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Wei W, Liu K, Huang X, Tian S, Wang H, Zhang C, Ye J, Dong Y, An Z, Ma X, Wang B, Huang Y, Zhang X. EIF4A3-mediated biogenesis of circSTX6 promotes bladder cancer metastasis and cisplatin resistance. J Exp Clin Cancer Res 2024; 43:2. [PMID: 38163881 PMCID: PMC10759346 DOI: 10.1186/s13046-023-02932-6] [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: 09/25/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Cisplatin (CDDP)-based chemotherapy is a standard first-line treatment for metastatic bladder cancer (BCa) patients, and chemoresistance remains a major challenge in clinical practice. Circular RNAs (circRNAs) have emerged as essential regulators in carcinogenesis and cancer progression. However, the role of circRNAs in mediating CDDP chemosensitivity has yet to be well elucidated in BCa. METHODS CircSTX6 (hsa_circ_0007905) was identified by mining the public circRNA datasets and verified by Sanger sequencing, agarose gel electrophoresis, RNase R treatment and qRT-PCR assays. Then, function experiments were performed to evaluate the effects of circSTX6 on BCa metastasis. Luciferase reporter assay, RNA pull-down, RNA immunoprecipitation (RIP), RNA stability assay, Fluorescence in situ hybridization (FISH) and Immunofluorescence (IF) were conducted to evaluate the interaction among circSTX6, miR-515-3p, PABPC1 and SUZ12. Animal experiments were performed to explore the function of circSTX6 in tumor metastasis and CDDP sensitivity. RESULTS We identified that circSTX6 was significantly upregulated in clinical samples and cells of BCa. Functionally, circSTX6 promoted cell migration and invasion both in vitro and in vivo. Mechanistically, circSTX6 could act as a miR-515-3p sponge and abolish its effect on SUZ12. Moreover, circSTX6 was confirmed to increase the stability of SUZ12 mRNA by interacting with a mRNA stabilizer PABPC1 and subsequently promote the expression of SUZ12. Importantly, silencing of circSTX6 improved the chemosensitivity of CDDP-resistant bladder cancer cells to CDDP. Furthermore, in vivo analysis supported that knockdown of circSTX6 attenuated CDDP resistance in BCa tumors. CONCLUSION These studies demonstrate that circSTX6 plays a pivotal role in BCa metastasis and chemoresistance, and has potential to serve as a therapeutic target for treatment of BCa.
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Affiliation(s)
- Wenjie Wei
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
- Medical School of PLA, Beijing, 100853, China
| | - Kan Liu
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Xing Huang
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
- Medical School of PLA, Beijing, 100853, China
| | - Shuo Tian
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
- Medical School of PLA, Beijing, 100853, China
| | - Hanfeng Wang
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
- Medical School of PLA, Beijing, 100853, China
| | - Chi Zhang
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Jiali Ye
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
- Medical School of PLA, Beijing, 100853, China
| | - Yuhao Dong
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
- Medical School of PLA, Beijing, 100853, China
| | - Ziyan An
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
- Medical School of PLA, Beijing, 100853, China
| | - Xin Ma
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Baojun Wang
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100039, China.
| | - Yan Huang
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100039, China.
| | - Xu Zhang
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100039, China.
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2
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Halbout M, Bury M, Hanet A, Gerin I, Graff J, Killian T, Gatto L, Vertommen D, Bommer GT. SUZ domain-containing proteins have multiple effects on nonsense-mediated decay target transcripts. J Biol Chem 2023; 299:105095. [PMID: 37507022 PMCID: PMC10470013 DOI: 10.1016/j.jbc.2023.105095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Many transcripts are targeted by nonsense-mediated decay (NMD), leading to their degradation and the inhibition of their translation. We found that the protein SUZ domain-containing protein 1 (SZRD1) interacts with the key NMD factor up-frameshift 1. When recruited to NMD-sensitive reporter gene transcripts, SZRD1 increased protein production, at least in part, by relieving translational inhibition. The conserved SUZ domain in SZRD1 was required for this effect. The SUZ domain is present in only three other human proteins besides SZRD1: R3H domain-containing protein 1 and 2 (R3HDM1, R3HDM2) and cAMP-regulated phosphoprotein 21 (ARPP21). We found that ARPP21, similarly to SZRD1, can increase protein production from NMD-sensitive reporter transcripts in an SUZ domain-dependent manner. This indicated that the SUZ domain-containing proteins could prevent translational inhibition of transcripts targeted by NMD. Consistent with the idea that SZRD1 mainly prevents translational inhibition, we did not observe a systematic decrease in the abundance of NMD targets when we knocked down SZRD1. Surprisingly, knockdown of SZRD1 in two different cell lines led to reduced levels of the NMD component UPF3B, which was accompanied by increased levels in a subset of NMD targets. This suggests that SZRD1 is required to maintain normal UPF3B levels and indicates that the effect of SZRD1 on NMD targets is not limited to a relief from translational inhibition. Overall, our study reveals that human SUZ domain-containing proteins play a complex role in regulating protein output from transcripts targeted by NMD.
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Affiliation(s)
- Mathias Halbout
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Marina Bury
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Aoife Hanet
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Isabelle Gerin
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Julie Graff
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Theodore Killian
- Computational Biology Laboratory, de Duve Institute, UCLouvain, Bruxelles, Belgium
| | - Laurent Gatto
- Computational Biology Laboratory, de Duve Institute, UCLouvain, Bruxelles, Belgium
| | - Didier Vertommen
- Protein Phosphorylation Unit, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Guido T Bommer
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium.
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3
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Qi Y, Wang M, Jiang Q. PABPC1--mRNA stability, protein translation and tumorigenesis. Front Oncol 2022; 12:1025291. [PMID: 36531055 PMCID: PMC9753129 DOI: 10.3389/fonc.2022.1025291] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/08/2022] [Indexed: 09/29/2023] Open
Abstract
Mammalian poly A-binding proteins (PABPs) are highly conserved multifunctional RNA-binding proteins primarily involved in the regulation of mRNA translation and stability, of which PABPC1 is considered a central regulator of cytoplasmic mRNA homing and is involved in a wide range of physiological and pathological processes by regulating almost every aspect of RNA metabolism. Alterations in its expression and function disrupt intra-tissue homeostasis and contribute to the development of various tumors. There is increasing evidence that PABPC1 is aberrantly expressed in a variety of tumor tissues and cancers such as lung, gastric, breast, liver, and esophageal cancers, and PABPC1 might be used as a potential biomarker for tumor diagnosis, treatment, and clinical application in the future. In this paper, we review the abnormal expression, functional role, and molecular mechanism of PABPC1 in tumorigenesis and provide directions for further understanding the regulatory role of PABPC1 in tumor cells.
