1
|
Abedeera SM, Davila-Calderon J, Haddad C, Henry B, King J, Penumutchu S, Tolbert BS. The Repurposing of Cellular Proteins during Enterovirus A71 Infection. Viruses 2023; 16:75. [PMID: 38257775 PMCID: PMC10821071 DOI: 10.3390/v16010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
Viruses pose a great threat to people's lives. Enterovirus A71 (EV-A71) infects children and infants all over the world with no FDA-approved treatment to date. Understanding the basic mechanisms of viral processes aids in selecting more efficient drug targets and designing more effective antivirals to thwart this virus. The 5'-untranslated region (5'-UTR) of the viral RNA genome is composed of a cloverleaf structure and an internal ribosome entry site (IRES). Cellular proteins that bind to the cloverleaf structure regulate viral RNA synthesis, while those that bind to the IRES also known as IRES trans-acting factors (ITAFs) regulate viral translation. In this review, we survey the cellular proteins currently known to bind the 5'-UTR and influence viral gene expression with emphasis on comparing proteins' functions and localizations pre- and post-(EV-A71) infection. A comprehensive understanding of how the host cell's machinery is hijacked and reprogrammed by the virus to facilitate its replication is crucial for developing effective antivirals.
Collapse
Affiliation(s)
- Sudeshi M. Abedeera
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Jesse Davila-Calderon
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Barrington Henry
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Josephine King
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Srinivasa Penumutchu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Blanton S. Tolbert
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| |
Collapse
|
2
|
Benavides-Serrato A, Saunders JT, Kumar S, Holmes B, Benavides KE, Bashir MT, Nishimura RN, Gera J. m 6A-modification of cyclin D1 and c-myc IRESs in glioblastoma controls ITAF activity and resistance to mTOR inhibition. Cancer Lett 2023; 562:216178. [PMID: 37061119 PMCID: PMC10805108 DOI: 10.1016/j.canlet.2023.216178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/17/2023] [Accepted: 04/07/2023] [Indexed: 04/17/2023]
Abstract
A major mechanism conferring resistance to mTOR inhibitors is activation of a salvage pathway stimulating internal ribosome entry site (IRES)-mediated mRNA translation, driving the synthesis of proteins promoting resistance of glioblastoma (GBM). Previously, we found this pathway is stimulated by the requisite IRES-trans-acting factor (ITAF) hnRNP A1, which itself is subject to phosphorylation and methylation events regulating cyclin D1 and c-myc IRES activity. Here we describe the requirement for m6A-modification of IRES RNAs for efficient translation and resistance to mTOR inhibition. DRACH-motifs within these IRES RNAs upon m6A modification resulted in enhanced IRES activity via increased hnRNP A1-binding following mTOR inhibitor exposure. Inhibitor exposure stimulated the expression of m6A-methylosome components resulting in increased activity in GBM. Silencing of METTL3-14 complexes reduced IRES activity upon inhibitor exposure and sensitized resistant GBM lines. YTHDF3 associates with m6A-modified cyclin D1 or c-myc IRESs, regulating IRES activity, and mTOR inhibitor sensitivity in vitro and in xenograft experiments. YTHDF3 interacted directly with hnRNP A1 and together stimulated hnRNP A1-dependent nucleic acid strand annealing activity. These data demonstrate that m6A-methylation of IRES RNAs regulate GBM responses to this class of inhibitors.
Collapse
Affiliation(s)
- Angelica Benavides-Serrato
- Department of Medicine, University of California, Los Angeles, CA, USA; Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA, USA
| | - Jacquelyn T Saunders
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA, USA
| | - Sunil Kumar
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA, USA
| | - Brent Holmes
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA, USA
| | - Kennedy E Benavides
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA, USA
| | - Muhammad T Bashir
- Department of Medicine, University of California, Los Angeles, CA, USA; Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA, USA
| | - Robert N Nishimura
- Neurology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA; Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA, USA
| | - Joseph Gera
- Department of Medicine, University of California, Los Angeles, CA, USA; Jonnson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, CA, USA; Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA, USA.
