1
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Schmidt T, Dabrowska A, Waldron JA, Hodge K, Koulouras G, Gabrielsen M, Munro J, Tack DC, Harris G, McGhee E, Scott D, Carlin L, Huang D, Le Quesne J, Zanivan S, Wilczynska A, Bushell M. eIF4A1-dependent mRNAs employ purine-rich 5'UTR sequences to activate localised eIF4A1-unwinding through eIF4A1-multimerisation to facilitate translation. Nucleic Acids Res 2023; 51:1859-1879. [PMID: 36727461 PMCID: PMC9976904 DOI: 10.1093/nar/gkad030] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/20/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023] Open
Abstract
Altered eIF4A1 activity promotes translation of highly structured, eIF4A1-dependent oncogene mRNAs at root of oncogenic translational programmes. It remains unclear how these mRNAs recruit and activate eIF4A1 unwinding specifically to facilitate their preferential translation. Here, we show that single-stranded RNA sequence motifs specifically activate eIF4A1 unwinding allowing local RNA structural rearrangement and translation of eIF4A1-dependent mRNAs in cells. Our data demonstrate that eIF4A1-dependent mRNAs contain AG-rich motifs within their 5'UTR which specifically activate eIF4A1 unwinding of local RNA structure to facilitate translation. This mode of eIF4A1 regulation is used by mRNAs encoding components of mTORC-signalling and cell cycle progression, and renders these mRNAs particularly sensitive to eIF4A1-inhibition. Mechanistically, we show that binding of eIF4A1 to AG-rich sequences leads to multimerization of eIF4A1 with eIF4A1 subunits performing distinct enzymatic activities. Our structural data suggest that RNA-binding of multimeric eIF4A1 induces conformational changes in the RNA resulting in an optimal positioning of eIF4A1 proximal to the RNA duplex enabling efficient unwinding. Our data proposes a model in which AG-motifs in the 5'UTR of eIF4A1-dependent mRNAs specifically activate eIF4A1, enabling assembly of the helicase-competent multimeric eIF4A1 complex, and positioning these complexes proximal to stable localised RNA structure allowing ribosomal subunit scanning.
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Affiliation(s)
- Tobias Schmidt
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Adrianna Dabrowska
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
- Department of Urology, University of California, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph A Waldron
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Kelly Hodge
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Grigorios Koulouras
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Mads Gabrielsen
- MVLS Structural Biology and Biophysical Characterisation Facility, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
| | - June Munro
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - David C Tack
- Spectrum Health Office of Research and Education, Spectrum Health System, 15 Michigan Street NE, Grand Rapids, MI 49503, USA
| | - Gemma Harris
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0FA, UK
| | - Ewan McGhee
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - David Scott
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0FA, UK
- ISIS Spallation Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, DidcotOX11 0QX, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington LE12 5RD, UK
| | - Leo M Carlin
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Danny Huang
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - John Le Quesne
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Sara Zanivan
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Ania Wilczynska
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
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2
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The Polyvalent Role of NF90 in RNA Biology. Int J Mol Sci 2022; 23:ijms232113584. [DOI: 10.3390/ijms232113584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022] Open
Abstract
Double-stranded RNA-binding proteins (dsRBPs) are major players in the regulation of gene expression patterns. Among them, Nuclear Factor 90 (NF90) has a plethora of well-known functions in viral infection, transcription, and translation as well as RNA stability and degradation. In addition, NF90 has been identified as a regulator of microRNA (miRNA) maturation by competing with Microprocessor for the binding of pri-miRNAs in the nucleus. NF90 was recently shown to control the biogenesis of a subset of human miRNAs, which ultimately influences, not only the abundance, but also the expression of the host gene and the fate of the mRNA target repertoire. Moreover, recent evidence suggests that NF90 is also involved in RNA-Induced Silencing Complex (RISC)-mediated silencing by binding to target mRNAs and controlling their translation and degradation. Here, we review the many, and growing, functions of NF90 in RNA biology, with a focus on the miRNA pathway and RISC-mediated gene silencing.
