1
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Shichino Y, Yamaguchi T, Kashiwagi K, Mito M, Takahashi M, Ito T, Ingolia NT, Kuba K, Iwasaki S. eIF4A1 enhances LARP1-mediated translational repression during mTORC1 inhibition. Nat Struct Mol Biol 2024:10.1038/s41594-024-01321-7. [PMID: 38773334 DOI: 10.1038/s41594-024-01321-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/18/2024] [Indexed: 05/23/2024]
Abstract
Eukaryotic translation initiation factor (eIF)4A-a DEAD-box RNA-binding protein-plays an essential role in translation initiation. Recent reports have suggested helicase-dependent and helicase-independent functions for eIF4A, but the multifaceted roles of eIF4A have not been fully explored. Here we show that eIF4A1 enhances translational repression during the inhibition of mechanistic target of rapamycin complex 1 (mTORC1), an essential kinase complex controlling cell proliferation. RNA pulldown followed by sequencing revealed that eIF4A1 preferentially binds to mRNAs containing terminal oligopyrimidine (TOP) motifs, whose translation is rapidly repressed upon mTORC1 inhibition. This selective interaction depends on a La-related RNA-binding protein, LARP1. Ribosome profiling revealed that deletion of EIF4A1 attenuated the translational repression of TOP mRNAs upon mTORC1 inactivation. Moreover, eIF4A1 increases the interaction between TOP mRNAs and LARP1 and, thus, ensures stronger translational repression upon mTORC1 inhibition. Our data show the multimodality of eIF4A1 in modulating protein synthesis through an inhibitory binding partner and provide a unique example of the repressive role of a universal translational activator.
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Affiliation(s)
- Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan.
| | - Tomokazu Yamaguchi
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, Akita, Japan
- Department of Pharmacology, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Kazuhiro Kashiwagi
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Mari Takahashi
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, Akita, Japan
- Department of Pharmacology, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
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2
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Brito Querido J, Díaz-López I, Ramakrishnan V. The molecular basis of translation initiation and its regulation in eukaryotes. Nat Rev Mol Cell Biol 2024; 25:168-186. [PMID: 38052923 DOI: 10.1038/s41580-023-00624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2023] [Indexed: 12/07/2023]
Abstract
The regulation of gene expression is fundamental for life. Whereas the role of transcriptional regulation of gene expression has been studied for several decades, it has been clear over the past two decades that post-transcriptional regulation of gene expression, of which translation regulation is a major part, can be equally important. Translation can be divided into four main stages: initiation, elongation, termination and ribosome recycling. Translation is controlled mainly during its initiation, a process which culminates in a ribosome positioned with an initiator tRNA over the start codon and, thus, ready to begin elongation of the protein chain. mRNA translation has emerged as a powerful tool for the development of innovative therapies, yet the detailed mechanisms underlying the complex process of initiation remain unclear. Recent studies in yeast and mammals have started to shed light on some previously unclear aspects of this process. In this Review, we discuss the current state of knowledge on eukaryotic translation initiation and its regulation in health and disease. Specifically, we focus on recent advances in understanding the processes involved in assembling the 43S pre-initiation complex and its recruitment by the cap-binding complex eukaryotic translation initiation factor 4F (eIF4F) at the 5' end of mRNA. In addition, we discuss recent insights into ribosome scanning along the 5' untranslated region of mRNA and selection of the start codon, which culminates in joining of the 60S large subunit and formation of the 80S initiation complex.
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Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Irene Díaz-López
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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3
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Gentry RC, Ide NA, Comunale VM, Hartwick EW, Kinz-Thompson CD, Gonzalez RL. The mechanism of mRNA activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.567265. [PMID: 38014128 PMCID: PMC10680758 DOI: 10.1101/2023.11.15.567265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
During translation initiation, messenger RNA molecules must be identified and activated for loading into a ribosome. In this rate-limiting step, the heterotrimeric protein eukaryotic initiation factor eIF4F must recognize and productively interact with the 7-methylguanosine cap at the 5' end of the messenger RNA and subsequently activate the message. Despite its fundamental, regulatory role in gene expression, the molecular events underlying cap recognition and messenger RNA activation remain mysterious. Here, we generate a unique, single-molecule fluorescence imaging system to interrogate the dynamics with which eIF4F discriminates productive and non-productive locations on full-length, native messenger RNA molecules. At the single-molecule level, we observe stochastic sampling of eIF4F along the length of the messenger RNA and identify allosteric communication between the eIF4F subunits which ultimately drive cap-recognition and subsequent activation of the message. Our experiments uncover novel functions for each subunit of eIF4F and we conclude by presenting a model for messenger RNA activation which precisely defines the composition of the activated message. This model provides a general framework for understanding how messenger RNA molecules may be discriminated from one another, and how other RNA-binding proteins may control the efficiency of translation initiation.
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Affiliation(s)
- Riley C Gentry
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Nicholas A Ide
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | | | - Erik W Hartwick
- Department of Chemistry, Columbia University, New York, NY, USA
- Current Address: BioChemistry Krios Electron Microscopy Facility, Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Colin D Kinz-Thompson
- Department of Chemistry, Columbia University, New York, NY, USA
- Current Address: Department of Chemistry, Rutgers University-Newark, Newark, NJ 07102
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4
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Brina D, Ponzoni A, Troiani M, Calì B, Pasquini E, Attanasio G, Mosole S, Mirenda M, D'Ambrosio M, Colucci M, Guccini I, Revandkar A, Alajati A, Tebaldi T, Donzel D, Lauria F, Parhizgari N, Valdata A, Maddalena M, Calcinotto A, Bolis M, Rinaldi A, Barry S, Rüschoff JH, Sabbadin M, Sumanasuriya S, Crespo M, Sharp A, Yuan W, Grinu M, Boyle A, Miller C, Trotman L, Delaleu N, Fassan M, Moch H, Viero G, de Bono J, Alimonti A. The Akt/mTOR and MNK/eIF4E pathways rewire the prostate cancer translatome to secrete HGF, SPP1 and BGN and recruit suppressive myeloid cells. NATURE CANCER 2023; 4:1102-1121. [PMID: 37460872 DOI: 10.1038/s43018-023-00594-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/13/2023] [Indexed: 08/25/2023]
Abstract
Cancer is highly infiltrated by myeloid-derived suppressor cells (MDSCs). Currently available immunotherapies do not completely eradicate MDSCs. Through a genome-wide analysis of the translatome of prostate cancers driven by different genetic alterations, we demonstrate that prostate cancer rewires its secretome at the translational level to recruit MDSCs. Among different secreted proteins released by prostate tumor cells, we identified Hgf, Spp1 and Bgn as the key factors that regulate MDSC migration. Mechanistically, we found that the coordinated loss of Pdcd4 and activation of the MNK/eIF4E pathways regulate the mRNAs translation of Hgf, Spp1 and Bgn. MDSC infiltration and tumor growth were dampened in prostate cancer treated with the MNK1/2 inhibitor eFT508 and/or the AKT inhibitor ipatasertib, either alone or in combination with a clinically available MDSC-targeting immunotherapy. This work provides a therapeutic strategy that combines translation inhibition with available immunotherapies to restore immune surveillance in prostate cancer.
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Affiliation(s)
- Daniela Brina
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Adele Ponzoni
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Ima Biotech, Lille, France
| | - Martina Troiani
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Bianca Calì
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Emiliano Pasquini
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Giuseppe Attanasio
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Simone Mosole
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Michela Mirenda
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Evotec, Toulouse, France
| | - Mariantonietta D'Ambrosio
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Imperial College London, London, UK
| | - Manuel Colucci
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Ilaria Guccini
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Ajinkya Revandkar
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Abdullah Alajati
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Department of Urology, Universitätklinikum Bonn, Bonn, Germany
| | - Toma Tebaldi
- Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Deborah Donzel
- Institute of Biophysics, CNR Unit at Trento, Povo, Italy
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Povo, Italy
| | - Nahjme Parhizgari
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Biosun Pharmed, Kordan, Iran
| | - Aurora Valdata
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Martino Maddalena
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Arianna Calcinotto
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Marco Bolis
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
- Bioinformatics Core Unit, Swiss Institute of Bioinformatics, Bellinzona, Switzerland
- Computational Oncology Unit, Department of Oncology, Istituto di Richerche Farmacologiche 'Mario Negri' IRCCS, Milano, Italy
| | - Andrea Rinaldi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Simon Barry
- IMED Oncology AstraZeneca, Li Ka Shing Centre, Cambridge, UK
| | - Jan Hendrik Rüschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
| | | | - Semini Sumanasuriya
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Mateus Crespo
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Adam Sharp
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Wei Yuan
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Mathew Grinu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Alexandra Boyle
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Cynthia Miller
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Lloyd Trotman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | | | - Matteo Fassan
- Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, Italy
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
| | | | - Johann de Bono
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
- The Royal Marsden Hospital, London, UK
| | - Andrea Alimonti
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland.