| |
Collapse
|
3
|
Angulo J, Cáceres CJ, Contreras N, Fernández-García L, Chamond N, Ameur M, Sargueil B, López-Lastra M. Polypyrimidine-Tract-Binding Protein Isoforms Differentially Regulate the Hepatitis C Virus Internal Ribosome Entry Site. Viruses 2022; 15:8. [PMID: 36680049 PMCID: PMC9864772 DOI: 10.3390/v15010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/03/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Translation initiation of the hepatitis C virus (HCV) mRNA depends on an internal ribosome entry site (IRES) that encompasses most of the 5'UTR and includes nucleotides of the core coding region. This study shows that the polypyrimidine-tract-binding protein (PTB), an RNA-binding protein with four RNA recognition motifs (RRMs), binds to the HCV 5'UTR, stimulating its IRES activity. There are three isoforms of PTB: PTB1, PTB2, and PTB4. Our results show that PTB1 and PTB4, but not PTB2, stimulate HCV IRES activity in HuH-7 and HEK293T cells. In HuH-7 cells, PTB1 promotes HCV IRES-mediated initiation more strongly than PTB4. Mutations in PTB1, PTB4, RRM1/RRM2, or RRM3/RRM4, which disrupt the RRM's ability to bind RNA, abrogated the protein's capacity to stimulate HCV IRES activity in HuH-7 cells. In HEK293T cells, PTB1 and PTB4 stimulate HCV IRES activity to similar levels. In HEK293T cells, mutations in RRM1/RRM2 did not impact PTB1's ability to promote HCV IRES activity; and mutations in PTB1 RRM3/RRM4 domains reduced, but did not abolish, the protein's capacity to stimulate HCV IRES activity. In HEK293T cells, mutations in PTB4 RRM1/RRM2 abrogated the protein's ability to promote HCV IRES activity, and mutations in RRM3/RRM4 have no impact on PTB4 ability to enhance HCV IRES activity. Therefore, PTB1 and PTB4 differentially stimulate the IRES activity in a cell type-specific manner. We conclude that PTB1 and PTB4, but not PTB2, act as IRES transacting factors of the HCV IRES.
Collapse
Affiliation(s)
- Jenniffer Angulo
- Laboratorio de Virología Molecular, Centro de Investigaciones Médicas, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
- Facultad de Odontología, Universidad Finis Terrae, Santiago 7501015, Chile
| | - C. Joaquín Cáceres
- Laboratorio de Virología Molecular, Centro de Investigaciones Médicas, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Nataly Contreras
- Laboratorio de Virología Molecular, Centro de Investigaciones Médicas, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
- Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago 7500975, Chile
| | - Leandro Fernández-García
- Laboratorio de Virología Molecular, Centro de Investigaciones Médicas, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
| | - Nathalie Chamond
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8038, Laboratoire CiTCoM, Université Paris Cité, 75006 Paris, France
| | - Melissa Ameur
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8038, Laboratoire CiTCoM, Université Paris Cité, 75006 Paris, France
| | - Bruno Sargueil
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8038, Laboratoire CiTCoM, Université Paris Cité, 75006 Paris, France
| | - Marcelo López-Lastra
- Laboratorio de Virología Molecular, Centro de Investigaciones Médicas, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
| |
Collapse
|
4
|
Andreev DE, Niepmann M, Shatsky IN. Elusive Trans-Acting Factors Which Operate with Type I (Poliovirus-like) IRES Elements. Int J Mol Sci 2022; 23:ijms232415497. [PMID: 36555135 PMCID: PMC9778869 DOI: 10.3390/ijms232415497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
The phenomenon of internal initiation of translation was discovered in 1988 on poliovirus mRNA. The prototypic cis-acting element in the 5' untranslated region (5'UTR) of poliovirus mRNA, which is able to direct initiation at an internal start codon without the involvement of a cap structure, has been called an IRES (Internal Ribosome Entry Site or Segment). Despite its early discovery, poliovirus and other related IRES elements of type I are poorly characterized, and it is not yet clear which host proteins (a.k.a. IRES trans-acting factors, ITAFs) are required for their full activity in vivo. Here we discuss recent and old results devoted to type I IRESes and provide evidence that Poly(rC) binding protein 2 (PCBP2), Glycyl-tRNA synthetase (GARS), and Cold Shock Domain Containing E1 (CSDE1, also known as UNR) are major regulators of type I IRES activity.
