101
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Hulea L, Gravel SP, Morita M, Cargnello M, Uchenunu O, Im YK, Lehuédé C, Ma EH, Leibovitch M, McLaughlan S, Blouin MJ, Parisotto M, Papavasiliou V, Lavoie C, Larsson O, Ohh M, Ferreira T, Greenwood C, Bridon G, Avizonis D, Ferbeyre G, Siegel P, Jones RG, Muller W, Ursini-Siegel J, St-Pierre J, Pollak M, Topisirovic I. Translational and HIF-1α-Dependent Metabolic Reprogramming Underpin Metabolic Plasticity and Responses to Kinase Inhibitors and Biguanides. Cell Metab 2018; 28:817-832.e8. [PMID: 30244971 PMCID: PMC7252493 DOI: 10.1016/j.cmet.2018.09.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 05/18/2018] [Accepted: 08/31/2018] [Indexed: 10/28/2022]
Abstract
There is increasing interest in therapeutically exploiting metabolic differences between normal and cancer cells. We show that kinase inhibitors (KIs) and biguanides synergistically and selectively target a variety of cancer cells. Synthesis of non-essential amino acids (NEAAs) aspartate, asparagine, and serine, as well as glutamine metabolism, are major determinants of the efficacy of KI/biguanide combinations. The mTORC1/4E-BP axis regulates aspartate, asparagine, and serine synthesis by modulating mRNA translation, while ablation of 4E-BP1/2 substantially decreases sensitivity of breast cancer and melanoma cells to KI/biguanide combinations. Efficacy of the KI/biguanide combinations is also determined by HIF-1α-dependent perturbations in glutamine metabolism, which were observed in VHL-deficient renal cancer cells. This suggests that cancer cells display metabolic plasticity by engaging non-redundant adaptive mechanisms, which allows them to survive therapeutic insults that target cancer metabolism.
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Affiliation(s)
- Laura Hulea
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3A 1A3, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 1A3, Canada
| | - Simon-Pierre Gravel
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Faculté de Pharmacie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada
| | - Masahiro Morita
- Department of Molecular Medicine and Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Institute of Resource Developmental and Analysis, Kumamoto University, Kumamoto 860-8111, Japan
| | - Marie Cargnello
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3A 1A3, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 1A3, Canada; Centre de Recherche en Cancérologie de Toulouse, 31100 Toulouse, France
| | - Oro Uchenunu
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3A 1A3, Canada; Department of Experimental Medicine, McGill University, Montreal, QC H3A 1A3, Canada
| | - Young Kyuen Im
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3A 1A3, Canada; Department of Experimental Medicine, McGill University, Montreal, QC H3A 1A3, Canada
| | - Camille Lehuédé
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Experimental Medicine, McGill University, Montreal, QC H3A 1A3, Canada
| | - Eric H Ma
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Physiology, McGill University, Montreal, QC H3A 1A3, Canada
| | - Matthew Leibovitch
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3A 1A3, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 1A3, Canada
| | - Shannon McLaughlan
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3A 1A3, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 1A3, Canada
| | - Marie-José Blouin
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3A 1A3, Canada
| | - Maxime Parisotto
- Département de Chimie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | | | - Cynthia Lavoie
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 171 16 Stockholm, Sweden
| | - Michael Ohh
- Department of Laboratory Medicine and Pathobiology and Department of Biochemistry, University of Toronto, Toronto, ON M5S1A8, Canada
| | - Tiago Ferreira
- McGill University Centre for Research in Neuroscience, Montreal General Hospital, Montreal, QC H3G 1A4, Canada
| | - Celia Greenwood
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3A 1A3, Canada; Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, QC H3A 1A3, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 1A3, Canada
| | - Gaëlle Bridon
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
| | - Daina Avizonis
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
| | - Gerardo Ferbeyre
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Peter Siegel
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Russell G Jones
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Physiology, McGill University, Montreal, QC H3A 1A3, Canada
| | - William Muller
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Department of Experimental Medicine, McGill University, Montreal, QC H3A 1A3, Canada
| | - Josie Ursini-Siegel
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3A 1A3, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 1A3, Canada; Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Department of Experimental Medicine, McGill University, Montreal, QC H3A 1A3, Canada
| | - Julie St-Pierre
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Michael Pollak
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3A 1A3, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 1A3, Canada; Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Experimental Medicine, McGill University, Montreal, QC H3A 1A3, Canada.
| | - Ivan Topisirovic
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3A 1A3, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Department of Experimental Medicine, McGill University, Montreal, QC H3A 1A3, Canada.
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102
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Ernlund AW, Schneider RJ, Ruggles KV. RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics data. BMC Genomics 2018; 19:809. [PMID: 30409155 PMCID: PMC6225633 DOI: 10.1186/s12864-018-5166-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/15/2018] [Indexed: 11/29/2022] Open
Abstract
Background Translatomics data, particularly genome-wide ribosome profiling and polysome profiling, provide multiple levels of gene regulatory information that can be used to assess general transcription and translation, as well translational efficiency. The increasing popularity of these techniques has resulted in multiple algorithms to detect translational regulation, typically distributed in the form of command line tools that require a basic level of programming ability. Additionally, due to the static nature of current software, dynamic transcriptional and translational comparative analysis cannot be adequately achieved. In order to streamline hypothesis generation, investigators must have the ability to manipulate and interact with their data in real-time. Results To address the lack of integration in current software, we introduce RIVET, Ribosomal Investigation and Visualization to Evaluate Translation, an R shiny based graphical user interface for translatomics data exploration and differential analysis. RIVET can analyze either microarray or RNA sequencing data from polysome profiling and ribosome profiling experiments. RIVET provides multiple choices for statistical analysis as well as integration of transcription, translation, and translational efficiency data analytics and the ability to visualize all results dynamically. Conclusions RIVET is a user-friendly tool designed for bench scientists with little to no programming background. RIVET facilitates the data analysis of translatomics data allowing for dynamic generation of results based on user-defined inputs and publication ready visualization. We expect RIVET will allow for scientists to efficiently make more comprehensive data observations that will lead to more robust hypothesis regarding translational regulation. Electronic supplementary material The online version of this article (10.1186/s12864-018-5166-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amanda W Ernlund
- Department of Microbiology, New York University School of Medicine, New York, 10016, USA
| | - Robert J Schneider
- Department of Microbiology, New York University School of Medicine, New York, 10016, USA.
| | - Kelly V Ruggles
- Department of Medicine, Department of Translational Medicine, New York University School of Medicine, New York, 10016, USA.
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103
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Rendleman J, Cheng Z, Maity S, Kastelic N, Munschauer M, Allgoewer K, Teo G, Zhang YBM, Lei A, Parker B, Landthaler M, Freeberg L, Kuersten S, Choi H, Vogel C. New insights into the cellular temporal response to proteostatic stress. eLife 2018; 7:39054. [PMID: 30272558 PMCID: PMC6185107 DOI: 10.7554/elife.39054] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
Abstract
Maintaining a healthy proteome involves all layers of gene expression regulation. By quantifying temporal changes of the transcriptome, translatome, proteome, and RNA-protein interactome in cervical cancer cells, we systematically characterize the molecular landscape in response to proteostatic challenges. We identify shared and specific responses to misfolded proteins and to oxidative stress, two conditions that are tightly linked. We reveal new aspects of the unfolded protein response, including many genes that escape global translation shutdown. A subset of these genes supports rerouting of energy production in the mitochondria. We also find that many genes change at multiple levels, in either the same or opposing directions, and at different time points. We highlight a variety of putative regulatory pathways, including the stress-dependent alternative splicing of aminoacyl-tRNA synthetases, and protein-RNA binding within the 3’ untranslated region of molecular chaperones. These results illustrate the potential of this information-rich resource.
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Affiliation(s)
- Justin Rendleman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Zhe Cheng
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Shuvadeep Maity
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Nicolai Kastelic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mathias Munschauer
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Kristina Allgoewer
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Guoshou Teo
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Yun Bin Matteo Zhang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Amy Lei
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Brian Parker
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Integrative Research Institute for the Life Sciences, Institute of Biology, Humboldt University, Berlin, Germany
| | | | | | - Hyungwon Choi
- National University of Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
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104
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Translation Links Nutrient Availability with Inflammation. Trends Biochem Sci 2018; 43:849-852. [PMID: 30224182 DOI: 10.1016/j.tibs.2018.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 08/29/2018] [Indexed: 11/22/2022]
Abstract
Translation plays a crucial role in shaping the proteome during adaptation to various types of stress. A recent study by Gameiro and Struhl identified an inflammatory response which comprises coordination of transcriptional and translational programs, and which appears to be required for recovery from nutrient deprivation.
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105
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Peters TL, Tillotson J, Yeomans AM, Wilmore S, Lemm E, Jiménez-Romero C, Amador LA, Li L, Amin AD, Pongtornpipat P, Zerio CJ, Ambrose AJ, Paine-Murrieta G, Greninger P, Vega F, Benes CH, Packham G, Rodríguez AD, Chapman E, Schatz JH. Target-Based Screening against eIF4A1 Reveals the Marine Natural Product Elatol as a Novel Inhibitor of Translation Initiation with In Vivo Antitumor Activity. Clin Cancer Res 2018; 24:4256-4270. [PMID: 29844128 PMCID: PMC6500731 DOI: 10.1158/1078-0432.ccr-17-3645] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 04/20/2018] [Accepted: 05/21/2018] [Indexed: 12/26/2022]
Abstract
Purpose: The DEAD-box RNA helicase eIF4A1 carries out the key enzymatic step of cap-dependent translation initiation and is a well-established target for cancer therapy, but no drug against it has entered evaluation in patients. We identified and characterized a natural compound with broad antitumor activities that emerged from the first target-based screen to identify novel eIF4A1 inhibitors.Experimental Design: We tested potency and specificity of the marine compound elatol versus eIF4A1 ATPase activity. We also assessed eIF4A1 helicase inhibition, binding between the compound and the target including binding site mutagenesis, and extensive mechanistic studies in cells. Finally, we determined maximum tolerated dosing in vivo and assessed activity against xenografted tumors.Results: We found elatol is a specific inhibitor of ATP hydrolysis by eIF4A1 in vitro with broad activity against multiple tumor types. The compound inhibits eIF4A1 helicase activity and binds the target with unexpected 2:1 stoichiometry at key sites in its helicase core. Sensitive tumor cells suffer acute loss of translationally regulated proteins, leading to growth arrest and apoptosis. In contrast to other eIF4A1 inhibitors, elatol induces markers of an integrated stress response, likely an off-target effect, but these effects do not mediate its cytotoxic activities. Elatol is less potent in vitro than the well-studied eIF4A1 inhibitor silvestrol but is tolerated in vivo at approximately 100× relative dosing, leading to significant activity against lymphoma xenografts.Conclusions: Elatol's identification as an eIF4A1 inhibitor with in vivo antitumor activities provides proof of principle for target-based screening against this highly promising target for cancer therapy. Clin Cancer Res; 24(17); 4256-70. ©2018 AACR.