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Affiliation(s)
- Ya Qi
- Department of Gynecology and Obstetrics, Shengjing Hospital Affiliated of China Medical University, Shenyang, Liaoning, China
| | - Min Wang
- Department of Gynecology and Obstetrics, Shengjing Hospital Affiliated of China Medical University, Shenyang, Liaoning, China
| | - Qi Jiang
- Second Department of Clinical Medicine, China Medical University, Shenyang, Liaoning, China
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4
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Embree CM, Abu-Alhasan R, Singh G. Features and factors that dictate if terminating ribosomes cause or counteract nonsense-mediated mRNA decay. J Biol Chem 2022; 298:102592. [PMID: 36244451 PMCID: PMC9661723 DOI: 10.1016/j.jbc.2022.102592] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality control pathway in eukaryotes that continuously monitors mRNA transcripts to ensure truncated polypeptides are not produced. The expression of many normal mRNAs that encode full-length polypeptides is also regulated by this pathway. Such transcript surveillance by NMD is intimately linked to translation termination. When a ribosome terminates translation at a normal termination codon, NMD is not activated, and mRNA can undergo repeated rounds of translation. On the other hand, when translation termination is deemed abnormal, such as that on a premature termination codon, it leads to a series of poorly understood events involving the NMD pathway, which destabilizes the transcript. In this review, we summarize our current understanding of how the NMD machinery interfaces with the translation termination factors to initiate NMD. We also discuss a variety of cis-acting sequence contexts and trans-acting factors that can cause readthrough, ribosome reinitiation, or ribosome frameshifting at stop codons predicted to induce NMD. These alternative outcomes can lead to the ribosome translating downstream of such stop codons and hence the transcript escaping NMD. NMD escape via these mechanisms can have wide-ranging implications on human health, from being exploited by viruses to hijack host cell systems to being harnessed as potential therapeutic possibilities to treat genetic diseases.
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Affiliation(s)
- Caleb M Embree
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA
| | - Rabab Abu-Alhasan
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA
| | - Guramrit Singh
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA.
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5
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Karousis ED, Mühlemann O. The broader sense of nonsense. Trends Biochem Sci 2022; 47:921-935. [PMID: 35780009 DOI: 10.1016/j.tibs.2022.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/30/2022] [Accepted: 06/08/2022] [Indexed: 12/21/2022]
Abstract
The term 'nonsense-mediated mRNA decay' (NMD) was initially coined to describe the translation-dependent degradation of mRNAs harboring premature termination codons (PTCs), but it is meanwhile known that NMD also targets many canonical mRNAs with numerous biological implications. The molecular mechanisms determining on which RNAs NMD ensues are only partially understood. Considering the broad range of NMD-sensitive RNAs and the variable degrees of their degradation, we highlight here the hallmarks of mammalian NMD and point out open questions. We review the links between NMD and disease by summarizing the role of NMD in cancer, neurodegeneration, and viral infections. Finally, we describe strategies to modulate NMD activity and specificity as potential therapeutic approaches for various diseases.
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Affiliation(s)
- Evangelos D Karousis
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
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6
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Marques AR, Santos JX, Martiniano H, Vilela J, Rasga C, Romão L, Vicente AM. Gene Variants Involved in Nonsense-Mediated mRNA Decay Suggest a Role in Autism Spectrum Disorder. Biomedicines 2022; 10:biomedicines10030665. [PMID: 35327467 PMCID: PMC8945030 DOI: 10.3390/biomedicines10030665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 02/07/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is a heterogeneous neurodevelopmental condition with unclear etiology. Many genes have been associated with ASD risk, but the underlying mechanisms are still poorly understood. An important post-transcriptional regulatory mechanism that plays an essential role during neurodevelopment, the Nonsense-Mediated mRNA Decay (NMD) pathway, may contribute to ASD risk. In this study, we gathered a list of 46 NMD factors and regulators and investigated the role of genetic variants in these genes in ASD. By conducting a comprehensive search for Single Nucleotide Variants (SNVs) in NMD genes using Whole Exome Sequencing data from 1828 ASD patients, we identified 270 SNVs predicted to be damaging in 28.7% of the population. We also analyzed Copy Number Variants (CNVs) from two cohorts of ASD patients (N = 3570) and discovered 38 CNVs in 1% of cases. Importantly, we discovered 136 genetic variants (125 SNVs and 11 CNVs) in 258 ASD patients that were located within protein domains required for NMD. These gene variants are classified as damaging using in silico prediction tools, and therefore may interfere with proper NMD function in ASD. The discovery of NMD genes as candidates for ASD in large patient genomic datasets provides evidence supporting the involvement of the NMD pathway in ASD pathophysiology.
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Affiliation(s)
- Ana Rita Marques
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - João Xavier Santos
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - Hugo Martiniano
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - Joana Vilela
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - Célia Rasga
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - Luísa Romão
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal
| | - Astrid Moura Vicente
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
- Correspondence:
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7
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Eberle AB, Mühlemann O. Tethered Function Assays to Elucidate the Role of RNA-Binding Proteins. Methods Mol Biol 2022; 2537:285-306. [PMID: 35895271 DOI: 10.1007/978-1-0716-2521-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The fate of each RNA molecule is strongly determined by RNA-binding proteins (RBPs) which accompany transcripts from its synthesis to its degradation. To elucidate the effect of a specific RBP on bound RNA, it can be artificially recruited to a specific site on a reporter mRNA that can be followed by a variety of methods. In this so-called tethering assay, the protein of interest (POI) is fused to the coat protein of the MS2 bacteriophage and expressed in your favorite cells together with a reporter gene containing MS2 binding sites. The MS2 binding sites are recognized by the MS2 coat protein (MS2CP) with high affinity and specificity and by doing so, the POI is tethered to the reporter RNA. Here, we describe how with the help of this assay the human cytoplasmic poly(A) binding protein is recruited to a mini-μ RNA reporter, thereby influencing the stability of the reporter transcript.
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Affiliation(s)
- Andrea B Eberle
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
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8
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Karousis ED, Gurzeler LA, Annibaldis G, Dreos R, Mühlemann O. Human NMD ensues independently of stable ribosome stalling. Nat Commun 2020; 11:4134. [PMID: 32807779 PMCID: PMC7431590 DOI: 10.1038/s41467-020-17974-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/20/2020] [Indexed: 12/18/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA degradation pathway that is important for the elimination of faulty, and the regulation of normal, mRNAs. The molecular details of the early steps in NMD are not fully understood but previous work suggests that NMD activation occurs as a consequence of ribosome stalling at the termination codon (TC). To test this hypothesis, we established an in vitro translation-coupled toeprinting assay based on lysates from human cells that allows monitoring of ribosome occupancy at the TC of reporter mRNAs. In contrast to the prevailing NMD model, our in vitro system reveals similar ribosomal occupancy at the stop codons of NMD-sensitive and NMD-insensitive reporter mRNAs. Moreover, ribosome profiling reveals a similar density of ribosomes at the TC of endogenous NMD-sensitive and NMD-insensitive mRNAs in vivo. Together, these data show that NMD activation is not accompanied by stable stalling of ribosomes at TCs. Nonsense-mediated mRNA decay (NMD) was thought to ensue when ribosomes fail to terminate translation properly. However, the authors observe similar ribosome occupancy at stop codons of NMD sensitive and insensitive mRNAs, showing that human NMD is not activated by stable ribosome stalling as previously suggested.
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Affiliation(s)
- Evangelos D Karousis
- Department of Chemistry and Biochemistry, University of Bern, CH-3012, Bern, Switzerland
| | - Lukas-Adrian Gurzeler
- Department of Chemistry and Biochemistry, University of Bern, CH-3012, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012, Bern, Switzerland
| | - Giuditta Annibaldis
- Department of Chemistry and Biochemistry, University of Bern, CH-3012, Bern, Switzerland
| | - René Dreos
- Center for Integrative Genomics, Université de Lausanne, CH-1015, Lausanne, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, CH-3012, Bern, Switzerland.
