1
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Farooq Z, Kusuma F, Burke P, Dufour CR, Lee D, Tabatabaei N, Toboz P, Radovani E, Greenblatt J, Rehman J, Class J, Khoutorsky A, Fonseca BD, Richner JM, Mercier E, Bourque G, Giguère V, Subramaniam AR, Han J, Tahmasebi S. The amino acid sensor GCN2 suppresses Terminal Oligopyrimidine (TOP) mRNA translation via La-related Protein 1 (LARP1). J Biol Chem 2022; 298:102277. [PMID: 35863436 PMCID: PMC9396407 DOI: 10.1016/j.jbc.2022.102277] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
La-related protein 1 (LARP1) has been identified as a key translational inhibitor of terminal oligopyrimidine (TOP) mRNAs downstream of the nutrient sensing protein kinase complex, mTORC1. LARP1 exerts this inhibitory effect on TOP mRNA translation by binding to the mRNA cap and the adjacent 5′TOP motif, resulting in the displacement of the cap-binding protein eIF4E from TOP mRNAs. However, the involvement of additional signaling pathway in regulating LARP1-mediated inhibition of TOP mRNA translation is largely unexplored. In the present study, we identify a second nutrient sensing kinase GCN2 that converges on LARP1 to control TOP mRNA translation. Using chromatin-immunoprecipitation followed by massive parallel sequencing (ChIP-seq) analysis of activating transcription factor 4 (ATF4), an effector of GCN2 in nutrient stress conditions, in WT and GCN2 KO mouse embryonic fibroblasts, we determined that LARP1 is a GCN2-dependent transcriptional target of ATF4. Moreover, we identified GCN1, a GCN2 activator, participates in a complex with LARP1 on stalled ribosomes, suggesting a role for GCN1 in LARP1-mediated translation inhibition in response to ribosome stalling. Therefore, our data suggest that the GCN2 pathway controls LARP1 activity via two mechanisms: ATF4-dependent transcriptional induction of LARP1 mRNA and GCN1-mediated recruitment of LARP1 to stalled ribosomes.
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Affiliation(s)
- Zeenat Farooq
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Fedho Kusuma
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea
| | - Phillip Burke
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Catherine R Dufour
- Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Duckgue Lee
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea
| | - Negar Tabatabaei
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Phoenix Toboz
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Ernest Radovani
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jack Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jalees Rehman
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Jacob Class
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL, USA
| | - Arkady Khoutorsky
- Department of Anesthesia and Faculty of Dentistry, McGill University, Montreal, QC H3A 0G1, Canada
| | | | - Justin M Richner
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL, USA
| | - Eloi Mercier
- Canadian Centre for Computational Genomics, and McGill University and Genome Québec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, and McGill University and Genome Québec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Vincent Giguère
- Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Arvind R Subramaniam
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jaeseok Han
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea.
| | - Soroush Tahmasebi
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA.
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2
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Galloway A, Kaskar A, Ditsova D, Atrih A, Yoshikawa H, Gomez-Moreira C, Suska O, Warminski M, Grzela R, Lamond AI, Darzynkiewicz E, Jemielity J, Cowling V. Upregulation of RNA cap methyltransferase RNMT drives ribosome biogenesis during T cell activation. Nucleic Acids Res 2021; 49:6722-6738. [PMID: 34125914 PMCID: PMC8266598 DOI: 10.1093/nar/gkab465] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/09/2021] [Accepted: 05/17/2021] [Indexed: 01/07/2023] Open
Abstract
The m7G cap is ubiquitous on RNAPII-transcribed RNA and has fundamental roles in eukaryotic gene expression, however its in vivo role in mammals has remained unknown. Here, we identified the m7G cap methyltransferase, RNMT, as a key mediator of T cell activation, which specifically regulates ribosome production. During T cell activation, induction of mRNA expression and ribosome biogenesis drives metabolic reprogramming, rapid proliferation and differentiation generating effector populations. We report that RNMT is induced by T cell receptor (TCR) stimulation and co-ordinates the mRNA, snoRNA and rRNA production required for ribosome biogenesis. Using transcriptomic and proteomic analyses, we demonstrate that RNMT selectively regulates the expression of terminal polypyrimidine tract (TOP) mRNAs, targets of the m7G-cap binding protein LARP1. The expression of LARP1 targets and snoRNAs involved in ribosome biogenesis is selectively compromised in Rnmt cKO CD4 T cells resulting in decreased ribosome synthesis, reduced translation rates and proliferation failure. By enhancing ribosome abundance, upregulation of RNMT co-ordinates mRNA capping and processing with increased translational capacity during T cell activation.
