1
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Sun X, Singla-Rastogi M, Wang J, Zhao C, Wang X, Li P. The uS10c-BPG2 module mediates ribosomal RNA processing in chloroplast nucleoids. Nucleic Acids Res 2024; 52:7893-7909. [PMID: 38686791 PMCID: PMC11260468 DOI: 10.1093/nar/gkae339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
In plant chloroplasts, certain ribosomal proteins (RPs) and ribosome biogenesis factors (RBFs) are present in nucleoids, implying an association between nucleoids and ribosome biogenesis. In Arabidopsis, the YqeH-type GTPase Brassinazole-Insensitive Pale Green2 (BPG2) is a chloroplast nucleoid-associated RBF. Here, we investigated the relationship between nucleoids and BPG2-involved ribosome biogenesis steps by exploring how BPG2 targets ribosomes. Our findings demonstrate that BPG2 interacts with an essential plastid RP, uS10c, in chloroplast nucleoids in a ribosomal RNA (rRNA)-independent manner. We also discovered that uS10c is a haploinsufficient gene, as the heterozygous deletion of this gene leads to variegated shoots and chlorophyll aggregation. uS10c is integrated into 30S ribosomal particles when rRNA is relatively exposed and also exists in polysome fractions. In contrast, BPG2 exclusively associates with 30S ribosomal particles. Notably, the interaction between BPG2 and 30S particles is influenced by the absence of uS10c, resulting in BPG2 diffusing in chloroplasts instead of targeting nucleoids. Further, our results reveal that the loss of BPG2 function and the heterozygous deletion of uS10c impair the processing of 16S and 23S-4.5S rRNAs, reduce plastid protein accumulation, and trigger the plastid signaling response. Together, these findings indicate that the uS10c-BPG2 module mediates ribosome biogenesis in chloroplast nucleoids.
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Affiliation(s)
- Xueping Sun
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, PR China
| | | | - Jingwen Wang
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, PR China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
| | - Pengcheng Li
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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2
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Akbari B, Ahmadi E, Zabihi MR, Zamir MR, Shaker MS, Noorbakhsh F. SARS-CoV-2 helicase might interfere with cellular nonsense-mediated RNA decay: insights from a bioinformatics study. BMC Genom Data 2023; 24:68. [PMID: 37980504 PMCID: PMC10657555 DOI: 10.1186/s12863-023-01173-y] [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: 03/15/2023] [Accepted: 11/10/2023] [Indexed: 11/20/2023] Open
Abstract
BACKGROUND Viruses employ diverse strategies to interfere with host defense mechanisms, including the production of proteins that mimic or resemble host proteins. This study aimed to analyze the similarities between SARS-CoV-2 and human proteins, investigate their impact on virus-host interactions, and elucidate underlying mechanisms. RESULTS Comparing the proteins of SARS-CoV-2 with human and mammalian proteins revealed sequence and structural similarities between viral helicase with human UPF1. The latter is a protein that is involved in nonsense-mediated RNA decay (NMD), an mRNA surveillance pathway which also acts as a cellular defense mechanism against viruses. Protein sequence similarities were also observed between viral nsp3 and human Poly ADP-ribose polymerase (PARP) family of proteins. Gene set enrichment analysis on transcriptomic data derived from SARS-CoV-2 positive samples illustrated the enrichment of genes belonging to the NMD pathway compared with control samples. Moreover, comparing transcriptomic data from SARS-CoV-2-infected samples with transcriptomic data derived from UPF1 knockdown cells demonstrated a significant overlap between datasets. CONCLUSIONS These findings suggest that helicase/UPF1 sequence and structural similarity might have the ability to interfere with the NMD pathway with pathogenic and immunological implications.
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Affiliation(s)
- Behnia Akbari
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ehsan Ahmadi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zabihi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mina Roshan Zamir
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mina Sadeghi Shaker
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farshid Noorbakhsh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran.
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3
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Nasif S, Colombo M, Uldry AC, Schröder M, de Brot S, Mühlemann O. Inhibition of nonsense-mediated mRNA decay reduces the tumorigenicity of human fibrosarcoma cells. NAR Cancer 2023; 5:zcad048. [PMID: 37681034 PMCID: PMC10480688 DOI: 10.1093/narcan/zcad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/08/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic RNA decay pathway with roles in cellular stress responses, differentiation, and viral defense. It functions in both quality control and post-transcriptional regulation of gene expression. NMD has also emerged as a modulator of cancer progression, although available evidence supports both a tumor suppressor and a pro-tumorigenic role, depending on the model. To further investigate the role of NMD in cancer, we knocked out the NMD factor SMG7 in the HT1080 human fibrosarcoma cell line, resulting in suppression of NMD function. We then compared the oncogenic properties of the parental cell line, the SMG7-knockout, and a rescue cell line in which we re-introduced both isoforms of SMG7. We also tested the effect of a drug inhibiting the NMD factor SMG1 to distinguish NMD-dependent effects from putative NMD-independent functions of SMG7. Using cell-based assays and a mouse xenograft tumor model, we showed that suppression of NMD function severely compromises the oncogenic phenotype. Molecular pathway analysis revealed that NMD suppression strongly reduces matrix metalloprotease 9 (MMP9) expression and that MMP9 re-expression partially rescues the oncogenic phenotype. Since MMP9 promotes cancer cell migration and invasion, metastasis and angiogenesis, its downregulation may contribute to the reduced tumorigenicity of NMD-suppressed cells. Collectively, our results highlight the potential value of NMD inhibition as a therapeutic approach.
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Affiliation(s)
- Sofia Nasif
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland
| | - Martino Colombo
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research, University of Bern, Switzerland
| | - Markus S Schröder
- NCCR RNA & Disease Bioinformatics Support,Department of Biology, ETH Zürich, Switzerland
| | - Simone de Brot
- COMPATH, Institute of Animal Pathology, University of Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland
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4
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He Y, Hewett SJ. The Cystine/Glutamate Antiporter, System xc– Contributes to Cortical Infarction After Moderate but Not Severe Focal Cerebral Ischemia in Mice. Front Cell Neurosci 2022; 16:821036. [PMID: 35669109 PMCID: PMC9165760 DOI: 10.3389/fncel.2022.821036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/04/2022] [Indexed: 12/14/2022] Open
Abstract
Understanding the mechanisms underlying ischemic brain injury is of importance to the goal of devising novel therapeutics for protection and/or recovery. Previous work in our laboratory and in others has shown that activation of cystine/glutamate antiporter, system xc– (Sxc–), facilitates neuronal injury in several in vitro models of energy deprivation. However, studies on the contribution of this antiporter to ischemic brain damage in vivo are more limited. Since embolic or thrombotic transient or permanent occlusion of a cerebral blood vessel eventually leads to brain infarction in most stroke cases, we evaluated the contribution of Sxc– to cerebral ischemic damage by comparing brain infarction between mice naturally null for SLC7a11 (SLC7a11sut/sut mice). The gene the encodes for the substrate specific light chain for system xcc– — with their wild type (SLC7a11 + / +)littermates following photothrombotic ischemic stroke of the middle cerebral artery (PTI) and permanent middle cerebral artery occlusion (pMCAo) rendered by cauterization. In the PTI model, we found a time-dependent reduction in cerebral blood flow that reached 50% from baseline in both genotypes 47–48 h post-illumination. Despite this, a remarkable reduction in incidence and total infarct volume of SLC7a11sut/sut mice was revealed 48 h following PTI as compared to SLC7a11+/+ mice. No difference in injury markers and/or infarct volume was measured between genotypes when occlusion of the MCA was permanent, however. Present data demonstrate a model-dependent differential role for Sxc– in focal cerebral ischemic damage, further highlighting that ischemic severity activates heterogeneous biochemical events that lead to damage engendered by stroke.
