1
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Sen MG, Sanislav O, Fisher PR, Annesley SJ. The Multifaceted Interactions of Dictyostelium Atg1 with Mitochondrial Function, Endocytosis, Growth, and Development. Cells 2024; 13:1191. [PMID: 39056773 PMCID: PMC11274416 DOI: 10.3390/cells13141191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Autophagy is a degradative recycling process central to the maintenance of homeostasis in all eukaryotes. By ensuring the degradation of damaged mitochondria, it plays a key role in maintaining mitochondrial health and function. Of the highly conserved autophagy proteins, autophagy-related protein 1 (Atg1) is essential to the process. The involvement of these proteins in intracellular signalling pathways, including those involving mitochondrial function, are still being elucidated. Here the role of Atg1 was investigated in the simple model organism Dictyostelium discoideum using an atg1 null mutant and mutants overexpressing or antisense-inhibiting atg1. When evaluated against the well-characterised outcomes of mitochondrial dysfunction in this model, altered atg1 expression resulted in an unconventional set of phenotypic outcomes in growth, endocytosis, multicellular development, and mitochondrial homeostasis. The findings here show that Atg1 is involved in a tightly regulated signal transduction pathway coordinating energy-consuming processes such as cell growth and multicellular development, along with nutrient status and energy production. Furthermore, Atg1's effects on energy homeostasis indicate a peripheral ancillary role in the mitochondrial signalling network, with effects on energy balance rather than direct effects on electron transport chain function. Further research is required to tease out these complex networks. Nevertheless, this study adds further evidence to the theory that autophagy and mitochondrial signalling are not opposing but rather linked, yet strictly controlled, homeostatic mechanisms.
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Affiliation(s)
| | | | | | - Sarah Jane Annesley
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Melbourne 3086, Australia; (M.G.S.); (O.S.); (P.R.F.)
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2
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Grosely R, Alvarado C, Ivanov IP, Nicholson OB, Puglisi JD, Dever TE, Lapointe CP. eIF1 and eIF5 dynamically control translation start site fidelity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602410. [PMID: 39026837 PMCID: PMC11257575 DOI: 10.1101/2024.07.10.602410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Translation initiation defines the identity of a synthesized protein through selection of a translation start site on a messenger RNA. This process is essential to well-controlled protein synthesis, modulated by stress responses, and dysregulated in many human diseases. The eukaryotic initiation factors eIF1 and eIF5 interact with the initiator methionyl-tRNAi Met on the 40S ribosomal subunit to coordinate start site selection. Here, using single-molecule analysis of in vitro reconstituted human initiation combined with translation assays in cells, we examine eIF1 and eIF5 function. During translation initiation on a panel of RNAs, we monitored both proteins directly and in real time using single-molecule fluorescence. As expected, eIF1 loaded onto mRNAs as a component of the 43S initiation complex. Rapid (~ 2 s) eIF1 departure required a translation start site and was delayed by alternative start sites and a longer 5' untranslated region (5'UTR). After its initial departure, eIF1 rapidly and transiently sampled initiation complexes, with more prolonged sampling events on alternative start sites. By contrast, eIF5 only transiently bound initiation complexes late in initiation immediately prior to association of eIF5B, which allowed joining of the 60S ribosomal subunit. eIF5 association required the presence of a translation start site and was inhibited and destabilized by alternative start sites. Using both knockdown and overexpression experiments in human cells, we validated that eIF1 and eIF5 have opposing roles during initiation. Collectively, our findings demonstrate how multiple eIF1 and eIF5 binding events control start-site selection fidelity throughout initiation, which is tuned in response to changes in the levels of both proteins.