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3
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Grasso G, Akkawi C, Franckhauser C, Nait-Saidi R, Bello M, Barbier J, Kiernan R. NF90 interacts with components of RISC and modulates association of Ago2 with mRNA. BMC Biol 2022; 20:194. [PMID: 36050755 PMCID: PMC9438302 DOI: 10.1186/s12915-022-01384-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 08/05/2022] [Indexed: 01/14/2023] Open
Abstract
Background Nuclear factor 90 (NF90) is a double-stranded RNA-binding protein involved in a multitude of different cellular mechanisms such as transcription, translation, viral infection, and mRNA stability. Recent data suggest that NF90 might influence the abundance of target mRNAs in the cytoplasm through miRNA- and Argonaute 2 (Ago2)-dependent activity. Results Here, we identified the interactome of NF90 in the cytoplasm, which revealed several components of the RNA-induced silencing complex (RISC) and associated factors. Co-immunoprecipitation analysis confirmed the interaction of NF90 with the RISC-associated RNA helicase, Moloney leukemia virus 10 (MOV10), and other proteins involved in RISC-mediated silencing, including Ago2. Furthermore, NF90 association with MOV10 and Ago2 was found to be RNA-dependent. Glycerol gradient sedimentation of NF90 immune complexes indicates that these proteins occur in the same protein complex. At target RNAs predicted to bind both NF90 and MOV10 in their 3′ UTRs, NF90 association was increased upon loss of MOV10 and vice versa. Interestingly, loss of NF90 led to an increase in association of Ago2 as well as a decrease in the abundance of the target mRNA. Similarly, during hypoxia, the binding of Ago2 to vascular endothelial growth factor (VEGF) mRNA increased after loss of NF90, while the level of VEGF mRNA decreased. Conclusions These findings reveal that, in the cytoplasm, NF90 can associate with components of RISC such as Ago2 and MOV10. In addition, the data indicate that NF90 and MOV10 may compete for the binding of common target mRNAs, suggesting a role for NF90 in the regulation of RISC-mediated silencing by stabilizing target mRNAs, such as VEGF, during cancer-induced hypoxia. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01384-2.
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Affiliation(s)
- Giuseppa Grasso
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France
| | - Charbel Akkawi
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France
| | - Celine Franckhauser
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France
| | - Rima Nait-Saidi
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France
| | - Maxime Bello
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France
| | - Jérôme Barbier
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France
| | - Rosemary Kiernan
- UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, 34396, Montpellier, France.
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4
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Chen G, Yang Y, Wu QJ, Cao L, Ruan W, Shao C, Jiang L, Tang P, Ma S, Jiang A, Wang Z, Wu K, Zhang QC, Fu XD, Zhou Y. ILF3 represses repeat-derived microRNAs targeting RIG-I mediated type I interferon response. J Mol Biol 2022; 434:167469. [PMID: 35120969 DOI: 10.1016/j.jmb.2022.167469] [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: 09/08/2021] [Revised: 01/05/2022] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
Abstract
MicroRNAs (miRNAs) play important roles in regulated gene expression and miRNA biogenesis is also subject to regulation, together constituting critical regulatory circuitries in numerous physiological and pathological processes. As a dsRNA binding protein, interleukin enhancer binding factor 3 (ILF3) has been implicated as a negative regulator in miRNA biogenesis, but the mechanism and specificity have remained undefined. Here, combining small-RNA-seq and CLIP-seq, we showed that ILF3 directly represses many miRNAs or perhaps other types of small RNAs annotated in both miRBase and MirGeneDB. We demonstrated that ILF3 preferentially binds to A/U-enriched motifs, which tend to lengthen and/or stabilize the stem-loop in pri-miRNAs, thereby effectively competing with the Microprocessor to block miRNA biogenesis. Focusing on the biological function of ILF3-suppressed miR-582-3p, we discovered that this LINE-derived miRNA targets a critical interferon-inducible gene RIG-I for repression, thus establishing a novel ILF3/miR-582/RIG-I axis in the antiviral response.