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5
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De S, Mühlemann O. A comprehensive coverage insurance for cells: revealing links between ribosome collisions, stress responses and mRNA surveillance. RNA Biol 2021; 19:609-621. [PMID: 35491909 PMCID: PMC9067528 DOI: 10.1080/15476286.2022.2065116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/02/2022] [Indexed: 11/02/2022] Open
Abstract
Cells of metazoans respond to internal and external stressors by activating stress response pathways that aim for re-establishing cellular homoeostasis or, if this cannot be achieved, triggering programmed cell death. Problems during translation, arising from defective mRNAs, tRNAs, ribosomes or protein misfolding, can activate stress response pathways as well as mRNA surveillance and ribosome quality control programs. Recently, ribosome collisions have emerged as a central signal for translational stress and shown to elicit different stress responses. Here, we review our current knowledge about the intricate mutual connections between ribosome collisions, stress response pathways and mRNA surveillance. A central factor connecting the sensing of collided ribosomes with degradation of the nascent polypeptides, dissociation of the stalled ribosomes and degradation of the mRNA by no-go or non-stop decay is the E3-ligase ZNF598. We tested whether ZNF598 also plays a role in nonsense-mediated mRNA decay (NMD) but found that it is dispensable for this translation termination-associated mRNA surveillance pathway, which in combination with other recent data argues against stable ribosome stalling at termination codons being the NMD-triggering signal.
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Affiliation(s)
- Soumasree De
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
| | - Oliver Mühlemann
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
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6
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SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity. Nat Commun 2021; 12:3965. [PMID: 34172724 PMCID: PMC8233366 DOI: 10.1038/s41467-021-24046-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 05/30/2021] [Indexed: 12/28/2022] Open
Abstract
Eukaryotic gene expression is constantly controlled by the translation-coupled nonsense-mediated mRNA decay (NMD) pathway. Aberrant translation termination leads to NMD activation, resulting in phosphorylation of the central NMD factor UPF1 and robust clearance of NMD targets via two seemingly independent and redundant mRNA degradation branches. Here, we uncover that the loss of the first SMG5-SMG7-dependent pathway also inactivates the second SMG6-dependent branch, indicating an unexpected functional connection between the final NMD steps. Transcriptome-wide analyses of SMG5-SMG7-depleted cells confirm exhaustive NMD inhibition resulting in massive transcriptomic alterations. Intriguingly, we find that the functionally underestimated SMG5 can substitute the role of SMG7 and individually activate NMD. Furthermore, the presence of either SMG5 or SMG7 is sufficient to support SMG6-mediated endonucleolysis of NMD targets. Our data support an improved model for NMD execution that features two-factor authentication involving UPF1 phosphorylation and SMG5-SMG7 recruitment to access SMG6 activity. Degradation of nonsense mediated mRNA decay (NMD) substrates is carried out by two seemingly independent pathways, SMG6-mediated endonucleolytic cleavage and/or SMG5-SMG7-induced accelerated deadenylation. Here the authors show that SMG5-SMG7 maintain NMD activity by permitting SMG6 activation.
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7
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Alzahrani F, Kuwahara H, Long Y, Al-Owain M, Tohary M, AlSayed M, Mahnashi M, Fathi L, Alnemer M, Al-Hamed MH, Lemire G, Boycott KM, Hashem M, Han W, Al-Maawali A, Al Mahrizi F, Al-Thihli K, Gao X, Alkuraya FS. Recessive, Deleterious Variants in SMG8 Expand the Role of Nonsense-Mediated Decay in Developmental Disorders in Humans. Am J Hum Genet 2020; 107:1178-1185. [PMID: 33242396 DOI: 10.1016/j.ajhg.2020.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
We have previously described a heart-, eye-, and brain-malformation syndrome caused by homozygous loss-of-function variants in SMG9, which encodes a critical component of the nonsense-mediated decay (NMD) machinery. Here, we describe four consanguineous families with four different likely deleterious homozygous variants in SMG8, encoding a binding partner of SMG9. The observed phenotype greatly resembles that linked to SMG9 and comprises severe global developmental delay, microcephaly, facial dysmorphism, and variable congenital heart and eye malformations. RNA-seq analysis revealed a general increase in mRNA expression levels with significant overrepresentation of core NMD substrates. We also identified increased phosphorylation of UPF1, a key SMG1-dependent step in NMD, which most likely represents the loss of SMG8--mediated inhibition of SMG1 kinase activity. Our data show that SMG8 and SMG9 deficiency results in overlapping developmental disorders that most likely converge mechanistically on impaired NMD.
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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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Beißel C, Grosse S, Krebber H. Dbp5/DDX19 between Translational Readthrough and Nonsense Mediated Decay. Int J Mol Sci 2020; 21:ijms21031085. [PMID: 32041247 PMCID: PMC7037193 DOI: 10.3390/ijms21031085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 01/21/2023] Open
Abstract
The DEAD-box protein Dbp5 (human DDX19) remodels RNA-protein complexes. Dbp5 functions in ribonucleoprotein export and translation termination. Termination occurs, when the ribosome has reached a stop codon through the Dbp5 mediated delivery of the eukaryotic termination factor eRF1. eRF1 contacts eRF3 upon dissociation of Dbp5, resulting in polypeptide chain release and subsequent ribosomal subunit splitting. Mutations in DBP5 lead to stop codon readthrough, because the eRF1 and eRF3 interaction is not controlled and occurs prematurely. This identifies Dbp5/DDX19 as a possible potent drug target for nonsense suppression therapy. Neurodegenerative diseases and cancer are caused in many cases by the loss of a gene product, because its mRNA contained a premature termination codon (PTC) and is thus eliminated through the nonsense mediated decay (NMD) pathway, which is described in the second half of this review. We discuss translation termination and NMD in the light of Dbp5/DDX19 and subsequently speculate on reducing Dbp5/DDX19 activity to allow readthrough of the PTC and production of a full-length protein to detract the RNA from NMD as a possible treatment for diseases.