Collapse
Affiliation(s)
- Dmitry E. Andreev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Michael Niepmann
- Institute of Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, Germany
| | - Ivan N. Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Correspondence:
| |
Collapse
|
5
|
Charpentier M, Dupré E, Fortun A, Briand F, Maillasson M, Com E, Pineau C, Labarrière N, Rabu C, Lang F. hnRNP-A1 binds to the IRES of MELOE-1 antigen to promote MELOE-1 translation in stressed melanoma cells. Mol Oncol 2022; 16:594-606. [PMID: 34418284 PMCID: PMC8807352 DOI: 10.1002/1878-0261.13088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/05/2021] [Accepted: 08/20/2021] [Indexed: 12/29/2022] Open
Abstract
The major challenge in antigen-specific immunotherapy of cancer is to select the most relevant tumor antigens to target. To this aim, understanding their mode of expression by tumor cells is critical. We previously identified a melanoma-specific antigen, melanoma-overexpressed antigen 1 (MELOE-1)-coded for by a long noncoding RNA-whose internal ribosomal entry sequence (IRES)-dependent translation is restricted to tumor cells. This restricted expression is associated with the presence of a broad-specific T-cell repertoire that is involved in tumor immunosurveillance in melanoma patients. In the present work, we explored the translation control of MELOE-1 and provide evidence that heterogeneous nuclear ribonucleoprotein A1 (hnRNP-A1) binds to the MELOE-1 IRES and acts as an IRES trans-activating factor (ITAF) to promote the translation of MELOE-1 in melanoma cells. In addition, we showed that endoplasmic reticulum (ER) stress induced by thapsigargin, which promotes hnRNP-A1 cytoplasmic translocation, enhances MELOE-1 translation and recognition of melanoma cells by a MELOE-1-specific T-cell clone. These findings suggest that pharmacological stimulation of stress pathways may enhance the efficacy of immunotherapies targeting stress-induced tumor antigens such as MELOE-1.
Collapse
Affiliation(s)
| | - Emilie Dupré
- InsermLabEx IGOCRCINAUniversité de NantesNantesFrance
| | - Agnès Fortun
- InsermLabEx IGOCRCINAUniversité de NantesNantesFrance
| | | | - Mike Maillasson
- InsermLabEx IGOCRCINAUniversité de NantesNantesFrance
- InsermCNRSSFR SantéInserm UMS 016CNRS UMS 3556Université de NantesNantesFrance
| | - Emmanuelle Com
- InsermEHESPIrset (Institut de recherche en santé, environnement et travail) – UMR‐S 1085Univ RennesRennesFrance
- ProtimBiosit – UMS 3480US‐S 018Univ RennesRennesFrance
| | - Charles Pineau
- InsermEHESPIrset (Institut de recherche en santé, environnement et travail) – UMR‐S 1085Univ RennesRennesFrance
- ProtimBiosit – UMS 3480US‐S 018Univ RennesRennesFrance
| | | | | | - François Lang
- InsermLabEx IGOCRCINAUniversité de NantesNantesFrance
| |
Collapse
|
6
|
Bera A, Lewis SM. Regulation of Epithelial-to-Mesenchymal Transition by Alternative Translation Initiation Mechanisms and Its Implications for Cancer Metastasis. Int J Mol Sci 2020; 21:ijms21114075. [PMID: 32517298 PMCID: PMC7312463 DOI: 10.3390/ijms21114075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
Translation initiation plays a critical role in the regulation of gene expression for development and disease conditions. During the processes of development and disease, cells select specific mRNAs to be translated by controlling the use of diverse translation initiation mechanisms. Cells often switch translation initiation from a cap-dependent to a cap-independent mechanism during epithelial-to-mesenchymal transition (EMT), a process that plays an important role in both development and disease. EMT is involved in tumor metastasis because it leads to cancer cell migration and invasion, and is also associated with chemoresistance. In this review we will provide an overview of both the internal ribosome entry site (IRES)-dependent and N6-methyladenosine (m6A)-mediated translation initiation mechanisms and discuss how cap-independent translation enables cells from primary epithelial tumors to achieve a motile mesenchymal-like phenotype, which in turn drives tumor metastasis.