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Affiliation(s)
- Geng Chen
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Yang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qi-Jia Wu
- Seqhealth Technology Co., Ltd, Wuhan, China
| | - Liu Cao
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wen Ruan
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Changwei Shao
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China; Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, USA
| | - Li Jiang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Peng Tang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Suping Ma
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ao Jiang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhen Wang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Kai Wu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, USA
| | - Yu Zhou
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.
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5
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Nitschko V, Kunzelmann S, Fröhlich T, Arnold GJ, Förstemann K. Trafficking of siRNA precursors by the dsRBD protein Blanks in Drosophila. Nucleic Acids Res 2020; 48:3906-3921. [PMID: 32025726 PMCID: PMC7144943 DOI: 10.1093/nar/gkaa072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 01/21/2020] [Accepted: 02/03/2020] [Indexed: 01/03/2023] Open
Abstract
RNA interference targets aberrant transcripts with cognate small interfering RNAs, which derive from double-stranded RNA precursors. Several functional screens have identified Drosophila blanks/lump (CG10630) as a facilitator of RNAi, yet its molecular function has remained unknown. The protein carries two dsRNA binding domains (dsRBD) and blanks mutant males have a spermatogenesis defect. We demonstrate that blanks selectively boosts RNAi triggered by dsRNA of nuclear origin. Blanks binds dsRNA via its second dsRBD in vitro, shuttles between nucleus and cytoplasm and the abundance of siRNAs arising at many sites of convergent transcription is reduced in blanks mutants. Since features of nascent RNAs - such as introns and transcription beyond the polyA site – contribute to the small RNA pool, we propose that Blanks binds dsRNA formed by cognate nascent RNAs in the nucleus and fosters its export to the cytoplasm for dicing. We refer to the resulting small RNAs as blanks exported siRNAs (bepsiRNAs). While bepsiRNAs were fully dependent on RNA binding to the second dsRBD of blanks in transgenic flies, male fertility was not. This is consistent with a previous report that linked fertility to the first dsRBD of Blanks. The role of blanks in spermatogenesis appears thus unrelated to its role in dsRNA export.
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Affiliation(s)
- Volker Nitschko
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Stefan Kunzelmann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Thomas Fröhlich
- Laboratory of Functional Genome Analysis, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Georg J Arnold
- Laboratory of Functional Genome Analysis, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Klaus Förstemann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
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6
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Ding D, Huang H, Li Q, Yu W, Wang C, Ma H, Wu J, Dang Y, Yu L, Jiang W. NF90 stabilizes cyclin E1 mRNA through phosphorylation of NF90-Ser382 by CDK2. Cell Death Discov 2020; 6:3. [PMID: 32123579 PMCID: PMC7026180 DOI: 10.1038/s41420-020-0236-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/17/2019] [Accepted: 01/02/2020] [Indexed: 12/19/2022] Open
Abstract
Nuclear factor 90 (NF90), an RNA-binding protein, has been implicated in regulating interleukin-2 (IL-2) and the immune response. It was recently reported that NF90 is upregulated in hepatocellular carcinoma (HCC) tissues and promotes HCC proliferation through upregulating cyclin E1 at the posttranscription level. However, the regulation of NF90 in HCC remains unclear. We demonstrate here that cyclin-dependent kinase (CDK) 2 interacts with NF90 and phosphorylated it at serine382. Mechanistically, phosphorylation of NF90-Ser382 determines the nuclear export of NF90 and stabilization of cyclin E1 mRNA. We also demonstrate that the phosphorylation deficient mutant NF90-S382A inhibits cell growth and induces cell cycle arrest at the G1 phase in HCC cells. Moreover, an NF90-S382A xenograft tumor had a decreased size and weight compared with the wildtype NF90. The NF90-S382A xenograft contained a significantly lower level of the proliferation marker Ki-67. Additionally, in HCC patients, NF90-Ser382 phosphorylation was stronger in tumor than in non-tumor tissues. Clinically, phosphorylation of NF90-Ser382 is significantly associated with larger tumor sizes, higher AFP levels, and shorter overall survival rates. These results suggest NF90-Ser382 phosphorylation serves as a potential diagnosis and prognostic marker and a promising pharmacological target for HCC.