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10
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Hong D, Park T, Jeong S. Nuclear UPF1 Is Associated with Chromatin for Transcription-Coupled RNA Surveillance. Mol Cells 2019; 42:523-529. [PMID: 31234619 PMCID: PMC6681869 DOI: 10.14348/molcells.2019.0116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/19/2019] [Accepted: 06/19/2019] [Indexed: 01/26/2023] Open
Abstract
mRNA quality is controlled by multiple RNA surveillance machineries to reduce errors during gene expression processes in eukaryotic cells. Nonsense-mediated mRNA decay (NMD) is a well-characterized mechanism that degrades error-containing transcripts during translation. The ATP-dependent RNA helicase up-frameshift 1 (UPF1) is a key player in NMD that is mostly prevalent in the cytoplasm. However, recent studies on UPF1-RNA interaction suggest more comprehensive roles of UPF1 on diverse forms of target transcripts. Here we used subcellular fractionation and immunofluorescence to understand such complex functions of UPF1. We demonstrated that UPF1 can be localized to the nucleus and predominantly associated with the chromatin. Moreover, we showed that UPF1 associates more strongly with the chromatin when the transcription elongation and translation inhibitors were used. These findings suggest a novel role of UPF1 in transcription elongation-coupled RNA machinery in the chromatin, as well as in translation-coupled NMD in the cytoplasm. Thus, we propose that cytoplasmic UPF1-centric RNA surveillance mechanism could be extended further up to the chromatin-associated UPF1 and cotranscriptional RNA surveillance. Our findings could provide the mechanistic insights on extensive regulatory roles of UPF1 for many cellular RNAs.
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Affiliation(s)
- Dawon Hong
- Graduate Department of Bioconvergence Science and Technology, Dankook University, Yongin 16892,
Korea
| | - Taeyoung Park
- Graduate Department of Bioconvergence Science and Technology, Dankook University, Yongin 16892,
Korea
| | - Sunjoo Jeong
- Graduate Department of Bioconvergence Science and Technology, Dankook University, Yongin 16892,
Korea
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11
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Kishor A, Fritz SE, Hogg JR. Nonsense-mediated mRNA decay: The challenge of telling right from wrong in a complex transcriptome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1548. [PMID: 31131562 DOI: 10.1002/wrna.1548] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/01/2019] [Accepted: 05/07/2019] [Indexed: 12/18/2022]
Abstract
The nonsense-mediated mRNA decay pathway selects and degrades its targets using a dense network of RNA-protein and protein-protein interactions. Together, these interactions allow the pathway to collect copious information about the translating mRNA, including translation termination status, splice junction positions, mRNP composition, and 3'UTR length and structure. The core NMD machinery, centered on the RNA helicase UPF1, integrates this information to determine the efficiency of decay. A picture of NMD is emerging in which many factors contribute to the dynamics of decay complex assembly and disassembly, thereby influencing the probability of decay. The ability of the NMD pathway to recognize mRNP features of diverse potential substrates allows it to simultaneously perform quality control and regulatory functions. In vertebrates, increased transcriptome complexity requires balance between these two functions since high NMD efficiency is desirable for maintenance of quality control fidelity but may impair expression of normal mRNAs. NMD has adapted to this challenge by employing mechanisms to enhance identification of certain potential substrates, while using sequence-specific RNA-binding proteins to shield others from detection. These elaborations on the conserved NMD mechanism permit more sensitive post-transcriptional gene regulation but can have severe deleterious consequences, including the failure to degrade pathogenic aberrant mRNAs in many B cell lymphomas. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Aparna Kishor
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Sarah E Fritz
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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12
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13
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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: 16] [Impact Index Per Article: 2.7] [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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14
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Zander G, Krebber H. Quick or quality? How mRNA escapes nuclear quality control during stress. RNA Biol 2017; 14:1642-1648. [PMID: 28708448 PMCID: PMC5731798 DOI: 10.1080/15476286.2017.1345835] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/19/2017] [Accepted: 06/20/2017] [Indexed: 10/19/2022] Open
Abstract
Understanding the mechanisms for mRNA production under normal conditions and in response to cytotoxic stresses has been subject of numerous studies for several decades. The shutdown of canonical mRNA transcription, export and translation is required to have enough free resources for the immediate production of heat shock proteins that act as chaperones to sustain cellular processes. In recent work we uncovered a simple mechanism, in which the export block of regular mRNAs and a fast export of heat shock mRNAs is achieved by deactivation of the nuclear mRNA quality control mediated by the guard proteins. In this point of view we combine long known data with recently gathered information that support this novel model, in which cells omit quality control of stress responsive transcripts to ensure survival.
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Affiliation(s)
- Gesa Zander
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
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15
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Silva S, Homolka D, Pillai RS. Characterization of the mammalian RNA exonuclease 5/NEF-sp as a testis-specific nuclear 3' → 5' exoribonuclease. RNA (NEW YORK, N.Y.) 2017; 23:1385-1392. [PMID: 28539487 PMCID: PMC5558908 DOI: 10.1261/rna.060723.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
Ribonucleases catalyze maturation of functional RNAs or mediate degradation of cellular transcripts, activities that are critical for gene expression control. Here we identify a previously uncharacterized mammalian nuclease family member NEF-sp (RNA exonuclease 5 [REXO5] or LOC81691) as a testis-specific factor. Recombinant human NEF-sp demonstrates a divalent metal ion-dependent 3' → 5' exoribonuclease activity. This activity is specific to single-stranded RNA substrates and is independent of their length. The presence of a 2'-O-methyl modification at the 3' end of the RNA substrate is inhibitory. Ectopically expressed NEF-sp localizes to the nucleolar/nuclear compartment in mammalian cell cultures and this is dependent on an amino-terminal nuclear localization signal. Finally, mice lacking NEF-sp are viable and display normal fertility, likely indicating overlapping functions with other nucleases. Taken together, our study provides the first biochemical and genetic exploration of the role of the NEF-sp exoribonuclease in the mammalian genome.
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Affiliation(s)
- Sara Silva
- Department of Molecular Biology, University of Geneva, CH-1211 Geneva 4, Switzerland
- European Molecular Biology Laboratory, Grenoble Outstation, 38042, France
| | - David Homolka
- Department of Molecular Biology, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Ramesh S Pillai
- Department of Molecular Biology, University of Geneva, CH-1211 Geneva 4, Switzerland
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16
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Colombo M, Karousis ED, Bourquin J, Bruggmann R, Mühlemann O. Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways. RNA (NEW YORK, N.Y.) 2017; 23:189-201. [PMID: 27864472 PMCID: PMC5238794 DOI: 10.1261/rna.059055.116] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/05/2016] [Indexed: 05/02/2023]
Abstract
Besides degrading aberrant mRNAs that harbor a premature translation termination codon (PTC), nonsense-mediated mRNA decay (NMD) also targets many seemingly "normal" mRNAs that encode for full-length proteins. To identify a bona fide set of such endogenous NMD targets in human cells, we applied a meta-analysis approach in which we combined transcriptome profiling of knockdowns and rescues of the three NMD factors UPF1, SMG6, and SMG7. We provide evidence that this combinatorial approach identifies NMD-targeted transcripts more reliably than previous attempts that focused on inactivation of single NMD factors. Our data revealed that SMG6 and SMG7 act on essentially the same transcripts, indicating extensive redundancy between the endo- and exonucleolytic decay routes. Besides mRNAs, we also identified as NMD targets many long noncoding RNAs as well as miRNA and snoRNA host genes. The NMD target feature with the most predictive value is an intron in the 3' UTR, followed by the presence of upstream open reading frames (uORFs) and long 3' UTRs. Furthermore, the 3' UTRs of NMD-targeted transcripts tend to have an increased GC content and to be phylogenetically less conserved when compared to 3' UTRs of NMD insensitive transcripts.