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Affiliation(s)
- Alison Galloway
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Aneesa Kaskar
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Dimitrinka Ditsova
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Abdelmadjid Atrih
- FingerPrints Proteomics Facility, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Harunori Yoshikawa
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Carolina Gomez-Moreira
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Olga Suska
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Marcin Warminski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Renata Grzela
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, and Division of Physics, 02-093 Warsaw, Poland
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Edward Darzynkiewicz
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, and Division of Physics, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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3
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Nagano S, Jinno J, Abdelhamid RF, Jin Y, Shibata M, Watanabe S, Hirokawa S, Nishizawa M, Sakimura K, Onodera O, Okada H, Okada T, Saito Y, Takahashi-Fujigasaki J, Murayama S, Wakatsuki S, Mochizuki H, Araki T. TDP-43 transports ribosomal protein mRNA to regulate axonal local translation in neuronal axons. Acta Neuropathol 2020; 140:695-713. [PMID: 32803350 DOI: 10.1007/s00401-020-02205-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/01/2020] [Accepted: 08/01/2020] [Indexed: 12/12/2022]
Abstract
Mislocalization and abnormal deposition of TDP-43 into the cytoplasm (TDP-43 proteinopathy) is a hallmark in neurons of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). However, the pathogenic mechanism of the diseases linked to TDP-43 is largely unknown. We hypothesized that the failure of mRNA transport to neuronal axons by TDP-43 may contribute to neurodegeneration in ALS and FTLD, and sought to examine the function of TDP-43 by identifying its target mRNA for axonal transport. We found that mRNAs related to translational function including ribosomal proteins (RPs) were decreased by shRNA-based TDP-43 knock-down in neurites of cortical neurons. TDP-43 binds to and transports the RP mRNAs through their 5' untranslated region, which contains a common 5' terminal oligopyrimidine tract motif and a downstream GC-rich region. We showed by employing in vitro and in vivo models that the RP mRNAs were translated and incorporated into native ribosomes locally in axons to maintain functionality of axonal ribosomes, which is required for local protein synthesis in response to stimulation and stress to axons. We also found that RP mRNAs were reduced in the pyramidal tract of sporadic ALS cases harboring TDP-43 pathology. Our results elucidated a novel function of TDP-43 to control transport of RP mRNAs and local translation by ribosomes to maintain morphological integrity of neuronal axons, and proved the influence of this function of TDP-43 on neurodegeneration in ALS and FTLD associated with TDP-43 proteinopathy.
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4
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TOP mRNPs: Molecular Mechanisms and Principles of Regulation. Biomolecules 2020; 10:biom10070969. [PMID: 32605040 PMCID: PMC7407576 DOI: 10.3390/biom10070969] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/20/2020] [Accepted: 06/23/2020] [Indexed: 02/08/2023] Open
Abstract
The cellular response to changes in the surrounding environment and to stress requires the coregulation of gene networks aiming to conserve energy and resources. This is often achieved by downregulating protein synthesis. The 5’ Terminal OligoPyrimidine (5’ TOP) motif-containing mRNAs, which encode proteins that are essential for protein synthesis, are the primary targets of translational control under stress. The TOP motif is a cis-regulatory RNA element that begins directly after the m7G cap structure and contains the hallmark invariant 5’-cytidine followed by an uninterrupted tract of 4–15 pyrimidines. Regulation of translation via the TOP motif coordinates global protein synthesis with simultaneous co-expression of the protein components required for ribosome biogenesis. In this review, we discuss architecture of TOP mRNA-containing ribonucleoprotein complexes, the principles of their assembly, and the modes of regulation of TOP mRNA translation.