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Affiliation(s)
- Donglin Ding
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN USA
| | - Huixing Huang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Quanfu Li
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wenbo Yu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Chenji Wang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Haijie Ma
- Laboratory of Cytobiology and Molecular Biology, The Affiliated Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang China
| | - Jiaxue Wu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Yongjun Dang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Long Yu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Wei Jiang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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7
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Watson SF, Bellora N, Macias S. ILF3 contributes to the establishment of the antiviral type I interferon program. Nucleic Acids Res 2020; 48:116-129. [PMID: 31701124 PMCID: PMC7145544 DOI: 10.1093/nar/gkz1060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/21/2019] [Accepted: 11/04/2019] [Indexed: 12/14/2022] Open
Abstract
Upon detection of viral infections, cells activate the expression of type I interferons (IFNs) and pro-inflammatory cytokines to control viral dissemination. As part of their antiviral response, cells also trigger the translational shutoff response which prevents translation of viral mRNAs and cellular mRNAs in a non-selective manner. Intriguingly, mRNAs encoding for antiviral factors bypass this translational shutoff, suggesting the presence of additional regulatory mechanisms enabling expression of the self-defence genes. Here, we identified the dsRNA binding protein ILF3 as an essential host factor required for efficient translation of the central antiviral cytokine, IFNB1, and a subset of interferon-stimulated genes. By combining polysome profiling and next-generation sequencing, ILF3 was also found to be necessary to establish the dsRNA-induced transcriptional and translational programs. We propose a central role for the host factor ILF3 in enhancing expression of the antiviral defence mRNAs in cellular conditions where cap-dependent translation is compromised.
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Affiliation(s)
- Samir F Watson
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh, UK
| | | | - Sara Macias
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh, UK
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8
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Fasolo F, Patrucco L, Volpe M, Bon C, Peano C, Mignone F, Carninci P, Persichetti F, Santoro C, Zucchelli S, Sblattero D, Sanges R, Cotella D, Gustincich S. The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs. FASEB J 2019; 33:13572-13589. [PMID: 31570000 PMCID: PMC6894054 DOI: 10.1096/fj.201901618rr] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Transposable elements (TEs) compose about half of the mammalian genome and, as embedded sequences, up to 40% of long noncoding RNA (lncRNA) transcripts. Embedded TEs may represent functional domains within lncRNAs, providing a structured RNA platform for protein interaction. Here we show the interactome profile of the mouse inverted short interspersed nuclear element (SINE) of subfamily B2 (invSINEB2) alone and embedded in antisense (AS) ubiquitin C-terminal hydrolase L1 (Uchl1), an lncRNA that is AS to Uchl1 gene. AS Uchl1 is the representative member of a functional class of AS lncRNAs, named SINEUPs, in which the invSINEB2 acts as effector domain (ED)-enhancing translation of sense protein-coding mRNAs. By using RNA-interacting domainome technology, we identify the IL enhancer-binding factor 3 (ILF3) as a protein partner of AS Uchl1 RNA. We determine that this interaction is mediated by the RNA-binding motif 2 of ILF3 and the invSINEB2. Furthermore, we show that ILF3 is able to bind a free right Arthrobacter luteus (Alu) monomer sequence, the embedded TE acting as ED in human SINEUPs. Bioinformatic analysis of Encyclopedia of DNA Elements-enhanced cross-linking immunoprecipitation data reveals that ILF3 binds transcribed human SINE sequences at transcriptome-wide levels. We then demonstrate that the embedded TEs modulate AS Uchl1 RNA nuclear localization to an extent moderately influenced by ILF3. This work unveils the existence of a specific interaction between embedded TEs and an RNA-binding protein, strengthening the model of TEs as functional modules in lncRNAs.-Fasolo, F., Patrucco, L., Volpe, M., Bon, C., Peano, C., Mignone, F., Carninci, P., Persichetti, F., Santoro, C., Zucchelli, S., Sblattero, D., Sanges, R., Cotella, D., Gustincich, S. The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs.