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Affiliation(s)
- Martino Colombo
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, CH-3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Evangelos D Karousis
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Joël Bourquin
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, 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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17
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Balistreri G, Bognanni C, Mühlemann O. Virus Escape and Manipulation of Cellular Nonsense-Mediated mRNA Decay. Viruses 2017; 9:v9010024. [PMID: 28124995 PMCID: PMC5294993 DOI: 10.3390/v9010024] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/05/2017] [Accepted: 01/13/2017] [Indexed: 12/13/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD), a cellular RNA turnover pathway targeting RNAs with features resulting in aberrant translation termination, has recently been found to restrict the replication of positive-stranded RNA ((+)RNA) viruses. As for every other antiviral immune system, there is also evidence of viruses interfering with and modulating NMD to their own advantage. This review will discuss our current understanding of why and how NMD targets viral RNAs, and elaborate counter-defense strategies viruses utilize to escape NMD.
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Affiliation(s)
- Giuseppe Balistreri
- Department of Biosciences, University of Helsinki, Helsinki FIN-00014, Finland.
| | - Claudia Bognanni
- Department of Chemistry and Biochemistry, University of Bern, Bern CH-3012, Switzerland.
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern CH-3012, Switzerland.
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern CH-3012, Switzerland.
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18
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Abstract
Viruses have evolved diverse strategies to maximize the functional and coding capacities of their genetic material. Individual viral RNAs are often used as substrates for both replication and translation and can contain multiple, sometimes overlapping open reading frames. Further, viral RNAs engage in a wide variety of interactions with both host and viral proteins to modify the activities of important cellular factors and direct their own trafficking, packaging, localization, stability, and translation. However, adaptations increasing the information density of small viral genomes can have unintended consequences. In particular, viral RNAs have developed features that mark them as potential targets of host RNA quality control pathways. This minireview focuses on ways in which viral RNAs run afoul of the cellular mRNA quality control and decay machinery, as well as on strategies developed by viruses to circumvent or exploit cellular mRNA surveillance.
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19
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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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20
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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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21
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Tucker JF, Ohle C, Schermann G, Bendrin K, Zhang W, Fischer T, Zhang K. A Novel Epigenetic Silencing Pathway Involving the Highly Conserved 5'-3' Exoribonuclease Dhp1/Rat1/Xrn2 in Schizosaccharomyces pombe. PLoS Genet 2016; 12:e1005873. [PMID: 26889830 PMCID: PMC4758730 DOI: 10.1371/journal.pgen.1005873] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 01/26/2016] [Indexed: 01/09/2023] Open
Abstract
Epigenetic gene silencing plays a critical role in regulating gene expression and contributes to organismal development and cell fate acquisition in eukaryotes. In fission yeast, Schizosaccharomyces pombe, heterochromatin-associated gene silencing is known to be mediated by RNA processing pathways including RNA interference (RNAi) and a 3’-5’ exoribonuclease complex, the exosome. Here, we report a new RNA-processing pathway that contributes to epigenetic gene silencing and assembly of heterochromatin mediated by 5’-3’ exoribonuclease Dhp1/Rat1/Xrn2. Dhp1 mutation causes defective gene silencing both at peri-centromeric regions and at the silent mating type locus. Intriguingly, mutation in either of the two well-characterized Dhp1-interacting proteins, the Din1 pyrophosphohydrolase or the Rhn1 transcription termination factor, does not result in silencing defects at the main heterochromatic regions. We demonstrate that Dhp1 interacts with heterochromatic factors and is essential in the sequential steps of establishing silencing in a manner independent of both RNAi and the exosome. Genomic and genetic analyses suggest that Dhp1 is involved in post-transcriptional silencing of repetitive regions through its RNA processing activity. The results describe the unexpected role of Dhp1/Rat1/Xrn2 in chromatin-based silencing and elucidate how various RNA-processing pathways, acting together or independently, contribute to epigenetic regulation of the eukaryotic genome. Epigenetic mechanisms regulate when, where, and how an organism uses the genetic information stored in its genome. They are essential to many cellular processes, such as the regulation of gene expression, genome organization, and cell-fate determination. They also govern growth, development, and ultimately human health. Heterochromatin constitutes silenced chromatic domains, in which gene silencing occurs through epigenetic mechanisms. RNA processing pathways, such as RNA interference (RNAi) and the exosome, are known to mediate the silencing of genes via degradation of unwanted or aberrant transcripts. In this study, we describe a new RNA processing mechanism in epigenetic silencing using fission yeast, a premier model for studying these processes. With genetic, cell biology, and genomic approaches, we uncovered a previously unrecognized function of Dhp1, a highly conserved 5’-3’ exoribonuclease and ortholog of budding yeast Rat1 and metazoan Xrn2. We show that Dhp1 mediates a novel RNA processing mechanism in epigenetic silencing which occurs independently of both RNAi and the exosome. Our results clarify how multiple RNA processing pathways are involved in the regulation of eukaryotic gene expression and chromatin organization.