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Affiliation(s)
- Rosslyn Grosely
- Dept. of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carlos Alvarado
- Dept. of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ivaylo P. Ivanov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | | | - Joseph D. Puglisi
- Dept. of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas E. Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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3
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Brito Querido J, Díaz-López I, Ramakrishnan V. The molecular basis of translation initiation and its regulation in eukaryotes. Nat Rev Mol Cell Biol 2024; 25:168-186. [PMID: 38052923 DOI: 10.1038/s41580-023-00624-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2023] [Indexed: 12/07/2023]
Abstract
The regulation of gene expression is fundamental for life. Whereas the role of transcriptional regulation of gene expression has been studied for several decades, it has been clear over the past two decades that post-transcriptional regulation of gene expression, of which translation regulation is a major part, can be equally important. Translation can be divided into four main stages: initiation, elongation, termination and ribosome recycling. Translation is controlled mainly during its initiation, a process which culminates in a ribosome positioned with an initiator tRNA over the start codon and, thus, ready to begin elongation of the protein chain. mRNA translation has emerged as a powerful tool for the development of innovative therapies, yet the detailed mechanisms underlying the complex process of initiation remain unclear. Recent studies in yeast and mammals have started to shed light on some previously unclear aspects of this process. In this Review, we discuss the current state of knowledge on eukaryotic translation initiation and its regulation in health and disease. Specifically, we focus on recent advances in understanding the processes involved in assembling the 43S pre-initiation complex and its recruitment by the cap-binding complex eukaryotic translation initiation factor 4F (eIF4F) at the 5' end of mRNA. In addition, we discuss recent insights into ribosome scanning along the 5' untranslated region of mRNA and selection of the start codon, which culminates in joining of the 60S large subunit and formation of the 80S initiation complex.
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Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Irene Díaz-López
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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4
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Gotoh S, Mori K, Fujino Y, Kawabe Y, Yamashita T, Omi T, Nagata K, Tagami S, Nagai Y, Ikeda M. eIF5 stimulates the CUG initiation of RAN translation of poly-GA dipeptide repeat protein (DPR) in C9orf72 FTLD/ALS. J Biol Chem 2024; 300:105703. [PMID: 38301895 PMCID: PMC10904283 DOI: 10.1016/j.jbc.2024.105703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
Tandem GGGGCC repeat expansion in C9orf72 is a genetic cause of frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Transcribed repeats are translated into dipeptide repeat proteins via repeat-associated non-AUG (RAN) translation. However, the regulatory mechanism of RAN translation remains unclear. Here, we reveal a GTPase-activating protein, eukaryotic initiation factor 5 (eIF5), which allosterically facilitates the conversion of eIF2-bound GTP into GDP upon start codon recognition, as a novel modifier of C9orf72 RAN translation. Compared to global translation, eIF5, but not its inactive mutants, preferentially stimulates poly-GA RAN translation. RAN translation is increased during integrated stress response, but the stimulatory effect of eIF5 on poly-GA RAN translation was additive to the increase of RAN translation during integrated stress response, with no further increase in phosphorylated eIF2α. Moreover, an alteration of the CUG near cognate codon to CCG or AUG in the poly-GA reading frame abolished the stimulatory effects, indicating that eIF5 primarily acts through the CUG-dependent initiation. Lastly, in a Drosophila model of C9orf72 FTLD/ALS that expresses GGGGCC repeats in the eye, knockdown of endogenous eIF5 by two independent RNAi strains significantly reduced poly-GA expressions, confirming in vivo effect of eIF5 on poly-GA RAN translation. Together, eIF5 stimulates the CUG initiation of poly-GA RAN translation in cellular and Drosophila disease models of C9orf72 FTLD/ALS.
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Affiliation(s)
- Shiho Gotoh
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kohji Mori
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan.