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5
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Fonseca BD, Zakaria C, Jia JJ, Graber TE, Svitkin Y, Tahmasebi S, Healy D, Hoang HD, Jensen JM, Diao IT, Lussier A, Dajadian C, Padmanabhan N, Wang W, Matta-Camacho E, Hearnden J, Smith EM, Tsukumo Y, Yanagiya A, Morita M, Petroulakis E, González JL, Hernández G, Alain T, Damgaard CK. La-related Protein 1 (LARP1) Represses Terminal Oligopyrimidine (TOP) mRNA Translation Downstream of mTOR Complex 1 (mTORC1). J Biol Chem 2015; 290:15996-6020. [PMID: 25940091 PMCID: PMC4481205 DOI: 10.1074/jbc.m114.621730] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 04/27/2015] [Indexed: 12/11/2022] Open
Abstract
The mammalian target of rapamycin complex 1 (mTORC1) is a critical regulator of protein synthesis. The best studied targets of mTORC1 in translation are the eukaryotic initiation factor-binding protein 1 (4E-BP1) and ribosomal protein S6 kinase 1 (S6K1). In this study, we identify the La-related protein 1 (LARP1) as a key novel target of mTORC1 with a fundamental role in terminal oligopyrimidine (TOP) mRNA translation. Recent genome-wide studies indicate that TOP and TOP-like mRNAs compose a large portion of the mTORC1 translatome, but the mechanism by which mTORC1 controls TOP mRNA translation is incompletely understood. Here, we report that LARP1 functions as a key repressor of TOP mRNA translation downstream of mTORC1. Our data show the following: (i) LARP1 associates with mTORC1 via RAPTOR; (ii) LARP1 interacts with TOP mRNAs in an mTORC1-dependent manner; (iii) LARP1 binds the 5'TOP motif to repress TOP mRNA translation; and (iv) LARP1 competes with the eukaryotic initiation factor (eIF) 4G for TOP mRNA binding. Importantly, from a drug resistance standpoint, our data also show that reducing LARP1 protein levels by RNA interference attenuates the inhibitory effect of rapamycin, Torin1, and amino acid deprivation on TOP mRNA translation. Collectively, our findings demonstrate that LARP1 functions as an important repressor of TOP mRNA translation downstream of mTORC1.
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Affiliation(s)
- Bruno D Fonseca
- From the Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada,
| | - Chadi Zakaria
- the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Jian-Jun Jia
- From the Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
| | - Tyson E Graber
- From the Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada, the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Yuri Svitkin
- the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Soroush Tahmasebi
- the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Danielle Healy
- From the Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
| | - Huy-Dung Hoang
- From the Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
| | - Jacob M Jensen
- the Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Ilo T Diao
- the Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Alexandre Lussier
- the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Christopher Dajadian
- the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Niranjan Padmanabhan
- the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Walter Wang
- the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Edna Matta-Camacho
- the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Jaclyn Hearnden
- the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Ewan M Smith
- the Medical Research Council Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, United Kingdom
| | - Yoshinori Tsukumo
- the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Akiko Yanagiya
- the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Masahiro Morita
- the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Emmanuel Petroulakis
- the Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada, Pfizer Canada Inc., Kirkland, Quebec H9J 2M5, Canada, and
| | - Jose L González
- the Division of Basic Science, National Institute of Cancer, 22 San Fernando Ave., Tlalpan, Mexico City 14080, Mexico
| | - Greco Hernández
- the Division of Basic Science, National Institute of Cancer, 22 San Fernando Ave., Tlalpan, Mexico City 14080, Mexico
| | - Tommy Alain
- From the Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada,
| | - Christian K Damgaard
- the Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark,
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6
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Nandagopal N, Roux PP. Regulation of global and specific mRNA translation by the mTOR signaling pathway. ACTA ACUST UNITED AC 2015; 3:e983402. [PMID: 26779414 DOI: 10.4161/21690731.2014.983402] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/22/2014] [Accepted: 10/29/2014] [Indexed: 11/19/2022]
Abstract
The translation of mRNA into polypeptides is a key step in eukaryotic gene expression. Translation is mostly controlled at the level of initiation, which is partly regulated by the mammalian/mechanistic target of rapamycin (mTOR) signaling pathway. Whereas mTOR controls global protein synthesis through specific effector proteins, its role in the translation of select groups of mRNAs, such as those harboring a terminal oligopyrimidine (TOP) tract at their 5' end, remains more enigmatic. In this article, we describe the current knowledge on the role of mTOR in global mRNA translation, but also focus on the potential molecular mechanisms underlying the regulation of specific translational programs.