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Affiliation(s)
- Tara L Peters
- Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami, Miami, Florida
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | | | - Alison M Yeomans
- Somers Cancer Science Building, University of Southampton, Southampton, United Kingdom
| | - Sarah Wilmore
- University of Southampton, Southampton, United Kingdom
| | - Elizabeth Lemm
- Cancer Research UK Centre, University of Southampton, Southampton, United Kingdom
| | - Carlos Jiménez-Romero
- Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Luis A Amador
- Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Lingxiao Li
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Amit D Amin
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | | | | | | | | | - Patricia Greninger
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Francisco Vega
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Division of Hematopathology, Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida
| | - Cyril H Benes
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Graham Packham
- Cancer Research UK Centre, University of Southampton, Southampton, United Kingdom
| | - Abimael D Rodríguez
- Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Eli Chapman
- College of Pharmacy, University of Arizona, Tucson, Arizona.
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida.
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
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106
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Fonseca BD, Lahr RM, Damgaard CK, Alain T, Berman AJ. LARP1 on TOP of ribosome production. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1480. [PMID: 29722158 PMCID: PMC6214789 DOI: 10.1002/wrna.1480] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 12/27/2022]
Abstract
The ribosome is an essential unit of all living organisms that commands protein synthesis, ultimately fuelling cell growth (accumulation of cell mass) and cell proliferation (increase in cell number). The eukaryotic ribosome consists of 4 ribosomal RNAs (rRNAs) and 80 ribosomal proteins (RPs). Despite its fundamental role in every living organism, our present understanding of how higher eukaryotes produce the various ribosome components is incomplete. Uncovering the mechanisms utilized by human cells to generate functional ribosomes will likely have far-reaching implications in human disease. Recent biochemical and structural studies revealed La-related protein 1 (LARP1) as a key new player in RP production. LARP1 is an RNA-binding protein that belongs to the LARP superfamily; it controls the translation and stability of the mRNAs that encode RPs and translation factors, which are characterized by a 5' terminal oligopyrimidine (5'TOP) motif and are thus known as TOP mRNAs. The activity of LARP1 is regulated by the mammalian target of rapamycin complex 1 (mTORC1): a eukaryotic protein kinase complex that integrates nutrient sensing with mRNA translation, particularly that of TOP mRNAs. In this review, we provide an overview of the role of LARP1 in the control of ribosome production in multicellular eukaryotes. This article is categorized under: Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
| | | | | | - Tommy Alain
- Children’s Hospital of Eastern Ontario, Ottawa, ON, Canada
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107
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Dynamic Interaction of Eukaryotic Initiation Factor 4G1 (eIF4G1) with eIF4E and eIF1 Underlies Scanning-Dependent and -Independent Translation. Mol Cell Biol 2018; 38:MCB.00139-18. [PMID: 29987188 DOI: 10.1128/mcb.00139-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/26/2018] [Indexed: 11/20/2022] Open
Abstract
Translation initiation of most mRNAs involves m7G-cap binding, ribosomal scanning, and AUG selection. Initiation from an m7G-cap-proximal AUG can be bypassed resulting in leaky scanning, except for mRNAs bearing the translation initiator of short 5' untranslated region (TISU) element. m7G-cap binding is mediated by the eukaryotic initiation factor 4E (eIF4E)-eIF4G1 complex. eIF4G1 also associates with eIF1, and both promote scanning and AUG selection. Understanding of the dynamics and significance of these interactions is lacking. We report that eIF4G1 exists in two complexes, either with eIF4E or with eIF1. Using an eIF1 mutant impaired in eIF4G1 binding, we demonstrate that eIF1-eIF4G1 interaction is important for leaky scanning and for avoiding m7G-cap-proximal initiation. Intriguingly, eIF4E-eIF4G1 antagonizes the scanning promoted by eIF1-eIF4G1 and is required for TISU. In mapping the eIF1-binding site on eIF4G1, we unexpectedly found that eIF4E also binds it indirectly. These findings uncover the RNA features underlying regulation by eIF4E-eIF4G1 and eIF1-eIF4G1 and suggest that 43S ribosome transition from the m7G-cap to scanning involves relocation of eIF4G1 from eIF4E to eIF1.
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108
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Zakaria C, Sean P, Hoang HD, Leroux LP, Watson M, Workenhe ST, Hearnden J, Pearl D, Truong VT, Robichaud N, Yanagiya A, Tahmasebi S, Jafarnejad SM, Jia JJ, Pelin A, Diallo JS, Le Boeuf F, Bell JC, Mossman KL, Graber TE, Jaramillo M, Sonenberg N, Alain T. Active-site mTOR inhibitors augment HSV1-dICP0 infection in cancer cells via dysregulated eIF4E/4E-BP axis. PLoS Pathog 2018; 14:e1007264. [PMID: 30138450 PMCID: PMC6124814 DOI: 10.1371/journal.ppat.1007264] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 09/05/2018] [Accepted: 08/07/2018] [Indexed: 12/21/2022] Open
Abstract
Herpes Simplex Virus 1 (HSV1) is amongst the most clinically advanced oncolytic virus platforms. However, efficient and sustained viral replication within tumours is limiting. Rapamycin can stimulate HSV1 replication in cancer cells, but active-site dual mTORC1 and mTORC2 (mammalian target of rapamycin complex 1 and 2) inhibitors (asTORi) were shown to suppress the virus in normal cells. Surprisingly, using the infected cell protein 0 (ICP0)-deleted HSV1 (HSV1-dICP0), we found that asTORi markedly augment infection in cancer cells and a mouse mammary cancer xenograft. Mechanistically, asTORi repressed mRNA translation in normal cells, resulting in defective antiviral response but also inhibition of HSV1-dICP0 replication. asTORi also reduced antiviral response in cancer cells, however in contrast to normal cells, transformed cells and cells transduced to elevate the expression of eukaryotic initiation factor 4E (eIF4E) or to silence the repressors eIF4E binding proteins (4E-BPs), selectively maintained HSV1-dICP0 protein synthesis during asTORi treatment, ultimately supporting increased viral replication. Our data show that altered eIF4E/4E-BPs expression can act to promote HSV1-dICP0 infection under prolonged mTOR inhibition. Thus, pharmacoviral combination of asTORi and HSV1 can target cancer cells displaying dysregulated eIF4E/4E-BPs axis. Dysregulated mRNA translation occurs frequently in tumours due to elevated eIF4E expression or a hyperactive mTOR complex 1 (mTORC1) signaling pathway that results in the inactivation of the eIF4E binding proteins (4E-BPs). Targeting the mTORC1/4E-BPs/eIF4E axis is a promising strategy in cancer therapies and for preventing resistance to treatment. Enhanced mTORC1 activity also drives innate immune responses by modulating protein expression of antiviral genes. It was previously shown that the mTORC1 inhibitor rapamycin limits antiviral responses and promotes replication of oncolytic viruses within tumour tissues. Active-site dual mTORC1 and mTORC2 inhibitors (asTORi) have been developed for superior mTOR inhibition and anti-cancer potency but have not been studied in the context of oncolytic viral infection. We show here that prolonged treatment with asTORi strongly augments infection of HSV1-dICP0 in cancer cells, but not in normal cells, an effect modulated via eIF4E/4E-BP expression. Thus, cancer cells with dysregulated translation could be amenable to the pharmacoviral combination of HSV1 and asTORi treatment.