| | - Yuzo Fujino
- Department of Neurology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan; Department of Neurology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuya Kawabe
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Tomoko Yamashita
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Tsubasa Omi
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kenichi Nagata
- Department of Precision Medicine for Dementia, Osaka University Graduate School of Medicine, Suita, Japan
| | - Shinji Tagami
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshitaka Nagai
- Department of Neurology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Manabu Ikeda
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
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5
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Friedrich D, Marintchev A, Arthanari H. The metaphorical swiss army knife: The multitude and diverse roles of HEAT domains in eukaryotic translation initiation. Nucleic Acids Res 2022; 50:5424-5442. [PMID: 35552740 PMCID: PMC9177959 DOI: 10.1093/nar/gkac342] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
Biomolecular associations forged by specific interaction among structural scaffolds are fundamental to the control and regulation of cell processes. One such structural architecture, characterized by HEAT repeats, is involved in a multitude of cellular processes, including intracellular transport, signaling, and protein synthesis. Here, we review the multitude and versatility of HEAT domains in the regulation of mRNA translation initiation. Structural and cellular biology approaches, as well as several biophysical studies, have revealed that a number of HEAT domain-mediated interactions with a host of protein factors and RNAs coordinate translation initiation. We describe the basic structural architecture of HEAT domains and briefly introduce examples of the cellular processes they dictate, including nuclear transport by importin and RNA degradation. We then focus on proteins in the translation initiation system featuring HEAT domains, specifically the HEAT domains of eIF4G, DAP5, eIF5, and eIF2Bϵ. Comparative analysis of their remarkably versatile interactions, including protein-protein and protein-RNA recognition, reveal the functional importance of flexible regions within these HEAT domains. Here we outline how HEAT domains orchestrate fundamental aspects of translation initiation and highlight open mechanistic questions in the area.
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Affiliation(s)
- Daniel Friedrich
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Assen Marintchev
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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6
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Kratzat H, Mackens-Kiani T, Ameismeier M, Potocnjak M, Cheng J, Dacheux E, Namane A, Berninghausen O, Herzog F, Fromont-Racine M, Becker T, Beckmann R. A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes. EMBO J 2020; 40:e105179. [PMID: 33289941 PMCID: PMC7780240 DOI: 10.15252/embj.2020105179] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/21/2020] [Accepted: 09/29/2020] [Indexed: 11/24/2022] Open
Abstract
In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub‐complexes. These comprise/include the large eIF3 complex, eIF3j (Hcr1 in yeast) and the ATP‐binding cassette protein ABCE1 (Rli1 in yeast). The ATPase is mainly active as a recycling factor, but it can remain bound to the dissociated 40S subunit until formation of the next 43S pre‐initiation complexes. However, its functional role and native architectural context remains largely enigmatic. Here, we present an architectural inventory of native yeast and human ABCE1‐containing pre‐initiation complexes by cryo‐EM. We found that ABCE1 was mostly associated with early 43S, but also with later 48S phases of initiation. It adopted a novel hybrid conformation of its nucleotide‐binding domains, while interacting with the N‐terminus of eIF3j. Further, eIF3j occupied the mRNA entry channel via its ultimate C‐terminus providing a structural explanation for its antagonistic role with respect to mRNA binding. Overall, the native human samples provide a near‐complete molecular picture of the architecture and sophisticated interaction network of the 43S‐bound eIF3 complex and the eIF2 ternary complex containing the initiator tRNA.