Collapse
Affiliation(s)
- Amit Bera
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada;
| | - Stephen M. Lewis
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada;
- Department of Chemistry & Biochemistry, Université de Moncton, Moncton, NB E1A 3E9, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
- Correspondence: ; Tel.: +1-506-869-2892
| |
Collapse
|
7
|
Abstract
Translation of the hepatitis C virus (HCV) RNA genome is regulated by the internal ribosome entry site (IRES), located in the 5’-untranslated region (5′UTR) and part of the core protein coding sequence, and by the 3′UTR. The 5′UTR has some highly conserved structural regions, while others can assume different conformations. The IRES can bind to the ribosomal 40S subunit with high affinity without any other factors. Nevertheless, IRES activity is modulated by additional cis sequences in the viral genome, including the 3′UTR and the cis-acting replication element (CRE). Canonical translation initiation factors (eIFs) are involved in HCV translation initiation, including eIF3, eIF2, eIF1A, eIF5, and eIF5B. Alternatively, under stress conditions and limited eIF2-Met-tRNAiMet availability, alternative initiation factors such as eIF2D, eIF2A, and eIF5B can substitute for eIF2 to allow HCV translation even when cellular mRNA translation is downregulated. In addition, several IRES trans-acting factors (ITAFs) modulate IRES activity by building large networks of RNA-protein and protein–protein interactions, also connecting 5′- and 3′-ends of the viral RNA. Moreover, some ITAFs can act as RNA chaperones that help to position the viral AUG start codon in the ribosomal 40S subunit entry channel. Finally, the liver-specific microRNA-122 (miR-122) stimulates HCV IRES-dependent translation, most likely by stabilizing a certain structure of the IRES that is required for initiation.
Collapse
|
8
|
Benavides-Serrato A, Saunders JT, Holmes B, Nishimura RN, Lichtenstein A, Gera J. Repurposing Potential of Riluzole as an ITAF Inhibitor in mTOR Therapy Resistant Glioblastoma. Int J Mol Sci 2020; 21:ijms21010344. [PMID: 31948038 PMCID: PMC6981868 DOI: 10.3390/ijms21010344] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/27/2019] [Accepted: 12/31/2019] [Indexed: 12/17/2022] Open
Abstract
Internal ribosome entry site (IRES)-mediated protein synthesis has been demonstrated to play an important role in resistance to mechanistic target of rapamycin (mTOR) targeted therapies. Previously, we have demonstrated that the IRES trans-acting factor (ITAF), hnRNP A1 is required to promote IRES activity and small molecule inhibitors which bind specifically to this ITAF and curtail IRES activity, leading to mTOR inhibitor sensitivity. Here we report the identification of riluzole (Rilutek®), an FDA-approved drug for amyotrophic lateral sclerosis (ALS), via an in silico docking analysis of FDA-approved compounds, as an inhibitor of hnRNP A1. In a riluzole-bead coupled binding assay and in surface plasmon resonance imaging analyses, riluzole was found to directly bind to hnRNP A1 and inhibited IRES activity via effects on ITAF/RNA-binding. Riluzole also demonstrated synergistic anti-glioblastoma (GBM) affects with mTOR inhibitors in vitro and in GBM xenografts in mice. These data suggest that repurposing riluzole, used in conjunction with mTOR inhibitors, may serve as an effective therapeutic option in glioblastoma.