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Affiliation(s)
- Chadi Zakaria
- Goodman Cancer Centre, Department of Biochemistry, McGill University, Montreal, Canada
| | - Polen Sean
- Goodman Cancer Centre, Department of Biochemistry, McGill University, Montreal, Canada
| | - Huy-Dung Hoang
- Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Margaret Watson
- Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Samuel Tekeste Workenhe
- Department of Pathology and Molecular Medicine, MG DeGroote Institute for Infectious Disease, McMaster University, Hamilton, Ontario, Canada
| | - Jaclyn Hearnden
- Goodman Cancer Centre, Department of Biochemistry, McGill University, Montreal, Canada
| | - Dana Pearl
- Goodman Cancer Centre, Department of Biochemistry, McGill University, Montreal, Canada
| | - Vinh Tai Truong
- Goodman Cancer Centre, Department of Biochemistry, McGill University, Montreal, Canada
| | - Nathaniel Robichaud
- Goodman Cancer Centre, Department of Biochemistry, McGill University, Montreal, Canada
| | - Akiko Yanagiya
- Goodman Cancer Centre, Department of Biochemistry, McGill University, Montreal, Canada
| | - Soroush Tahmasebi
- Goodman Cancer Centre, Department of Biochemistry, McGill University, Montreal, Canada
| | | | - Jian-Jun Jia
- Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Adrian Pelin
- Center for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Jean-Simon Diallo
- Center for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Fabrice Le Boeuf
- Center for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - John Cameron Bell
- Center for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Karen Louise Mossman
- Department of Pathology and Molecular Medicine, MG DeGroote Institute for Infectious Disease, McMaster University, Hamilton, Ontario, Canada
| | - Tyson Ernst Graber
- Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Maritza Jaramillo
- INRS Institut Armand-Frappier Research Centre, Laval, Quebec, Canada
| | - Nahum Sonenberg
- Goodman Cancer Centre, Department of Biochemistry, McGill University, Montreal, Canada
- * E-mail: (NS); (TA)
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- * E-mail: (NS); (TA)
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109
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The Protozoan Parasite Toxoplasma gondii Selectively Reprograms the Host Cell Translatome. Infect Immun 2018; 86:IAI.00244-18. [PMID: 29967092 DOI: 10.1128/iai.00244-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/22/2018] [Indexed: 12/18/2022] Open
Abstract
The intracellular parasite Toxoplasma gondii promotes infection by targeting multiple host cell processes; however, whether it modulates mRNA translation is currently unknown. Here, we show that infection of primary murine macrophages with type I or II T. gondii strains causes a profound perturbation of the host cell translatome. Notably, translation of transcripts encoding proteins involved in metabolic activity and components of the translation machinery was activated upon infection. In contrast, the translational efficiency of mRNAs related to immune cell activation and cytoskeleton/cytoplasm organization was largely suppressed. Mechanistically, T. gondii bolstered mechanistic target of rapamycin (mTOR) signaling to selectively activate the translation of mTOR-sensitive mRNAs, including those with a 5'-terminal oligopyrimidine (5' TOP) motif and those encoding mitochondrion-related proteins. Consistent with parasite modulation of host mTOR-sensitive translation to promote infection, inhibition of mTOR activity suppressed T. gondii replication. Thus, selective reprogramming of host mRNA translation represents an important subversion strategy during T. gondii infection.
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Differential Requirement for Translation Initiation Factor Pathways during Ecdysone-Dependent Neuronal Remodeling in Drosophila. Cell Rep 2018; 24:2287-2299.e4. [DOI: 10.1016/j.celrep.2018.07.074] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 06/22/2018] [Accepted: 07/23/2018] [Indexed: 11/23/2022] Open
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111
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Im YK, Najyb O, Gravel SP, McGuirk S, Ahn R, Avizonis DZ, Chénard V, Sabourin V, Hudson J, Pawson T, Topisirovic I, Pollak M, St-Pierre J, Ursini-Siegel J. Interplay between ShcA Signaling and PGC-1α Triggers Targetable Metabolic Vulnerabilities in Breast Cancer. Cancer Res 2018; 78:4826-4838. [DOI: 10.1158/0008-5472.can-17-3696] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/07/2018] [Accepted: 06/18/2018] [Indexed: 11/16/2022]
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112
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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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113
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Zhong X, Persaud L, Muharam H, Francis A, Das D, Aktas BH, Sauane M. Eukaryotic Translation Initiation Factor 4A Down-Regulation Mediates Interleukin-24-Induced Apoptosis through Inhibition of Translation. Cancers (Basel) 2018; 10:cancers10050153. [PMID: 29786657 PMCID: PMC5977126 DOI: 10.3390/cancers10050153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/13/2018] [Accepted: 05/17/2018] [Indexed: 12/13/2022] Open
Abstract
Dysregulated activity of helicase eIF4A drives transformation to and maintenance of cancer cell phenotype by reprogramming cellular translation. Interleukin 24 (IL-24) is a tumor-suppressing protein, which has the ability to inhibit angiogenesis, sensitize cancer cells to chemotherapy, and induce cancer cell-specific apoptosis. In this study, we found that eIF4A is inhibited by IL-24. Consequently, selective reduction of translation was observed for mRNAs harboring strong secondary structures in their 5′-untranslated regions (5′UTRs). These mRNAs encode proteins, which function in cell survival and proliferation. Consistently, overexpression of eIF4A conferred cancer cells with resistance to IL-24-induced cell death. It has been established that inhibition of eIF4A triggers mitochondrial-mediated apoptosis. We showed that IL-24 induces eIF4A-dependent mitochondrial depolarization. We also showed that IL-24 induces Sigma 1 Receptor-dependent eIF4A down-regulation and mitochondrial depolarization. Thus, the progress of apoptosis triggered by IL-24 is characterized by a complex program of changes in regulation of several initiation factors, including the eIF4A.
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Affiliation(s)
- Xuelin Zhong
- Department of Biological Sciences, Herbert H. Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY 10468, USA.
- Department of Biology, The Graduate Center, City University of New York, 365 Fifth Avenue, Room 4315, New York, NY 10016, USA.
| | - Leah Persaud
- Department of Biological Sciences, Herbert H. Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY 10468, USA.
- Department of Biology, The Graduate Center, City University of New York, 365 Fifth Avenue, Room 4315, New York, NY 10016, USA.
| | - Hilal Muharam
- Department of Biological Sciences, Herbert H. Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY 10468, USA.
| | - Ashleigh Francis
- Department of Biological Sciences, Herbert H. Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY 10468, USA.
| | - Dibash Das
- Department of Biological Sciences, Herbert H. Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY 10468, USA.
- Department of Biology, The Graduate Center, City University of New York, 365 Fifth Avenue, Room 4315, New York, NY 10016, USA.
| | - Bertal Huseyin Aktas
- Department of Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA.
- Harvard Medical School, Laboratory for Translational Research, One Kendall Square, Building 600, 3rd Floor, Cambridge, MA 02139, USA.
| | - Moira Sauane
- Department of Biological Sciences, Herbert H. Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY 10468, USA.
- Department of Biology, The Graduate Center, City University of New York, 365 Fifth Avenue, Room 4315, New York, NY 10016, USA.
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114
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William M, Leroux LP, Chaparro V, Lorent J, Graber TE, M'Boutchou MN, Charpentier T, Fabié A, Dozois CM, Stäger S, van Kempen LC, Alain T, Larsson O, Jaramillo M. eIF4E-Binding Proteins 1 and 2 Limit Macrophage Anti-Inflammatory Responses through Translational Repression of IL-10 and Cyclooxygenase-2. THE JOURNAL OF IMMUNOLOGY 2018; 200:4102-4116. [PMID: 29712774 DOI: 10.4049/jimmunol.1701670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/10/2018] [Indexed: 01/10/2023]
Abstract
Macrophages represent one of the first lines of defense during infections and are essential for resolution of inflammation following pathogen clearance. Rapid activation or suppression of protein synthesis via changes in translational efficiency allows cells of the immune system, including macrophages, to quickly respond to external triggers or cues without de novo mRNA synthesis. The translational repressors eIF4E-binding proteins 4E-BP1 and 4E-BP2 (4E-BP1/2) are central regulators of proinflammatory cytokine synthesis during viral and parasitic infections. However, it remains to be established whether 4E-BP1/2 play a role in translational control of anti-inflammatory responses. By comparing translational efficiencies of immune-related transcripts in macrophages from wild-type and 4E-BP1/2 double-knockout mice, we found that translation of mRNAs encoding two major regulators of inflammation, IL-10 and PG-endoperoxide synthase 2/cyclooxygenase-2, is controlled by 4E-BP1/2. Genetic deletion of 4E-BP1/2 in macrophages increased endogenous IL-10 and PGE2 protein synthesis in response to TLR4 stimulation and reduced their bactericidal capacity. The molecular mechanism involves enhanced anti-inflammatory gene expression (sIl1ra, Nfil3, Arg1, Serpinb2) owing to upregulation of IL-10-STAT3 and PGE2-C/EBPβ signaling. These data provide evidence that 4E-BP1/2 limit anti-inflammatory responses in macrophages and suggest that dysregulated activity of 4E-BP1/2 might be involved in reprogramming of the translational and downstream transcriptional landscape of macrophages during pathological conditions, such as infections and cancer.
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Affiliation(s)
- Mirtha William
- Institut National de la Recherche Scientifique-Institut Armand-Frappier et Centre de Recherche sur les Interactions Hôte-Parasite, Laval, Quebec H7V 1B7, Canada
| | - Louis-Philippe Leroux
- Institut National de la Recherche Scientifique-Institut Armand-Frappier et Centre de Recherche sur les Interactions Hôte-Parasite, Laval, Quebec H7V 1B7, Canada
| | - Visnu Chaparro
- Institut National de la Recherche Scientifique-Institut Armand-Frappier et Centre de Recherche sur les Interactions Hôte-Parasite, Laval, Quebec H7V 1B7, Canada
| | - Julie Lorent
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Marie-Noël M'Boutchou
- Department of Pathology, McGill University, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada; and.,Department of Pathology and Medical Biology, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Tania Charpentier
- Institut National de la Recherche Scientifique-Institut Armand-Frappier et Centre de Recherche sur les Interactions Hôte-Parasite, Laval, Quebec H7V 1B7, Canada
| | - Aymeric Fabié
- Institut National de la Recherche Scientifique-Institut Armand-Frappier et Centre de Recherche sur les Interactions Hôte-Parasite, Laval, Quebec H7V 1B7, Canada
| | - Charles M Dozois
- Institut National de la Recherche Scientifique-Institut Armand-Frappier et Centre de Recherche sur les Interactions Hôte-Parasite, Laval, Quebec H7V 1B7, Canada
| | - Simona Stäger
- Institut National de la Recherche Scientifique-Institut Armand-Frappier et Centre de Recherche sur les Interactions Hôte-Parasite, Laval, Quebec H7V 1B7, Canada
| | - Léon C van Kempen
- Department of Pathology, McGill University, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada; and.,Department of Pathology and Medical Biology, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Maritza Jaramillo
- Institut National de la Recherche Scientifique-Institut Armand-Frappier et Centre de Recherche sur les Interactions Hôte-Parasite, Laval, Quebec H7V 1B7, Canada;
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115
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Karamysheva ZN, Tikhonova EB, Grozdanov PN, Huffman JC, Baca KR, Karamyshev A, Denison RB, MacDonald CC, Zhang K, Karamyshev AL. Polysome Profiling in Leishmania, Human Cells and Mouse Testis. J Vis Exp 2018. [PMID: 29683462 DOI: 10.3791/57600] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Proper protein expression at the right time and in the right amounts is the basis of normal cell function and survival in a fast-changing environment. For a long time, the gene expression studies were dominated by research on the transcriptional level. However, the steady-state levels of mRNAs do not correlate well with protein production, and the translatability of mRNAs varies greatly depending on the conditions. In some organisms, like the parasite Leishmania, the protein expression is regulated mostly at the translational level. Recent studies demonstrated that protein translation dysregulation is associated with cancer, metabolic, neurodegenerative and other human diseases. Polysome profiling is a powerful method to study protein translation regulation. It allows to measure the translational status of individual mRNAs or examine translation on a genome-wide scale. The basis of this technique is the separation of polysomes, ribosomes, their subunits and free mRNAs during centrifugation of a cytoplasmic lysate through a sucrose gradient. Here, we present a universal polysome profiling protocol used on three different models - parasite Leishmania major, cultured human cells and animal tissues. Leishmania cells freely grow in suspension and cultured human cells grow in adherent monolayer, while mouse testis represents an animal tissue sample. Thus, the technique is adapted to all of these sources. The protocol for the analysis of polysomal fractions includes detection of individual mRNA levels by RT-qPCR, proteins by Western blot and analysis of ribosomal RNAs by electrophoresis. The method can be further extended by examination of mRNAs association with the ribosome on a transcriptome level by deep RNA-seq and analysis of ribosome-associated proteins by mass spectroscopy of the fractions. The method can be easily adjusted to other biological models.