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Affiliation(s)
- Hanna Kratzat
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Timur Mackens-Kiani
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Michael Ameismeier
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Mia Potocnjak
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Jingdong Cheng
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Estelle Dacheux
- Génétique des Interactions Macromoléculaires, UMR3525 CNRS, Institut Pasteur, Paris, France
| | - Abdelkader Namane
- Génétique des Interactions Macromoléculaires, UMR3525 CNRS, Institut Pasteur, Paris, France
| | - Otto Berninghausen
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Franz Herzog
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | | | - Thomas Becker
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
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7
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Gerdol M, Visintin A, Kaleb S, Spazzali F, Pallavicini A, Falace A. Gene expression response of the alga Fucus virsoides (Fucales, Ochrophyta) to glyphosate solution exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 267:115483. [PMID: 32889518 DOI: 10.1016/j.envpol.2020.115483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Fucus virsoides is an ecologically important canopy-forming brown algae endemic to the Adriatic Sea. Once widespread in marine coastal areas, this species underwent a rapid population decline and is now confined to small residual areas. Although the reasons behind this progressive disappearance are still a matter of debate, F. virsoides may suffer, like other macroalgae, from the potential toxic effects of glyphosate-based herbicides. Here, through a transcriptomic approach, we investigate the molecular basis of the high susceptibility of this species to glyphosate solution, previously observed at the morphological and eco-physiological levels. By simulating runoff event in a factorial experiment, we exposed F. virsoides to glyphosate (Roundup® 2.0), either alone or in association with nutrient enrichment, highlighting significant alterations of gene expression profiles that were already visible after three days of exposure. In particular, glyphosate exposure determined the near-complete expression shutdown of several genes involved in photosynthesis, protein synthesis and stress response molecular pathways. Curiously, these detrimental effects were partially mitigated by nutrient supplementation, which may explain the survival of relict population in confined areas with high nutrient inputs.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Andrea Visintin
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Sara Kaleb
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Francesca Spazzali
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy; CoNISMa, Piazzale Flaminio 9, 00196, Roma, Italy; Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Annalisa Falace
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy; CoNISMa, Piazzale Flaminio 9, 00196, Roma, Italy; Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy.
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8
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Ma RH, Ni ZJ, Thakur K, Zhang F, Zhang YY, Zhang JG, Wei ZJ. Natural Compounds Play Therapeutic Roles in Various Human Pathologies via Regulating Endoplasmic Reticulum Pathway. MEDICINE IN DRUG DISCOVERY 2020. [DOI: 10.1016/j.medidd.2020.100065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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9
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Firczuk H, Teahan J, Mendes P, McCarthy JEG. Multisite rate control analysis identifies ribosomal scanning as the sole high-capacity/low-flux-control step in mRNA translation. FEBS J 2019; 287:925-940. [PMID: 31520451 PMCID: PMC7054134 DOI: 10.1111/febs.15059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/26/2019] [Accepted: 09/09/2019] [Indexed: 11/30/2022]
Abstract
Control of complex intracellular pathways such as protein synthesis is critical to organism survival, but is poorly understood. Translation of a reading frame in eukaryotic mRNA is preceded by a scanning process in which a subset of translation factors helps guide ribosomes to the start codon. Here, we perform comparative analysis of the control status of this scanning step that sits between recruitment of the small ribosomal subunit to the m7GpppG‐capped 5′end of mRNA and of the control exerted by downstream phases of polypeptide initiation, elongation and termination. We have utilized a detailed predictive model as guidance for designing quantitative experimental interrogation of control in the yeast translation initiation pathway. We have built a synthetic orthogonal copper‐responsive regulatory promoter (PCuR3) that is used here together with the tet07 regulatory system in a novel dual‐site in vivo rate control analysis strategy. Combining this two‐site strategy with calibrated mass spectrometry to determine translation factor abundance values, we have tested model‐based predictions of rate control properties of the in vivo system. We conclude from the results that the components of the translation machinery that promote scanning collectively function as a low‐flux‐control system with a capacity to transfer ribosomes into the core process of polypeptide production that exceeds the respective capacities of the steps of polypeptide initiation, elongation and termination. In contrast, the step immediately prior to scanning, that is, ribosome recruitment via the mRNA 5′ cap‐binding complex, is a high‐flux‐control step.