- Department of Medicine, Venetian Institute of Molecular Medicine, University of Padova, Padova, Italy.
- Department of Health Sciences and Technology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland.
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5
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Lee EJ, Neppl RL. Influence of Age on Skeletal Muscle Hypertrophy and Atrophy Signaling: Established Paradigms and Unexpected Links. Genes (Basel) 2021; 12:genes12050688. [PMID: 34063658 PMCID: PMC8147613 DOI: 10.3390/genes12050688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022] Open
Abstract
Skeletal muscle atrophy in an inevitable occurrence with advancing age, and a consequence of disease including cancer. Muscle atrophy in the elderly is managed by a regimen of resistance exercise and increased protein intake. Understanding the signaling that regulates muscle mass may identify potential therapeutic targets for the prevention and reversal of muscle atrophy in metabolic and neuromuscular diseases. This review covers the major anabolic and catabolic pathways that regulate skeletal muscle mass, with a focus on recent progress and potential new players.
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6
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Abstract
RNA helicases are ubiquitous, highly conserved RNA-binding enzymes that use the energy derived from the hydrolysis of nucleoside triphosphate to modify the structure of RNA molecules and/or the functionality of ribonucleoprotein complexes. Ultimately, the action of RNA helicases results in changes in gene expression that allow the cell to perform crucial functions. In this chapter, we review established and emerging concepts for DEAD-box and DExH-box RNA helicases. We mention examples from both eukaryotic and prokaryotic systems, in order to highlight common themes and specific actions.
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Affiliation(s)
- Martina Valentini
- Faculty of Medicine, Department of Microbiology and Molecular Medicine, University of Geneva, Genève, Switzerland
| | - Patrick Linder
- Faculty of Medicine, Department of Microbiology and Molecular Medicine, University of Geneva, Genève, Switzerland.
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7
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Nelson CR, Mrozowich T, Park SM, D’souza S, Henrickson A, Vigar JRJ, Wieden HJ, Owens RJ, Demeler B, Patel TR. Human DDX17 Unwinds Rift Valley Fever Virus Non-Coding RNAs. Int J Mol Sci 2020; 22:E54. [PMID: 33374561 PMCID: PMC7793125 DOI: 10.3390/ijms22010054] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 01/20/2023] Open
Abstract
Rift Valley fever virus (RVFV) is a mosquito-transmitted virus from the Bunyaviridae family that causes high rates of mortality and morbidity in humans and ruminant animals. Previous studies indicated that DEAD-box helicase 17 (DDX17) restricts RVFV replication by recognizing two primary non-coding RNAs in the S-segment of the genome: the intergenic region (IGR) and 5' non-coding region (NCR). However, we lack molecular insights into the direct binding of DDX17 with RVFV non-coding RNAs and information on the unwinding of both non-coding RNAs by DDX17. Therefore, we performed an extensive biophysical analysis of the DDX17 helicase domain (DDX17135-555) and RVFV non-coding RNAs, IGR and 5' NCR. The homogeneity studies using analytical ultracentrifugation indicated that DDX17135-555, IGR, and 5' NCR are pure. Next, we performed small-angle X-ray scattering (SAXS) experiments, which suggested that DDX17 and both RNAs are homogenous as well. SAXS analysis also demonstrated that DDX17 is globular to an extent, whereas the RNAs adopt an extended conformation in solution. Subsequently, microscale thermophoresis (MST) experiments were performed to investigate the direct binding of DDX17 to the non-coding RNAs. The MST experiments demonstrated that DDX17 binds with the IGR and 5' NCR with a dissociation constant of 5.77 ± 0.15 µM and 9.85 ± 0.11 µM, respectively. As DDX17135-555 is an RNA helicase, we next determined if it could unwind IGR and NCR. We developed a helicase assay using MST and fluorescently-labeled oligos, which suggested DDX17135-555 can unwind both RNAs. Overall, our study provides direct evidence of DDX17135-555 interacting with and unwinding RVFV non-coding regions.
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Affiliation(s)
- Corey R. Nelson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
| | - Tyler Mrozowich
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
| | - Sean M. Park
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
| | - Simmone D’souza
- Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
| | - Justin R. J. Vigar
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
| | - Hans-Joachim Wieden
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
| | - Raymond J. Owens
- Research Complex at Harwell, R92 Rutherford Appleton Laboratories, Harwell, Oxford OX1 0QX, UK;
| | - Borries Demeler
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
- NorthWest Biophysics Consortium, University of Lethbridge, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Trushar R. Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
- Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, AB T6G 2E1, Canada
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8
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Brito Querido J, Sokabe M, Kraatz S, Gordiyenko Y, Skehel JM, Fraser CS, Ramakrishnan V. Structure of a human 48 S translational initiation complex. Science 2020; 369:1220-1227. [PMID: 32883864 DOI: 10.1126/science.aba4904] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/07/2020] [Indexed: 12/20/2022]
Abstract
A key step in translational initiation is the recruitment of the 43S preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48S initiation complex (i.e., the 48S). The 48S then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48S The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43S The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40S subunit during scanning.
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Affiliation(s)
| | - Masaaki Sokabe
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | | | | | | | - Christopher S Fraser
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA.
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9
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Emerging molecular functions and novel roles for the DEAD-box protein Dbp5/DDX19 in gene expression. Cell Mol Life Sci 2020; 78:2019-2030. [PMID: 33205304 DOI: 10.1007/s00018-020-03680-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/21/2020] [Accepted: 10/06/2020] [Indexed: 12/23/2022]
Abstract
The DEAD-box protein (DBP) Dbp5, a member of the superfamily II (SFII) helicases, has multiple reported roles in gene expression. First identified as an essential regulator of mRNA export in Saccharomyces cerevisiae, the enzyme now has reported functions in non-coding RNA export, translation, transcription, and DNA metabolism. Localization of the protein to various cellular compartments (nucleoplasm, nuclear envelope, and cytoplasm) highlights the ability of Dbp5 to modulate different stages of the RNA lifecycle. While Dbp5 has been well studied for > 20 years, several critical questions remain regarding the mechanistic principles that govern Dbp5 localization, substrate selection, and functions in gene expression. This review aims to take a holistic view of the proposed functions of Dbp5 and evaluate models that accommodate current published data.
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10
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Huggins HP, Keiper BD. Regulation of Germ Cell mRNPs by eIF4E:4EIP Complexes: Multiple Mechanisms, One Goal. Front Cell Dev Biol 2020; 8:562. [PMID: 32733883 PMCID: PMC7358283 DOI: 10.3389/fcell.2020.00562] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/15/2020] [Indexed: 11/29/2022] Open
Abstract
Translational regulation of mRNAs is critically important for proper gene expression in germ cells, gametes, and embryos. The ability of the nucleus to control gene expression in these systems may be limited due to spatial or temporal constraints, as well as the breadth of gene products they express to prepare for the rapid animal development that follows. During development germ granules are hubs of post-transcriptional regulation of mRNAs. They assemble and remodel messenger ribonucleoprotein (mRNP) complexes for translational repression or activation. Recently, mRNPs have been appreciated as discrete regulatory units, whose function is dictated by the many positive and negative acting factors within the complex. Repressed mRNPs must be activated for translation on ribosomes to introduce novel proteins into germ cells. The binding of eIF4E to interacting proteins (4EIPs) that sequester it represents a node that controls many aspects of mRNP fate including localization, stability, poly(A) elongation, deadenylation, and translational activation/repression. Furthermore, plants and animals have evolved to express multiple functionally distinct eIF4E and 4EIP variants within germ cells, giving rise to different modes of translational regulation.
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Affiliation(s)
- Hayden P Huggins
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Brett D Keiper
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
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11
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Abstract
The stage at which ribosomes are recruited to messenger RNAs (mRNAs) is an elaborate and highly regulated phase of protein synthesis. Upon completion of this step, a ribosome is positioned at an appropriate initiation codon and primed to synthesize the encoded polypeptide product. In most circumstances, this step commits the ribosome to translate the mRNA. We summarize the knowledge regarding the initiation factors implicated in this activity as well as review different mechanisms by which this process is conducted.