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Affiliation(s)
- Francesca Fasolo
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Laura Patrucco
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Massimiliano Volpe
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Carlotta Bon
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Clelia Peano
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Flavio Mignone
- Department of Sciences and Innovation, Università del Piemonte Orientale, Alessandria, Italy
| | - Piero Carninci
- Division of Genomic Technologies, Riken Center for Life Science Technologies, Yokohama, Japan
| | | | - Claudio Santoro
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Silvia Zucchelli
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.,Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | | | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Diego Cotella
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Stefano Gustincich
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
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9
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Meyer A, Golbik RP, Sänger L, Schmidt T, Behrens SE, Friedrich S. The RGG/RG motif of AUF1 isoform p45 is a key modulator of the protein's RNA chaperone and RNA annealing activities. RNA Biol 2019; 16:960-971. [PMID: 30951406 DOI: 10.1080/15476286.2019.1602438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The RNA-binding protein AUF1 regulates post-transcriptional gene expression by affecting the steady state and translation levels of numerous target RNAs. Remodeling of RNA structures by the largest isoform AUF1 p45 was recently demonstrated in the context of replicating RNA viruses, and involves two RNA remodeling activities, i.e. an RNA chaperone and an RNA annealing activity. AUF1 contains two non-identical RNA recognition motifs (RRM) and one RGG/RG motif located in the C-terminus. In order to determine the functional significance of each motif to AUF1's RNA-binding and remodeling activities we performed a comprehensive mutagenesis study and characterized the wildtype AUF1, and several variants thereof. We demonstrate that each motif contributes to efficient RNA binding and remodeling by AUF1 indicating a tight cooperation of the RRMs and the RGG/RG motif. Interestingly, the data identify two distinct roles for the arginine residues of the RGG/RG motif for each RNA remodeling activity. First, arginine-mediated stacking interactions promote AUF1's helix-destabilizing RNA chaperone activity. Second, the electropositive character of the arginine residues is the major driving force for the RNA annealing activity. Thus, we provide the first evidence that arginine residues of an RGG/RG motif contribute to the mechanism of RNA annealing and RNA chaperoning.