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Affiliation(s)
- Helena Firczuk
- Warwick Integrative Synthetic Biology Centre [WISB] and School of Life Sciences, University of Warwick, Coventry, UK
| | - James Teahan
- Warwick Integrative Synthetic Biology Centre [WISB] and School of Life Sciences, University of Warwick, Coventry, UK
| | - Pedro Mendes
- Center for Quantitative Medicine, UConn Health, Farmington, CT, USA
| | - John E G McCarthy
- Warwick Integrative Synthetic Biology Centre [WISB] and School of Life Sciences, University of Warwick, Coventry, UK
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10
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Ye Y, Chen M, Kato K, Yao M. The pH-dependent conformational change of eukaryotic translation initiation factor 5: Insights into partner-binding manner. Biochem Biophys Res Commun 2019; 519:186-191. [PMID: 31492496 DOI: 10.1016/j.bbrc.2019.08.128] [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: 08/16/2019] [Accepted: 08/23/2019] [Indexed: 10/26/2022]
Abstract
In the process of eukaryotic translation, the formation of preinitiation complex 43S, which consists of a 40S subunit, the eIF2-GTP-Met-tRNAiMet ternary complex, eIF3, eIF1, eIF1A, and eIF5, is essential for translational quality control. Of those factors, eIF5 promotes the hydrolysis of eIF2-bound GTP to release eIF2-GDP in the complex for the recycling of eIF2. eIF5 appears to bind to the β subunit of eIF2 (eIF2β) via an interaction between aromatic/acidic residue-rich regions (AA-boxes) in the C-terminal domain of eIF5 (eIF5CTD) and three lysine clusters (K-boxes) in the N-terminal domain of eIF2β (eIF2βNTD). However, the details of this interaction are unclear, due to the lack of a structure for the eIF5-eIF2β complex, and the unavailability of an intact structure of eIF5, in which the AA-boxes are always disordered, with high flexibility. In this study, we solved two crystal structures of eIF5CTD from Candida albicans, which for the first time showed the AA-box2 of eIF5 presenting as an ordered helical structure. The structures exhibited different arrangements of AA-box2 under different pH values, which may reflect the dynamic nature of the interactions of eIF5CTD, and eIF2βNTD in the preinitiation complex.
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Affiliation(s)
- Yuxin Ye
- Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, 060-0810, Japan
| | - Meirong Chen
- Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, 060-0810, Japan; College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Koji Kato
- Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, 060-0810, Japan
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, 060-0810, Japan.
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11
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Gordiyenko Y, Llácer JL, Ramakrishnan V. Structural basis for the inhibition of translation through eIF2α phosphorylation. Nat Commun 2019; 10:2640. [PMID: 31201334 PMCID: PMC6572841 DOI: 10.1038/s41467-019-10606-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/10/2019] [Indexed: 11/29/2022] Open
Abstract
One of the responses to stress by eukaryotic cells is the down-regulation of protein synthesis by phosphorylation of translation initiation factor eIF2. Phosphorylation results in low availability of the eIF2 ternary complex (eIF2-GTP-tRNAi) by affecting the interaction of eIF2 with its GTP-GDP exchange factor eIF2B. We have determined the cryo-EM structure of yeast eIF2B in complex with phosphorylated eIF2 at an overall resolution of 4.2 Å. Two eIF2 molecules bind opposite sides of an eIF2B hetero-decamer through eIF2α-D1, which contains the phosphorylated Ser51. eIF2α-D1 is mainly inserted between the N-terminal helix bundle domains of δ and α subunits of eIF2B. Phosphorylation of Ser51 enhances binding to eIF2B through direct interactions of phosphate groups with residues in eIF2Bα and indirectly by inducing contacts of eIF2α helix 58–63 with eIF2Bδ leading to a competition with Met-tRNAi. During stress, protein synthesis is inhibited through phosphorylation of the initiation factor eIF2 on its alpha subunit and its interaction with eIF2B. Here the authors describe a structure of the yeast eIF2B in complex with its substrate - the GDP-bound phosphorylated eIF2, providing insights into how phosphorylation results in a tighter interaction with eIF2B.
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Affiliation(s)
- Yuliya Gordiyenko
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - José Luis Llácer
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK. .,Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas and CIBERER-ISCIII, Valencia, 46010, Spain.