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Affiliation(s)
- Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada; , .,Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Oncology, McGill University, Montreal, Quebec H4A 3T2, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada; , .,Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3A 1A3, Canada
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12
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General and Target-Specific DExD/H RNA Helicases in Eukaryotic Translation Initiation. Int J Mol Sci 2020; 21:ijms21124402. [PMID: 32575790 PMCID: PMC7352612 DOI: 10.3390/ijms21124402] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
DExD (DDX)- and DExH (DHX)-box RNA helicases, named after their Asp-Glu-x-Asp/His motifs, are integral to almost all RNA metabolic processes in eukaryotic cells. They play myriad roles in processes ranging from transcription and mRNA-protein complex remodeling, to RNA decay and translation. This last facet, translation, is an intricate process that involves DDX/DHX helicases and presents a regulatory node that is highly targetable. Studies aimed at better understanding this family of conserved proteins have revealed insights into their structures, catalytic mechanisms, and biological roles. They have also led to the development of chemical modulators that seek to exploit their essential roles in diseases. Herein, we review the most recent insights on several general and target-specific DDX/DHX helicases in eukaryotic translation initiation.
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13
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Naineni SK, Itoua Maïga R, Cencic R, Putnam AA, Amador LA, Rodriguez AD, Jankowsky E, Pelletier J. A comparative study of small molecules targeting eIF4A. RNA (NEW YORK, N.Y.) 2020; 26:541-549. [PMID: 32014999 PMCID: PMC7161356 DOI: 10.1261/rna.072884.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 01/30/2020] [Indexed: 05/13/2023]
Abstract
The PI3K/Akt/mTOR kinase pathway is extensively deregulated in human cancers. One critical node under regulation of this signaling axis is eukaryotic initiation factor (eIF) 4F, a complex involved in the control of translation initiation rates. eIF4F-dependent addictions arise during tumor initiation and maintenance due to increased eIF4F activity-generally in response to elevated PI3K/Akt/mTOR signaling flux. There is thus much interest in exploring eIF4F as a small molecule target for the development of new anticancer drugs. The DEAD-box RNA helicase, eIF4A, is an essential subunit of eIF4F, and several potent small molecules (rocaglates, hippuristanol, pateamine A) affecting its activity have been identified and shown to demonstrate anticancer activity in vitro and in vivo in preclinical models. Recently, a number of new small molecules have been reported as having the capacity to target and inhibit eIF4A. Here, we undertook a comparative analysis of their biological activity and specificity relative to the eIF4A inhibitor, hippuristanol.
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Affiliation(s)
- Sai Kiran Naineni
- Department of Biochemistry, McGill University, Montreal, Québec H3G 1Y6, Canada
| | - Rayelle Itoua Maïga
- Department of Biochemistry, McGill University, Montreal, Québec H3G 1Y6, Canada
| | - Regina Cencic
- Department of Biochemistry, McGill University, Montreal, Québec H3G 1Y6, Canada
| | - Andrea A Putnam
- School of Medicine, Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Luis A Amador
- Department of Chemistry, Faculty of Natural Sciences, University of Puerto Rico, San Juan, 00931-3346, Puerto Rico
| | - Abimael D Rodriguez
- Department of Chemistry, Faculty of Natural Sciences, University of Puerto Rico, San Juan, 00931-3346, Puerto Rico
| | - Eckhard Jankowsky
- School of Medicine, Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Québec H3G 1Y6, Canada
- Department of Oncology, McGill University, Montreal, Québec H4A 3T2, Canada
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, Québec H3A 1A3, Canada
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14
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The DEAD-box RNA helicase eIF4A regulates plant development and interacts with the hnRNP LIF2L1 in Physcomitrella patens. Mol Genet Genomics 2019; 295:373-389. [PMID: 31781862 DOI: 10.1007/s00438-019-01628-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 11/20/2019] [Indexed: 12/26/2022]
Abstract
eIF4A is a RNA-stimulated ATPase and helicase. Besides its key role in regulating cap-dependent translation initiation in eukaryotes, it also performs specific functions in regulating cell cycle progression, plant growth and abiotic stress tolerance. Flowering plants encode three eIF4A paralogues, eIF4A1, eIF4A2 and eIF4A3 that share conserved sequence motifs but differ in functions. To date, however, no information is available on eIF4A in basal land plants. In this study we report that genome of the moss Physcomitrella patens encodes multiple eIF4A genes. The encoded proteins possess the highly conserved motifs characteristic of the DEAD box helicases. Spatial expression analysis shows these genes to be ubiquitously expressed in all tissue types with Pp3c6_1080V3.1 showing high expression in filamentous protonemata. Targeted deletion of conserved core motifs in Pp3c6_1080V3.1 slowed protonemata growth and resulted in dwarfing of leafy gametophores suggesting a role for Pp3c6_1080V3.1 in regulating cell division/elongation. Rapid and strong induction of Pp3c6_1080V3.1 under salt stress and slow recovery of knockout plants upon exposure to high salt further suggest Pp3c6_1080V3.1 to be involved in stress management in P. patens. Protein-protein interaction studies that show Pp3c6_1080V3.1 to interact with the Physcomitrella heterogenous ribonucleoprotein, LIF2L1, a transcriptional regulator of stress-responsive genes in Arabidopsis. The results presented in this study provide insight into evolutionary conserved functions of eIF4A and shed light on the novel link between eIF4A activities and stress mitigation pathways/RNA metabolic processes in P. patens.
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15
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Characterization of influenza H1N1 Gag virus-like particles and extracellular vesicles co-produced in HEK-293SF. Vaccine 2019; 37:7100-7107. [DOI: 10.1016/j.vaccine.2019.07.057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/06/2019] [Accepted: 07/05/2019] [Indexed: 01/02/2023]
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16
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Janapala Y, Preiss T, Shirokikh NE. Control of Translation at the Initiation Phase During Glucose Starvation in Yeast. Int J Mol Sci 2019; 20:E4043. [PMID: 31430885 PMCID: PMC6720308 DOI: 10.3390/ijms20164043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/10/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Glucose is one of the most important sources of carbon across all life. Glucose starvation is a key stress relevant to all eukaryotic cells. Glucose starvation responses have important implications in diseases, such as diabetes and cancer. In yeast, glucose starvation causes rapid and dramatic effects on the synthesis of proteins (mRNA translation). Response to glucose deficiency targets the initiation phase of translation by different mechanisms and with diverse dynamics. Concomitantly, translationally repressed mRNAs and components of the protein synthesis machinery may enter a variety of cytoplasmic foci, which also form with variable kinetics and may store or degrade mRNA. Much progress has been made in understanding these processes in the last decade, including with the use of high-throughput/omics methods of RNA and RNA:protein detection. This review dissects the current knowledge of yeast reactions to glucose starvation systematized by the stage of translation initiation, with the focus on rapid responses. We provide parallels to mechanisms found in higher eukaryotes, such as metazoans, for the most critical responses, and point out major remaining gaps in knowledge and possible future directions of research on translational responses to glucose starvation.
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Affiliation(s)
- Yoshika Janapala
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.
| | - Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
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17
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Toribio R, Díaz-López I, Boskovic J, Ventoso I. Translation initiation of alphavirus mRNA reveals new insights into the topology of the 48S initiation complex. Nucleic Acids Res 2019; 46:4176-4187. [PMID: 29415133 PMCID: PMC5934618 DOI: 10.1093/nar/gky071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 02/01/2018] [Indexed: 02/02/2023] Open
Abstract
The topology and dynamics of the scanning ribosomal 43S pre-initiation complex (PIC) bound to mRNA and initiation factors (eIFs) are probably the least understood aspects of translation initiation in eukaryotes. Recently, we described a trapping mechanism in alphavirus that stalls the PIC during scanning of viral mRNA. Using this model, we were able to snapshot for the first time the eIF4A helicase bound to mRNA in a 48S initiation complex assembled in vitro. This interaction was only detected in the presence of the natural stem loop structure (DLP) located downstream from the AUG in viral mRNA that promoted stalling of the PIC, suggesting that DLP stability was enough to jam the helicase activity of eIF4A in a fraction of assembled 48S complexes. However, a substantial proportion of DLP mRNA molecules were effectively unwound by eIF4A in vitro, an activity that alphaviruses counteract in infected cells by excluding eIF4A from viral factories. Our data indicated that eIF4A–mRNA contact occurred in (or near) the ES6S region of the 40S subunit, suggesting that incoming mRNA sequences penetrate through the ES6S region during the scanning process. We propose a topological model of the scanning PIC and how some viruses have exploited this topology to translate their mRNAs with fewer eIF requirements.