Collapse
Affiliation(s)
- Angelica Benavides-Serrato
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA 91343, USA
| | - Jacquelyn T. Saunders
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA 91343, USA
| | - Brent Holmes
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA 91343, USA
| | - Robert N. Nishimura
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA 91343, USA
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Alan Lichtenstein
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA 91343, USA
- Jonnson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA 90095, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Joseph Gera
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA 91343, USA
- Jonnson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA 90095, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA 90095, USA
- Correspondence: ; Tel.: +00-1-818-895-9416
| |
Collapse
|
9
|
Yang Y, Wang Z. IRES-mediated cap-independent translation, a path leading to hidden proteome. J Mol Cell Biol 2019; 11:911-919. [PMID: 31504667 PMCID: PMC6884710 DOI: 10.1093/jmcb/mjz091] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/05/2019] [Accepted: 07/18/2019] [Indexed: 01/06/2023] Open
Abstract
Most eukaryotic mRNAs are translated in a cap-dependent fashion; however, under stress conditions, the cap-independent translation driven by internal ribosomal entry sites (IRESs) can serve as an alternative mechanism for protein production. Many IRESs have been discovered from viral or cellular mRNAs to promote ribosome assembly and initiate translation by recruiting different trans-acting factors. Although the mechanisms of translation initiation driven by viral IRESs are relatively well understood, the existence of cellular IRESs is still under debate due to the limitations of translation reporter systems used to assay IRES activities. A recent screen identified > 1000 putative IRESs from viral and human mRNAs, expanding the scope and mechanism for cap-independent translation. Additionally, a large number of circular RNAs lacking free ends were identified in eukaryotic cells, many of which are found to be translated through IRESs. These findings suggest that IRESs may play a previously unappreciated role in driving translation of the new type of mRNA, implying a hidden proteome produced from cap-independent translation.
Collapse
Affiliation(s)
- Yun Yang
- CAS Key Laboratory of Computational Biology, Biomedical Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, Biomedical Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| |
Collapse
|
10
|
Godet AC, David F, Hantelys F, Tatin F, Lacazette E, Garmy-Susini B, Prats AC. IRES Trans-Acting Factors, Key Actors of the Stress Response. Int J Mol Sci 2019; 20:ijms20040924. [PMID: 30791615 PMCID: PMC6412753 DOI: 10.3390/ijms20040924] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 12/16/2022] Open
Abstract
The cellular stress response corresponds to the molecular changes that a cell undergoes in response to various environmental stimuli. It induces drastic changes in the regulation of gene expression at transcriptional and posttranscriptional levels. Actually, translation is strongly affected with a blockade of the classical cap-dependent mechanism, whereas alternative mechanisms are activated to support the translation of specific mRNAs. A major mechanism involved in stress-activated translation is the internal ribosome entry site (IRES)-driven initiation. IRESs, first discovered in viral mRNAs, are present in cellular mRNAs coding for master regulators of cell responses, whose expression must be tightly controlled. IRESs allow the translation of these mRNAs in response to different stresses, including DNA damage, amino-acid starvation, hypoxia or endoplasmic reticulum stress, as well as to physiological stimuli such as cell differentiation or synapse network formation. Most IRESs are regulated by IRES trans-acting factor (ITAFs), exerting their action by at least nine different mechanisms. This review presents the history of viral and cellular IRES discovery as well as an update of the reported ITAFs regulating cellular mRNA translation and of their different mechanisms of action. The impact of ITAFs on the coordinated expression of mRNA families and consequences in cell physiology and diseases are also highlighted.
Collapse
Affiliation(s)
- Anne-Claire Godet
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florian David
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Fransky Hantelys
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florence Tatin
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Eric Lacazette
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Barbara Garmy-Susini
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Anne-Catherine Prats
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| |
Collapse
|
11
|
James CC, Smyth JW. Alternative mechanisms of translation initiation: An emerging dynamic regulator of the proteome in health and disease. Life Sci 2018; 212:138-144. [PMID: 30290184 DOI: 10.1016/j.lfs.2018.09.054] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/18/2018] [Accepted: 09/27/2018] [Indexed: 01/06/2023]
Abstract
Eukaryotic mRNAs were historically thought to rely exclusively on recognition and binding of their 5' cap by initiation factors to effect protein translation. While internal ribosome entry sites (IRESs) are well accepted as necessary for the cap-independent translation of many viral genomes, there is now recognition that eukaryotic mRNAs also undergo non-canonical modes of translation initiation. Recently, high-throughput assays have identified thousands of mammalian transcripts with translation initiation occurring at non-canonical start codons, upstream of and within protein coding regions. In addition to IRES-mediated events, regulatory mechanisms of translation initiation have been described involving alternate 5' cap recognition, mRNA sequence elements, and ribosome selection. These mechanisms ensure translation of specific mRNAs under conditions where cap-dependent translation is shut down and contribute to pathological states including cardiac hypertrophy and cancer. Such global and gene-specific dynamic regulation of translation presents us with an increasing number of novel therapeutic targets. While these newly discovered modes of translation initiation have been largely studied in isolation, it is likely that several act on the same mRNA and exquisite coordination is necessary to maintain 'normal' translation. In this short review, we summarize the current state of knowledge of these alternative mechanisms of eukaryotic protein translation, their contribution to normal and pathological cell biology, and the potential of targeting translation initiation therapeutically in human disease.