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9
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Lavysh D, Neu-Yilik G. UPF1-Mediated RNA Decay-Danse Macabre in a Cloud. Biomolecules 2020; 10:E999. [PMID: 32635561 PMCID: PMC7407380 DOI: 10.3390/biom10070999] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/18/2020] [Accepted: 06/29/2020] [Indexed: 12/21/2022] Open
Abstract
Nonsense-mediated RNA decay (NMD) is the prototype example of a whole family of RNA decay pathways that unfold around a common central effector protein called UPF1. While NMD in yeast appears to be a linear pathway, NMD in higher eukaryotes is a multifaceted phenomenon with high variability with respect to substrate RNAs, degradation efficiency, effector proteins and decay-triggering RNA features. Despite increasing knowledge of the mechanistic details, it seems ever more difficult to define NMD and to clearly distinguish it from a growing list of other UPF1-mediated RNA decay pathways (UMDs). With a focus on mammalian, we here critically examine the prevailing NMD models and the gaps and inconsistencies in these models. By exploring the minimal requirements for NMD and other UMDs, we try to elucidate whether they are separate and definable pathways, or rather variations of the same phenomenon. Finally, we suggest that the operating principle of the UPF1-mediated decay family could be considered similar to that of a computing cloud providing a flexible infrastructure with rapid elasticity and dynamic access according to specific user needs.
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Affiliation(s)
- Daria Lavysh
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany;
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany
- Department Clinical Pediatric Oncology, Hopp Kindertumorzentrum am NCT Heidelberg, 69120 Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany;
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany
- Department Clinical Pediatric Oncology, Hopp Kindertumorzentrum am NCT Heidelberg, 69120 Heidelberg, Germany
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10
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Kurosaki T, Popp MW, Maquat LE. Quality and quantity control of gene expression by nonsense-mediated mRNA decay. Nat Rev Mol Cell Biol 2020; 20:406-420. [PMID: 30992545 DOI: 10.1038/s41580-019-0126-2] [Citation(s) in RCA: 428] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is one of the best characterized and most evolutionarily conserved cellular quality control mechanisms. Although NMD was first found to target one-third of mutated, disease-causing mRNAs, it is now known to also target ~10% of unmutated mammalian mRNAs to facilitate appropriate cellular responses - adaptation, differentiation or death - to environmental changes. Mutations in NMD genes in humans are associated with intellectual disability and cancer. In this Review, we discuss how NMD serves multiple purposes in human cells by degrading both mutated mRNAs to protect the integrity of the transcriptome and normal mRNAs to control the quantities of unmutated transcripts.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.,Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Maximilian W Popp
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.,Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA. .,Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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11
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Sulkowska A, Auber A, Sikorski PJ, Silhavy DN, Auth M, Sitkiewicz E, Jean V, Merret RM, Bousquet-Antonelli CC, Kufel J. RNA Helicases from the DEA(D/H)-Box Family Contribute to Plant NMD Efficiency. PLANT & CELL PHYSIOLOGY 2020; 61:144-157. [PMID: 31560399 DOI: 10.1093/pcp/pcz186] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic RNA surveillance mechanism that degrades aberrant mRNAs comprising a premature translation termination codon. The adenosine triphosphate (ATP)-dependent RNA helicase up-frameshift 1 (UPF1) is a major NMD factor in all studied organisms; however, the complexity of this mechanism has not been fully characterized in plants. To identify plant NMD factors, we analyzed UPF1-interacting proteins using tandem affinity purification coupled to mass spectrometry. Canonical members of the NMD pathway were found along with numerous NMD candidate factors, including conserved DEA(D/H)-box RNA helicase homologs of human DDX3, DDX5 and DDX6, translation initiation factors, ribosomal proteins and transport factors. Our functional studies revealed that depletion of DDX3 helicases enhances the accumulation of NMD target reporter mRNAs but does not result in increased protein levels. In contrast, silencing of DDX6 group leads to decreased accumulation of the NMD substrate. The inhibitory effect of DDX6-like helicases on NMD was confirmed by transient overexpression of RH12 helicase. These results indicate that DDX3 and DDX6 helicases in plants have a direct and opposing contribution to NMD and act as functional NMD factors.
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Affiliation(s)
- Aleksandra Sulkowska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andor Auber
- Agricultural Biotechnology Institute, Szent-Gy�rgyi 4, H-2100 G�d�llő, Hungary
| | - Pawel J Sikorski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Dï Niel Silhavy
- Agricultural Biotechnology Institute, Szent-Gy�rgyi 4, H-2100 G�d�llő, Hungary
| | - Mariann Auth
- Agricultural Biotechnology Institute, Szent-Gy�rgyi 4, H-2100 G�d�llő, Hungary
| | - Ewa Sitkiewicz
- Proteomics Laboratory, Biophysics Department, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Viviane Jean
- UMR5096 LGDP, Universit� de Perpignan Via Domitia, UMR5096 LGDP58, Avenue Paul Alduy, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, Perpignan Cedex, France
| | - Rï My Merret
- UMR5096 LGDP, Universit� de Perpignan Via Domitia, UMR5096 LGDP58, Avenue Paul Alduy, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, Perpignan Cedex, France
| | - Cï Cile Bousquet-Antonelli
- UMR5096 LGDP, Universit� de Perpignan Via Domitia, UMR5096 LGDP58, Avenue Paul Alduy, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, Perpignan Cedex, France
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
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12
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The Interactome analysis of the Respiratory Syncytial Virus protein M2-1 suggests a new role in viral mRNA metabolism post-transcription. Sci Rep 2019; 9:15258. [PMID: 31649314 PMCID: PMC6813310 DOI: 10.1038/s41598-019-51746-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/07/2019] [Indexed: 01/18/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is a globally prevalent negative-stranded RNA virus, which can cause life-threatening respiratory infections in young children, elderly people and immunocompromised patients. Its transcription termination factor M2-1 plays an essential role in viral transcription, but the mechanisms underpinning its function are still unclear. We investigated the cellular interactome of M2-1 using green fluorescent protein (GFP)-trap immunoprecipitation on RSV infected cells coupled with mass spectrometry analysis. We identified 137 potential cellular partners of M2-1, among which many proteins associated with mRNA metabolism, and particularly mRNA maturation, translation and stabilization. Among these, the cytoplasmic polyA-binding protein 1 (PABPC1), a candidate with a major role in both translation and mRNA stabilization, was confirmed to interact with M2-1 using protein complementation assay and specific immunoprecipitation. PABPC1 was also shown to colocalize with M2-1 from its accumulation in inclusion bodies associated granules (IBAGs) to its liberation in the cytoplasm. Altogether, these results strongly suggest that M2-1 interacts with viral mRNA and mRNA metabolism factors from transcription to translation, and imply that M2-1 may have an additional role in the fate of viral mRNA downstream of transcription.