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Affiliation(s)
| | - Elena B Tikhonova
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center
| | - Petar N Grozdanov
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center
| | - James C Huffman
- Department of Biological Sciences, Texas Tech University; CISER (Center for the Integration of STEM Education & Research), Texas Tech University
| | - Kristen R Baca
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center; CISER (Center for the Integration of STEM Education & Research), Texas Tech University
| | - Alexander Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center
| | - R Brian Denison
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center
| | - Clinton C MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center
| | - Kai Zhang
- Department of Biological Sciences, Texas Tech University
| | - Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center;
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116
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Shirokikh NE, Preiss T. Translation initiation by cap-dependent ribosome recruitment: Recent insights and open questions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1473. [PMID: 29624880 DOI: 10.1002/wrna.1473] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 12/14/2022]
Abstract
Gene expression universally relies on protein synthesis, where ribosomes recognize and decode the messenger RNA template by cycling through translation initiation, elongation, and termination phases. All aspects of translation have been studied for decades using the tools of biochemistry and molecular biology available at the time. Here, we focus on the mechanism of translation initiation in eukaryotes, which is remarkably more complex than prokaryotic initiation and is the target of multiple types of regulatory intervention. The "consensus" model, featuring cap-dependent ribosome entry and scanning of mRNA leader sequences, represents the predominantly utilized initiation pathway across eukaryotes, although several variations of the model and alternative initiation mechanisms are also known. Recent advances in structural biology techniques have enabled remarkable molecular-level insights into the functional states of eukaryotic ribosomes, including a range of ribosomal complexes with different combinations of translation initiation factors that are thought to represent bona fide intermediates of the initiation process. Similarly, high-throughput sequencing-based ribosome profiling or "footprinting" approaches have allowed much progress in understanding the elongation phase of translation, and variants of them are beginning to reveal the remaining mysteries of initiation, as well as aspects of translation termination and ribosomal recycling. A current view on the eukaryotic initiation mechanism is presented here with an emphasis on how recent structural and footprinting results underpin axioms of the consensus model. Along the way, we further outline some contested mechanistic issues and major open questions still to be addressed. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
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117
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Terenzio M, Koley S, Samra N, Rishal I, Zhao Q, Sahoo PK, Urisman A, Marvaldi L, Oses-Prieto JA, Forester C, Gomes C, Kalinski AL, Di Pizio A, Doron-Mandel E, Perry RBT, Koppel I, Twiss JL, Burlingame AL, Fainzilber M. Locally translated mTOR controls axonal local translation in nerve injury. Science 2018; 359:1416-1421. [PMID: 29567716 PMCID: PMC6501578 DOI: 10.1126/science.aan1053] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 12/13/2017] [Accepted: 01/30/2018] [Indexed: 12/12/2022]
Abstract
How is protein synthesis initiated locally in neurons? We found that mTOR (mechanistic target of rapamycin) was activated and then up-regulated in injured axons, owing to local translation of mTOR messenger RNA (mRNA). This mRNA was transported into axons by the cell size-regulating RNA-binding protein nucleolin. Furthermore, mTOR controlled local translation in injured axons. This included regulation of its own translation and that of retrograde injury signaling molecules such as importin β1 and STAT3 (signal transducer and activator of transcription 3). Deletion of the mTOR 3' untranslated region (3'UTR) in mice reduced mTOR in axons and decreased local translation after nerve injury. Both pharmacological inhibition of mTOR in axons and deletion of the mTOR 3'UTR decreased proprioceptive neuronal survival after nerve injury. Thus, mRNA localization enables spatiotemporal control of mTOR pathways regulating local translation and long-range intracellular signaling.
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Affiliation(s)
- Marco Terenzio
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sandip Koley
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nitzan Samra
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ida Rishal
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Qian Zhao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Pabitra K Sahoo
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Anatoly Urisman
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Letizia Marvaldi
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Craig Forester
- Division of Pediatric Allergy, Immunology and Bone Marrow Transplantation, University of California, San Francisco, CA 94158, USA
| | - Cynthia Gomes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Ashley L Kalinski
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Agostina Di Pizio
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ella Doron-Mandel
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Ben-Tov Perry
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Indrek Koppel
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jeffery L Twiss
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Mike Fainzilber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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118
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Leppek K, Das R, Barna M. Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat Rev Mol Cell Biol 2018; 19:158-174. [PMID: 29165424 PMCID: PMC5820134 DOI: 10.1038/nrm.2017.103] [Citation(s) in RCA: 482] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5' untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5' UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms.
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Affiliation(s)
- Kathrin Leppek
- Department of Developmental Biology, Stanford University, Stanford, California 94305, USA
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Rhiju Das
- Departments of Biochemistry and Physics, Stanford University, Stanford, California 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, California 94305, USA
- Department of Genetics, Stanford University, Stanford, California 94305, USA
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119
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Andreev DE, Dmitriev SE, Loughran G, Terenin IM, Baranov PV, Shatsky IN. Translation control of mRNAs encoding mammalian translation initiation factors. Gene 2018; 651:174-182. [PMID: 29414693 DOI: 10.1016/j.gene.2018.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/25/2018] [Accepted: 02/04/2018] [Indexed: 10/18/2022]
Abstract
Eukaryotic cells evolved highly complex and accurate protein synthesis machinery that is finely tuned by various signaling pathways. Dysregulation of translation is a hallmark of many diseases, including cancer, and thus pharmacological approaches to modulate translation become very promising. While there has been much progress in our understanding of mammalian mRNA-specific translation control, surprisingly, relatively little is known about whether and how the protein components of the translation machinery shape translation of their own mRNAs. Here we analyze mammalian mRNAs encoding components of the translation initiation machinery for potential regulatory features such as 5'TOP motifs, TISU motifs, poor start codon nucleotide context and upstream open reading frames.
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Affiliation(s)
- Dmitri E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Department of Biochemistry, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
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120
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A Unique ISR Program Determines Cellular Responses to Chronic Stress. Mol Cell 2017; 68:885-900.e6. [PMID: 29220654 DOI: 10.1016/j.molcel.2017.11.007] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 09/27/2017] [Accepted: 11/07/2017] [Indexed: 02/05/2023]
Abstract
The integrated stress response (ISR) is a homeostatic mechanism induced by endoplasmic reticulum (ER) stress. In acute/transient ER stress, decreased global protein synthesis and increased uORF mRNA translation are followed by normalization of protein synthesis. Here, we report a dramatically different response during chronic ER stress. This chronic ISR program is characterized by persistently elevated uORF mRNA translation and concurrent gene expression reprogramming, which permits simultaneous stress sensing and proteostasis. The program includes PERK-dependent switching to an eIF3-dependent translation initiation mechanism, resulting in partial, but not complete, translational recovery, which, together with transcriptional reprogramming, selectively bolsters expression of proteins with ER functions. Coordination of transcriptional and translational reprogramming prevents ER dysfunction and inhibits "foamy cell" development, thus establishing a molecular basis for understanding human diseases associated with ER dysfunction.
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121
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Lindqvist LM, Tandoc K, Topisirovic I, Furic L. Cross-talk between protein synthesis, energy metabolism and autophagy in cancer. Curr Opin Genet Dev 2017; 48:104-111. [PMID: 29179096 DOI: 10.1016/j.gde.2017.11.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/05/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Abstract
Translation is a pivotal step in the regulation of gene expression as well as one of the most energy consuming processes in the cell. Dysregulation of translation caused by the aberrant function of upstream signaling pathways and/or perturbations in the expression or function of components of the translation machinery is frequent in cancer. In this review, we discuss emerging findings that highlight hitherto unappreciated aspects of signaling to the translation apparatus with the particular focus on emerging connections between protein synthesis, autophagy and energy homeostasis in cancer.
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Affiliation(s)
- Lisa M Lindqvist
- Cell Signalling and Cell Death Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Melbourne, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3050, Australia.
| | - Kristofferson Tandoc
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada H3T 1E2; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3T2, Canada
| | - Ivan Topisirovic
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada H3T 1E2; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3T2, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada; Department of Biochemistry, McGill University, Montreal, QC H4A 3T2, Canada
| | - Luc Furic
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia.
