions after nonsense codon recognition during steps that involve the translation initiation factor eIF3 and mRNA decay factors. Phospho-Upf1 interacts directly with eIF3 and inhibits the eIF3-dependent conversion of 40S/Met-tRNA(i)(Met)/mRNA to translationally competent 80S/Met-tRNA(i)(Met)/mRNA initiation complexes to repress continued translation initiation. Consistent with phospho-Upf1 impairing eIF3 function, NMD fails to detectably target nonsense-containing transcripts that initiate translation independently of eIF3 from the CrPV IRES. There is growing evidence that translational repression is a key transition that precedes mRNA delivery to the degradation machinery. Our results uncover a critical step during NMD that converts a pioneer translation initiation complex to a translationally compromised mRNP.
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Affiliation(s)
- Olaf Isken
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, 601 Elmwood Avenue, Box 712, University of Rochester, Rochester, NY 14642, USA
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Woeller CF, Gaspari M, Isken O, Maquat LE. NMD resulting from encephalomyocarditis virus IRES-directed translation initiation seems to be restricted to CBP80/20-bound mRNA. EMBO Rep 2008; 9:446-51. [PMID: 18369367 DOI: 10.1038/embor.2008.36] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 02/12/2008] [Accepted: 02/14/2008] [Indexed: 11/10/2022] Open
Abstract
Nonsense-mediated messenger RNA decay (NMD) generally degrades mRNAs that prematurely terminate translation as a means of quality control. NMD in mammalian cells targets newly spliced mRNA that is bound by the cap-binding protein heterodimer CBP80/20 and one or more post-splicing exon junction complexes during a pioneer round of translation. NMD targets mRNA that initiates translation using the encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES), therefore NMD might target not only CBP80/20-bound mRNA but also its remodelled product, eIF4E-bound mRNA. Here, we provide evidence that NMD triggered by translation initiation at the EMCV IRES, similar to NMD triggered by translation initiation at an mRNA cap, targets CBP80/20-bound mRNA but does not detectably target eIF4E-bound mRNA. We show that EMCV IRES-initiated translation undergoes a CBP80/20-associated pioneer round of translation that results in CBP80/20-dependent and Upf factor-dependent NMD when translation terminates prematurely.
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Affiliation(s)
- Collynn F Woeller
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, USA
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Silva AL, Ribeiro P, Inácio A, Liebhaber SA, Romão L. Proximity of the poly(A)-binding protein to a premature termination codon inhibits mammalian nonsense-mediated mRNA decay. RNA (NEW YORK, N.Y.) 2008; 14:563-76. [PMID: 18230761 PMCID: PMC2248256 DOI: 10.1261/rna.815108] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
mRNA surveillance pathways selectively clear defective mRNAs from the cell. As such, these pathways serve as important modifiers of genetic disorders. Nonsense-mediated decay (NMD), the most intensively studied surveillance pathway, recognizes mRNAs with premature termination codons (PTCs). In mammalian systems the location of a PTC more than 50 nucleotides 5' to the terminal exon-exon junction is a critical determinant of NMD. However, mRNAs with nonsense codons that fulfill this requirement but are located very early in the open reading frame can effectively evade NMD. The unexpected resistance of such mRNAs with AUG-proximal PTCs to accelerated decay suggests that important determinants of NMD remain to be identified. Here, we report that an NMD-sensitive mRNA can be stabilized by artificially tethering the cytoplasmic poly(A) binding protein 1, PABPC1, at a PTC-proximal position. Remarkably, the data further suggest that NMD of an mRNA with an AUG-proximal PTC can also be repressed by PABPC1, which might be brought into proximity with the PTC during cap-dependent translation and 43S scanning. These results reveal a novel parameter of NMD in mammalian cells that can account for the stability of mRNAs with AUG-proximal PTCs. These findings serve to expand current mechanistic models of NMD and mRNA translation.
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Affiliation(s)
- Ana Luísa Silva
- Centro de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, 1649-016 Lisboa, Portugal
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Neu-Yilik G, Kulozik AE. NMD: multitasking between mRNA surveillance and modulation of gene expression. ADVANCES IN GENETICS 2008; 62:185-243. [PMID: 19010255 DOI: 10.1016/s0065-2660(08)00604-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Gene expression is a highly specific and regulated multilayer process with a plethora of interconnections as well as safeguard and feedback mechanisms. Messenger RNA, long neglected as a mere subcarrier of genetic information, is more recently recognized as a linchpin of regulation and control of gene expression. Moreover, the awareness of not only proteins but also mRNA as a modulator of genetic disorders has vastly increased in recent years. Nonsense-mediated mRNA decay (NMD) is a posttranscriptional surveillance mechanism that uses an intricate network of nuclear and cytoplasmic processes to eliminate mRNAs, containing premature termination codons. It thus helps limit the synthesis of potentially harmful truncated proteins. However, recent results suggest functions of NMD that go far beyond this role and affect the expression of wild-type genes and the modulation of whole pathways. In both respects--the elimination of faulty transcripts and the regulation of error-free mRNAs--NMD has many medical implications. Therefore, it has earned increasing interest from researchers of all fields of the life sciences. In the following text, we (1) present current knowledge about the NMD mechanism and its targets, (2) define its relevance in the regulation of important biochemical pathways, (3) explore its medical significance and the prospects of therapeutic interventions, and (4) discuss additional functions of NMD effectors, some of which may be networked to NMD. The main focus of this chapter lies on mammalian NMD and resorts to the features and factors of NMD in other organisms if these help to complete or illuminate the picture.
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Affiliation(s)
- Gabriele Neu-Yilik
- Department for Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg and Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Im Neuenheimer Feld 156, 69120 Heidelberg, Germany
| | - Andreas E Kulozik
- Department for Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg and Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Im Neuenheimer Feld 156, 69120 Heidelberg, Germany
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Isken O, Maquat LE. Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev 2007; 21:1833-56. [PMID: 17671086 DOI: 10.1101/gad.1566807] [Citation(s) in RCA: 433] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Cells routinely make mistakes. Some mistakes are encoded by the genome and may manifest as inherited or acquired diseases. Other mistakes occur because metabolic processes can be intrinsically inefficient or inaccurate. Consequently, cells have developed mechanisms to minimize the damage that would result if mistakes went unchecked. Here, we provide an overview of three quality control mechanisms--nonsense-mediated mRNA decay, nonstop mRNA decay, and no-go mRNA decay. Each surveys mRNAs during translation and degrades those mRNAs that direct aberrant protein synthesis. Along with other types of quality control that occur during the complex processes of mRNA biogenesis, these mRNA surveillance mechanisms help to ensure the integrity of protein-encoding gene expression.
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Affiliation(s)
- Olaf Isken
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
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Abstract
Nonsense-mediated mRNA decay (NMD) is a quality-control mechanism that selectively degrades mRNAs harboring premature termination (nonsense) codons. If translated, these mRNAs can produce truncated proteins with dominant-negative or deleterious gain-of-function activities. In this review, we describe the molecular mechanism of NMD. We first cover conserved factors known to be involved in NMD in all eukaryotes. We then describe a unique protein complex that is deposited on mammalian mRNAs during splicing, which defines a stop codon as premature. Interaction between this exon-junction complex (EJC) and NMD factors assembled at the upstream stop codon triggers a series of steps that ultimately lead to mRNA decay. We discuss whether these proofreading events preferentially occur during a "pioneer" round of translation in higher and lower eukaryotes, their cellular location, and whether they can use alternative EJC factors or act independent of the EJC.
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Affiliation(s)
- Yao-Fu Chang
- Department of Biochemistry and Molecular Biology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA.
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