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13
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Destabilization of Eukaryote mRNAs by 5' Proximal Stop Codons Can Occur Independently of the Nonsense-Mediated mRNA Decay Pathway. Cells 2019; 8:cells8080800. [PMID: 31370247 PMCID: PMC6721604 DOI: 10.3390/cells8080800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/17/2022] Open
Abstract
In eukaryotes, the binding of poly(A) binding protein (PAB) to the poly(A) tail is central to maintaining mRNA stability. PABP interacts with the translation termination apparatus, and with eIF4G to maintain 3′–5′ mRNA interactions as part of an mRNA closed loop. It is however unclear how ribosome recycling on a closed loop mRNA is influenced by the proximity of the stop codon to the poly(A) tail, and how post-termination ribosome recycling affects mRNA stability. We show that in a yeast disabled for nonsense mediated mRNA decay (NMD), a PGK1 mRNA with an early stop codon at codon 22 of the reading frame is still highly unstable, and that this instability cannot be significantly countered even when 50% stop codon readthrough is triggered. In an NMD-deficient mutant yeast, stable reporter alleles with more 3′ proximal stop codons could not be rendered unstable through Rli1-depletion, inferring defective Rli1 ribosome recycling is insufficient in itself to trigger mRNA instability. Mathematical modelling of a translation system including the effect of ribosome recycling and poly(A) tail shortening supports the hypothesis that impaired ribosome recycling from 5′ proximal stop codons may compromise initiation processes and thus destabilize the mRNA. A model is proposed wherein ribosomes undergo a maturation process during early elongation steps, and acquire competency to re-initiate on the same mRNA as translation elongation progresses beyond the very 5′ proximal regions of the mRNA.
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14
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Karousis ED, Mühlemann O. Nonsense-Mediated mRNA Decay Begins Where Translation Ends. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032862. [PMID: 29891560 DOI: 10.1101/cshperspect.a032862] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is arguably the best-studied eukaryotic messenger RNA (mRNA) surveillance pathway, yet fundamental questions concerning the molecular mechanism of target RNA selection remain unsolved. Besides degrading defective mRNAs harboring premature termination codons (PTCs), NMD also targets many mRNAs encoding functional full-length proteins. Thus, NMD impacts on a cell's transcriptome and is implicated in a range of biological processes that affect a broad spectrum of cellular homeostasis. Here, we focus on the steps involved in the recognition of NMD targets and the activation of NMD. We summarize the accumulating evidence that tightly links NMD to translation termination and we further discuss the recruitment and activation of the mRNA degradation machinery and the regulation of this complex series of events. Finally, we review emerging ideas concerning the mechanistic details of NMD activation and the potential role of NMD as a general surveyor of translation efficacy.
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Affiliation(s)
- Evangelos D Karousis
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
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15
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Zhou Z, Chen Y, Jin M, He J, Guli A, Yan C, Ding S. Comprehensive Analysis of Lysine Acetylome Reveals a Site-Specific Pattern in Rapamycin-Induced Autophagy. J Proteome Res 2019; 18:865-877. [PMID: 30592415 DOI: 10.1021/acs.jproteome.8b00533] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein acetylation reportedly acts as a key regulator of autophagy. However, up to now, the relationship between acetylome and autophagy has remained unclear. Here stable isotope labeling of amino acids in cell culture and high-throughput quantitative mass spectrometry were used to perform an acetylome analysis of rapamycin-induced autophagy in vitro. Our data revealed that 2135 sites were quantified on 1081 proteins. During autophagy, 421 sites were significantly regulated on 296 proteins, with 80.8% of sites downregulated and 19.2% upregulated. Motif enrichment analysis revealed five main motifs. Most of the downregulated sites conformed to the classical functional motif of p300/CBP [G-AcK]. Furthermore, acetylation targeted proteins involved mainly in ribosomes, spliceosomes, and AcCoA-related metabolic process. In-depth analysis indicated that most of the acetylation sites were in the critical domain, were functional sites, or could change their enzymatic activity by acetylation, highlighting the importance of site-specific acetylation patterns. Subsequently, we demonstrated that K1549 of p300 was also a functional site that could regulate the autophagic process in vitro. In conclusion, our data reveal a deacetylation-preponderant profile with autophagy. The specificity of the related motifs and the identification of site-specific acetylation patterns will assist searches for potential targets or subsequent mechanism-focused studies to elucidate site-specific protein networks in autophagy.
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Affiliation(s)
- Zhuo Zhou
- The National Education Base for Basic Medical Sciences , Zhejiang University School of Medicine , 866 Yuhangtang Road , Hangzhou 310058 , Zhejiang Province , China
| | - Yu Chen
- The National Education Base for Basic Medical Sciences , Zhejiang University School of Medicine , 866 Yuhangtang Road , Hangzhou 310058 , Zhejiang Province , China
| | - Mengqi Jin
- The National Education Base for Basic Medical Sciences , Zhejiang University School of Medicine , 866 Yuhangtang Road , Hangzhou 310058 , Zhejiang Province , China
| | - Jianqin He
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital , Zhejiang University School of Medicine , 79 Qingchun Road , Hangzhou 310003 , Zhejiang Province , China
| | - Ayiding Guli
- The National Education Base for Basic Medical Sciences , Zhejiang University School of Medicine , 866 Yuhangtang Road , Hangzhou 310058 , Zhejiang Province , China
| | - Chunlan Yan
- Department of Biophysics, Key Laboratory of Medical Neurobiology, Ministry of Health of China , Zhejiang University School of Medicine , 866 Yuhangtang Road , Hangzhou 310058 , Zhejiang Province , China
| | - Shiping Ding
- The National Education Base for Basic Medical Sciences , Zhejiang University School of Medicine , 866 Yuhangtang Road , Hangzhou 310058 , Zhejiang Province , China
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16
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Fernandes R, Nogueira G, da Costa PJ, Pinto F, Romão L. Nonsense-Mediated mRNA Decay in Development, Stress and Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:41-83. [DOI: 10.1007/978-3-030-19966-1_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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17
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Paolantoni C, Ricciardi S, De Paolis V, Okenwa C, Catalanotto C, Ciotti MT, Cattaneo A, Cogoni C, Giorgi C. Arc 3' UTR Splicing Leads to Dual and Antagonistic Effects in Fine-Tuning Arc Expression Upon BDNF Signaling. Front Mol Neurosci 2018; 11:145. [PMID: 29755318 PMCID: PMC5934489 DOI: 10.3389/fnmol.2018.00145] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/10/2018] [Indexed: 01/02/2023] Open
Abstract
Activity-regulated cytoskeletal associated protein (Arc) is an immediate-early gene critically involved in synaptic plasticity and memory consolidation. Arc mRNA is rapidly induced by synaptic activation and a portion is locally translated in dendrites where it modulates synaptic strength. Being an activity-dependent effector of homeostatic balance, regulation of Arc is uniquely tuned to result in short-lived bursts of expression. Cis-Acting elements that control its transitory expression post-transcriptionally reside primarily in Arc mRNA 3′ UTR. These include two conserved introns which distinctively modulate Arc mRNA stability by targeting it for destruction via the nonsense mediated decay pathway. Here, we further investigated how splicing of the Arc mRNA 3′ UTR region contributes to modulate Arc expression in cultured neurons. Unexpectedly, upon induction with brain derived neurotrophic factor, translational efficiency of a luciferase reporter construct harboring Arc 3′ UTR is significantly upregulated and this effect is dependent on splicing of Arc introns. We find that, eIF2α dephosphorylation, mTOR, ERK, PKC, and PKA activity are key to this process. Additionally, CREB-dependent transcription is required to couple Arc 3′ UTR-splicing to its translational upregulation, suggesting the involvement of de novo transcribed trans-acting factors. Overall, splicing of Arc 3′ UTR exerts a dual and unique effect in fine-tuning Arc expression upon synaptic signaling: while inducing mRNA decay to limit the time window of Arc expression, it also elicits translation of the decaying mRNA. This antagonistic effect likely contributes to the achievement of a confined yet efficient burst of Arc protein expression, facilitating its role as an effector of synapse-specific plasticity.