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122
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Chu J, Ramon Y Cajal S, Sonenberg N, Pelletier J. Eukaryotic initiation factor 4F-sidestepping resistance mechanisms arising from expression heterogeneity. Curr Opin Genet Dev 2017; 48:89-96. [PMID: 29169064 DOI: 10.1016/j.gde.2017.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 12/31/2022]
Abstract
There is enormous diversity in the genetic makeup and gene expression profiles between and within tumors. This heterogeneity leads to phenotypic variation and is a major mechanism of resistance to molecular targeted therapies. Here we describe a conceptual framework for targeting eukaryotic initiation factor (eIF) 4F in cancer-an essential complex that drives and promotes multiple Cancer Hallmarks. The unique nature of eIF4F and its druggability bypasses several of the heterogeneity issues that plague molecular targeted drugs developed for cancer therapy.
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Affiliation(s)
- Jennifer Chu
- Departments of Biochemistry and Oncology, McGill University, Montreal, Quebec, Canada
| | - Santiago Ramon Y Cajal
- Pathology Department, Vall d'Hebron Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain; Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Spain
| | - Nahum Sonenberg
- Departments of Biochemistry and Oncology, McGill University, Montreal, Quebec, Canada; Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
| | - Jerry Pelletier
- Departments of Biochemistry and Oncology, McGill University, Montreal, Quebec, Canada; Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada.
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de la Parra C, Walters BA, Geter P, Schneider RJ. Translation initiation factors and their relevance in cancer. Curr Opin Genet Dev 2017; 48:82-88. [PMID: 29153484 DOI: 10.1016/j.gde.2017.11.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/24/2017] [Accepted: 11/01/2017] [Indexed: 12/31/2022]
Abstract
Deregulation of several translation initiation factors occurs in numerous types of cancers. Translation initiation factors are not merely ancillary players in cancer development and progression, but rather, they are key participants in cellular transformation and tumor development. In fact, the altered expression of translation initiation factors is involved in cancer cell survival, metastasis and tumor angiogenesis. Although the exact mechanisms remain to be fully characterized, translation initiation factors comprise novel targets for pharmacologic intervention. Here we review the most recently established roles of initiation factors in cancer development and progression, as well as unique methods used to study translational regulation.
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Affiliation(s)
- Columba de la Parra
- Department of Microbiology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Beth A Walters
- Department of Microbiology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Phillip Geter
- Department of Microbiology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Robert J Schneider
- Department of Microbiology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
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124
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Biffo S, Manfrini N, Ricciardi S. Crosstalks between translation and metabolism in cancer. Curr Opin Genet Dev 2017; 48:75-81. [PMID: 29153483 DOI: 10.1016/j.gde.2017.10.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 12/26/2022]
Abstract
Albeit cancer patients' heterogeneity, all tumor cells have alterations of both metabolism and translation. The simplest explanation for this common feature is that several oncogenes coordinate a translational and metabolic reprogramming that is necessary for tumor cells to thrive. Overall, at least three oncogenic pathways, namely c-Myc, RAS and PI3K-mTOR, are known to affect both translation and metabolism by stimulating glycolysis and protein synthesis. The crosstalk between metabolite production and the translational machinery is, instead, less understood. What is known is that, on one side, translation initiation factors, such as eIF4E and eIF6, drive tumor growth and regulate metabolism through selective translation of nucleotide biosynthesis, glycolysis and fatty acid synthesis rate-limiting mRNAs, and on the other, that nutrient levels regulate the translational machinery by inducing full activity of translation factors. Therefore, translation and metabolism offer several therapeutic targets to be fully exploited in future studies.
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Affiliation(s)
- Stefano Biffo
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", INGM, 20122 Milano, Italy; Department of Biosciences, University of Milano, 20133 Milano, Italy.
| | - Nicola Manfrini
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", INGM, 20122 Milano, Italy
| | - Sara Ricciardi
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", INGM, 20122 Milano, Italy
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125
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Quek H, Lim YC, Lavin MF, Roberts TL. PIKKing a way to regulate inflammation. Immunol Cell Biol 2017; 96:8-20. [DOI: 10.1111/imcb.1001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/31/2017] [Accepted: 09/02/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Hazel Quek
- The University of Queensland Centre for Clinical Research; Herston Qld Australia
- QIMR Berghofer Medical Research Institute; Herston Qld Australia
| | - Yi Chieh Lim
- QIMR Berghofer Medical Research Institute; Herston Qld Australia
| | - Martin F Lavin
- The University of Queensland Centre for Clinical Research; Herston Qld Australia
| | - Tara L Roberts
- The University of Queensland Centre for Clinical Research; Herston Qld Australia
- The Ingham Institute for Applied Medical Research and School of Medicine; Western Sydney University; Liverpool New South Wales Australia
- South West Sydney Clinical School; Sydney UNSW Australia
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126
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Harvey RF, Willis AE. Post-transcriptional control of stress responses in cancer. Curr Opin Genet Dev 2017; 48:30-35. [PMID: 29100210 DOI: 10.1016/j.gde.2017.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/04/2017] [Accepted: 10/11/2017] [Indexed: 01/30/2023]
Abstract
The processes by which the canonical protein synthesis machinery is modified by environmental stresses to allow healthy cells to respond to external conditions to maintain homeostasis, are frequently hijacked by tumour cells to enhance their survival. Two major stress response pathways that play a major role in this regard are the unfolded protein response (UPR) and the DNA damage response (DDR). Recent data have shown that key proteins which coordinate post-transcriptional control, and which are regulated by signalling through the UPR and DDR, are upregulated in cancers and that targeting these proteins/pathways will provide new therapeutic avenues for cancer treatments.
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Affiliation(s)
- Robert F Harvey
- Medical Research Council Toxicology Unit, Lancaster Rd, Leicester LE1 9HN, UK
| | - Anne E Willis
- Medical Research Council Toxicology Unit, Lancaster Rd, Leicester LE1 9HN, UK.
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127
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Leibovitch M, Topisirovic I. Dysregulation of mRNA translation and energy metabolism in cancer. Adv Biol Regul 2017; 67:30-39. [PMID: 29150352 DOI: 10.1016/j.jbior.2017.11.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 10/26/2017] [Accepted: 11/01/2017] [Indexed: 12/20/2022]
Abstract
Dysregulated mRNA translation and aberrant energy metabolism are frequent in cancer. Considering that mRNA translation is an energy demanding process, cancer cells must produce sufficient ATP to meet energy demand of hyperactive translational machinery. In recent years, the mammalian/mechanistic target of rapamycin (mTOR) emerged as a central regulatory node which coordinates energy consumption by the translation apparatus and ATP production in mitochondria. Aberrant mTOR signaling underpins the vast majority of cancers whereby increased mTOR activity is thought to be a major determinant of both malignant translatomes and metabolomes. Nonetheless, the role of mTOR and other related signaling nodes (e.g. AMPK) in orchestrating protein synthesis and cancer energetics is only recently being unraveled. In this review, we discuss recent findings that provide insights into the molecular underpinnings of coordination of translational and metabolic programs of cancer cells, and potential strategies to translate these findings into clinical treatments.
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Affiliation(s)
- Matthew Leibovitch
- Lady Davis Institute, SMBD JGH, McGill University, Montréal, QC, H3T 1E2, Canada.
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology, Montréal, QC, H3A 1A3, Canada; Department of Biochemistry, Montréal, QC, H3A 1A3, Canada; Department of Experimental Medicine McGill University, Montréal, QC, H3A 1A3, Canada; Lady Davis Institute, SMBD JGH, McGill University, Montréal, QC, H3T 1E2, Canada
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128
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Laguesse S, Morisot N, Shin JH, Liu F, Adrover MF, Sakhai SA, Lopez MF, Phamluong K, Griffin WC, Becker HC, Bender KJ, Alvarez VA, Ron D. Prosapip1-Dependent Synaptic Adaptations in the Nucleus Accumbens Drive Alcohol Intake, Seeking, and Reward. Neuron 2017; 96:145-159.e8. [PMID: 28890345 PMCID: PMC6014831 DOI: 10.1016/j.neuron.2017.08.037] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/13/2017] [Accepted: 08/24/2017] [Indexed: 12/15/2022]
Abstract
The mammalian target of rapamycin complex 1 (mTORC1), a transducer of local dendritic translation, participates in learning and memory processes as well as in mechanisms underlying alcohol-drinking behaviors. Using an unbiased RNA-seq approach, we identified Prosapip1 as a novel downstream target of mTORC1 whose translation and consequent synaptic protein expression are increased in the nucleus accumbens (NAc) of mice excessively consuming alcohol. We demonstrate that alcohol-dependent increases in Prosapip1 levels promote the formation of actin filaments, leading to changes in dendritic spine morphology of NAc medium spiny neurons (MSNs). We further demonstrate that Prosapip1 is required for alcohol-dependent synaptic localization of GluA2 lacking AMPA receptors in NAc shell MSNs. Finally, we present data implicating Prosapip1 in mechanisms underlying alcohol self-administration and reward. Together, these data suggest that Prosapip1 in the NAc is a molecular transducer of structural and synaptic alterations that drive and/or maintain excessive alcohol use.
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Affiliation(s)
- Sophie Laguesse
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Nadege Morisot
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Jung Hoon Shin
- Laboratory on Neurobiology of Compulsive Behaviors, National Institute of Alcohol Abuse and Alcoholism, US National Institutes of Health, Bethesda, MD, USA
| | - Feng Liu
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Martin F Adrover
- Laboratory on Neurobiology of Compulsive Behaviors, National Institute of Alcohol Abuse and Alcoholism, US National Institutes of Health, Bethesda, MD, USA
| | - Samuel A Sakhai
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Marcelo F Lopez
- Charleston Alcohol Research Center, Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Khanhky Phamluong
- Department of Neurology, University of California, San Francisco, CA, USA
| | - William C Griffin
- Charleston Alcohol Research Center, Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Howard C Becker
- Charleston Alcohol Research Center, Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA; Department of Neurosciences, Medical University of South Carolina, Charleston, SC, USA; RHJ Department of Veterans Affairs Medical Center, Charleston, SC, USA
| | - Kevin J Bender
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Veronica A Alvarez
- Laboratory on Neurobiology of Compulsive Behaviors, National Institute of Alcohol Abuse and Alcoholism, US National Institutes of Health, Bethesda, MD, USA
| | - Dorit Ron
- Department of Neurology, University of California, San Francisco, CA, USA.