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Affiliation(s)
- Neethi Nandagopal
- Institute for Research in Immunology and Cancer (IRIC); Université de Montréal ; Montréal, Québec, Canada
| | - Philippe P Roux
- Institute for Research in Immunology and Cancer (IRIC); Université de Montréal; Montréal, Québec, Canada; Department of Pathology and Cell Biology; Faculty of Medicine; Université de Montréal; Montréal, Québec, Canada
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7
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Fonseca BD, Smith EM, Yelle N, Alain T, Bushell M, Pause A. The ever-evolving role of mTOR in translation. Semin Cell Dev Biol 2014; 36:102-12. [PMID: 25263010 DOI: 10.1016/j.semcdb.2014.09.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/12/2014] [Accepted: 09/15/2014] [Indexed: 02/06/2023]
Abstract
Control of translation allows for the production of stoichiometric levels of each protein in the cell. Attaining such a level of fine-tuned regulation of protein production requires the coordinated temporal and spatial control of numerous cellular signalling cascades impinging on the various components of the translational machinery. Foremost among these is the mTOR signalling pathway. The mTOR pathway regulates both the initiation and elongation steps of protein synthesis through the phosphorylation of numerous translation factors, while simultaneously ensuring adequate folding of nascent polypeptides through co-translational degradation of misfolded proteins. Perhaps most remarkably, mTOR is also a key regulator of the synthesis of ribosomal proteins and translation factors themselves. Two seminal studies have recently shown in translatome analysis that the mTOR pathway preferentially regulates the translation of mRNAs encoding ribosomal proteins and translation factors. Therefore, the role of the mTOR pathway in the control of protein synthesis extends far beyond immediate translational control. By controlling ribosome production (and ultimately ribosome availability), mTOR is a master long-term controller of protein synthesis. Herein, we review the literature spanning the early discoveries of mTOR on translation to the latest advances in our understanding of how the mTOR pathway controls the synthesis of ribosomal proteins.
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Affiliation(s)
- Bruno D Fonseca
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada.
| | - Ewan M Smith
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - Nicolas Yelle
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada
| | - Martin Bushell
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - Arnim Pause
- Goodman Cancer Research Centre, Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada.
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8
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Kakegawa T, Takase S, Masubuchi E, Yasukawa K. Diarylheptanoids from Alpinia officinarum Cause Distinct but Overlapping Effects on the Translatome of B Lymphoblastoid Cells. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2014; 2014:204797. [PMID: 25254051 PMCID: PMC4164264 DOI: 10.1155/2014/204797] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/25/2014] [Accepted: 07/25/2014] [Indexed: 12/01/2022]
Abstract
Diarylheptanoids (AO-0001, AO-0002, and AO-0003) isolated from Alpinia officinarum inhibit proinflammatory mediators and exhibit cytotoxic and antiviral activity. However, the precise mechanisms of action of these diarylheptanoids are unknown as are their effects on expression of specific genes. Here, we used a translatome analysis to investigate the mechanisms and modes of action of these three diarylheptanoids. Polysome-associated messenger RNAs (mRNAs) were prepared from diarylheptanoids-treated and control cells from a human B lymphoblastoid cell line; these mRNA samples were then used for microarray analysis. Microarray Data Analysis Tool version 3.2 was used to analyze the microarray data analysis; this software uses pathway information of the WikiPathways for gene ontology analysis. Each of the diarylheptanoids caused upregulation or downregulation of the same 37 and 286 genes, respectively. Among the 37 upregulated genes, 16 were related to mRNA processing based on the WikiPathways analysis. Our findings provided new insights into the mode of action of diarylheptanoids from A. officinarum.
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Affiliation(s)
- Tomohito Kakegawa
- Faculty of Pharmaceutical Sciences, Josai International University, 1 Gumyo, Togane, Chiba 283-8555, Japan
| | - Saeko Takase
- Faculty of Pharmaceutical Sciences, Josai International University, 1 Gumyo, Togane, Chiba 283-8555, Japan
| | - Eri Masubuchi
- Faculty of Pharmaceutical Sciences, Josai International University, 1 Gumyo, Togane, Chiba 283-8555, Japan
| | - Ken Yasukawa
- School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Funabashi, Chiba 274-8555, Japan
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9
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Tcherkezian J, Cargnello M, Romeo Y, Huttlin EL, Lavoie G, Gygi SP, Roux PP. Proteomic analysis of cap-dependent translation identifies LARP1 as a key regulator of 5'TOP mRNA translation. Genes Dev 2014; 28:357-71. [PMID: 24532714 PMCID: PMC3937514 DOI: 10.1101/gad.231407.113] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 01/06/2014] [Indexed: 12/20/2022]
Abstract
The mammalian target of rapamycin (mTOR) promotes cell growth and proliferation by promoting mRNA translation and increasing the protein synthetic capacity of the cell. Although mTOR globally promotes translation by regulating the mRNA 5' cap-binding protein eIF4E (eukaryotic initiation factor 4E), it also preferentially regulates the translation of certain classes of mRNA via unclear mechanisms. To help fill this gap in knowledge, we performed a quantitative proteomic screen to identify proteins that associate with the mRNA 5' cap in an mTOR-dependent manner. Using this approach, we identified many potential regulatory factors, including the putative RNA-binding protein LARP1 (La-related protein 1). Our results indicate that LARP1 associates with actively translating ribosomes via PABP and that LARP1 stimulates the translation of mRNAs containing a 5' terminal oligopyrimidine (TOP) motif, encoding for components of the translational machinery. We found that LARP1 associates with the mTOR complex 1 (mTORC1) and is required for global protein synthesis as well as cell growth and proliferation. Together, these data reveal important molecular mechanisms involved in TOP mRNA translation and implicate LARP1 as an important regulator of cell growth and proliferation.