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Affiliation(s)
- Chiara Paolantoni
- European Brain Research Institute Rita Levi-Montalcini Rome, Rome, Italy.,Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Simona Ricciardi
- European Brain Research Institute Rita Levi-Montalcini Rome, Rome, Italy.,Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Veronica De Paolis
- European Brain Research Institute Rita Levi-Montalcini Rome, Rome, Italy.,Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Chinenye Okenwa
- European Brain Research Institute Rita Levi-Montalcini Rome, Rome, Italy
| | - Caterina Catalanotto
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy
| | - Maria T Ciotti
- Institute of Cell Biology and Neurobiology, National Research Council, Rome, Italy
| | - Antonino Cattaneo
- European Brain Research Institute Rita Levi-Montalcini Rome, Rome, Italy.,Bio@SNS Laboratory, Scuola Normale Superiore, Pisa, Italy
| | - Carlo Cogoni
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy
| | - Corinna Giorgi
- European Brain Research Institute Rita Levi-Montalcini Rome, Rome, Italy
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18
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New insights into the interplay between the translation machinery and nonsense-mediated mRNA decay factors. Biochem Soc Trans 2018; 46:503-512. [PMID: 29626148 PMCID: PMC6008592 DOI: 10.1042/bst20170427] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 12/13/2022]
Abstract
Faulty mRNAs with a premature stop codon (PTC) are recognized and degraded by nonsense-mediated mRNA decay (NMD). Recognition of a nonsense mRNA depends on translation and on the presence of NMD-enhancing or the absence of NMD-inhibiting factors in the 3'-untranslated region. Our review summarizes our current understanding of the molecular function of the conserved NMD factors UPF3B and UPF1, and of the anti-NMD factor Poly(A)-binding protein, and their interactions with ribosomes translating PTC-containing mRNAs. Our recent discovery that UPF3B interferes with human translation termination and enhances ribosome dissociation in vitro, whereas UPF1 is inactive in these assays, suggests a re-interpretation of previous experiments and modification of prevalent NMD models. Moreover, we discuss recent work suggesting new functions of the key NMD factor UPF1 in ribosome recycling, inhibition of translation re-initiation and nascent chain ubiquitylation. These new findings suggest that the interplay of UPF proteins with the translation machinery is more intricate than previously appreciated, and that this interplay quality-controls the efficiency of termination, ribosome recycling and translation re-initiation.
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19
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Nicholson P, Gkratsou A, Josi C, Colombo M, Mühlemann O. Dissecting the functions of SMG5, SMG7, and PNRC2 in nonsense-mediated mRNA decay of human cells. RNA (NEW YORK, N.Y.) 2018; 24:557-573. [PMID: 29348139 PMCID: PMC5855955 DOI: 10.1261/rna.063719.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/08/2018] [Indexed: 05/04/2023]
Abstract
The term "nonsense-mediated mRNA decay" (NMD) originally described the degradation of mRNAs with premature translation-termination codons (PTCs), but its meaning has recently been extended to be a translation-dependent post-transcriptional regulator of gene expression affecting 3%-10% of all mRNAs. The degradation of NMD target mRNAs involves both exonucleolytic and endonucleolytic pathways in mammalian cells. While the latter is mediated by the endonuclease SMG6, the former pathway has been reported to require a complex of SMG5-SMG7 or SMG5-PNRC2 binding to UPF1. However, the existence, dominance, and mechanistic details of these exonucleolytic pathways are divisive. Therefore, we have investigated the possible exonucleolytic modes of mRNA decay in NMD by examining the roles of UPF1, SMG5, SMG7, and PNRC2 using a combination of functional assays and interaction mapping. Confirming previous work, we detected an interaction between SMG5 and SMG7 and also a functional need for this complex in NMD. In contrast, we found no evidence for the existence of a physical or functional interaction between SMG5 and PNRC2. Instead, we show that UPF1 interacts with PNRC2 and that it triggers 5'-3' exonucleolytic decay of reporter transcripts in tethering assays. PNRC2 interacts mainly with decapping factors and its knockdown does not affect the RNA levels of NMD reporters. We conclude that PNRC2 is probably an important mRNA decapping factor but that it does not appear to be required for NMD.
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Affiliation(s)
- Pamela Nicholson
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
| | - Asimina Gkratsou
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Christoph Josi
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Martino Colombo
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
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20
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Valášek LS, Zeman J, Wagner S, Beznosková P, Pavlíková Z, Mohammad MP, Hronová V, Herrmannová A, Hashem Y, Gunišová S. Embraced by eIF3: structural and functional insights into the roles of eIF3 across the translation cycle. Nucleic Acids Res 2017; 45:10948-10968. [PMID: 28981723 PMCID: PMC5737393 DOI: 10.1093/nar/gkx805] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/31/2017] [Indexed: 12/31/2022] Open
Abstract
Protein synthesis is mediated via numerous molecules including the ribosome, mRNA, tRNAs, as well as translation initiation, elongation and release factors. Some of these factors play several roles throughout the entire process to ensure proper assembly of the preinitiation complex on the right mRNA, accurate selection of the initiation codon, errorless production of the encoded polypeptide and its proper termination. Perhaps, the most intriguing of these multitasking factors is the eukaryotic initiation factor eIF3. Recent evidence strongly suggests that this factor, which coordinates the progress of most of the initiation steps, does not come off the initiation complex upon subunit joining, but instead it remains bound to 80S ribosomes and gradually falls off during the first few elongation cycles to: (1) promote resumption of scanning on the same mRNA molecule for reinitiation downstream—in case of translation of upstream ORFs short enough to preserve eIF3 bound; or (2) come back during termination on long ORFs to fine tune its fidelity or, if signaled, promote programmed stop codon readthrough. Here, we unite recent structural views of the eIF3–40S complex and discus all known eIF3 roles to provide a broad picture of the eIF3’s impact on translational control in eukaryotic cells.
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Affiliation(s)
- Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Jakub Zeman
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Susan Wagner
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Zuzana Pavlíková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Mahabub Pasha Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Vladislava Hronová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Yaser Hashem
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France
| | - Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
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21
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Ottens F, Boehm V, Sibley CR, Ule J, Gehring NH. Transcript-specific characteristics determine the contribution of endo- and exonucleolytic decay pathways during the degradation of nonsense-mediated decay substrates. RNA (NEW YORK, N.Y.) 2017; 23:1224-1236. [PMID: 28461625 PMCID: PMC5513067 DOI: 10.1261/rna.059659.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/17/2017] [Indexed: 06/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) controls gene expression by eliminating mRNAs with premature or aberrant translation termination. Degradation of NMD substrates is initiated by the central NMD factor UPF1, which recruits the endonuclease SMG6 and the deadenylation-promoting SMG5/7 complex. The extent to which SMG5/7 and SMG6 contribute to the degradation of individual substrates and their regulation by UPF1 remains elusive. Here we map transcriptome-wide sites of SMG6-mediated endocleavage via 3' fragment capture and degradome sequencing. This reveals that endogenous transcripts can have NMD-eliciting features at various positions, including upstream open reading frames (uORFs), premature termination codons (PTCs), and long 3' UTRs. We find that NMD substrates with PTCs undergo constitutive SMG6-dependent endocleavage, rather than SMG7-dependent exonucleolytic decay. In contrast, the turnover of NMD substrates containing uORFs and long 3' UTRs involves both SMG6- and SMG7-dependent endo- and exonucleolytic decay, respectively. This suggests that the extent to which SMG6 and SMG7 degrade NMD substrates is determined by the mRNA architecture.