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Affiliation(s)
- René Toribio
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
| | - Irene Díaz-López
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
| | - Jasminka Boskovic
- Structural Biology Programme, Electron Microscopy Unit, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Iván Ventoso
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
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18
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Nero TM, Dalia TN, Wang JCY, Kysela DT, Bochman ML, Dalia AB. ComM is a hexameric helicase that promotes branch migration during natural transformation in diverse Gram-negative species. Nucleic Acids Res 2019; 46:6099-6111. [PMID: 29722872 PMCID: PMC6158740 DOI: 10.1093/nar/gky343] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 04/19/2018] [Indexed: 12/16/2022] Open
Abstract
Acquisition of foreign DNA by natural transformation is an important mechanism of adaptation and evolution in diverse microbial species. Here, we characterize the mechanism of ComM, a broadly conserved AAA+ protein previously implicated in homologous recombination of transforming DNA (tDNA) in naturally competent Gram-negative bacterial species. In vivo, we found that ComM was required for efficient comigration of linked genetic markers in Vibrio cholerae and Acinetobacter baylyi, which is consistent with a role in branch migration. Also, ComM was particularly important for integration of tDNA with increased sequence heterology, suggesting that its activity promotes the acquisition of novel DNA sequences. In vitro, we showed that purified ComM binds ssDNA, oligomerizes into a hexameric ring, and has bidirectional helicase and branch migration activity. Based on these data, we propose a model for tDNA integration during natural transformation. This study provides mechanistic insight into the enigmatic steps involved in tDNA integration and uncovers the function of a protein required for this conserved mechanism of horizontal gene transfer.
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Affiliation(s)
- Thomas M Nero
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Triana N Dalia
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - David T Kysela
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Ankur B Dalia
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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19
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Eliseev B, Yeramala L, Leitner A, Karuppasamy M, Raimondeau E, Huard K, Alkalaeva E, Aebersold R, Schaffitzel C. Structure of a human cap-dependent 48S translation pre-initiation complex. Nucleic Acids Res 2019; 46:2678-2689. [PMID: 29401259 PMCID: PMC5861459 DOI: 10.1093/nar/gky054] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 01/21/2018] [Indexed: 01/13/2023] Open
Abstract
Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load the mRNA onto the 43S pre-initiation complex comprising 40S and initiation factors 1, 1A, 2, 3 and 5 as well as initiator-tRNA. Binding of the mRNA is followed by mRNA scanning in the 48S pre-initiation complex, until a start codon is recognised. Here, we use a reconstituted system to prepare human 48S complexes assembled on capped mRNA in the presence of eIF4B and eIF4F. The highly purified h-48S complexes are used for cross-linking/mass spectrometry, revealing the protein interaction network in this complex. We report the electron cryo-microscopy structure of the h-48S complex at 6.3 Å resolution. While the majority of eIF4B and eIF4F appear to be flexible with respect to the ribosome, additional density is detected at the entrance of the 40S mRNA channel which we attribute to the RNA-recognition motif of eIF4B. The eight core subunits of eIF3 are bound at the 40S solvent-exposed side, as well as the subunits eIF3d, eIF3b and eIF3i. elF2 and initiator-tRNA bound to the start codon are present at the 40S intersubunit side. This cryo-EM structure represents a molecular snap-shot revealing the h-48S complex following start codon recognition.
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Affiliation(s)
- Boris Eliseev
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Lahari Yeramala
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Alexander Leitner
- ETH Zürich, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, 8093 Zürich, Switzerland
| | - Manikandan Karuppasamy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Etienne Raimondeau
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Karine Huard
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ruedi Aebersold
- ETH Zürich, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, 8093 Zürich, Switzerland.,Faculty of Science, University of Zürich, 8057 Zürich, Switzerland
| | - Christiane Schaffitzel
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France.,School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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20
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Otsuka H, Fukao A, Funakami Y, Duncan KE, Fujiwara T. Emerging Evidence of Translational Control by AU-Rich Element-Binding Proteins. Front Genet 2019; 10:332. [PMID: 31118942 PMCID: PMC6507484 DOI: 10.3389/fgene.2019.00332] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/28/2019] [Indexed: 12/27/2022] Open
Abstract
RNA-binding proteins (RBPs) are key regulators of posttranscriptional gene expression and control many important biological processes including cell proliferation, development, and differentiation. RBPs bind specific motifs in their target mRNAs and regulate mRNA fate at many steps. The AU-rich element (ARE) is one of the major cis-regulatory elements in the 3′ untranslated region (UTR) of labile mRNAs. Many of these encode factors requiring very tight regulation, such as inflammatory cytokines and growth factors. Disruption in the control of these factors’ expression can cause autoimmune diseases, developmental disorders, or cancers. Therefore, these mRNAs are strictly regulated by various RBPs, particularly ARE-binding proteins (ARE-BPs). To regulate mRNA metabolism, ARE-BPs bind target mRNAs and affect some factors on mRNAs directly, or recruit effectors, such as mRNA decay machinery and protein kinases to target mRNAs. Importantly, some ARE-BPs have stabilizing roles, whereas others are destabilizing, and ARE-BPs appear to compete with each other when binding to target mRNAs. The function of specific ARE-BPs is modulated by posttranslational modifications (PTMs) including methylation and phosphorylation, thereby providing a means for cellular signaling pathways to regulate stability of specific target mRNAs. In this review, we summarize recent studies which have revealed detailed molecular mechanisms of ARE-BP-mediated regulation of gene expression and also report on the importance of ARE-BP function in specific physiological contexts and how this relates to disease. We also propose an mRNP regulatory network based on competition between stabilizing ARE-BPs and destabilizing ARE-BPs.
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Affiliation(s)
- Hiroshi Otsuka
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | | | | | - Kent E Duncan
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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21
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Abstract
The eukaryotic translation pathway has been studied for more than four decades, but the molecular mechanisms that regulate each stage of the pathway are not completely defined. This is in part because we have very little understanding of the kinetic framework for the assembly and disassembly of pathway intermediates. Steps of the pathway are thought to occur in the subsecond to second time frame, but most assays to monitor these events require minutes to hours to complete. Understanding translational control in sufficient detail will therefore require the development of assays that can precisely monitor the kinetics of the translation pathway in real time. Here, we describe the translation pathway from the perspective of its kinetic parameters, discuss advances that are helping us move toward the goal of a rigorous kinetic understanding, and highlight some of the challenges that remain.
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22
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Translational Control of Canonical and Non-Canonical Translation Initiation Factors at the Sea Urchin Egg to Embryo Transition. Int J Mol Sci 2019; 20:ijms20030626. [PMID: 30717141 PMCID: PMC6387300 DOI: 10.3390/ijms20030626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 02/06/2023] Open
Abstract
Sea urchin early development is a powerful model to study translational regulation under physiological conditions. Fertilization triggers an activation of the translation machinery responsible for the increase of protein synthesis necessary for the completion of the first embryonic cell cycles. The cap-binding protein eIF4E, the helicase eIF4A and the large scaffolding protein eIF4G are assembled upon fertilization to form an initiation complex on mRNAs involved in cap-dependent translation initiation. The presence of these proteins in unfertilized and fertilized eggs has already been demonstrated, however data concerning the translational status of translation factors are still scarce. Using polysome fractionation, we analyzed the impact of fertilization on the recruitment of mRNAs encoding initiation factors. Strikingly, whereas the mRNAs coding eIF4E, eIF4A, and eIF4G were not recruited into polysomes at 1 h post-fertilization, mRNAs for eIF4B and for non-canonical initiation factors such as DAP5, eIF4E2, eIF4E3, or hnRNP Q, are recruited and are differentially sensitive to the activation state of the mechanistic target of rapamycin (mTOR) pathway. We discuss our results suggesting alternative translation initiation in the context of the early development of sea urchins.
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23
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Merrick WC, Pavitt GD. Protein Synthesis Initiation in Eukaryotic Cells. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a033092. [PMID: 29735639 DOI: 10.1101/cshperspect.a033092] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review summarizes our current understanding of the major pathway for the initiation phase of protein synthesis in eukaryotic cells, with a focus on recent advances. We describe the major scanning or messenger RNA (mRNA) m7G cap-dependent mechanism, which is a highly coordinated and stepwise regulated process that requires the combined action of at least 12 distinct translation factors with initiator transfer RNA (tRNA), ribosomes, and mRNAs. We limit our review to studies involving either mammalian or budding yeast cells and factors, as these represent the two best-studied experimental systems, and only include a reference to other organisms where particular insight has been gained. We close with a brief description of what we feel are some of the major unknowns in eukaryotic initiation.