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Affiliation(s)
- James Franklin Tucker
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Corina Ohle
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Géza Schermann
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Katja Bendrin
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Wei Zhang
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Tamás Fischer
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Ke Zhang
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
- * E-mail:
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22
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Wery M, Descrimes M, Vogt N, Dallongeville AS, Gautheret D, Morillon A. Nonsense-Mediated Decay Restricts LncRNA Levels in Yeast Unless Blocked by Double-Stranded RNA Structure. Mol Cell 2016; 61:379-392. [PMID: 26805575 PMCID: PMC4747904 DOI: 10.1016/j.molcel.2015.12.020] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 10/23/2015] [Accepted: 12/14/2015] [Indexed: 12/16/2022]
Abstract
Antisense long non-coding (aslnc)RNAs represent a substantial part of eukaryotic transcriptomes that are, in yeast, controlled by the Xrn1 exonuclease. Nonsense-Mediated Decay (NMD) destabilizes the Xrn1-sensitive aslncRNAs (XUT), but what determines their sensitivity remains unclear. We report that 3′ single-stranded (3′-ss) extension mediates XUTs degradation by NMD, assisted by the Mtr4 and Dbp2 helicases. Single-gene investigation, genome-wide RNA analyses, and double-stranded (ds)RNA mapping revealed that 3′-ss extensions discriminate the NMD-targeted XUTs from stable lncRNAs. Ribosome profiling showed that XUT are translated, locking them for NMD activity. Interestingly, mutants of the Mtr4 and Dbp2 helicases accumulated XUTs, suggesting that dsRNA unwinding is a critical step for degradation. Indeed, expression of anticomplementary transcripts protects cryptic intergenic lncRNAs from NMD. Our results indicate that aslncRNAs form dsRNA that are only translated and targeted to NMD if dissociated by Mtr4 and Dbp2. We propose that NMD buffers genome expression by discarding pervasive regulatory transcripts. Xrn1-sensitive Unstable Transcripts (XUTs) are 3′-extended isoforms of stable lncRNAs Nonsense-Mediated Decay preferentially targets long XUTs with single-stranded 3′ end Antisense XUTs form double-stranded RNA in vivo Formation of double-stranded RNA protects XUTs from Nonsense-Mediated Decay
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Affiliation(s)
- Maxime Wery
- ncRNA, Epigenetic, and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Marc Descrimes
- ncRNA, Epigenetic, and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Nicolas Vogt
- ncRNA, Epigenetic, and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Anne-Sophie Dallongeville
- ncRNA, Epigenetic, and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, CNRS, CEA, Université Paris-Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
| | - Antonin Morillon
- ncRNA, Epigenetic, and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France.
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23
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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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24
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Fiorini F, Bagchi D, Le Hir H, Croquette V. Human Upf1 is a highly processive RNA helicase and translocase with RNP remodelling activities. Nat Commun 2015; 6:7581. [PMID: 26138914 PMCID: PMC4506499 DOI: 10.1038/ncomms8581] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/21/2015] [Indexed: 12/26/2022] Open
Abstract
RNA helicases are implicated in most cellular RNA-dependent events. In eukaryotes however, only few have been functionally characterized. Upf1 is a RNA helicase essential for nonsense-mediated mRNA decay (NMD). Here, using magnetic tweezers and bulk assays, we observe that human Upf1 is able to translocate slowly over long single-stranded nucleic acids with a processivity >10 kb. Upf1 efficiently translocates through double-stranded structures and protein-bound sequences, demonstrating that Upf1 is an efficient ribonucleoprotein complex remodeler. Our observation of processive unwinding by an eukaryotic RNA helicase reveals that Upf1, once recruited onto NMD mRNA targets, can scan the entire transcript to irreversibly remodel the mRNP, facilitating its degradation by the NMD machinery. Upf1 is a multifunctional helicase involved in various DNA- and RNA-related processes, including nonsense-mediated mRNA decay (NMD). Here the authors demonstrate that Upf1 is a highly processive ribonucleoprotein complex remodeler—a capability likely important for Upf1's NMD function.
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Affiliation(s)
- Francesca Fiorini
- 1] Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, Paris 75230, France [2] Institut de Biologie de l'Ecole Normale Supérieure, INSERM U1024, Paris 75230, France
| | - Debjani Bagchi
- 1] Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, Paris 75230, France [2] Institut de Biologie de l'Ecole Normale Supérieure, INSERM U1024, Paris 75230, France [3] Laboratoire de Physique Statistique, Ecole Normale Supérieure, Université Pierre et Marie Curie Paris, Université Paris Diderot, CNRS, 24 rue Lhomond, Paris 75005, France
| | - Hervé Le Hir
- 1] Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, Paris 75230, France [2] Institut de Biologie de l'Ecole Normale Supérieure, INSERM U1024, Paris 75230, France
| | - Vincent Croquette
- 1] Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, Paris 75230, France [2] Institut de Biologie de l'Ecole Normale Supérieure, INSERM U1024, Paris 75230, France [3] Laboratoire de Physique Statistique, Ecole Normale Supérieure, Université Pierre et Marie Curie Paris, Université Paris Diderot, CNRS, 24 rue Lhomond, Paris 75005, France
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25
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Feng D, Su RC, Zou L, Triggs-Raine B, Huang S, Xie J. Increase of a group of PTC(+) transcripts by curcumin through inhibition of the NMD pathway. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1104-15. [PMID: 25934542 DOI: 10.1016/j.bbagrm.2015.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/07/2015] [Accepted: 04/22/2015] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated mRNA decay (NMD), an mRNA surveillance mechanism, eliminates premature termination codon-containing (PTC⁺) transcripts. For instance, it maintains the homeostasis of splicing factors and degrades aberrant transcripts of human genetic disease genes. Here we examine the inhibitory effect on the NMD pathway and consequent increase of PTC+ transcripts by the dietary compound curcumin. We have found that several PTC⁺ transcripts including that of serine/arginine-rich splicing factor 1 (SRSF1) were specifically increased in cells by curcumin. We also observed a similar curcumin effect on the PTC⁺ mutant transcript from a Tay-Sachs-causing HEXA allele or from a beta-globin reporter gene. The curcumin effect was accompanied by significantly reduced expression of the NMD factors UPF1, 2, 3A and 3B. Consistently, in chromatin immunoprecipitation assays, curcumin specifically reduced the occupancy of acetyl-histone H3 and RNA polymerase II at the promoter region (-376 to -247nt) of human UPF1, in a time- and dosage-dependent way. Importantly, knocking down UPF1 abolished or substantially reduced the difference of PTC(+) transcript levels between control and curcumin-treated cells. The disrupted curcumin effect was efficiently rescued by expression of exogenous Myc-UPF1 in the knockdown cells. Together, our data demonstrate that a group of PTC⁺ transcripts are stabilized by a dietary compound curcumin through the inhibition of UPF factor expression and the NMD pathway.
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Affiliation(s)
- Dairong Feng
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100005, China; Department of Physiology and Pathophysiology, Faculty of Medicine, University of Manitoba, Winnipeg MB R3E 0J9, Canada
| | - Ruey-Chyi Su
- Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg MB R3E 0J9, Canada
| | - Liping Zou
- Department of Pediatrics, Chinese PLA General Hospital, Beijing 100853, China
| | - Barbara Triggs-Raine
- Department of Biochemistry & Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg MB R3E 0J9, Canada
| | - Shangzhi Huang
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100005, China.
| | - Jiuyong Xie
- Department of Physiology and Pathophysiology, Faculty of Medicine, University of Manitoba, Winnipeg MB R3E 0J9, Canada.