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Affiliation(s)
- Franziska Ottens
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Volker Boehm
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Christopher R Sibley
- Division of Brain Sciences, Imperial College London, London W12 0NN, United Kingdom
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
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22
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da Costa PJ, Menezes J, Romão L. The role of alternative splicing coupled to nonsense-mediated mRNA decay in human disease. Int J Biochem Cell Biol 2017; 91:168-175. [PMID: 28743674 DOI: 10.1016/j.biocel.2017.07.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/15/2017] [Accepted: 07/18/2017] [Indexed: 12/29/2022]
Abstract
Alternative pre-mRNA splicing (AS) affects gene expression as it generates proteome diversity. Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that recognizes and selectively degrades mRNAs carrying premature translation-termination codons (PTCs), preventing the production of truncated proteins that could result in disease. Several studies have also implicated NMD in the regulation of steady-state levels of physiological mRNAs. In addition, it is known that several regulated AS events do not lead to generation of protein products, as they lead to transcripts that carry PTCs and thus, they are committed to NMD. Indeed, an estimated one-third of naturally occurring, alternatively spliced mRNAs is targeted for NMD, being AS coupled to NMD (AS-NMD) an efficient strategy to regulate gene expression. In this review, we will focus on how AS mechanism operates and how can be coupled to NMD to fine-tune gene expression levels. Furthermore, we will demonstrate the physiological significance of the interplay among AS and NMD in human disease, such as cancer and neurological disorders. The understanding of how AS-NMD orchestrates expression of vital genes is of utmost importance for the advance in diagnosis, prognosis and treatment of many human disorders.
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Affiliation(s)
- Paulo J da Costa
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Juliane Menezes
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
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23
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Fatscher T, Gehring NH. Harnessing short poly(A)-binding protein-interacting peptides for the suppression of nonsense-mediated mRNA decay. Sci Rep 2016; 6:37311. [PMID: 27874031 PMCID: PMC5118804 DOI: 10.1038/srep37311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/27/2016] [Indexed: 11/17/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a cellular process that eliminates messenger RNA (mRNA) substrates with premature translation termination codons (PTCs). In addition, NMD regulates the expression of a number of physiological mRNAs, for example transcripts containing long 3′ UTRs. Current models implicate the interaction between cytoplasmic poly(A)-binding protein (PABPC1) and translation termination in NMD. Accordingly, PABPC1 present within close proximity of a termination codon antagonizes NMD. Here, we use reporter mRNAs with different NMD-inducing 3′ UTRs to establish a general NMD-inhibiting property of PABPC1. NMD-inhibition is not limited to PABPC1, but can also be achieved by peptides consisting of the PABP-interacting motif 2 (PAM2) of different proteins when recruited to an NMD-inhibiting position of NMD reporter transcripts. The short PAM2 peptides efficiently suppress NMD activated by a long 3′ UTR, an exon-junction complex (EJC) and individual EJC components, and stabilize a PTC-containing β-globin mRNA. In conclusion, our results establish short PABPC1-recruiting peptides as potent but position-dependent inhibitors of mammalian NMD.
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Affiliation(s)
- Tobias Fatscher
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, Cologne, Germany
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24
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Nkiliza A, Mutez E, Simonin C, Leprêtre F, Duflot A, Figeac M, Villenet C, Semaille P, Comptdaer T, Genet A, Sablonnière B, Devos D, Defebvre L, Destée A, Chartier-Harlin MC. RNA-binding disturbances as a continuum from spinocerebellar ataxia type 2 to Parkinson disease. Neurobiol Dis 2016; 96:312-322. [PMID: 27663142 DOI: 10.1016/j.nbd.2016.09.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/07/2016] [Accepted: 09/17/2016] [Indexed: 12/13/2022] Open
Abstract
CAG triplet expansions in Ataxin-2 gene (ATXN2) cause spinocerebellar ataxia type 2 and have a role that remains to be clarified in Parkinson's disease (PD). To study the molecular events associated with these expansions, we sequenced them and analyzed the transcriptome from blood cells of controls and three patient groups diagnosed with spinocerebellar ataxia type 2 (herein referred to as SCA2c) or PD with or without ATXN2 triplet expansions (named SCA2p). The transcriptome profiles of these 40 patients revealed three main observations: i) a specific pattern of pathways related to cellular contacts, proliferation and differentiation associated with SCA2p group, ii) similarities between the SCA2p and sporadic PD groups in genes and pathways known to be altered in PD such as Wnt, Ephrin and Leukocyte extravasation signaling iii) RNA metabolism disturbances with "RNA-binding" and "poly(A) RNA-binding" as a common feature in all groups. Remarkably, disturbances of ALS signaling were shared between SCA2p and sporadic PD suggesting common molecular dysfunctions in PD and ALS including CACNA1, hnRNP, DDX and PABPC gene family perturbations. Interestingly, the transcriptome profiles of patients with parkinsonian phenotypes were prevalently associated with alterations of translation while SCA2c and PD patients presented perturbations of splicing. While ATXN2 RNA expression was not perturbed, its protein expression in immortalized lymphoblastoid cells was significantly decreased in SCA2c and SCA2p versus control groups assuming post-transcriptional biological perturbations. In conclusion, the transcriptome data do not exclude the role of ATXN2 mutated alleles in PD but its decrease protein expression in both SCA2c and SCA2p patients suggest a potential involvement of this gene in PD. The perturbations of "RNA-binding" and "poly(A) RNA-binding" molecular functions in the three patient groups as well as gene deregulations of factors not yet described in PD but known to be deleterious in other neurological conditions, suggest the existence of RNA-binding disturbances as a continuum between spinocerebellar ataxia type 2 and Parkinson's disease.
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Affiliation(s)
- Aurore Nkiliza
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France
| | - Eugénie Mutez
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France; CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Clémence Simonin
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France; CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Frédéric Leprêtre
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Univ. Lille, CHU Lille, IRCL, Structural and Functional Genomics Core Facility, F-59000 Lille, France
| | - Aurélie Duflot
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France
| | - Martin Figeac
- Univ. Lille, CHU Lille, IRCL, Structural and Functional Genomics Core Facility, F-59000 Lille, France
| | - Céline Villenet
- Univ. Lille, CHU Lille, IRCL, Structural and Functional Genomics Core Facility, F-59000 Lille, France
| | - Pierre Semaille
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France; CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Thomas Comptdaer
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France
| | - Alexandre Genet
- CHU Lille, Centre de Biologie Pathologie, Unité de Neurobiologie, F-59000 Lille, France
| | - Bernard Sablonnière
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; CHU Lille, Centre de Biologie Pathologie, Unité de Neurobiologie, F-59000 Lille, France
| | - David Devos
- CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Luc Defebvre
- CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Alain Destée
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France; CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Marie-Christine Chartier-Harlin
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France.