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Affiliation(s)
- William C Merrick
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester M13 9PT, United Kingdom
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24
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Ali W, Shafique S, Rashid S. Structural characterization of β-catenin and RX-5902 binding to phospho-p68 RNA helicase by molecular dynamics simulation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 140:79-89. [DOI: 10.1016/j.pbiomolbio.2018.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/03/2018] [Accepted: 04/30/2018] [Indexed: 01/24/2023]
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25
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Yun SJ, Kim H, Jung SH, Kim JH, Ryu JE, Singh NJ, Jeon J, Han JK, Kim CH, Kim S, Jang SK, Kim WJ. The mechanistic insight of a specific interaction between 15d-Prostaglandin-J2 and eIF4A suggests an evolutionary conserved role across species. Biol Open 2018; 7:bio035402. [PMID: 30257829 PMCID: PMC6262856 DOI: 10.1242/bio.035402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 09/03/2018] [Indexed: 12/24/2022] Open
Abstract
15-deoxy-delta 12,14-prostaglandin J2 (15d-PGJ2) is an anti-inflammatory/anti-neoplastic prostaglandin that functions through covalent binding to cysteine residues of various target proteins. We previously showed that 15d-PGJ2 mediated anti-inflammatory responses are dependent on the translational inhibition through its interaction with eIF4A (Kim et al., 2007). Binding of 15d-PGJ2 to eIF4A specifically blocks the interaction between eIF4G and eIF4A, which leads to the formation of stress granules (SGs), which then cluster mRNAs with inhibited translation. Here, we show that the binding between 15d-PGJ2 and eIF4A specifically blocks the interaction between the MIF4G domain of eIF4G and eIF4A. To reveal the mechanism of this interaction, we used computational simulation-based docking studies and identified that the carboxyl tail of 15d-PGJ2 could stabilize the binding of 15d-PGJ2 to eIF4A through arginine 295 of eIF4A, which is the first suggestion that the 15d-PGJ2 tail plays a physiological role. Interestingly, the putative 15d-PGJ2 binding site on eiF4A is conserved across many species, suggesting a biological role. Our data propose that studying 15d-PGJ2 and its targets may uncover new therapeutic approaches in anti-inflammatory drug discovery.
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Affiliation(s)
- So Jeong Yun
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Hyunjoon Kim
- PBC, Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Seung-Hyun Jung
- Department of Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Joon Hyun Kim
- PBC, Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Jeong Eun Ryu
- PBC, Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - N Jiten Singh
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Jouhyun Jeon
- Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Jin-Kwan Han
- PBC, Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Sanguk Kim
- Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Sung Key Jang
- PBC, Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Woo Jae Kim
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5, Canada
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26
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Abstract
Translation is a key step in the regulation of gene expression and one of the most energy-consuming processes in the cell. In response to various stimuli, multiple signaling pathways converge on the translational machinery to regulate its function. To date, the roles of phosphoinositide 3-kinase (PI3K)/AKT and the mitogen-activated protein kinase (MAPK) pathways in the regulation of translation are among the best understood. Both pathways engage the mechanistic target of rapamycin (mTOR) to regulate a variety of components of the translational machinery. While these pathways regulate protein synthesis in homeostasis, their dysregulation results in aberrant translation leading to human diseases, including diabetes, neurological disorders, and cancer. Here we review the roles of the PI3K/AKT and MAPK pathways in the regulation of mRNA translation. We also highlight additional signaling mechanisms that have recently emerged as regulators of the translational apparatus.
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27
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Hashem Y, Frank J. The Jigsaw Puzzle of mRNA Translation Initiation in Eukaryotes: A Decade of Structures Unraveling the Mechanics of the Process. Annu Rev Biophys 2018; 47:125-151. [PMID: 29494255 DOI: 10.1146/annurev-biophys-070816-034034] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Translation initiation in eukaryotes is a highly regulated and rate-limiting process. It results in the assembly and disassembly of numerous transient and intermediate complexes involving over a dozen eukaryotic initiation factors (eIFs). This process culminates in the accommodation of a start codon marking the beginning of an open reading frame at the appropriate ribosomal site. Although this process has been extensively studied by hundreds of groups for nearly half a century, it has been only recently, especially during the last decade, that we have gained deeper insight into the mechanics of the eukaryotic translation initiation process. This advance in knowledge is due in part to the contributions of structural biology, which have shed light on the molecular mechanics underlying the different functions of various eukaryotic initiation factors. In this review, we focus exclusively on the contribution of structural biology to the understanding of the eukaryotic initiation process, a long-standing jigsaw puzzle that is just starting to yield the bigger picture.
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Affiliation(s)
- Yaser Hashem
- INSERM U1212, Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France;
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY 10032, USA;
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28
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Lee T, Pelletier J. The biology of DHX9 and its potential as a therapeutic target. Oncotarget 2018; 7:42716-42739. [PMID: 27034008 PMCID: PMC5173168 DOI: 10.18632/oncotarget.8446] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/16/2016] [Indexed: 12/25/2022] Open
Abstract
DHX9 is member of the DExD/H-box family of helicases with a “DEIH” sequence at its eponymous DExH-box motif. Initially purified from human and bovine cells and identified as a homologue of the Drosophila Maleless (MLE) protein, it is an NTP-dependent helicase consisting of a conserved helicase core domain, two double-stranded RNA-binding domains at the N-terminus, and a nuclear transport domain and a single-stranded DNA-binding RGG-box at the C-terminus. With an ability to unwind DNA and RNA duplexes, as well as more complex nucleic acid structures, DHX9 appears to play a central role in many cellular processes. Its functions include regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. Because of its central role in gene regulation and RNA metabolism, there are growing implications for DHX9 in human diseases and their treatment. This review will provide an overview of the structure, biochemistry, and biology of DHX9, its role in cancer and other human diseases, and the possibility of targeting DHX9 in chemotherapy.
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Affiliation(s)
- Teresa Lee
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
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29
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Andreou AZ, Harms U, Klostermeier D. eIF4B stimulates eIF4A ATPase and unwinding activities by direct interaction through its 7-repeats region. RNA Biol 2016; 14:113-123. [PMID: 27858515 DOI: 10.1080/15476286.2016.1259782] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Eukaryotic translation initiation starts with binding of the eIF4F complex to the 5'-m7G cap of the mRNA. Recruitment of the 43S pre-initiation complex (PIC), formed by the 40S ribosomal subunit and other translation initiation factors, leads to formation of the 48S PIC that then scans the 5'-untranslated region (5'-UTR) toward the start codon. The eIF4F complex consists of eIF4E, the cap binding protein, eIF4A, a DEAD-box RNA helicase that is believed to unwind secondary structures in the 5'-UTR during scanning, and eIF4G, a scaffold protein that binds to both eIF4E and eIF4A. The ATPase and helicase activities of eIF4A are jointly stimulated by eIF4G and the translation initiation factor eIF4B. Yeast eIF4B mediates recruitment of the 43S PIC to the cap-bound eIF4F complex by interacting with the 40S subunit and possibly with eIF4A. However, a direct interaction between yeast eIF4A and eIF4B has not been demonstrated yet. Here we show that eIF4B binds to eIF4A in the presence of RNA and ADPNP, independent of the presence of eIF4G. A stretch of seven moderately conserved repeats, the r1-7 region, is responsible for complex formation, for modulation of the conformational energy landscape of eIF4A by eIF4B, and for stimulating the RNA-dependent ATPase- and ATP-dependent RNA unwinding activities of eIF4A. The isolated r1-7 region only slightly stimulates eIF4A conformational changes and activities, suggesting that communication of the repeats with other regions of eIF4B is required for full stimulation of eIF4A activity, for recruitment of the PIC to the mRNA and for translation initiation.
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Affiliation(s)
| | - Ulf Harms
- a University of Muenster, Institute for Physical Chemistry , Muenster , Germany
| | - Dagmar Klostermeier
- a University of Muenster, Institute for Physical Chemistry , Muenster , Germany
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30
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Liu Z, Cho NJ. Muscarinic acetylcholine receptors mediate eIF4B phosphorylation in SNU-407 colon cancer cells. Biochem Biophys Res Commun 2016; 480:450-454. [DOI: 10.1016/j.bbrc.2016.10.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 10/19/2016] [Indexed: 01/21/2023]
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31
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Vaysse C, Philippe C, Martineau Y, Quelen C, Hieblot C, Renaud C, Nicaise Y, Desquesnes A, Pannese M, Filleron T, Escourrou G, Lawson M, Rintoul RC, Delisle MB, Pyronnet S, Brousset P, Prats H, Touriol C. Key contribution of eIF4H-mediated translational control in tumor promotion. Oncotarget 2016; 6:39924-40. [PMID: 26498689 PMCID: PMC4741870 DOI: 10.18632/oncotarget.5442] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/03/2015] [Indexed: 02/06/2023] Open
Abstract
Dysregulated expression of translation initiation factors has been associated with carcinogenesis, but underlying mechanisms remains to be fully understood. Here we show that eIF4H (eukaryotic translation initiation factor 4H), an activator of the RNA helicase eIF4A, is overexpressed in lung carcinomas and predictive of response to chemotherapy. In lung cancer cells, depletion of eIF4H enhances sensitization to chemotherapy, decreases cell migration and inhibits tumor growth in vivo, in association with reduced translation of mRNA encoding cell-proliferation (c-Myc, cyclin D1) angiogenic (FGF-2) and anti-apoptotic factors (CIAP-1, BCL-xL). Conversely, each isoform of eIF4H acts as an oncogene in NIH3T3 cells by stimulating transformation, invasion, tumor growth and resistance to drug-induced apoptosis together with increased translation of IRES-containing or structured 5′UTR mRNAs. These results demonstrate that eIF4H plays a crucial role in translational control and can promote cellular transformation by preferentially regulating the translation of potent growth and survival factor mRNAs, indicating that eIF4H is a promising new molecular target for cancer therapy.