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129
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Morita M, Prudent J, Basu K, Goyon V, Katsumura S, Hulea L, Pearl D, Siddiqui N, Strack S, McGuirk S, St-Pierre J, Larsson O, Topisirovic I, Vali H, McBride HM, Bergeron JJ, Sonenberg N. mTOR Controls Mitochondrial Dynamics and Cell Survival via MTFP1. Mol Cell 2017; 67:922-935.e5. [PMID: 28918902 DOI: 10.1016/j.molcel.2017.08.013] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 06/27/2017] [Accepted: 08/18/2017] [Indexed: 02/02/2023]
Abstract
The mechanisms that link environmental and intracellular stimuli to mitochondrial functions, including fission/fusion, ATP production, metabolite biogenesis, and apoptosis, are not well understood. Here, we demonstrate that the nutrient-sensing mechanistic/mammalian target of rapamycin complex 1 (mTORC1) stimulates translation of mitochondrial fission process 1 (MTFP1) to control mitochondrial fission and apoptosis. Expression of MTFP1 is coupled to pro-fission phosphorylation and mitochondrial recruitment of the fission GTPase dynamin-related protein 1 (DRP1). Potent active-site mTOR inhibitors engender mitochondrial hyperfusion due to the diminished translation of MTFP1, which is mediated by translation initiation factor 4E (eIF4E)-binding proteins (4E-BPs). Uncoupling MTFP1 levels from the mTORC1/4E-BP pathway upon mTOR inhibition blocks the hyperfusion response and leads to apoptosis by converting mTOR inhibitor action from cytostatic to cytotoxic. These data provide direct evidence for cell survival upon mTOR inhibition through mitochondrial hyperfusion employing MTFP1 as a critical effector of mTORC1 to govern cell fate decisions.
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Affiliation(s)
- Masahiro Morita
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A1A3, Canada; Department of Molecular Medicine and Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Julien Prudent
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Kaustuv Basu
- Department of Anatomy and Cell Biology and Facility for Electron Microscopy Research, McGill University, Montreal, QC H3A 0C7, Canada
| | - Vanessa Goyon
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Sakie Katsumura
- Department of Molecular Medicine and Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Laura Hulea
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada; Department of Oncology, McGill University, Montreal, QC H3T 1E2, Canada
| | - Dana Pearl
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A1A3, Canada
| | - Nadeem Siddiqui
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A1A3, Canada
| | - Stefan Strack
- Department of Pharmacology, University of Iowa, Iowa City, IA 52242, USA
| | - Shawn McGuirk
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A1A3, Canada
| | - Julie St-Pierre
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A1A3, Canada
| | - Ola Larsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm 171 76, Sweden
| | - Ivan Topisirovic
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A1A3, Canada; Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada; Department of Oncology, McGill University, Montreal, QC H3T 1E2, Canada
| | - Hojatollah Vali
- Department of Anatomy and Cell Biology and Facility for Electron Microscopy Research, McGill University, Montreal, QC H3A 0C7, Canada
| | - Heidi M McBride
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada.
| | - John J Bergeron
- Department of Medicine, McGill University Health Centre Research Institute, Montreal, QC H4A 3J1, Canada.
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A1A3, Canada.
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130
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Kimball SR. Leucine-Induced Upregulation of Terminal Oligopyrimidine mRNA Translation in Skeletal Muscle: Just the Tip of the Iceberg? J Nutr 2017; 147:1603-1604. [PMID: 28768833 PMCID: PMC5572500 DOI: 10.3945/jn.117.256289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- Scot R Kimball
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA
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131
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Dual abrogation of MNK and mTOR: a novel therapeutic approach for the treatment of aggressive cancers. Future Med Chem 2017; 9:1539-1555. [PMID: 28841037 DOI: 10.4155/fmc-2017-0062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Targeting the translational machinery has emerged as a promising therapeutic option for cancer treatment. Cancer cells require elevated protein synthesis and exhibit augmented activity to meet the increased metabolic demand. Eukaryotic translation initiation factor 4E is necessary for mRNA translation, its availability and phosphorylation are regulated by the PI3K/AKT/mTOR and MNK1/2 pathways. The phosphorylated form of eIF4E drives the expression of oncogenic proteins including those involved in metastasis. In this article, we will review the role of eIF4E in cancer, its regulation and discuss the benefit of dual inhibition of upstream pathways. The discernible interplay between the MNK and mTOR signaling pathways provides a novel therapeutic opportunity to target aggressive migratory cancers through the development of hybrid molecules.
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132
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Efficient and Accurate Translation Initiation Directed by TISU Involves RPS3 and RPS10e Binding and Differential Eukaryotic Initiation Factor 1A Regulation. Mol Cell Biol 2017; 37:MCB.00150-17. [PMID: 28584194 DOI: 10.1128/mcb.00150-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/17/2017] [Indexed: 01/20/2023] Open
Abstract
Canonical translation initiation involves ribosomal scanning, but short 5' untranslated region (5'UTR) mRNAs are translated in a scanning-independent manner. The extent and mechanism of scanning-independent translation are not fully understood. Here we report that short 5'UTR mRNAs constitute a substantial fraction of the translatome. Short 5'UTR mRNAs are enriched with TISU (translation initiator of short 5'UTR), a 12-nucleotide element directing efficient scanning-independent translation. Comprehensive mutagenesis revealed that each AUG codon-flanking nucleotide of TISU contributes to translational strength, but only a few are important for accuracy. Using site-specific UV cross-linking of ribosomal complexes assembled on TISU mRNA, we demonstrate specific binding of TISU to ribosomal proteins at the E and A sites. We identified RPS3 as the major TISU binding protein in the 48S complex A site. Upon 80S complex formation, RPS3 interaction is weakened and switched to RPS10e (formerly called RPS10). We further demonstrate that TISU is particularly dependent on eukaryotic initiation factor 1A (eIF1A) which interacts with both RPS3 and RPS10e. Our findings suggest that the cap-recruited ribosome specifically binds the TISU nucleotides at the A and E sites in cooperation with eIF1A to promote scanning arrest.
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133
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Translational control and the cancer cell response to stress. Curr Opin Cell Biol 2017; 45:102-109. [PMID: 28582681 DOI: 10.1016/j.ceb.2017.05.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/24/2017] [Accepted: 05/02/2017] [Indexed: 11/24/2022]
Abstract
The evidence for the importance of aberrant translation in cancer cells is overwhelming. Reflecting the wealth of data, there are excellent reviews delineating how ribosomes and initiation factors are linked to cancer [1-3], and the therapeutic strategies being devised to target them [4]. Changes in translational efficiency can engender a malignant phenotype without the need for chromatin reorganization, transcription, splicing and mRNA export [5,6]. Thus, cancer-related modulations of the translational machinery are ideally suited to allow cancer cells to respond to the various stresses encountered along the path of tumorigenesis and organism-wide dissemination [7•,8,9,10•]. Emerging findings supporting this notion are the focus of this review.
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134
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Liu X, Zhang Y, Ni M, Cao H, Signer RA, Li D, Li M, Gu Z, Hu Z, Dickerson KE, Weinberg SE, Chandel NS, DeBerardinis RJ, Zhou F, Shao Z, Xu J. Regulation of mitochondrial biogenesis in erythropoiesis by mTORC1-mediated protein translation. Nat Cell Biol 2017; 19:626-638. [PMID: 28504707 PMCID: PMC5771482 DOI: 10.1038/ncb3527] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 04/06/2017] [Indexed: 12/15/2022]
Abstract
Advances in genomic profiling present new challenges of explaining how changes in DNA and RNA are translated into proteins linking genotype to phenotype. Here we compare the genome-scale proteomic and transcriptomic changes in human primary haematopoietic stem/progenitor cells and erythroid progenitors, and uncover pathways related to mitochondrial biogenesis enhanced through post-transcriptional regulation. Mitochondrial factors including TFAM and PHB2 are selectively regulated through protein translation during erythroid specification. Depletion of TFAM in erythroid cells alters intracellular metabolism, leading to elevated histone acetylation, deregulated gene expression, and defective mitochondria and erythropoiesis. Mechanistically, mTORC1 signalling is enhanced to promote translation of mitochondria-associated transcripts through TOP-like motifs. Genetic and pharmacological perturbation of mitochondria or mTORC1 specifically impairs erythropoiesis in vitro and in vivo. Our studies support a mechanism for post-transcriptional control of erythroid mitochondria and may have direct relevance to haematologic defects associated with mitochondrial diseases and ageing.
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Affiliation(s)
- Xin Liu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Key Laboratory of Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Min Ni
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hui Cao
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert A.J. Signer
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Dan Li
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mushan Li
- Key Laboratory of Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhimin Gu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zeping Hu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kathryn E. Dickerson
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Samuel E. Weinberg
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Navdeep S. Chandel
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ralph J. DeBerardinis
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Feng Zhou
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Zhen Shao
- Key Laboratory of Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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135
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Gobet C, Naef F. Ribosome profiling and dynamic regulation of translation in mammals. Curr Opin Genet Dev 2017; 43:120-127. [PMID: 28363112 DOI: 10.1016/j.gde.2017.03.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 10/19/2022]
Abstract
Protein synthesis is an energy-demanding cellular process. Consequently, a well-timed, fine-tuned and plastic regulation of translation is needed to adjust and maintain cell states under dynamically changing environments. Genome-wide monitoring of translation was recently facilitated by ribosome profiling, which uncovered key features of translation regulation. In this review, we summarize recent ribosome profiling studies in mammals providing novel insight in dynamic translation regulation, notably related to circadian rhythms, diurnal feeding/fasting cycles, cell cycle progression, stress responses, and tRNA landscapes. In particular, recent results show that regulating translation initiation and elongation represent important mechanisms used in mammalian cells to rapidly modulate protein expression in dynamically changing environments.