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Affiliation(s)
- Joseph Tcherkezian
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Marie Cargnello
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Yves Romeo
- Centre National de la Recherche Scientifique, Laboratoire de Biologie Moléculaire Eucaryote, 31062 Toulouse, Cedex 04, France
- Université de Toulouse, Université Paul Sabatier (UPS), F-31000 Toulouse, France
| | - Edward L. Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Taplin Biological Mass Spectrometry Facility, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Genevieve Lavoie
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Taplin Biological Mass Spectrometry Facility, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Philippe P. Roux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
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10
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Pichon X, Wilson LA, Stoneley M, Bastide A, King HA, Somers J, Willis AEE. RNA binding protein/RNA element interactions and the control of translation. Curr Protein Pept Sci 2013; 13:294-304. [PMID: 22708490 PMCID: PMC3431537 DOI: 10.2174/138920312801619475] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/10/2012] [Accepted: 01/20/2012] [Indexed: 01/18/2023]
Abstract
A growing body of work demonstrates the importance of post-transcriptional control, in particular translation
initiation, in the overall regulation of gene expression. Here we focus on the contribution of regulatory elements within the
5’ and 3’ untranslated regions of mRNA to gene expression in eukaryotic cells including terminal oligopyrimidine tracts,
internal ribosome entry segments, upstream open reading frames and cytoplasmic polyadenylation elements. These
mRNA regulatory elements may adopt complex secondary structures and/or contain sequence motifs that allow their interaction
with a variety of regulatory proteins, RNAs and RNA binding proteins, particularly hnRNPs. The resulting interactions
are context-sensitive, and provide cells with a sensitive and fast response to cellular signals such as hormone exposure
or cytotoxic stress. Importantly, an increasing number of diseases have been identified, particularly cancers and
those associated with neurodegeneration, which originate either from mutation of these regulatory motifs, or from deregulation
of their cognate binding partners.
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Affiliation(s)
- Xavier Pichon
- Medical Research Council Toxicology Unit, Leicester, UK
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Abstract
Small nucleolar RNAs (snoRNAs) have long been considered important but unglamorous elements in the production of the protein synthesis machinery of the cell. Recently, however, several independent lines of evidence have indicated that these non-coding RNAs might have crucial roles in controlling cell behaviour, and snoRNA dysfunction could consequently contribute to oncogenesis in previously unsuspected ways.
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Affiliation(s)
- Gwyn T Williams
- Institute for Science and Technology in Medicine, Huxley Building, Keele University, Keele ST5 5BG, UK.
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12
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Lund N, Milev MP, Wong R, Sanmuganantham T, Woolaway K, Chabot B, Abou Elela S, Mouland AJ, Cochrane A. Differential effects of hnRNP D/AUF1 isoforms on HIV-1 gene expression. Nucleic Acids Res 2011; 40:3663-75. [PMID: 22187150 PMCID: PMC3333888 DOI: 10.1093/nar/gkr1238] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Control of RNA processing plays a major role in HIV-1 gene expression. To explore the role of several hnRNP proteins in this process, we carried out a siRNA screen to examine the effect of depletion of hnRNPs A1, A2, D, H, I and K on HIV-1 gene expression. While loss of hnRNPs H, I or K had little effect, depletion of A1 and A2 increased expression of viral structural proteins. In contrast, reduced hnRNP D expression decreased synthesis of HIV-1 Gag and Env. Loss of hnRNP D induced no changes in viral RNA abundance but reduced the accumulation of HIV-1 unspliced and singly spliced RNAs in the cytoplasm. Subsequent analyses determined that hnRNP D underwent relocalization to the cytoplasm upon HIV-1 infection and was associated with Gag protein. Screening of the four isoforms of hnRNP D determined that, upon overexpression, they had differential effects on HIV-1 Gag expression, p45 and p42 isoforms increased viral Gag synthesis while p40 and p37 suppressed it. The differential effect of hnRNP D isoforms on HIV-1 expression suggests that their relative abundance could contribute to the permissiveness of cell types to replicate the virus, a hypothesis subsequently confirmed by selective depletion of p45 and p42.