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26
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Moon SL, Blackinton JG, Anderson JR, Dozier MK, Dodd BJT, Keene JD, Wilusz CJ, Bradrick SS, Wilusz J. XRN1 stalling in the 5' UTR of Hepatitis C virus and Bovine Viral Diarrhea virus is associated with dysregulated host mRNA stability. PLoS Pathog 2015; 11:e1004708. [PMID: 25747802 PMCID: PMC4352041 DOI: 10.1371/journal.ppat.1004708] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 01/26/2015] [Indexed: 01/11/2023] Open
Abstract
We demonstrate that both Hepatitis C virus (HCV) and Bovine Viral Diarrhea virus (BVDV) contain regions in their 5’ UTRs that stall and repress the enzymatic activity of the cellular 5’-3’ exoribonuclease XRN1, resulting in dramatic changes in the stability of cellular mRNAs. We used biochemical assays, virus infections, and transfection of the HCV and BVDV 5’ untranslated regions in the absence of other viral gene products to directly demonstrate the existence and mechanism of this novel host-virus interaction. In the context of HCV infection, we observed globally increased stability of mRNAs resulting in significant increases in abundance of normally short-lived mRNAs encoding a variety of relevant oncogenes and angiogenesis factors. These findings suggest that non-coding regions from multiple genera of the Flaviviridae interfere with XRN1 and impact post-transcriptional processes, causing global dysregulation of cellular gene expression which may promote cell growth and pathogenesis. Understanding how a persistent virus like Hepatitis C Virus (HCV) interfaces with the cellular machinery during infection can provide significant insights into mechanisms of pathogenesis. We demonstrate that while trying to degrade HCV transcripts, a major cellular exonuclease called XRN1 stalls and gets repressed in the 5’ noncoding region of the viral mRNA. Interestingly, the region where XRN1 stalls in the 5’ UTR includes the viral IRES that is required for translation initiation, uncovering a novel, unexpected function for this well-studied region. Differential mRNA stability is a major regulator of gene expression in cells. Curiously, repression of the cellular XRN1 exonuclease is associated with a general repression of mRNA decay in general in HCV-infected cells. Thus numerous cellular mRNAs are stabilized and accumulate in a dysregulated fashion during HCV infection. Normally short-lived mRNAs are disproportionately affected—including mRNAs that encode immune regulators and oncogenes. Thus, this study suggests a novel role for the 5’ UTR of HCV in molecular pathogenesis—including hepatocellular carcinoma. Furthermore, the 5’ UTR of Bovine Viral Diarrhea virus also represses the XRN1 enzyme and stabilizes cellular mRNA. Therefore a strategy of 5’ UTR-mediated XRN1 repression appears to be conserved among the vector-independent members of the Flaviviridae.
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Affiliation(s)
- Stephanie L. Moon
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jeffrey G. Blackinton
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - John R. Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Mary K. Dozier
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Benjamin J. T. Dodd
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jack D. Keene
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Carol J. Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Shelton S. Bradrick
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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27
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Lykke-Andersen S, Chen Y, Ardal BR, Lilje B, Waage J, Sandelin A, Jensen TH. Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes. Genes Dev 2015; 28:2498-517. [PMID: 25403180 PMCID: PMC4233243 DOI: 10.1101/gad.246538.114] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Eukaryotic RNAs with premature termination codons (PTCs) are eliminated by nonsense-mediated decay (NMD). Lykke-Andersen et al. discover that SMG6-catalyzed endonucleolysis widely initiates the degradation of human nonsense RNAs, whereas decapping is used to a lesser extent. A large proportion of genes hosting snoRNAs in their introns produce considerable amounts of NMD-sensitive splice variants, indicating that these RNAs are merely by-products of a primary snoRNA production process. Eukaryotic RNAs with premature termination codons (PTCs) are eliminated by nonsense-mediated decay (NMD). While human nonsense RNA degradation can be initiated either by an endonucleolytic cleavage event near the PTC or through decapping, the individual contribution of these activities on endogenous substrates has remained unresolved. Here we used concurrent transcriptome-wide identification of NMD substrates and their 5′–3′ decay intermediates to establish that SMG6-catalyzed endonucleolysis widely initiates the degradation of human nonsense RNAs, whereas decapping is used to a lesser extent. We also show that a large proportion of genes hosting snoRNAs in their introns produce considerable amounts of NMD-sensitive splice variants, indicating that these RNAs are merely by-products of a primary snoRNA production process. Additionally, transcripts from genes encoding multiple snoRNAs often yield alternative transcript isoforms that allow for differential expression of individual coencoded snoRNAs. Based on our findings, we hypothesize that snoRNA host genes need to be highly transcribed to accommodate high levels of snoRNA production and that the expression of individual snoRNAs and their cognate spliced RNA can be uncoupled via alternative splicing and NMD.
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Affiliation(s)
- Søren Lykke-Andersen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark
| | - Yun Chen
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Britt R Ardal
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark
| | - Berit Lilje
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Johannes Waage
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Torben Heick Jensen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark
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Roque S, Cerciat M, Gaugué I, Mora L, Floch AG, de Zamaroczy M, Heurgué-Hamard V, Kervestin S. Interaction between the poly(A)-binding protein Pab1 and the eukaryotic release factor eRF3 regulates translation termination but not mRNA decay in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2015; 21:124-134. [PMID: 25411355 PMCID: PMC4274632 DOI: 10.1261/rna.047282.114] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/26/2014] [Indexed: 06/04/2023]
Abstract
Eukaryotic release factor 3 (eRF3) is implicated in translation termination and also interacts with the poly(A)-binding protein (PABP, Pab1 in yeast), a major player in mRNA metabolism. Despite conservation of this interaction, its precise function remains elusive. First, we showed experimentally that yeast eRF3 does not contain any obvious consensus PAM2 (PABP-interacting motif 2). Thus, in yeast this association is different from the well described interaction between the metazoan factors. To gain insight into the exact function of this interaction, we then analyzed the phenotypes resulting from deleting the respective binding domains. Deletion of the Pab1 interaction domain on eRF3 did not affect general mRNA stability or nonsense-mediated mRNA decay (NMD) pathway and induced a decrease in translational readthrough. Furthermore, combined deletions of the respective interacting domains on eRF3 and on Pab1 were viable, did not affect Pab1 function in mRNA stability and harbored an antisuppression phenotype. Our results show that in Saccharomyces cerevisiae the role of the Pab1 C-terminal domain in mRNA stability is independent of eRF3 and the association of these two factors negatively regulates translation termination.