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Affiliation(s)
- Cédric Gobet
- The Institute of Bioengineering (IBI), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Switzerland
| | - Felix Naef
- The Institute of Bioengineering (IBI), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Switzerland.
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136
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Masvidal L, Hulea L, Furic L, Topisirovic I, Larsson O. mTOR-sensitive translation: Cleared fog reveals more trees. RNA Biol 2017; 14:1299-1305. [PMID: 28277937 PMCID: PMC5711451 DOI: 10.1080/15476286.2017.1290041] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Translation is fundamental for many biologic processes as it enables cells to rapidly respond to stimuli without requiring de novo mRNA synthesis. The mammalian/mechanistic target of rapamycin (mTOR) is a key regulator of translation. Although mTOR affects global protein synthesis, translation of a subset of mRNAs appears to be exceptionally sensitive to changes in mTOR activity. Recent efforts to catalog these mTOR-sensitive mRNAs resulted in conflicting results. Whereas ribosome-profiling almost exclusively identified 5'-terminal oligopyrimidine (TOP) mRNAs as mTOR-sensitive, polysome-profiling suggested that mTOR also regulates translation of non-TOP mRNAs. This inconsistency was explained by analytical and technical biases limiting the efficiency of ribosome-profiling in detecting mRNAs showing differential translation. Moreover, genome-wide characterization of 5'UTRs of non-TOP mTOR-sensitive mRNAs revealed 2 subsets of transcripts which differ in their requirement for translation initiation factors and biologic functions. We summarize these recent advances and their impact on the understanding of mTOR-sensitive translation.
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Affiliation(s)
- Laia Masvidal
- a Department of Oncology-Pathology , Science for Life Laboratory, Karolinska Institutet , Stockholm , Sweden
| | - Laura Hulea
- b Lady Davis Institute, SMBD Jewish General Hospital , Montreal , Canada.,c Gerald-Bronfman Department of Oncology, Departments of Experimental Medicine , and Biochemistry McGill University , Montreal , Canada
| | - Luc Furic
- d Cancer Program , Biomedicine Discovery Institute and Department of Anatomy & Developmental Biology, Monash University , Victoria , Australia.,e Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre , Melbourne , Victoria , Australia
| | - Ivan Topisirovic
- b Lady Davis Institute, SMBD Jewish General Hospital , Montreal , Canada.,c Gerald-Bronfman Department of Oncology, Departments of Experimental Medicine , and Biochemistry McGill University , Montreal , Canada
| | - Ola Larsson
- a Department of Oncology-Pathology , Science for Life Laboratory, Karolinska Institutet , Stockholm , Sweden
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137
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Joyce CE, Yanez AG, Mori A, Yoda A, Carroll JS, Novina CD. Differential Regulation of the Melanoma Proteome by eIF4A1 and eIF4E. Cancer Res 2017; 77:613-622. [PMID: 27879264 PMCID: PMC5362820 DOI: 10.1158/0008-5472.can-16-1298] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 11/16/2016] [Accepted: 11/16/2016] [Indexed: 11/16/2022]
Abstract
Small molecules and antisense oligonucleotides that inhibit the translation initiation factors eIF4A1 and eIF4E have been explored as broad-based therapeutic agents for cancer treatment, based on the frequent upregulation of these two subunits of the eIF4F cap-binding complex in many cancer cells. Here, we provide support for these therapeutic approaches with mechanistic studies of eIF4F-driven tumor progression in a preclinical model of melanoma. Silencing eIF4A1 or eIF4E decreases melanoma proliferation and invasion. There were common effects on the level of cell-cycle proteins that could explain the antiproliferative effects in vitro Using clinical specimens, we correlate the common cell-cycle targets of eIF4A1 and eIF4E with patient survival. Finally, comparative proteomic and transcriptomic analyses reveal extensive mechanistic divergence in response to eIF4A1 or eIF4E silencing. Current models indicate that eIF4A1 and eIF4E function together through the 5'UTR to increase translation of oncogenes. In contrast, our data demonstrate that the common effects of eIF4A1 and eIF4E on translation are mediated by the coding region and 3'UTR. Moreover, their divergent effects occur through the 5'UTR. Overall, our work shows that it will be important to evaluate subunit-specific inhibitors of eIF4F in different disease contexts to fully understand their anticancer actions. Cancer Res; 77(3); 613-22. ©2016 AACR.
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Affiliation(s)
- Cailin E Joyce
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Adrienne G Yanez
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Akihiro Mori
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts, Worcester, Massachusetts
- Onami team, The Systems Biology Institute, Tokyo, Japan
- Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Hyogo, Japan
| | - Akinori Yoda
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Johanna S Carroll
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Carl D Novina
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
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138
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Sesma A, Castresana C, Castellano MM. Regulation of Translation by TOR, eIF4E and eIF2α in Plants: Current Knowledge, Challenges and Future Perspectives. FRONTIERS IN PLANT SCIENCE 2017; 8:644. [PMID: 28491073 PMCID: PMC5405063 DOI: 10.3389/fpls.2017.00644] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/10/2017] [Indexed: 05/06/2023]
Abstract
An important step in eukaryotic gene expression is the synthesis of proteins from mRNA, a process classically divided into three stages, initiation, elongation, and termination. Translation is a precisely regulated and conserved process in eukaryotes. The presence of plant-specific translation initiation factors and the lack of well-known translational regulatory pathways in this kingdom nonetheless indicate how a globally conserved process can diversify among organisms. The control of protein translation is a central aspect of plant development and adaptation to environmental stress, but the mechanisms are still poorly understood. Here we discuss current knowledge of the principal mechanisms that regulate translation initiation in plants, with special attention to the singularities of this eukaryotic kingdom. In addition, we highlight the major recent breakthroughs in the field and the main challenges to address in the coming years.
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Affiliation(s)
- Ane Sesma
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
- Departamento Biotecnología y Biología Vegetal, Universidad Politécnica de MadridMadrid, Spain
| | - Carmen Castresana
- Centro Nacional de Biotecnología – Consejo Superior de Investigaciones Científicas (CSIC)Madrid, Spain
| | - M. Mar Castellano
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
- *Correspondence: M. Mar Castellano,
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139
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Andreev DE, O'Connor PBF, Loughran G, Dmitriev SE, Baranov PV, Shatsky IN. Insights into the mechanisms of eukaryotic translation gained with ribosome profiling. Nucleic Acids Res 2016; 45:513-526. [PMID: 27923997 PMCID: PMC5314775 DOI: 10.1093/nar/gkw1190] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/31/2016] [Accepted: 11/18/2016] [Indexed: 12/29/2022] Open
Abstract
The development of Ribosome Profiling (RiboSeq) has revolutionized functional genomics. RiboSeq is based on capturing and sequencing of the mRNA fragments enclosed within the translating ribosome and it thereby provides a ‘snapshot’ of ribosome positions at the transcriptome wide level. Although the method is predominantly used for analysis of differential gene expression and discovery of novel translated ORFs, the RiboSeq data can also be a rich source of information about molecular mechanisms of polypeptide synthesis and translational control. This review will focus on how recent findings made with RiboSeq have revealed important details of the molecular mechanisms of translation in eukaryotes. These include mRNA translation sensitivity to drugs affecting translation initiation and elongation, the roles of upstream ORFs in response to stress, the dynamics of elongation and termination as well as details of intrinsic ribosome behavior on the mRNA after translation termination. As the RiboSeq method is still at a relatively early stage we will also discuss the implications of RiboSeq artifacts on data interpretation.
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Affiliation(s)
- Dmitry E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | | | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
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140
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Akulich KA, Andreev DE, Terenin IM, Smirnova VV, Anisimova AS, Makeeva DS, Arkhipova VI, Stolboushkina EA, Garber MB, Prokofjeva MM, Spirin PV, Prassolov VS, Shatsky IN, Dmitriev SE. Four translation initiation pathways employed by the leaderless mRNA in eukaryotes. Sci Rep 2016; 6:37905. [PMID: 27892500 PMCID: PMC5124965 DOI: 10.1038/srep37905] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/02/2016] [Indexed: 01/09/2023] Open
Abstract
mRNAs lacking 5′ untranslated regions (leaderless mRNAs) are molecular relics of an ancient translation initiation pathway. Nevertheless, they still represent a significant portion of transcriptome in some taxons, including a number of eukaryotic species. In bacteria and archaea, the leaderless mRNAs can bind non-dissociated 70 S ribosomes and initiate translation without protein initiation factors involved. Here we use the Fleeting mRNA Transfection technique (FLERT) to show that translation of a leaderless reporter mRNA is resistant to conditions when eIF2 and eIF4F, two key eukaryotic translation initiation factors, are inactivated in mammalian cells. We report an unconventional translation initiation pathway utilized by the leaderless mRNA in vitro, in addition to the previously described 80S-, eIF2-, or eIF2D-mediated modes. This mechanism is a bacterial-like eIF5B/IF2-assisted initiation that has only been reported for hepatitis C virus-like internal ribosome entry sites (IRESs). Therefore, the leaderless mRNA is able to take any of four different translation initiation pathways in eukaryotes.
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Affiliation(s)
- Kseniya A Akulich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Dmitry E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ilya M Terenin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Victoria V Smirnova
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Aleksandra S Anisimova
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Desislava S Makeeva
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Valentina I Arkhipova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Elena A Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Maria B Garber
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Maria M Prokofjeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Pavel V Spirin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Vladimir S Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Sergey E Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.,Department of Biochemistry, Biological Faculty, Lomonosov Moscow State University, Moscow, 119991, Russia
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141
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Song J, Perreault JP, Topisirovic I, Richard S. RNA G-quadruplexes and their potential regulatory roles in translation. ACTA ACUST UNITED AC 2016; 4:e1244031. [PMID: 28090421 PMCID: PMC5173311 DOI: 10.1080/21690731.2016.1244031] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/26/2016] [Accepted: 09/28/2016] [Indexed: 12/11/2022]
Abstract
DNA guanine (G)-rich 4-stranded helical nucleic acid structures called G-quadruplexes (G4), have been extensively studied during the last decades. However, emerging evidence reveals that 5′- and 3′-untranslated regions (5′- and 3′-UTRs) as well as open reading frames (ORFs) contain putative RNA G-quadruplexes. These stable secondary structures play key roles in telomere homeostasis and RNA metabolism including pre-mRNA splicing, polyadenylation, mRNA targeting and translation. Interestingly, multiple RNA binding proteins such as nucleolin, FMRP, DHX36, and Aven were identified to bind RNA G-quadruplexes. Moreover, accumulating reports suggest that RNA G-quadruplexes regulate translation in cap-dependent and -independent manner. Herein, we discuss potential roles of RNA G-quadruplexes and associated trans-acting factors in the regulation of mRNA translation.