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Affiliation(s)
- Alexandra Meyer
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Ralph P Golbik
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Lennart Sänger
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Tobias Schmidt
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Sven-Erik Behrens
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Susann Friedrich
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
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Garcia-Moreno M, Järvelin AI, Castello A. Unconventional RNA-binding proteins step into the virus-host battlefront. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1498. [PMID: 30091184 PMCID: PMC7169762 DOI: 10.1002/wrna.1498] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 12/15/2022]
Abstract
The crucial participation of cellular RNA‐binding proteins (RBPs) in virtually all steps of virus infection has been known for decades. However, most of the studies characterizing this phenomenon have focused on well‐established RBPs harboring classical RNA‐binding domains (RBDs). Recent proteome‐wide approaches have greatly expanded the census of RBPs, discovering hundreds of proteins that interact with RNA through unconventional RBDs. These domains include protein–protein interaction platforms, enzymatic cores, and intrinsically disordered regions. Here, we compared the experimentally determined census of RBPs to gene ontology terms and literature, finding that 472 proteins have previous links with viruses. We discuss what these proteins are and what their roles in infection might be. We also review some of the pioneering examples of unorthodox RBPs whose RNA‐binding activity has been shown to be critical for virus infection. Finally, we highlight the potential of these proteins for host‐based therapies against viruses. This article is categorized under:
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
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Affiliation(s)
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, Oxford, UK
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Pertermann R, Tamilarasan S, Gursinsky T, Gambino G, Schuck J, Weinholdt C, Lilie H, Grosse I, Golbik RP, Pantaleo V, Behrens SE. A Viral Suppressor Modulates the Plant Immune Response Early in Infection by Regulating MicroRNA Activity. mBio 2018; 9:e00419-18. [PMID: 29691336 PMCID: PMC5915741 DOI: 10.1128/mbio.00419-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/28/2018] [Indexed: 02/06/2023] Open
Abstract
Many viral suppressors (VSRs) counteract antiviral RNA silencing, a central component of the plant's immune response by sequestration of virus-derived antiviral small interfering RNAs (siRNAs). Here, we addressed how VSRs affect the activities of cellular microRNAs (miRNAs) during a viral infection by characterizing the interactions of two unrelated VSRs, the Tombusvirus p19 and the Cucumovirus 2b, with miRNA 162 (miR162), miR168, and miR403. These miRNAs regulate the expression of the important silencing factors Dicer-like protein 1 (DCL1) and Argonaute proteins 1 and 2 (AGO1 and AGO2), respectively. Interestingly, while the two VSRs showed similar binding profiles, the miRNAs were bound with significantly different affinities, for example, with the affinity of miR162 greatly exceeding that of miR168. In vitro silencing experiments revealed that p19 and 2b affect miRNA-mediated silencing of the DCL1, AGO1, and AGO2 mRNAs in strict accordance with the VSR's miRNA-binding profiles. In Tombusvirus-infected plants, the miRNA-binding behavior of p19 closely corresponded to that in vitro Most importantly, in contrast to controls with a Δp19 virus, infections with wild-type (wt) virus led to changes of the levels of the miRNA-targeted mRNAs, and these changes correlated with the miRNA-binding preferences of p19. This was observed exclusively in the early stage of infection when viral genomes are proposed to be susceptible to silencing and viral siRNA (vsiRNA) concentrations are low. Accordingly, our study suggests that differential binding of miRNAs by VSRs is a widespread viral mechanism to coordinately modulate cellular gene expression and the antiviral immune response during infection initiation.IMPORTANCE Plant viruses manipulate their hosts in various ways. Viral suppressor proteins (VSRs) interfere with the plant's immune response by sequestering small, antivirally acting vsiRNAs, which are processed from viral RNAs during the plant's RNA-silencing response. Here, we examined the effects of VSRs on cellular microRNAs (miRNAs), which show a high degree of similarity with vsiRNAs. Binding experiments with two unrelated VSRs and three important regulatory miRNAs revealed that the proteins exhibit similar miRNA-binding profiles but bind different miRNAs at considerably different affinities. Most interestingly, experiments in plants showed that in the early infection phase, the Tombusvirus VSR p19 modulates the activity of these miRNAs on their target mRNAs very differently and that this differential regulation strictly correlates with the binding affinities of p19 for the respective miRNAs. Our data suggest that VSRs may specifically control plant gene expression and the early immune response by differential sequestration of miRNAs.