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Affiliation(s)
- Sylvain Roque
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Marie Cerciat
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Isabelle Gaugué
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Liliana Mora
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Aurélie G Floch
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Miklos de Zamaroczy
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Valérie Heurgué-Hamard
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Stephanie Kervestin
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France Metabolism and function of RNA in the nucleus, Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris 75013, France
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29
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Joncourt R, Eberle AB, Rufener SC, Mühlemann O. Eukaryotic initiation factor 4G suppresses nonsense-mediated mRNA decay by two genetically separable mechanisms. PLoS One 2014; 9:e104391. [PMID: 25148142 PMCID: PMC4141738 DOI: 10.1371/journal.pone.0104391] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/08/2014] [Indexed: 11/19/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD), which is best known for degrading mRNAs with premature termination codons (PTCs), is thought to be triggered by aberrant translation termination at stop codons located in an environment of the mRNP that is devoid of signals necessary for proper termination. In mammals, the cytoplasmic poly(A)-binding protein 1 (PABPC1) has been reported to promote correct termination and therewith antagonize NMD by interacting with the eukaryotic release factors 1 (eRF1) and 3 (eRF3). Using tethering assays in which proteins of interest are recruited as MS2 fusions to a NMD reporter transcript, we show that the three N-terminal RNA recognition motifs (RRMs) of PABPC1 are sufficient to antagonize NMD, while the eRF3-interacting C-terminal domain is dispensable. The RRM1-3 portion of PABPC1 interacts with eukaryotic initiation factor 4G (eIF4G) and tethering of eIF4G to the NMD reporter also suppresses NMD. We identified the interactions of the eIF4G N-terminus with PABPC1 and the eIF4G core domain with eIF3 as two genetically separable features that independently enable tethered eIF4G to inhibit NMD. Collectively, our results reveal a function of PABPC1, eIF4G and eIF3 in translation termination and NMD suppression, and they provide additional evidence for a tight coupling between translation termination and initiation.
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Affiliation(s)
- Raphael Joncourt
- University of Bern, Department of Chemistry and Biochemistry, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrea B. Eberle
- University of Bern, Department of Chemistry and Biochemistry, Bern, Switzerland
| | - Simone C. Rufener
- University of Bern, Department of Chemistry and Biochemistry, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Oliver Mühlemann
- University of Bern, Department of Chemistry and Biochemistry, Bern, Switzerland
- * E-mail:
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Flury V, Restuccia U, Bachi A, Mühlemann O. Characterization of phosphorylation- and RNA-dependent UPF1 interactors by quantitative proteomics. J Proteome Res 2014; 13:3038-53. [PMID: 24762188 DOI: 10.1021/pr5002143] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human up-frameshift 1 (UPF1) is an ATP-dependent RNA helicase and phosphoprotein implicated in several biological processes but is best known for its key function in nonsense-mediated mRNA decay (NMD). Here we employed a combination of stable isotope labeling of amino acids in cell culture experiments to determine by quantitative proteomics UPF1 interactors. We used this approach to distinguish between RNA-mediated and protein-mediated UPF1 interactors and to determine proteins that preferentially bind the hypo- or the hyper-phosphorylated form of UPF1. Confirming and expanding previous studies, we identified the eukaryotic initiation factor 3 (eIF3) as a prominent protein-mediated interactor of UPF1. However, unlike previously reported, eIF3 binds to UPF1 independently of UPF1's phosphorylation state. Furthermore, our data revealed many nucleus-associated RNA-binding proteins that preferentially associate with hyper-phosphorylated UPF1 in an RNase-sensitive manner, suggesting that UPF1 gets recruited to mRNA and becomes phosphorylated before being exported to the cytoplasm as part of the mRNP.
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Affiliation(s)
- Valentin Flury
- Department of Chemistry and Biochemistry, University of Bern , Freiestr. 3, Bern 3012, Switzerland
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31
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Malagon F. RNase III is required for localization to the nucleoid of the 5' pre-rRNA leader and for optimal induction of rRNA synthesis in E. coli. RNA (NEW YORK, N.Y.) 2013; 19:1200-7. [PMID: 23893733 PMCID: PMC3753927 DOI: 10.1261/rna.038588.113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/14/2013] [Indexed: 05/24/2023]
Abstract
It has recently been demonstrated that ribosomes are preferentially localized outside the nucleoid in Escherichia coli, but little is known about the spatial regulation of pre-rRNA processing. In this work, I investigate the cellular distribution of leader pre-rRNAs using RNA-FISH. In contrast to mature rRNA, the 5' proximal leader region associates with the nucleoid, and this association occurs in an RNase III-dependent manner. Moreover, RNase III plays a role in the rapid induction of ribosomal operons during outgrowth and is essential in the absence of the transcriptional regulator Fis, suggesting a linkage of transcription and RNA processing for ribosomal operons in E. coli.
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Affiliation(s)
- Francisco Malagon
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4264, USA.
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32
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Lubas M, Damgaard CK, Tomecki R, Cysewski D, Jensen TH, Dziembowski A. Exonuclease hDIS3L2 specifies an exosome-independent 3'-5' degradation pathway of human cytoplasmic mRNA. EMBO J 2013; 32:1855-68. [PMID: 23756462 DOI: 10.1038/emboj.2013.135] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 05/15/2013] [Indexed: 12/27/2022] Open
Abstract
Turnover of mRNA in the cytoplasm of human cells is thought to be redundantly conducted by the monomeric 5'-3' exoribonuclease hXRN1 and the 3'-5' exoribonucleolytic RNA exosome complex. However, in addition to the exosome-associated 3'-5' exonucleases hDIS3 and hDIS3L, the human genome encodes another RNase II/R domain protein-hDIS3L2. Here, we show that hDIS3L2 is an exosome-independent cytoplasmic mRNA 3'-5' exonuclease, which exhibits processive activity on structured RNA substrates in vitro. hDIS3L2 associates with hXRN1 in an RNA-dependent manner and can, like hXRN1, be found on polysomes. The impact of hDIS3L2 on cytoplasmic RNA metabolism is revealed by an increase in levels of cytoplasmic RNA processing bodies (P-bodies) upon hDIS3L2 depletion, which also increases half-lives of investigated mRNAs. Consistently, RNA sequencing (RNA-seq) analyses demonstrate that depletion of hDIS3L2, like downregulation of hXRN1 and hDIS3L, causes changed levels of multiple mRNAs. We suggest that hDIS3L2 is a key exosome-independent effector of cytoplasmic mRNA metabolism.
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Affiliation(s)
- Michal Lubas
- Centre for mRNP Biogenesis and Metabolism, Aarhus University, Aarhus C, Denmark
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33
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Emerging roles for ribonucleoprotein modification and remodeling in controlling RNA fate. Trends Cell Biol 2013; 23:504-10. [PMID: 23756094 DOI: 10.1016/j.tcb.2013.05.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/01/2013] [Accepted: 05/02/2013] [Indexed: 12/26/2022]
Abstract
In the cell, mRNAs and non-coding RNAs exist in association with proteins to form ribonucleoprotein (RNP) complexes. Regulation of RNP stability and function is achieved by alterations to the RNP through poorly understood mechanisms into which recent studies have now begun to provide insight. This emerging body of work points to chemical modification of RNPs at the RNA or protein level and ATP-dependent RNP remodeling by RNA helicases/RNA-dependent ATPases as central events that dictate RNA fate. Some RNP modifications serve as tags for recruitment of regulatory proteins, with RNP modifiers and recruited proteins analogous to the writers and readers of chromatin modification, respectively. This review highlights examples in which RNP modification and ATP-dependent remodeling play key roles in the control of eukaryotic RNA fate, suggesting that we are only at the beginning of uncovering the multitude of ways in which RNP modification and remodeling impact RNA regulation.