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Affiliation(s)
- Nicole Lund
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A8, Canada
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13
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Abstract
Under conditions of limited nutrients, eukaryotic cells reprogram protein expression in a way that slows growth but enhances survival. Recent data implicate stress granules, discrete cytoplasmic foci into which untranslated mRNPs are assembled during stress, in this process. In the October 1, 2011, issue of Genes & Development, Damgaard and Lykke-Andersen (p. 2057-2068) provide mechanistic insights into the regulation of a specific subset of mRNAs bearing 5'-terminal oligopyrimidine tracts (5'TOPs) by the structurally related stress granule proteins TIA-1 and TIAR.
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Affiliation(s)
- Pavel Ivanov
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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14
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Damgaard CK, Lykke-Andersen J. Translational coregulation of 5'TOP mRNAs by TIA-1 and TIAR. Genes Dev 2011; 25:2057-68. [PMID: 21979918 DOI: 10.1101/gad.17355911] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The response of cells to changes in their environment often requires coregulation of gene networks, but little is known about how this can occur at the post-transcriptional level. An important example of post-transcriptional coregulation is the selective translational regulation in response to growth conditions of mammalian mRNAs that encode protein biosynthesis factors and contain hallmark 5'-terminal oligopyrimidine tracts (5'TOP). However, the responsible trans-factors and the mechanism by which they coregulate 5'TOP mRNAs have remained elusive. Here we identify stress granule-associated TIA-1 and TIAR proteins as key factors in human 5'TOP mRNA regulation, which upon amino acid starvation assemble onto the 5' end of 5'TOP mRNAs and arrest translation at the initiation step, as evidenced by TIA-1/TIAR-dependent 5'TOP mRNA translation repression, polysome release, and accumulation in stress granules. This requires starvation-mediated activation of the GCN2 (general control nonderepressible 2) kinase and inactivation of the mTOR (mammalian target of rapamycin) signaling pathway. Our findings provide a mechanistic explanation to the long-standing question of how the network of 5'TOP mRNAs are coregulated according to amino acid availability, thereby allowing redirection of limited resources to mount a nutrient deprivation response. This presents a fundamental example of how a group of mRNAs can be translationally coregulated in response to changes in the cellular environment.
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Affiliation(s)
- Christian Kroun Damgaard
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA.
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15
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Ing NH. Estradiol up-regulates expression of the A + U-rich binding factor 1 (AUF1) gene in the sheep uterus. J Steroid Biochem Mol Biol 2010; 122:172-9. [PMID: 20621185 DOI: 10.1016/j.jsbmb.2010.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 06/21/2010] [Accepted: 07/03/2010] [Indexed: 10/19/2022]
Abstract
The A+U-rich binding factor 1 (AUF1 or HNRPD) gene produces predominant RNA binding proteins. The AUF1 transcript is alternatively spliced to produce four protein isoforms that stabilize or destabilize hundreds of mRNAs. Previously, we discovered that estradiol (E2) treatment of ovariectomized sheep increased concentrations of AUF1p45 protein which stabilized estrogen receptor alpha (ER) mRNA in the uterus. This study examined E2 regulation of AUF1 mRNAs in the sheep uterus. Northern analysis determined that E2 treatment increased concentrations of total AUF1 mRNAs twofold in endometrial and myometrial tissue compartments. In situ hybridization indicated that the increase was most intense in the glandular epithelium of endometrium. In a well characterized in vitro RNA stability assay, AUF1 3'UTR sequences were much more stable in uterine extracts from E2-treated ewes compared to extracts from control ewes. AUF1 mRNAs with alternative splicing of exons 2 and 7 (in the coding sequence) and exon 9 (in the 3'UTR) were identified. The only effect of E2 treatment on alternative splicing was that it reduced the percentage of AUF1 mRNAs containing exon 9-derived sequences. These data indicate that E2 up-regulates AUF1 and ER genes coordinately by a post-transcriptional mechanism.
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Affiliation(s)
- Nancy H Ing
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, TX 77843-2471, United States
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