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Affiliation(s)
- Charlotte Vaysse
- INSERM U1037, CRCT, Cancer Research Center of Toulouse, Toulouse, France.,Toulouse University, Paul Sabatier, Toulouse, France
| | - Céline Philippe
- INSERM U1037, CRCT, Cancer Research Center of Toulouse, Toulouse, France.,Toulouse University, Paul Sabatier, Toulouse, France
| | - Yvan Martineau
- INSERM U1037, CRCT, Cancer Research Center of Toulouse, Toulouse, France.,Toulouse University, Paul Sabatier, Toulouse, France
| | - Cathy Quelen
- INSERM U1037, CRCT, Cancer Research Center of Toulouse, Toulouse, France.,Toulouse University, Paul Sabatier, Toulouse, France
| | - Corinne Hieblot
- INSERM U1037, CRCT, Cancer Research Center of Toulouse, Toulouse, France.,Toulouse University, Paul Sabatier, Toulouse, France
| | - Claire Renaud
- Department of Thoracic Surgery, Rangueil-Larrey Hospital, Toulouse, France
| | - Yvan Nicaise
- Department of Pathology, CHU Rangueil, Toulouse, France
| | | | | | - Thomas Filleron
- Clinical Trial Office, Cellule Biostatistique Institut Universitaire du Cancer Toulouse, Toulouse, France
| | - Ghislaine Escourrou
- INSERM U1037, CRCT, Cancer Research Center of Toulouse, Toulouse, France.,Department of Pathology, CHU Rangueil, Toulouse, France
| | - Malcolm Lawson
- Department of Respiratory Medicine, Broomfield Hospital, Chelmsford, Essex, UK
| | - Robert C Rintoul
- Department of Thoracic Oncology, Papworth Hospital, Cambridge, UK
| | - Marie Bernadette Delisle
- INSERM U1037, CRCT, Cancer Research Center of Toulouse, Toulouse, France.,Department of Pathology, CHU Rangueil, Toulouse, France
| | - Stéphane Pyronnet
- INSERM U1037, CRCT, Cancer Research Center of Toulouse, Toulouse, France.,Toulouse University, Paul Sabatier, Toulouse, France
| | - Pierre Brousset
- INSERM U1037, CRCT, Cancer Research Center of Toulouse, Toulouse, France.,Toulouse University, Paul Sabatier, Toulouse, France.,Department of Pathology, Institut Universitaire du Cancer, Toulouse, France
| | - Hervé Prats
- INSERM U1037, CRCT, Cancer Research Center of Toulouse, Toulouse, France.,Toulouse University, Paul Sabatier, Toulouse, France
| | - Christian Touriol
- INSERM U1037, CRCT, Cancer Research Center of Toulouse, Toulouse, France.,Toulouse University, Paul Sabatier, Toulouse, France
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32
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The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q Rev Biophys 2016; 49:e11. [PMID: 27658712 DOI: 10.1017/s0033583516000056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints. The stochastic nature of biological processes would allow different pathways to occur during translation that are biased by the interaction of the ribosome with other translation factors, with many of the steps kinetically controlled. These multiple pathways and branchpoints are potential regulatory nexus, allowing gene expression to be tuned at the translational level. As research focus shifts toward eukaryotic translation, certain themes will be echoed from studies on prokaryotic translation. This review provides a general overview of the dynamic data related to prokaryotic and eukaryotic translation, in particular recent findings with single-molecule methods, complemented by biochemical, kinetic, and structural findings. We will underscore the importance of viewing the process through the viewpoints of regulation, translational control, and heterogeneous pathways.
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33
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Satoh R. [Regulation of translation initiation via signal transduction]. Nihon Yakurigaku Zasshi 2016; 147:368-369. [PMID: 27301312 DOI: 10.1254/fpj.147.368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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34
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Abstract
The past several years have seen dramatic leaps in our understanding of how gene expression is rewired at the translation level during tumorigenesis to support the transformed phenotype. This work has been driven by an explosion in technological advances and is revealing previously unimagined regulatory mechanisms that dictate functional expression of the cancer genome. In this Review we discuss emerging trends and exciting new discoveries that reveal how this translational circuitry contributes to specific aspects of tumorigenesis and cancer cell function, with a particular focus on recent insights into the role of translational control in the adaptive response to oncogenic stress conditions.
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Affiliation(s)
- Morgan L Truitt
- Department of Urology, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94158, USA
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94158, USA
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35
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Targeting the eIF4A RNA helicase as an anti-neoplastic approach. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:781-91. [DOI: 10.1016/j.bbagrm.2014.09.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 09/03/2014] [Indexed: 01/22/2023]
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36
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Nandagopal N, Roux PP. Regulation of global and specific mRNA translation by the mTOR signaling pathway. ACTA ACUST UNITED AC 2015; 3:e983402. [PMID: 26779414 DOI: 10.4161/21690731.2014.983402] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/22/2014] [Accepted: 10/29/2014] [Indexed: 11/19/2022]
Abstract
The translation of mRNA into polypeptides is a key step in eukaryotic gene expression. Translation is mostly controlled at the level of initiation, which is partly regulated by the mammalian/mechanistic target of rapamycin (mTOR) signaling pathway. Whereas mTOR controls global protein synthesis through specific effector proteins, its role in the translation of select groups of mRNAs, such as those harboring a terminal oligopyrimidine (TOP) tract at their 5' end, remains more enigmatic. In this article, we describe the current knowledge on the role of mTOR in global mRNA translation, but also focus on the potential molecular mechanisms underlying the regulation of specific translational programs.
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Affiliation(s)
- Neethi Nandagopal
- Institute for Research in Immunology and Cancer (IRIC); Université de Montréal ; Montréal, Québec, Canada
| | - Philippe P Roux
- Institute for Research in Immunology and Cancer (IRIC); Université de Montréal; Montréal, Québec, Canada; Department of Pathology and Cell Biology; Faculty of Medicine; Université de Montréal; Montréal, Québec, Canada
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37
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Abstract
Human rhinoviruses (HRV) are the major etiological agents of the common cold and asthma exacerbations, with significant worldwide health and economic impact. Although large-scale population vaccination has proved successful in limiting or even eradicating many viruses, the more than 100 distinct serotypes mean that conventional vaccination is not a feasible strategy to combat HRV. An alternative strategy is to target conserved viral proteins such as the HRV proteases, 2A(pro) and 3C(pro), the focus of this review. Necessary for host cell shutoff, virus replication, and pathogenesis, 2A(pro) and 3C(pro) are clearly viable drug targets, and indeed, 3C(pro) has been successfully targeted for treating the common cold in experimental infection. 2A(pro) and 3C(pro) are crucial for virus replication due to their role in polyprotein processing as well as cleavage of key cellular proteins to inhibit cellular transcription and translation. Intriguingly, the action of the HRV proteases also disrupts nucleocytoplasmic trafficking, contributing to HRV cytopathic effects. Improved understanding of the protease-cell interactions should enable new therapeutic approaches to be identified for drug development.
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Affiliation(s)
- Lora M Jensen
- Faculty of Education, Science, Technology and Mathematics, Centre for Research in Therapeutic Solutions, University of Canberra, 1 Kirinari Street, Bruce, Canberra, ACT, 2601, Australia
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38
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Abstract
RNA helicases of the DEAD-box family are found in all eukaryotes, most bacteria and many archaea. They play important roles in rearranging RNA-RNA and RNA-protein interactions. DEAD-box proteins are ATP-dependent RNA binding proteins and RNA-dependent ATPases. The first helicases of this large family of proteins were described in the 1980s. Since then our perception of these proteins has dramatically changed. From bona fide helicases, they became RNA binding proteins that separate duplex RNAs, in a local manner, by binding and bending the target RNA. In the present review we describe some of the experiments that were important milestones in the life of DEAD-box proteins since their birth 25 years ago.