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Schweingruber C, Rufener SC, Zünd D, Yamashita A, Mühlemann O. Nonsense-mediated mRNA decay - mechanisms of substrate mRNA recognition and degradation in mammalian cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:612-23. [PMID: 23435113 DOI: 10.1016/j.bbagrm.2013.02.005] [Citation(s) in RCA: 247] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/10/2013] [Accepted: 02/12/2013] [Indexed: 12/15/2022]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway is well known as a translation-coupled quality control system that recognizes and degrades aberrant mRNAs with truncated open reading frames (ORF) due to the presence of a premature termination codon (PTC). However, a more general role of NMD in posttranscriptional regulation of gene expression is indicated by transcriptome-wide mRNA profilings that identified a plethora of physiological mRNAs as NMD targets. In this review, we focus on mechanistic aspects of target mRNA identification and degradation in mammalian cells, based on the available biochemical and genetic data, and point out knowledge gaps. Translation termination in a messenger ribonucleoprotein particle (mRNP) environment lacking necessary factors for proper translation termination emerges as a key determinant for subjecting an mRNA to NMD, and we therefore review recent structural and mechanistic insight into translation termination. In addition, the central role of UPF1, its crucial phosphorylation/dephosphorylation cycle and dynamic interactions with other NMD factors are discussed. Moreover, we address the role of exon junction complexes (EJCs) in NMD and summarize the functions of SMG5, SMG6 and SMG7 in promoting mRNA decay through different routes. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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35
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Moon SL, Anderson JR, Kumagai Y, Wilusz CJ, Akira S, Khromykh AA, Wilusz J. A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability. RNA (NEW YORK, N.Y.) 2012; 18:2029-40. [PMID: 23006624 PMCID: PMC3479393 DOI: 10.1261/rna.034330.112] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/17/2012] [Indexed: 05/25/2023]
Abstract
All arthropod-borne flaviviruses generate a short noncoding RNA (sfRNA) from the viral 3' untranslated region during infection due to stalling of the cellular 5'-to-3' exonuclease XRN1. We show here that formation of sfRNA also inhibits XRN1 activity. Cells infected with Dengue or Kunjin viruses accumulate uncapped mRNAs, decay intermediates normally targeted by XRN1. XRN1 repression also resulted in the increased overall stability of cellular mRNAs in flavivirus-infected cells. Importantly, a mutant Kunjin virus that cannot form sfRNA but replicates to normal levels failed to affect host mRNA stability or XRN1 activity. Expression of sfRNA in the absence of viral infection demonstrated that sfRNA formation was directly responsible for the stabilization of cellular mRNAs. Finally, numerous cellular mRNAs were differentially expressed in an sfRNA-dependent fashion in a Kunjin virus infection. We conclude that flaviviruses incapacitate XRN1 during infection and dysregulate host mRNA stability as a result of sfRNA formation.
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Affiliation(s)
- Stephanie L. Moon
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - John R. Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Yutaro Kumagai
- Laboratory of Host Defense, Immunology Frontier Research Center, Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Carol J. Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Shizuo Akira
- Laboratory of Host Defense, Immunology Frontier Research Center, Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Alexander A. Khromykh
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
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36
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Mischo HE, Proudfoot NJ. Disengaging polymerase: terminating RNA polymerase II transcription in budding yeast. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:174-85. [PMID: 23085255 PMCID: PMC3793857 DOI: 10.1016/j.bbagrm.2012.10.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 11/29/2022]
Abstract
Termination of transcription by RNA polymerase II requires two distinct processes: The formation of a defined 3′ end of the transcribed RNA, as well as the disengagement of RNA polymerase from its DNA template. Both processes are intimately connected and equally pivotal in the process of functional messenger RNA production. However, research in recent years has elaborated how both processes can additionally be employed to control gene expression in qualitative and quantitative ways. This review embraces these new findings and attempts to paint a broader picture of how this final step in the transcription cycle is of critical importance to many aspects of gene regulation. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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Affiliation(s)
- Hannah E Mischo
- Cancer Research UK London Research Institute, Blanche Lane South Mimms, Herts, UK.
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37
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Schmid M, Jensen TH. Transcription-associated quality control of mRNP. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:158-68. [PMID: 22982197 DOI: 10.1016/j.bbagrm.2012.08.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 08/24/2012] [Accepted: 08/29/2012] [Indexed: 01/06/2023]
Abstract
Although a prime purpose of transcription is to produce RNA, a substantial amount of transcript is nevertheless turned over very early in its lifetime. During transcription RNAs are matured by nucleases from longer precursors and activities are also employed to exert quality control over the RNA synthesis process so as to discard, retain or transcriptionally silence unwanted molecules. In this review we discuss the somewhat paradoxical circumstance that the retention or turnover of RNA is often linked to its synthesis. This occurs via the association of chromatin, or the transcription elongation complex, with RNA degradation (co)factors. Although our main focus is on protein-coding genes, we also discuss mechanisms of transcription-connected turnover of non-protein-coding RNA from where important general principles are derived. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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Affiliation(s)
- Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C., Denmark
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38
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Schmid M, Poulsen MB, Olszewski P, Pelechano V, Saguez C, Gupta I, Steinmetz LM, Moore C, Jensen TH. Rrp6p controls mRNA poly(A) tail length and its decoration with poly(A) binding proteins. Mol Cell 2012; 47:267-80. [PMID: 22683267 DOI: 10.1016/j.molcel.2012.05.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 03/30/2012] [Accepted: 05/01/2012] [Indexed: 11/17/2022]
Abstract
Poly(A) (pA) tail binding proteins (PABPs) control mRNA polyadenylation, stability, and translation. In a purified system, S. cerevisiae PABPs, Pab1p and Nab2p, are individually sufficient to provide normal pA tail length. However, it is unknown how this occurs in more complex environments. Here we find that the nuclear exosome subunit Rrp6p counteracts the in vitro and in vivo extension of mature pA tails by the noncanonical pA polymerase Trf4p. Moreover, PABP loading onto nascent pA tails is controlled by Rrp6p; while Pab1p is the major PABP, Nab2p only associates in the absence of Rrp6p. This is because Rrp6p can interact with Nab2p and displace it from pA tails, potentially leading to RNA turnover, as evidenced for certain pre-mRNAs. We suggest that a nuclear mRNP surveillance step involves targeting of Rrp6p by Nab2p-bound pA-tailed RNPs and that pre-mRNA abundance is regulated at this level.
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Affiliation(s)
- Manfred Schmid
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, DK-8000 Aarhus C., Denmark
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39
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Lubas M, Chlebowski A, Dziembowski A, Jensen TH. Biochemistry and Function of RNA Exosomes. EUKARYOTIC RNASES AND THEIR PARTNERS IN RNA DEGRADATION AND BIOGENESIS, PART A 2012; 31:1-30. [DOI: 10.1016/b978-0-12-404740-2.00001-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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