Collapse
Affiliation(s)
- Carissa C James
- Virginia Tech Carilion Research Institute and School of Medicine, Roanoke, VA, USA; Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA, USA; Center for Heart and Regenerative Medicine, Virginia Tech Carilion Research Institute, Roanoke, VA, USA
| | - James W Smyth
- Virginia Tech Carilion Research Institute and School of Medicine, Roanoke, VA, USA; Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; Center for Heart and Regenerative Medicine, Virginia Tech Carilion Research Institute, Roanoke, VA, USA.
| |
Collapse
|
12
|
Karginov TA, Pastor DPH, Semler BL, Gomez CM. Mammalian Polycistronic mRNAs and Disease. Trends Genet 2016; 33:129-142. [PMID: 28012572 DOI: 10.1016/j.tig.2016.11.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/22/2016] [Accepted: 11/28/2016] [Indexed: 01/08/2023]
Abstract
Our understanding of gene expression has come far since the 'one-gene one-polypeptide' hypothesis proposed by Beadle and Tatum. In this review, we address the gradual recognition that a growing number of polycistronic genes, originally discovered in viruses, are being identified within the mammalian genome, and that these may provide new insights into disease mechanisms and treatment. We carried out a systematic literature review identifying 13 mammalian genes for which there is evidence for polycistronic expression via translation through an internal ribosome entry site (IRES). Although the canonical mechanism of translation initiation has been studied extensively, here we highlight a process of noncanonical translation, IRES-mediated translation, that is a growing source for understanding complex inheritance, the elucidation of disease mechanisms, and the discovery of novel therapeutic targets. Identification of additional polycistronic genes may provide new insights into disease therapy and allow for new discoveries of both translational and disease mechanisms.
Collapse
Affiliation(s)
| | | | - Bert L Semler
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, CA, USA
| | | |
Collapse
|
13
|
Holmes B, Lee J, Landon KA, Benavides-Serrato A, Bashir T, Jung ME, Lichtenstein A, Gera J. Mechanistic Target of Rapamycin (mTOR) Inhibition Synergizes with Reduced Internal Ribosome Entry Site (IRES)-mediated Translation of Cyclin D1 and c-MYC mRNAs to Treat Glioblastoma. J Biol Chem 2016; 291:14146-14159. [PMID: 27226604 DOI: 10.1074/jbc.m116.726927] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 12/18/2022] Open
Abstract
Our previous work has demonstrated an intrinsic mRNA-specific protein synthesis salvage pathway operative in glioblastoma (GBM) tumor cells that is resistant to mechanistic target of rapamycin (mTOR) inhibitors. The activation of this internal ribosome entry site (IRES)-dependent mRNA translation initiation pathway results in continued translation of critical transcripts involved in cell cycle progression in the face of global eIF-4E-mediated translation inhibition. Recently we identified compound 11 (C11), a small molecule capable of inhibiting c-MYC IRES translation as a consequence of blocking the interaction of a requisite c-MYC IRES trans-acting factor, heterogeneous nuclear ribonucleoprotein A1, with its IRES. Here we demonstrate that C11 also blocks cyclin D1 IRES-dependent initiation and demonstrates synergistic anti-GBM properties when combined with the mechanistic target of rapamycin kinase inhibitor PP242. The structure-activity relationship of C11 was investigated and resulted in the identification of IRES-J007, which displayed improved IRES-dependent initiation blockade and synergistic anti-GBM effects with PP242. Mechanistic studies with C11 and IRES-J007 revealed binding of the inhibitors within the UP1 fragment of heterogeneous nuclear ribonucleoprotein A1, and docking analysis suggested a small pocket within close proximity to RRM2 as the potential binding site. We further demonstrate that co-therapy with IRES-J007 and PP242 significantly reduces tumor growth of GBM xenografts in mice and that combined inhibitor treatments markedly reduce the mRNA translational state of cyclin D1 and c-MYC transcripts in these tumors. These data support the combined use of IRES-J007 and PP242 to achieve synergistic antitumor responses in GBM.