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Affiliation(s)
- Jingwen Song
- Terry Fox Molecular Oncology Group and Segal Cancer Center, McGill University, Montréal, Québec, Canada; Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, McGill University, Montréal, Québec, Canada; Department of Oncology, McGill University, Montréal, Québec, Canada; Department of Medicine, McGill University, Montréal, Québec, Canada
| | | | - Ivan Topisirovic
- Terry Fox Molecular Oncology Group and Segal Cancer Center, McGill University, Montréal, Québec, Canada; Department of Oncology, McGill University, Montréal, Québec, Canada; Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Stéphane Richard
- Terry Fox Molecular Oncology Group and Segal Cancer Center, McGill University, Montréal, Québec, Canada; Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, McGill University, Montréal, Québec, Canada; Department of Oncology, McGill University, Montréal, Québec, Canada; Department of Medicine, McGill University, Montréal, Québec, Canada
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142
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Curran JA, Weiss B. What Is the Impact of mRNA 5' TL Heterogeneity on Translational Start Site Selection and the Mammalian Cellular Phenotype? Front Genet 2016; 7:156. [PMID: 27630668 PMCID: PMC5005323 DOI: 10.3389/fgene.2016.00156] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/16/2016] [Indexed: 12/23/2022] Open
Abstract
A major determinant in the efficiency of ribosome loading onto mRNAs is the 5′ TL (transcript leader or 5′ UTR). In addition, elements within this region also impact on start site selection demonstrating that it can modulate the protein readout at both quantitative and qualitative levels. With the increasing wealth of data generated by the mining of the mammalian transcriptome, it has become evident that a genes 5′ TL is not homogeneous but actually exhibits significant heterogeneity. This arises due to the utilization of alternative promoters, and is further compounded by significant variability with regards to the precise transcriptional start sites of each (not to mention alternative splicing). Consequently, the transcript for a protein coding gene is not a unique mRNA, but in-fact a complexed quasi-species of variants whose composition may respond to the changing physiological environment of the cell. Here we examine the potential impact of these events with regards to the protein readout.
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Affiliation(s)
- Joseph A Curran
- Department of Microbiology and Molecular Medicine, Medical School, University of GenevaGeneva, Switzerland; Institute of Genetics and Genomics of Geneva, University of GenevaGeneva, Switzerland
| | - Benjamin Weiss
- Department of Microbiology and Molecular Medicine, Medical School, University of Geneva Geneva, Switzerland
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143
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A Transcript-Specific eIF3 Complex Mediates Global Translational Control of Energy Metabolism. Cell Rep 2016; 16:1891-902. [PMID: 27477275 DOI: 10.1016/j.celrep.2016.07.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 05/19/2016] [Accepted: 07/03/2016] [Indexed: 01/20/2023] Open
Abstract
The multi-subunit eukaryotic translation initiation factor eIF3 is thought to assist in the recruitment of ribosomes to mRNA. The expression of eIF3 subunits is frequently disrupted in human cancers, but the specific roles of individual subunits in mRNA translation and cancer remain elusive. Using global transcriptomic, proteomic, and metabolomic profiling, we found a striking failure of Schizosaccharomyces pombe cells lacking eIF3e and eIF3d to synthesize components of the mitochondrial electron transport chain, leading to a defect in respiration, endogenous oxidative stress, and premature aging. Energy balance was maintained, however, by a switch to glycolysis with increased glucose uptake, upregulation of glycolytic enzymes, and strict dependence on a fermentable carbon source. This metabolic regulatory function appears to be conserved in human cells where eIF3e binds metabolic mRNAs and promotes their translation. Thus, via its eIF3d-eIF3e module, eIF3 orchestrates an mRNA-specific translational mechanism controlling energy metabolism that may be disrupted in cancer.
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144
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IL-15 activates mTOR and primes stress-activated gene expression leading to prolonged antitumor capacity of NK cells. Blood 2016; 128:1475-89. [PMID: 27465917 DOI: 10.1182/blood-2016-02-698027] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 07/13/2016] [Indexed: 12/21/2022] Open
Abstract
Treatment of hematological malignancies by adoptive transfer of activated natural killer (NK) cells is limited by poor postinfusion persistence. We compared the ability of interleukin-2 (IL-2) and IL-15 to sustain human NK-cell functions following cytokine withdrawal to model postinfusion performance. In contrast to IL-2, IL-15 mediated stronger signaling through the IL-2/15 receptor complex and provided cell function advantages. Genome-wide analysis of cytosolic and polysome-associated messenger RNA (mRNA) revealed not only cytokine-dependent differential mRNA levels and translation during cytokine activation but also that most gene expression differences were primed by IL-15 and only manifested after cytokine withdrawal. IL-15 augmented mammalian target of rapamycin (mTOR) signaling, which correlated with increased expression of genes related to cell metabolism and respiration. Consistently, mTOR inhibition abrogated IL-15-induced cell function advantages. Moreover, mTOR-independent STAT-5 signaling contributed to improved NK-cell function during cytokine activation but not following cytokine withdrawal. The superior performance of IL-15-stimulated NK cells was also observed using a clinically applicable protocol for NK-cell expansion in vitro and in vivo. Finally, expression of IL-15 correlated with cytolytic immune functions in patients with B-cell lymphoma and favorable clinical outcome. These findings highlight the importance of mTOR-regulated metabolic processes for immune cell functions and argue for implementation of IL-15 in adoptive NK-cell cancer therapy.
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145
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eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation. Nature 2016; 536:96-9. [PMID: 27462815 PMCID: PMC5003174 DOI: 10.1038/nature18954] [Citation(s) in RCA: 231] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 06/21/2016] [Indexed: 12/19/2022]
Abstract
Eukaryotic mRNAs contain a 5' cap structure critical for recruitment of the translation machinery and initiation of protein synthesis. mRNA recognition is thought to require direct interactions between eukaryotic initiation factor 4E (eIF4E) and the mRNA cap. However, translation of numerous capped mRNAs remains robust during cellular stress, early development, and cell cycle progression1 despite eIF4E inactivation. Here we describe a new cellular cap-dependent pathway of translation initiation that relies on a previously unknown cap-binding activity of eIF3d, a subunit of the 800-kilodalton eukaryotic initiation factor 3 (eIF3) complex. A 1.4 Å crystal structure of the eIF3d cap-binding domain reveals unexpected homology to endonucleases involved in RNA turnover, and allows modeling of cap recognition by eIF3d. eIF3d makes specific contacts to the cap, as exemplified by cap analog competition, and these interactions are essential for assembly of translation initiation complexes on eIF3-specialized mRNAs2 such as the cell proliferation regulator c-Jun. The c-Jun mRNA further encodes an inhibitory RNA element that blocks eIF4E recruitment, thus enforcing alternative cap recognition by eIF3d. Our results reveal a new mechanism of cap-dependent translation independent of eIF4E, and illustrate how modular RNA elements work in concert to direct specialized forms of translation initiation.
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146
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Chu J, Cargnello M, Topisirovic I, Pelletier J. Translation Initiation Factors: Reprogramming Protein Synthesis in Cancer. Trends Cell Biol 2016; 26:918-933. [PMID: 27426745 DOI: 10.1016/j.tcb.2016.06.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/03/2016] [Accepted: 06/13/2016] [Indexed: 12/11/2022]
Abstract
Control of mRNA translation plays a crucial role in the regulation of gene expression and is critical for cellular homeostasis. Dysregulation of translation initiation factors has been documented in several pathologies including cancer. Aberrant function of translation initiation factors leads to translation reprogramming that promotes proliferation, survival, angiogenesis, and metastasis. In such context, understanding how altered levels (and presumably activity) of initiation factors can contribute to tumor initiation and/or maintenance is of major interest for the development of novel therapeutic strategies. In this review we provide an overview of translation initiation mechanisms and focus on recent findings describing the role of individual initiation factors and their aberrant activity in cancer.
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Affiliation(s)
- Jennifer Chu
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Marie Cargnello
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, McGill University, Quebec, Canada
| | - Ivan Topisirovic
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada; Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, McGill University, Quebec, Canada.
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, McGill University, Quebec, Canada; The Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada.
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147
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Hinnebusch AG, Ivanov IP, Sonenberg N. Translational control by 5'-untranslated regions of eukaryotic mRNAs. Science 2016; 352:1413-6. [PMID: 27313038 DOI: 10.1126/science.aad9868] [Citation(s) in RCA: 654] [Impact Index Per Article: 81.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The eukaryotic 5' untranslated region (UTR) is critical for ribosome recruitment to the messenger RNA (mRNA) and start codon choice and plays a major role in the control of translation efficiency and shaping the cellular proteome. The ribosomal initiation complex is assembled on the mRNA via a cap-dependent or cap-independent mechanism. We describe various mechanisms controlling ribosome scanning and initiation codon selection by 5' upstream open reading frames, translation initiation factors, and primary and secondary structures of the 5'UTR, including particular sequence motifs. We also discuss translational control via phosphorylation of eukaryotic initiation factor 2, which is implicated in learning and memory, neurodegenerative diseases, and cancer.
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Affiliation(s)
- Alan G Hinnebusch
- Group on Cell Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivaylo P Ivanov
- Group on Cell Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.
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