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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12
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Llácer JL, Hussain T, Saini AK, Nanda JS, Kaur S, Gordiyenko Y, Kumar R, Hinnebusch AG, Lorsch JR, Ramakrishnan V. Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition. eLife 2018; 7:e39273. [PMID: 30475211 PMCID: PMC6298780 DOI: 10.7554/elife.39273] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/21/2018] [Indexed: 12/22/2022] Open
Abstract
In eukaryotic translation initiation, AUG recognition of the mRNA requires accommodation of Met-tRNAi in a 'PIN' state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) of eIF2 that additionally promotes stringent AUG selection, but the molecular basis of its dual function was unknown. We present a cryo-electron microscopy (cryo-EM) reconstruction of a yeast 48S pre-initiation complex (PIC), at an overall resolution of 3.0 Å, featuring the N-terminal domain (NTD) of eIF5 bound to the 40S subunit at the location vacated by eIF1. eIF5 interacts with and allows a more accommodated orientation of Met-tRNAi. Substitutions of eIF5 residues involved in the eIF5-NTD/tRNAi interaction influenced initiation at near-cognate UUG codonsin vivo, and the closed/open PIC conformation in vitro, consistent with direct stabilization of the codon:anticodon duplex by the wild-type eIF5-NTD. The present structure reveals the basis for a key role of eIF5 in start-codon selection.
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Affiliation(s)
- Jose Luis Llácer
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
- Instituto de Biomedicina de Valencia (IBV-CSIC)ValenciaSpain
| | - Tanweer Hussain
- Department of Molecular Reproduction, Development and GeneticsIndian Institute of ScienceBangaloreIndia
| | - Adesh K Saini
- Shoolini University of Biotechnology and Management SciencesHimachal PradeshIndia
| | - Jagpreet Singh Nanda
- Laboratory on the Mechanism and Regulation of Protein SynthesisEunice K Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Sukhvir Kaur
- Shoolini University of Biotechnology and Management SciencesHimachal PradeshIndia
| | | | - Rakesh Kumar
- Shoolini University of Biotechnology and Management SciencesHimachal PradeshIndia
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and DevelopmentEunice K Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Jon R Lorsch
- Laboratory on the Mechanism and Regulation of Protein SynthesisEunice K Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - V Ramakrishnan
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
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13
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Manalo RVM, Medina PMB. The endoplasmic reticulum stress response in disease pathogenesis and pathophysiology. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2018. [DOI: 10.1016/j.ejmhg.2017.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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14
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Loughran G, Firth AE, Atkins JF, Ivanov IP. Translational autoregulation of BZW1 and BZW2 expression by modulating the stringency of start codon selection. PLoS One 2018; 13:e0192648. [PMID: 29470543 PMCID: PMC5823381 DOI: 10.1371/journal.pone.0192648] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/26/2018] [Indexed: 01/20/2023] Open
Abstract
The efficiency of start codon selection during ribosomal scanning in eukaryotic translation initiation is influenced by the context or flanking nucleotides surrounding the AUG codon. The levels of eukaryotic translation initiation factors 1 (eIF1) and 5 (eIF5) play critical roles in controlling the stringency of translation start site selection. The basic leucine zipper and W2 domain-containing proteins 1 and 2 (BZW1 and BZW2), also known as eIF5-mimic proteins, are paralogous human proteins containing C-terminal HEAT domains that resemble the HEAT domain of eIF5. We show that translation of mRNAs encoding BZW1 and BZW2 homologs in fungi, plants and metazoans is initiated by AUG codons in conserved unfavorable initiation contexts. This conservation is reminiscent of the conserved unfavorable initiation context that enables autoregulation of EIF1. We show that overexpression of BZW1 and BZW2 proteins enhances the stringency of start site selection, and that their poor initiation codons confer autoregulation on BZW1 and BZW2 mRNA translation. We also show that overexpression of these two proteins significantly diminishes the effect of overexpressing eIF5 on stringency of start codon selection, suggesting they antagonize this function of eIF5. These results reveal a surprising role for BZW1 and BZW2 in maintaining homeostatic stringency of start codon selection, and taking into account recent biochemical, genetic and structural insights into eukaryotic initiation, suggest a model for BZW1 and BZW2 function.