Collapse
Affiliation(s)
- Brent Holmes
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California 90048; Department of Research and Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, California 91343
| | - Jihye Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90048
| | - Kenna A Landon
- Department of Research and Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, California 91343
| | - Angelica Benavides-Serrato
- Department of Research and Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, California 91343
| | - Tariq Bashir
- Department of Research and Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, California 91343
| | - Michael E Jung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90048; Jonnson Comprehensive Cancer Center, University of California, Los Angeles, California 90048; Molecular Biology Institute, University of California, Los Angeles, California 90048
| | - Alan Lichtenstein
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California 90048; Department of Research and Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, California 91343; Jonnson Comprehensive Cancer Center, University of California, Los Angeles, California 90048
| | - Joseph Gera
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California 90048; Department of Research and Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, California 91343; Jonnson Comprehensive Cancer Center, University of California, Los Angeles, California 90048; Molecular Biology Institute, University of California, Los Angeles, California 90048.
| |
Collapse
|
14
|
Kunze MM, Benz F, Brauß TF, Lampe S, Weigand JE, Braun J, Richter FM, Wittig I, Brüne B, Schmid T. sST2 translation is regulated by FGF2 via an hnRNP A1-mediated IRES-dependent mechanism. Biochim Biophys Acta 2016; 1859:848-59. [PMID: 27168114 DOI: 10.1016/j.bbagrm.2016.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 04/15/2016] [Accepted: 05/05/2016] [Indexed: 11/23/2022]
Abstract
Translation is an energy-intensive process and tightly regulated. Generally, translation is initiated in a cap-dependent manner. Under stress conditions, typically found within the tumor microenvironment in association with e.g. nutrient deprivation or hypoxia, cap-dependent translation decreases, and alternative modes of translation initiation become more important. Specifically, internal ribosome entry sites (IRES) facilitate translation of specific mRNAs under otherwise translation-inhibitory conditions. This mechanism is controlled by IRES trans-acting factors (ITAF), i.e. by RNA-binding proteins, which interact with and determine the activity of selected IRESs. We aimed at characterizing the translational regulation of the IL-33 decoy receptor sST2, which was enhanced by fibroblast growth factor 2 (FGF2). We identified and verified an IRES within the 5'UTR of sST2. Furthermore, we found that MEK/ERK signaling contributes to FGF2-induced, sST2-IRES activation and translation. Determination of the sST2-5'UTR structure by in-line probing followed by deletion analyses identified 23 nucleotides within the sST2-5'UTR to be required for optimal IRES activity. Finally, we show that the RNA-binding protein heterogeneous ribonucleoprotein A1 (hnRNP A1) binds to the sST2-5'UTR, acts as an ITAF, and thus controls the activity of the sST2-IRES and consequently sST2 translation. Specifically, FGF2 enhances nuclear-cytoplasmic translocation of hnRNP A1, which requires intact MEK/ERK activity. In summary, we provide evidence that the sST2-5'UTR contains an IRES element, which is activated by a MEK/ERK-dependent increase in cytoplasmic localization of hnRNP A1 in response to FGF2, enhancing the translation of sST2.