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Affiliation(s)
- Patrick Linder
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, Genève 4, 1211, Switzerland,
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39
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Deficiency in either 4E-BP1 or 4E-BP2 augments innate antiviral immune responses. PLoS One 2014; 9:e114854. [PMID: 25531441 PMCID: PMC4273997 DOI: 10.1371/journal.pone.0114854] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 11/14/2014] [Indexed: 01/08/2023] Open
Abstract
Genetic deletion of both 4E-BP1 and 4E-BP2 was found to protect cells against viral infections. Here we demonstrate that the individual loss of either 4E-BP1 or 4E-BP2 in mouse embryonic fibroblasts (MEFs) is sufficient to confer viral resistance. shRNA-mediated silencing of 4E-BP1 or 4E-BP2 renders MEFs resistant to viruses, and compared to wild type cells, MEFs knockout for either 4E-BP1 or 4E-BP2 exhibit enhanced translation of Irf-7 and consequently increased innate immune response to viruses. Accordingly, the replication of vesicular stomatitis virus, encephalomyocarditis virus, influenza virus and Sindbis virus is markedly suppressed in these cells. Importantly, expression of either 4E-BP1 or 4E-BP2 in double knockout or respective single knockout cells diminishes their resistance to viral infection. Our data show that loss of 4E-BP1 or 4E-BP2 potentiates innate antiviral immunity. These results provide further evidence for translational control of innate immunity and support targeting translational effectors as an antiviral strategy.
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40
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Gao B, Roux PP. Translational control by oncogenic signaling pathways. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:753-65. [PMID: 25477072 DOI: 10.1016/j.bbagrm.2014.11.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 11/17/2014] [Accepted: 11/19/2014] [Indexed: 01/04/2023]
Abstract
Messenger RNA (mRNA) translation is highly regulated in cells and plays an integral role in the overall process of gene expression. The initiation phase of translation is considered to be the most rate-limiting and is often targeted by oncogenic signaling pathways to promote global protein synthesis and the selective translation of tumor-promoting mRNAs. Translational control is a crucial component of cancer development as it allows cancer cells to adapt to the altered metabolism that is generally associated with the tumor state. The phosphoinositide 3-kinase (PI3K)/Akt and Ras/mitogen-activated protein kinase (MAPK) pathways are strongly implicated in cancer etiology, and they exert their biological effects by modulating both global and specific mRNA translation. In addition to having respective translational targets, these pathways also impinge on the mechanistic/mammalian target of rapamycin (mTOR), which acts as a critical signaling node linking nutrient sensing to the coordinated regulation of cellular metabolism. mTOR is best known as a central regulator of protein synthesis and has been implicated in an increasing number of pathological conditions, including cancer. In this article, we describe the current knowledge on the roles and regulation of mRNA translation by various oncogenic signaling pathways, as well as the relevance of these molecular mechanisms to human malignancies. This article is part of a Special Issue entitled: Translation and cancer.
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Affiliation(s)
- Beichen Gao
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec, Canada
| | - Philippe P Roux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec, Canada; Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada.
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41
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Umate P, Tuteja N, Tuteja R. Genome-wide comprehensive analysis of human helicases. Commun Integr Biol 2014. [DOI: 10.4161/cib.13844] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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42
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Pisareva VP, Pisarev AV. eIF5 and eIF5B together stimulate 48S initiation complex formation during ribosomal scanning. Nucleic Acids Res 2014; 42:12052-69. [PMID: 25260592 PMCID: PMC4231746 DOI: 10.1093/nar/gku877] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
48S initiation complex (48S IC) formation is the first stage in the eukaryotic translation process. According to the canonical mechanism, 40S ribosomal subunit binds to the 5′-end of messenger RNA (mRNA) and scans its 5′-untranslated region (5′-UTR) to the initiation codon where it forms the 48S IC. Entire process is mediated by initiation factors. Here we show that eIF5 and eIF5B together stimulate 48S IC formation influencing initiation codon selection during ribosomal scanning. Initiation on non-optimal start codons—following structured 5′-UTRs, in bad AUG context, within few nucleotides from 5′-end of mRNA and CUG start codon—is the most affected. eIF5-induced hydrolysis of eIF2-bound GTP is essential for stimulation. GTP hydrolysis increases the probability that scanning ribosomal complexes will recognize and arrest scanning at a non-optimal initiation codon. Such 48S ICs are less stable owing to dissociation of eIF2*GDP from initiator tRNA, and eIF5B is then required to stabilize the initiator tRNA in the P site of 40S subunit. Alternative model that eIF5 and eIF5B cause 43S pre-initiation complex rearrangement favoring more efficient initiation codon recognition during ribosomal scanning is equally possible. Mutational analysis of eIF1A and eIF5B revealed distinct functions of eIF5B in 48S IC formation and subunit joining.
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Affiliation(s)
- Vera P Pisareva
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Ave, Brooklyn, NY 11203, USA
| | - Andrey V Pisarev
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Ave, Brooklyn, NY 11203, USA
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43
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Insights from a Paradigm Shift: How the Poly(A)-Binding Protein Brings Translating mRNAs Full Circle. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/873084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In recent years, our thinking of how the initiation of protein synthesis occurs has changed dramatically. Initiation was thought to involve only events occurring at or near the 5′-cap structure, which serves as the binding site for the cap-binding complex, a group of translation initiation factors (eIFs) that facilitate the binding of the 40 S ribosomal subunit to an mRNA. Because the poly(A)-binding protein (PABP) binds the poly(A) tail present at the 3′-terminus of an mRNA, it was long thought to play no role in translation initiation. In this review, I present evidence from my laboratory that has contributed to the paradigm shift in how we think of mRNAs during translation. The depiction of mRNAs as straight molecules in which the poly(A) tail is far from events occurring at the 5′-end has now been replaced by the concept of a circular mRNA where the interaction between PABP and the cap-binding complex bridges the termini of an mRNA and promotes translation initiation. The research from my laboratory supports the new paradigm that translation of most mRNAs requires a functional and physical interaction between the termini of an mRNA.
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44
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Harms U, Andreou AZ, Gubaev A, Klostermeier D. eIF4B, eIF4G and RNA regulate eIF4A activity in translation initiation by modulating the eIF4A conformational cycle. Nucleic Acids Res 2014; 42:7911-22. [PMID: 24848014 PMCID: PMC4081068 DOI: 10.1093/nar/gku440] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Eukaryotic translation initiation factor eIF4A is a DEAD-box helicase that resolves secondary structure elements in the 5'-UTR of mRNAs during ribosome scanning. Its RNA-stimulated ATPase and ATP-dependent helicase activities are enhanced by other translation initiation factors, but the underlying mechanisms are unclear. DEAD-box proteins alternate between open and closed conformations during RNA unwinding. The transition to the closed conformation is linked to duplex destabilization. eIF4A is a special DEAD-box protein that can adopt three different conformations, an open state in the absence of ligands, a half-open state stabilized by the translation initiation factor eIF4G and a closed state in the presence of eIF4G and eIF4B. We show here that eIF4A alone does not measurably sample the closed conformation. The translation initiation factors eIF4B and eIF4G accelerate the eIF4A conformational cycle. eIF4G increases the rate of closing more than the opening rate, and eIF4B selectively increases the closing rate. Strikingly, the rate constants and the effect of eIF4B are different for different RNAs, and are related to the presence of single-stranded regions. Modulating the kinetics of the eIF4A conformational cycle is thus central for the multi-layered regulation of its activity, and for its role as a regulatory hub in translation initiation.
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Affiliation(s)
- Ulf Harms
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Alexandra Zoi Andreou
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Airat Gubaev
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Dagmar Klostermeier
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
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45
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Human DExD/H RNA helicases: emerging roles in stress survival regulation. Clin Chim Acta 2014; 436:45-58. [PMID: 24835919 DOI: 10.1016/j.cca.2014.05.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/05/2014] [Accepted: 05/06/2014] [Indexed: 12/13/2022]
Abstract
Environmental stresses threatening cell homeostasis trigger various cellular responses ranging from the activation of survival pathways to eliciting programmed cell death. Cellular stress response highly depends on the nature and level of the insult as well as the cell type. Notably, the interplay among all these responses will ultimately determine the fate of the stressed cell. Human DExD/H RNA helicases are ubiquitous molecular motors rearranging RNA secondary structure in an ATP-dependent fashion. These highly conserved enzymes participate in nearly all aspects of cellular process involving RNA metabolism. Although numerous functions of DExD/H RNA helicases are well documented, their importance in stress response is only just becoming evident. This review outlines our current knowledge on major mechanistic themes of human DExD/H RNA helicases in response to stressful stimuli, especially on emerging molecular models for the functional roles of these enzymes in the stress survival regulation.