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25
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Brogna S, McLeod T, Petric M. The Meaning of NMD: Translate or Perish. Trends Genet 2016; 32:395-407. [PMID: 27185236 DOI: 10.1016/j.tig.2016.04.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 04/02/2016] [Accepted: 04/25/2016] [Indexed: 02/08/2023]
Abstract
Premature translation termination leads to a reduced mRNA level in all types of organisms. In eukaryotes, the phenomenon is known as nonsense-mediated mRNA decay (NMD). This is commonly regarded as the output of a specific surveillance and destruction mechanism that is activated by the presence of a premature translation termination codon (PTC) in an atypical sequence context. Despite two decades of research, it is still unclear how NMD discriminates between PTCs and normal stop codons. We suggest that cells do not possess any such mechanism and instead propose a new model in which this mRNA depletion is a consequence of the appearance of long tracts of mRNA that are unprotected by scanning ribosomes.
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Affiliation(s)
- Saverio Brogna
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK.
| | - Tina McLeod
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK
| | - Marija Petric
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK
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26
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Karousis ED, Nasif S, Mühlemann O. Nonsense-mediated mRNA decay: novel mechanistic insights and biological impact. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:661-82. [PMID: 27173476 PMCID: PMC6680220 DOI: 10.1002/wrna.1357] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 12/19/2022]
Abstract
Nonsense‐mediated mRNA decay (NMD) was originally coined to define a quality control mechanism that targets mRNAs with truncated open reading frames due to the presence of a premature termination codon. Meanwhile, it became clear that NMD has a much broader impact on gene expression and additional biological functions beyond quality control are continuously being discovered. We review here the current views regarding the molecular mechanisms of NMD, according to which NMD ensues on mRNAs that fail to terminate translation properly, and point out the gaps in our understanding. We further summarize the recent literature on an ever‐rising spectrum of biological processes in which NMD appears to be involved, including homeostatic control of gene expression, development and differentiation, as well as viral defense. WIREs RNA 2016, 7:661–682. doi: 10.1002/wrna.1357 This article is categorized under:
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability
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Affiliation(s)
| | - Sofia Nasif
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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27
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Schweingruber C, Soffientini P, Ruepp MD, Bachi A, Mühlemann O. Identification of Interactions in the NMD Complex Using Proximity-Dependent Biotinylation (BioID). PLoS One 2016; 11:e0150239. [PMID: 26934103 PMCID: PMC4774922 DOI: 10.1371/journal.pone.0150239] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/02/2016] [Indexed: 01/09/2023] Open
Abstract
Proximity-dependent trans-biotinylation by the Escherichia coli biotin ligase BirA mutant R118G (BirA*) allows stringent streptavidin affinity purification of proximal proteins. This so-called BioID method provides an alternative to the widely used co-immunoprecipitation (co-IP) to identify protein-protein interactions. Here, we used BioID, on its own and combined with co-IP, to identify proteins involved in nonsense-mediated mRNA decay (NMD), a post-transcriptional mRNA turnover pathway that targets mRNAs that fail to terminate translation properly. In particular, we expressed BirA* fused to the well characterized NMD factors UPF1, UPF2 and SMG5 and detected by liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) the streptavidin-purified biotinylated proteins. While the identified already known interactors confirmed the usefulness of BioID, we also found new potentially important interactors that have escaped previous detection by co-IP, presumably because they associate only weakly and/or very transiently with the NMD machinery. Our results suggest that SMG5 only transiently contacts the UPF1-UPF2-UPF3 complex and that it provides a physical link to the decapping complex. In addition, BioID revealed among others CRKL and EIF4A2 as putative novel transient interactors with NMD factors, but whether or not they have a function in NMD remains to be elucidated.
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Affiliation(s)
- Christoph Schweingruber
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Angela Bachi
- IFOM-FIRC Institute of Molecular Oncology, Milan, Italy
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
- * E-mail:
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28
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Abstract
Nonsense-mediated mRNA decay (NMD) is an mRNA quality-control mechanism that typifies all eukaryotes examined to date. NMD surveys newly synthesized mRNAs and degrades those that harbor a premature termination codon (PTC), thereby preventing the production of truncated proteins that could result in disease in humans. This is evident from dominantly inherited diseases that are due to PTC-containing mRNAs that escape NMD. Although many cellular NMD targets derive from mistakes made during, for example, pre-mRNA splicing and, possibly, transcription initiation, NMD also targets ∼10% of normal physiological mRNAs so as to promote an appropriate cellular response to changing environmental milieus, including those that induce apoptosis, maturation or differentiation. Over the past ∼35 years, a central goal in the NMD field has been to understand how cells discriminate mRNAs that are targeted by NMD from those that are not. In this Cell Science at a Glance and the accompanying poster, we review progress made towards this goal, focusing on human studies and the role of the key NMD factor up-frameshift protein 1 (UPF1).
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
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29
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Vexler K, Cymerman MA, Berezin I, Fridman A, Golani L, Lasnoy M, Saul H, Shaul O. The Arabidopsis NMD Factor UPF3 Is Feedback-Regulated at Multiple Levels and Plays a Role in Plant Response to Salt Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:1376. [PMID: 27746786 PMCID: PMC5040709 DOI: 10.3389/fpls.2016.01376] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 08/29/2016] [Indexed: 05/22/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic RNA surveillance mechanism that degrades aberrant transcripts and controls the levels of many normal mRNAs. It was shown that balanced expression of the NMD factor UPF3 is essential for the maintenance of proper NMD homeostasis in Arabidopsis. UPF3 expression is controlled by a negative feedback loop that exposes UPF3 transcript to NMD. It was shown that the long 3' untranslated region (3' UTR) of UPF3 exposes its transcript to NMD. Long 3' UTRs that subject their transcripts to NMD were identified in several eukaryotic NMD factors. Interestingly, we show here that a construct that contains all the regulatory regions of the UPF3 gene except this long 3' UTR is also feedback-regulated by NMD. This indicates that UPF3 expression is feedback-regulated at multiple levels. UPF3 is constitutively expressed in different plant tissues, and its expression is equal in leaves of plants of different ages. This finding is in agreement with the possibility that UPF3 is ubiquitously operative in the Arabidopsis NMD pathway. Expression mediated by the regulatory regions of UPF3 is significantly induced by salt stress. We found that both a deficiency and a strong excess of UPF3 expression are detrimental to plant resistance to salt stress. This indicates that UPF3 plays a role in plant response to salt stress, and that balanced expression of the UPF3 gene is essential for coping with this stress.
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30
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Park J, Ahn S, Jayabalan AK, Ohn T, Koh HC, Hwang J. Insulin Signaling Augments eIF4E-Dependent Nonsense-Mediated mRNA Decay in Mammalian Cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:896-905. [PMID: 26708722 DOI: 10.1016/j.bbagrm.2015.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 12/14/2015] [Accepted: 12/17/2015] [Indexed: 12/13/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) modulates the level of mRNA harboring a premature termination codon (PTC) in a translation-dependent manner. Inhibition of translation is known to impair NMD; however, few studies have investigated the correlation between enhanced translation and increased NMD. Here, we demonstrate that insulin signaling events increase translation, leading to an increase in NMD of eIF4E-bound transcripts. We provide evidence that (i) insulin-mediated enhancement of translation augments NMD and rapamycin abrogates this enhancement; (ii) an increase in AKT phosphorylation due to inhibition of PTEN facilitates NMD; (iii) insulin stimulation increases the binding of up-frameshift factor 1 (UPF1), most likely to eIF4E-bound PTC-containing transcripts; and (iv) insulin stimulation induces the colocalization of UPF1 and eIF4E in processing bodies. These results illustrate how extracellular signaling promotes the removal of eIF4E-bound NMD targets.