Collapse
|
15
|
Kanda T, Ozawa M, Tsukiyama-Kohara K. IRES-mediated translation of foot-and-mouth disease virus (FMDV) in cultured cells derived from FMDV-susceptible and -insusceptible animals. BMC Vet Res 2016; 12:66. [PMID: 27036295 PMCID: PMC4815274 DOI: 10.1186/s12917-016-0694-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 03/23/2016] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Foot-and-mouth disease virus (FMDV) possess a positive sense, single stranded RNA genome. Internal ribosomal entry site (IRES) element exists within its 5' untranslated region (5'UTR) of the viral RNA. Translation of the viral RNA is initiated by internal entry of the 40S ribosome within the IRES element. This process is facilitated by cellular factors known as IRES trans-acting factors (ITAFs). Foot-and-mouth disease (FMD) is host-restricted disease for cloven-hoofed animals such as cattle and pigs, but the factors determining the host range have not been identified yet. Although, ITAFs are known to promote IRES-mediated translation, these findings were confirmed only in cells derived from FMDV-insusceptible animals so far. We evaluated and compared the IRES-mediated translation activities among cell lines derived from four different animal species using bicistronic luciferase reporter plasmid, which possesses an FMDV-IRES element between Renilla and Firefly luciferase genes. Furthermore, we analyzed the effect of the cellular factors on IRES-mediated translation by silencing the cellular factors using siRNA in both FMDV-susceptible and -insusceptible animal cells. RESULTS Our data indicated that IRES-mediated translational activity was not linked to FMDV host range. ITAF45 promoted IRES-mediated translation in all cell lines, and the effects of poly-pyrimidine tract binding protein (PTB) and eukaryotic initiation factor 4E-binding protein 1 (4E-BP1) were observed only in FMDV-susceptible cells. Thus, PTB and 4E-BP1 may influence the host range of FMDV. CONCLUSIONS IRES-mediated translation activity of FMDV was not predictive of its host range. ITAF45 promoted IRES-mediated translation in all cells, and the effects of PTB and 4E-BP1 were observed only in FMDV-susceptible cells.
Collapse
Affiliation(s)
- Takehiro Kanda
- Department of Animal Hygiene, Joint Facility of Veterinary Medicine, Kagoshima University, Kagoshima, Kagoshima, Japan
| | - Makoto Ozawa
- Department of Animal Hygiene, Joint Facility of Veterinary Medicine, Kagoshima University, Kagoshima, Kagoshima, Japan.,Transboundary Animal Disease Center, Joint Facility of Veterinary Medicine, Kagoshima University, Kagoshima, Kagoshima, Japan
| | - Kyoko Tsukiyama-Kohara
- Department of Animal Hygiene, Joint Facility of Veterinary Medicine, Kagoshima University, Kagoshima, Kagoshima, Japan. .,Transboundary Animal Disease Center, Joint Facility of Veterinary Medicine, Kagoshima University, Kagoshima, Kagoshima, Japan.
| |
Collapse
|
16
|
Abstract
BclxL is a key prosurvival factor that in addition to controlling mitochondrial membrane permeability regulates mitochondrial network dynamics. The expression of BclxL is regulated at the level of transcription, splicing and selective translation. In this study, we show that the RNA-binding protein HuR, which is known to orchestrate an anti-apoptotic cellular program, functions as a translational repressor of BclxL. We show that HuR binds directly to the 5`UTR of BclxL, and represses BclxL translation through the inhibition of its internal ribosome entry site (IRES). Reduction of HuR levels leads to the derepression of BclxL translation and subsequent rearrangement of the mitochondrial network. Our results place BclxL into the HuR-regulated operon and provide further insight into the regulation of cellular stress response by HuR.
Collapse
Affiliation(s)
- Danielle Durie
- Apoptosis Research Center, Children's Hospital of Eastern Ontario Research Institute
| | - Maria Hatzoglou
- Department of Nutrition, Case Western Reserve University, School of Medicine, Cleveland, Ohio, U.S.A
| | - Pranesh Chakraborty
- Department of Pediatrics, University of Ottawa ; Newborn Screening Ontario, Children's Hospital of Eastern Ontario, 401 Smyth Road, Ottawa, K1H 8L1, Canada
| | - Martin Holcik
- Apoptosis Research Center, Children's Hospital of Eastern Ontario Research Institute ; Department of Pediatrics, University of Ottawa
| |
Collapse
|