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Affiliation(s)
- Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E. Firth
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - John F. Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Ivaylo P. Ivanov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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15
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RAN translation at C9orf72-associated repeat expansions is selectively enhanced by the integrated stress response. Nat Commun 2017; 8:2005. [PMID: 29222490 PMCID: PMC5722904 DOI: 10.1038/s41467-017-02200-0] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 11/12/2017] [Indexed: 12/22/2022] Open
Abstract
Repeat-associated non-AUG (RAN) translation allows for unconventional initiation at disease-causing repeat expansions. As RAN translation contributes to pathogenesis in multiple neurodegenerative disorders, determining its mechanistic underpinnings may inform therapeutic development. Here we analyze RAN translation at G4C2 repeat expansions that cause C9orf72-associated amyotrophic lateral sclerosis and frontotemporal dementia (C9RAN) and at CGG repeats that cause fragile X-associated tremor/ataxia syndrome. We find that C9RAN translation initiates through a cap- and eIF4A-dependent mechanism that utilizes a CUG start codon. C9RAN and CGG RAN are both selectively enhanced by integrated stress response (ISR) activation. ISR-enhanced RAN translation requires an eIF2α phosphorylation-dependent alteration in start codon fidelity. In parallel, both CGG and G4C2 repeats trigger phosphorylated-eIF2α-dependent stress granule formation and global translational suppression. These findings support a model whereby repeat expansions elicit cellular stress conditions that favor RAN translation of toxic proteins, creating a potential feed-forward loop that contributes to neurodegeneration. A nucleotide repeat expansion in C9orf72 is a common genetic cause of neurodegenerative disorders. Here, the authors provide insight into the molecular mechanism by which this repeat undergoes Repeat-Associated Non-AUG (RAN) translation, implicating the integrated stress response and eIF2α phosphorylation.
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16
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Yourik P, Aitken CE, Zhou F, Gupta N, Hinnebusch AG, Lorsch JR. Yeast eIF4A enhances recruitment of mRNAs regardless of their structural complexity. eLife 2017; 6:31476. [PMID: 29192585 PMCID: PMC5726853 DOI: 10.7554/elife.31476] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/23/2017] [Indexed: 12/11/2022] Open
Abstract
eIF4A is a DEAD-box RNA-dependent ATPase thought to unwind RNA secondary structure in the 5'-untranslated regions (UTRs) of mRNAs to promote their recruitment to the eukaryotic translation pre-initiation complex (PIC). We show that eIF4A's ATPase activity is markedly stimulated in the presence of the PIC, independently of eIF4E•eIF4G, but dependent on subunits i and g of the heteromeric eIF3 complex. Surprisingly, eIF4A accelerated the rate of recruitment of all mRNAs tested, regardless of their degree of structural complexity. Structures in the 5'-UTR and 3' of the start codon synergistically inhibit mRNA recruitment in a manner relieved by eIF4A, indicating that the factor does not act solely to melt hairpins in 5'-UTRs. Our findings that eIF4A functionally interacts with the PIC and plays important roles beyond unwinding 5'-UTR structure is consistent with a recent proposal that eIF4A modulates the conformation of the 40S ribosomal subunit to promote mRNA recruitment.
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Affiliation(s)
- Paul Yourik
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Colin Echeverría Aitken
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Fujun Zhou
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Neha Gupta
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Jon R Lorsch
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
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17
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Manalo RVM. Anastasis and the ER stress response: Solving the paradox of the unfolded protein response in cancer. Med Hypotheses 2017; 109:25-27. [PMID: 29150287 DOI: 10.1016/j.mehy.2017.09.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/01/2017] [Accepted: 09/15/2017] [Indexed: 01/27/2023]
Abstract
In recent years, studies have suggested a novel pathway for cell survival, which faces scientific skepticism and interest in its concept of cell 'resurrection' - that is, the anastasis of cells at late-stage apoptosis. While biomarkers have been discovered, many of these are related to the endoplasmic reticulum (ER) stress response - acting also to promote cell survival in the presence of perturbation. The promises of anastasis, if accepted, will greatly impact translational medicine especially in the treatment of cancer, since apoptosis is generally irreversible in the late stages, and chemotherapy is performed to maximize tumor death and minimize off-target effects. As with all new concepts, there is a need to demarcate anastasis from a well-studied survival mechanism - the ER stress response - if the concept is to progress any further. In this article, it is proposed that anastasis and the ER stress response are one and the same mechanism, demarcated only by the presence of persistent stress. Further, anastasis solves the paradox of the unfolded protein response (UPR) in cancer by providing rationale in C/EBP homologous protein (CHOP)-induced tumor survival, such that CHOP-mediated apoptosis initiates genetic alterations in favor of its survival. After which, the cell regenerates through an enhanced ER stress response. Hence, anastatic cell recovery is the ER stress response post-apoptosis.