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46
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Ostareck DH, Naarmann-de Vries IS, Ostareck-Lederer A. DDX6 and its orthologs as modulators of cellular and viral RNA expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:659-78. [PMID: 24788243 DOI: 10.1002/wrna.1237] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/19/2014] [Accepted: 03/21/2014] [Indexed: 12/21/2022]
Abstract
DDX6 (Rck/p54), a member of the DEAD-box family of helicases, is highly conserved from unicellular eukaryotes to vertebrates. Functions of DDX6 and its orthologs in dynamic ribonucleoproteins contribute to global and transcript-specific messenger RNA (mRNA) storage, translational repression, and decay during development and differentiation in the germline and somatic cells. Its role in pathways that promote mRNA-specific alternative translation initiation has been shown to be linked to cellular homeostasis, deregulated tissue development, and the control of gene expression in RNA viruses. Recently, DDX6 was found to participate in mRNA regulation mediated by miRNA-mediated silencing. DDX6 and its orthologs have versatile functions in mRNA metabolism, which characterize them as important post-transcriptional regulators of gene expression.
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Affiliation(s)
- Dirk H Ostareck
- Experimental Research Unit, Department of Intensive Care and Intermediate Care, University Hospital, RWTH Aachen University, Aachen, Germany
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47
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Akcakanat A, Hong DS, Meric-Bernstam F. Targeting translation initiation in breast cancer. ACTA ACUST UNITED AC 2014; 2:e28968. [PMID: 26779407 PMCID: PMC4705830 DOI: 10.4161/trla.28968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/09/2014] [Accepted: 04/22/2014] [Indexed: 12/23/2022]
Abstract
Over the past 20 years, a better understanding of cancer biology, screening for early detection, improved adjuvant treatment, and targeted therapies have decreased the rate of breast cancer deaths. However, resistance to treatment is common, and new approaches are needed. Deregulation of translation initiation is associated with the commencement and progression of cancer. Often, translation initiation factors are overexpressed and the related signaling pathways activated in human tumors. Recently, a significant number of inhibitors that target translation factors and pathways have become available. These inhibitors are being tested alone or in combination with chemotherapeutic agents in clinical trials. The results are varied, and it is not yet clear which drug treatments most effectively inhibit tumor growth. This review highlights the pathways and downstream effects of the activation of translation and discusses targeting the control of translation initiation as a therapeutic approach in cancer, focusing on breast cancer clinical trials.
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Affiliation(s)
- Argun Akcakanat
- Department of Investigational Cancer Therapeutics; Houston, TX USA
| | - David S Hong
- Department of Investigational Cancer Therapeutics; Houston, TX USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics; Houston, TX USA; Department of Surgical Oncology; The University of Texas MD Anderson Cancer Center; Houston, TX USA
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48
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Abstract
Superfamily 2 helicase proteins are ubiquitous in RNA biology and have an extraordinarily broad set of functional roles. Central among these roles are the promotion of rearrangements of structured RNAs and the remodeling of ribonucleoprotein complexes (RNPs), allowing formation of native RNA structure or progression through a functional cycle of structures. Although all superfamily 2 helicases share a conserved helicase core, they are divided evolutionarily into several families, and it is principally proteins from three families, the DEAD-box, DEAH/RHA, and Ski2-like families, that function to manipulate structured RNAs and RNPs. Strikingly, there are emerging differences in the mechanisms of these proteins, both between families and within the largest family (DEAD-box), and these differences appear to be tuned to their RNA or RNP substrates and their specific roles. This review outlines basic mechanistic features of the three families and surveys individual proteins and the current understanding of their biological substrates and mechanisms.
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Affiliation(s)
- Inga Jarmoskaite
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712; ,
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Galicia-Vázquez G, Di Marco S, Lian XJ, Ma JF, Gallouzi IE, Pelletier J. Regulation of eukaryotic initiation factor 4AII by MyoD during murine myogenic cell differentiation. PLoS One 2014; 9:e87237. [PMID: 24466343 PMCID: PMC3900710 DOI: 10.1371/journal.pone.0087237] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 12/23/2013] [Indexed: 11/18/2022] Open
Abstract
Gene expression during muscle cell differentiation is tightly regulated at multiple levels, including translation initiation. The PI3K/mTOR signalling pathway exerts control over protein synthesis by regulating assembly of eukaryotic initiation factor (eIF) 4F, a heterotrimeric complex that stimulates recruitment of ribosomes to mRNA templates. One of the subunits of eIF4F, eIF4A, supplies essential helicase function during this phase of translation. The presence of two cellular eIF4A isoforms, eIF4AI and eIF4AII, has long thought to impart equivalent functions to eIF4F. However, recent experiments have alluded to distinct activities between them. Herein, we characterize distinct regulatory mechanisms between the eIF4A isoforms during muscle cell differentiation. We find that eIF4AI levels decrease during differentiation whereas eIF4AII levels increase during myofiber formation in a MyoD-dependent manner. This study characterizes a previously undefined mechanism for eIF4AII regulation in differentiation and highlights functional differences between eIF4AI and eIF4AII. Finally, RNAi-mediated alterations in eIF4AI and eIF4AII levels indicate that the myogenic process can tolerate short term reductions in eIF4AI or eIF4AII levels, but not both.
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Affiliation(s)
| | - Sergio Di Marco
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Xian J. Lian
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jennifer F. Ma
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Imed E. Gallouzi
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
- * E-mail:
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Degen M, Barron P, Natarajan E, Widlund HR, Rheinwald JG. RSK activation of translation factor eIF4B drives abnormal increases of laminin γ2 and MYC protein during neoplastic progression to squamous cell carcinoma. PLoS One 2013; 8:e78979. [PMID: 24205356 PMCID: PMC3810258 DOI: 10.1371/journal.pone.0078979] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 09/26/2013] [Indexed: 12/17/2022] Open
Abstract
Overexpression of the basement membrane protein Laminin γ2 (Lamγ2) is a feature of many epidermal and oral dysplasias and all invasive squamous cell carcinomas (SCCs). This abnormality has potential value as an immunohistochemical biomarker of premalignancy but its mechanism has remained unknown. We recently reported that Lamγ2 overexpression in culture is the result of deregulated translation controls and depends on the MAPK-RSK signaling cascade. Here we identify eIF4B as the RSK downstream effector responsible for elevated Lamγ2 as well as MYC protein in neoplastic epithelial cells. Premalignant dysplastic keratinocytes, SCC cells, and keratinocytes expressing the E6 oncoprotein of human papillomavirus (HPV) type 16 displayed MAPK-RSK and mTOR-S6K1 activation and overexpressed Lamγ2 and MYC in culture. Immunohistochemical staining of oral dysplasias and SCCs for distinct, RSK- and S6K1-specific S6 phosphorylation events revealed that their respective upstream pathways become hyperactive at the same time during neoplastic progression. However, pharmacologic kinase inhibitor studies in culture revealed that Lamγ2 and MYC overexpression depends on MAPK-RSK activity, independent of PI3K-mTOR-S6K1. eIF4B knockdown reduced Lamγ2 and MYC protein expression, consistent with the known requirement for eIF4B to translate mRNAs with long, complex 5′ untranslated regions (5′-UTRs). Accordingly, expression of a luciferase reporter construct preceded by the Lamγ2 5′-UTR proved to be RSK-dependent and mTOR-independent. These results demonstrate that RSK activation of eIF4B is causally linked to elevated Lamγ2 and MYC protein levels during neoplastic progression to invasive SCC. These findings have potential clinical significance for identifying premalignant lesions and for developing targeted drugs to treat SCC.
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Affiliation(s)
- Martin Degen
- Department of Dermatology, Brigham and Women's Hospital and Harvard Skin Disease Research Center, Boston, Massachusetts, United States of America
| | - Patricia Barron
- Department of Dermatology, Brigham and Women's Hospital and Harvard Skin Disease Research Center, Boston, Massachusetts, United States of America
| | - Easwar Natarajan
- Section of Oral and Maxillofacial Pathology, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Hans R. Widlund
- Department of Dermatology, Brigham and Women's Hospital and Harvard Skin Disease Research Center, Boston, Massachusetts, United States of America
| | - James G. Rheinwald
- Department of Dermatology, Brigham and Women's Hospital and Harvard Skin Disease Research Center, Boston, Massachusetts, United States of America
- * E-mail:
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