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Affiliation(s)
- Jungyun Park
- Graduate School for Biomedical Science & Engineering, FTC1202-8, Hanyang University, 222 Wangimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Seyoung Ahn
- Graduate School for Biomedical Science & Engineering, FTC1202-8, Hanyang University, 222 Wangimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Aravinth K Jayabalan
- Department of Cellular and Molecular Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Takbum Ohn
- Department of Cellular and Molecular Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Hyun Chul Koh
- Department of Pharmacology, College of Medicine, Hanyang University, 222 Wangimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea.
| | - Jungwook Hwang
- Graduate School for Biomedical Science & Engineering, FTC1202-8, Hanyang University, 222 Wangimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea; Department of Medical Genetics, College of Medicine, FTC1202-8, Hanyang University, 222 Wangimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea.
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31
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Fatscher T, Boehm V, Gehring NH. Mechanism, factors, and physiological role of nonsense-mediated mRNA decay. Cell Mol Life Sci 2015; 72:4523-44. [PMID: 26283621 PMCID: PMC11113733 DOI: 10.1007/s00018-015-2017-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/10/2015] [Accepted: 08/06/2015] [Indexed: 02/04/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a translation-dependent, multistep process that degrades irregular or faulty messenger RNAs (mRNAs). NMD mainly targets mRNAs with a truncated open reading frame (ORF) due to premature termination codons (PTCs). In addition, NMD also regulates the expression of different types of endogenous mRNA substrates. A multitude of factors are involved in the tight regulation of the NMD mechanism. In this review, we focus on the molecular mechanism of mammalian NMD. Based on the published data, we discuss the involvement of translation termination in NMD initiation. Furthermore, we provide a detailed overview of the core NMD machinery, as well as several peripheral NMD factors, and discuss their function. Finally, we present an overview of diseases associated with NMD factor mutations and summarize the current state of treatment for genetic disorders caused by nonsense mutations.
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Affiliation(s)
- Tobias Fatscher
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Volker Boehm
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, Cologne, Germany.
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32
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Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity. Mol Cell 2015; 59:413-25. [PMID: 26253027 DOI: 10.1016/j.molcel.2015.06.036] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/27/2015] [Accepted: 06/29/2015] [Indexed: 12/17/2022]
Abstract
RNA quality-control pathways get rid of faulty RNAs and therefore must be able to discriminate these RNAs from those that are normal. Here we present evidence that the adenosine triphosphatase (ATPase) cycle of the SF1 helicase Upf1 is required for mRNA discrimination during nonsense-mediated decay (NMD). Mutations affecting the Upf1 ATPase cycle disrupt the mRNA selectivity of Upf1, leading to indiscriminate accumulation of NMD complexes on both NMD target and non-target mRNAs. In addition, two modulators of NMD-translation and termination codon-proximal poly(A) binding protein-depend on the ATPase activity of Upf1 to limit Upf1-non-target association. Preferential ATPase-dependent dissociation of Upf1 from non-target mRNAs in vitro suggests that selective release of Upf1 contributes to the ATPase dependence of Upf1 target discrimination. Given the prevalence of helicases in RNA regulation, ATP hydrolysis may be a widely used activity in target RNA discrimination.
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33
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Shaul O. Unique Aspects of Plant Nonsense-Mediated mRNA Decay. TRENDS IN PLANT SCIENCE 2015; 20:767-779. [PMID: 26442679 DOI: 10.1016/j.tplants.2015.08.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 08/17/2015] [Accepted: 08/20/2015] [Indexed: 05/20/2023]
Abstract
Nonsense-mediated mRNA Decay (NMD) is a eukaryotic quality-control mechanism that governs the stability of both aberrant and normal transcripts. Although plant and mammalian NMD share great similarity, they differ in certain mechanistic and regulatory aspects. Whereas SMG6 (from Caenorhabditis elegans 'suppressor with morphogenetic effect on genitalia')-catalyzed endonucleolytic cleavage is a prominent step in mammalian NMD, plant NMD targets are degraded by an SMG7-induced exonucleolytic pathway. Both mammalian and plant NMD are downregulated by stress, thereby enhancing the expression of defense response genes. However, the target genes and processes affected differ. Several plant and mammalian NMD factors are regulated by negative feedback-loops. However, while the loop regulating UPF3 (up-frameshift 3) expression in not vital for mammalian NMD, the sensitivity of UPF3 to NMD is crucial for the overall regulation of plant NMD.
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Affiliation(s)
- Orit Shaul
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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34
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Lykke-Andersen S, Jensen TH. Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes. Nat Rev Mol Cell Biol 2015; 16:665-77. [PMID: 26397022 DOI: 10.1038/nrm4063] [Citation(s) in RCA: 522] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is probably the best characterized eukaryotic RNA degradation pathway. Through intricate steps, a set of NMD factors recognize and degrade mRNAs with translation termination codons that are positioned in abnormal contexts. However, NMD is not only part of a general cellular quality control system that prevents the production of aberrant proteins. Mammalian cells also depend on NMD to dynamically adjust their transcriptomes and their proteomes to varying physiological conditions. In this Review, we discuss how NMD targets mRNAs, the types of mRNAs that are targeted, and the roles of NMD in cellular stress, differentiation and maturation processes.
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Affiliation(s)
- Søren Lykke-Andersen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Torben Heick Jensen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
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35
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Pereira FJC, Teixeira A, Kong J, Barbosa C, Silva AL, Marques-Ramos A, Liebhaber SA, Romão L. Resistance of mRNAs with AUG-proximal nonsense mutations to nonsense-mediated decay reflects variables of mRNA structure and translational activity. Nucleic Acids Res 2015; 43:6528-44. [PMID: 26068473 PMCID: PMC4513866 DOI: 10.1093/nar/gkv588] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/23/2015] [Indexed: 11/25/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that recognizes and selectively degrades mRNAs carrying premature termination codons (PTCs). The level of sensitivity of a PTC-containing mRNA to NMD is multifactorial. We have previously shown that human β-globin mRNAs carrying PTCs in close proximity to the translation initiation AUG codon escape NMD. This was called the ‘AUG-proximity effect’. The present analysis of nonsense codons in the human α-globin mRNA illustrates that the determinants of the AUG-proximity effect are in fact quite complex, reflecting the ability of the ribosome to re-initiate translation 3′ to the PTC and the specific sequence and secondary structure of the translated ORF. These data support a model in which the time taken to translate the short ORF, impacted by distance, sequence, and structure, not only modulates translation re-initiation, but also impacts on the exact boundary of AUG-proximity protection from NMD.
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Affiliation(s)
- Francisco J C Pereira
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal
| | - Alexandre Teixeira
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal Centro de Investigação em Genética Molecular Humana, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1349-008 Lisboa, Portugal
| | - Jian Kong
- Departments of Genetics and Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cristina Barbosa
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Ana Luísa Silva
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal
| | - Ana Marques-Ramos
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal
| | - Stephen A Liebhaber
- Departments of Genetics and Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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