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Affiliation(s)
- Robert Pertermann
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Selvaraj Tamilarasan
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Torsten Gursinsky
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection-Consiglio Nazionale delle Ricerche, Turin, Italy
| | - Jana Schuck
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Claus Weinholdt
- Institute of Informatics, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Ivo Grosse
- Institute of Informatics, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Ralph Peter Golbik
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection-Consiglio Nazionale delle Ricerche, Research Unit of Bari, Bari, Italy
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
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Schmidt T, Friedrich S, Golbik RP, Behrens SE. NF90-NF45 is a selective RNA chaperone that rearranges viral and cellular riboswitches: biochemical analysis of a virus host factor activity. Nucleic Acids Res 2017; 45:12441-12454. [PMID: 29040738 PMCID: PMC5716087 DOI: 10.1093/nar/gkx931] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/10/2017] [Indexed: 01/28/2023] Open
Abstract
The heterodimer NF90-NF45 is an RNA-binding protein complex that modulates the expression of various cellular mRNAs on the post-transcriptional level. Furthermore, it acts as a host factor that supports the replication of several RNA viruses. The molecular mechanisms underlying these activities have yet to be elucidated. Recently, we showed that the RNA-binding capabilities and binding specificity of NF90 considerably improves when it forms a complex with NF45. Here, we demonstrate that NF90 has a substrate-selective RNA chaperone activity (RCA) involving RNA annealing and strand displacement activities. The mechanism of the NF90-catalyzed RNA annealing was elucidated to comprise a combination of 'matchmaking' and compensation of repulsive charges, which finally results in the population of dsRNA products. Heterodimer formation with NF45 enhances 'matchmaking' of complementary ssRNAs and substantially increases the efficiency of NF90's RCA. During investigations of the relevance of the NF90-NF45 RCA, the complex was shown to stimulate the first step in the RNA replication process of hepatitis C virus (HCV) in vitro and to stabilize a regulatory element within the mRNA of vascular endothelial growth factor (VEGF) by protein-guided changes of the RNAs' structures. Thus, our study reveals how the intrinsic properties of an RNA-binding protein determine its biological activities.
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Affiliation(s)
- Tobias Schmidt
- Institute of Biochemistry and Biotechnology (NFI), Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle/Saale, Germany
- To whom correspondence should be addressed. Tel: +49 3455 5249 60; Fax: +49 3455 5273 87; . Correspondence may also be addressed to Tobias Schmidt.
| | - Susann Friedrich
- Institute of Biochemistry and Biotechnology (NFI), Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle/Saale, Germany
| | - Ralph Peter Golbik
- Institute of Biochemistry and Biotechnology (NFI), Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle/Saale, Germany
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology (NFI), Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle/Saale, Germany
- To whom correspondence should be addressed. Tel: +49 3455 5249 60; Fax: +49 3455 5273 87; . Correspondence may also be addressed to Tobias Schmidt.
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The properties of the RNA-binding protein NF90 are considerably modulated by complex formation with NF45. Biochem J 2016; 474:259-280. [PMID: 28062840 DOI: 10.1042/bcj20160790] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/07/2016] [Accepted: 11/11/2016] [Indexed: 12/31/2022]
Abstract
Nuclear factor 90 (NF90) is an RNA-binding protein (RBP) that regulates post-transcriptionally the expression of various mRNAs. NF90 was recently shown to be capable of discriminating between different RNA substrates. This is mediated by an adaptive and co-operative interplay between three RNA-binding motifs (RBMs) in the protein's C-terminus. In many cell types, NF90 exists predominantly in a complex with NF45. Here, we compared the RNA-binding properties of the purified NF90 monomer and the NF90-NF45 heterodimer by biophysical and biochemical means, and demonstrate that the interaction with NF45 considerably affects the characteristics of NF90. Along with a thermodynamic stabilization, complex formation substantially improves the RNA-binding capacity of NF90 by modulating its binding mode and by enhancing its affinity for single- and double-stranded RNA substrates. Our data suggest that features of both the N- and C-termini of NF90 participate in the heterodimerization with NF45 and that the formation of NF90-NF45 changes the conformation of NF90's RBMs to a status in which the co-operative interplay of the RBMs is optimal. NF45 is considered to act as a conformational scaffold for NF90's RBMs, which alters the RNA-binding specificity of NF90. Accordingly, the monomeric NF90 and the NF90-NF45 heterodimer may exert different functions in the cell.
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