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Affiliation(s)
- Rafael Vincent M Manalo
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Ermita, Manila 1000, Philippines.
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18
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Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae. Genetics 2017; 203:65-107. [PMID: 27183566 DOI: 10.1534/genetics.115.186221] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/24/2016] [Indexed: 12/18/2022] Open
Abstract
In this review, we provide an overview of protein synthesis in the yeast Saccharomyces cerevisiae The mechanism of protein synthesis is well conserved between yeast and other eukaryotes, and molecular genetic studies in budding yeast have provided critical insights into the fundamental process of translation as well as its regulation. The review focuses on the initiation and elongation phases of protein synthesis with descriptions of the roles of translation initiation and elongation factors that assist the ribosome in binding the messenger RNA (mRNA), selecting the start codon, and synthesizing the polypeptide. We also examine mechanisms of translational control highlighting the mRNA cap-binding proteins and the regulation of GCN4 and CPA1 mRNAs.
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19
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Terenin IM, Akulich KA, Andreev DE, Polyanskaya SA, Shatsky IN, Dmitriev SE. Sliding of a 43S ribosomal complex from the recognized AUG codon triggered by a delay in eIF2-bound GTP hydrolysis. Nucleic Acids Res 2016; 44:1882-93. [PMID: 26717981 PMCID: PMC4770231 DOI: 10.1093/nar/gkv1514] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 02/05/2023] Open
Abstract
During eukaryotic translation initiation, 43S ribosomal complex scans mRNA leader unless an AUG codon in an appropriate context is found. Establishing the stable codon-anticodon base-pairing traps the ribosome on the initiator codon and triggers structural rearrangements, which lead to Pi release from the eIF2-bound GTP. It is generally accepted that AUG recognition by the scanning 43S complex sets the final point in the process of start codon selection, while latter stages do not contribute to this process. Here we use translation reconstitution approach and kinetic toe-printing assay to show that after the 48S complex is formed on an AUG codon, in case GTP hydrolysis is impaired, the ribosomal subunit is capable to resume scanning and slides downstream to the next AUG. In contrast to leaky scanning, this sliding is not limited to AUGs in poor nucleotide contexts and occurs after a relatively long pause at the recognized AUG. Thus, recognition of an AUG per se does not inevitably lead to this codon being selected for initiation of protein synthesis. Instead, it is eIF5-induced GTP hydrolysis and Pi release that irreversibly trap the 48S complex, and this complex is further stabilized by eIF5B and 60S joining.
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Affiliation(s)
- Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Kseniya A Akulich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, 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
| | - Sofya A Polyanskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia Department of Molecular Biology, Biological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia Department of Biochemistry, Biological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia
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20
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Aktas BH, Bordelois P, Peker S, Merajver S, Halperin JA. Depletion of eIF2·GTP·Met-tRNAi translation initiation complex up-regulates BRCA1 expression in vitro and in vivo. Oncotarget 2016; 6:6902-14. [PMID: 25762631 PMCID: PMC4466658 DOI: 10.18632/oncotarget.3125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/09/2015] [Indexed: 01/27/2023] Open
Abstract
Most sporadic breast and ovarian cancers express low levels of the breast cancer susceptibility gene, BRCA1. The BRCA1 gene produces two transcripts, mRNAa and mRNAb. mRNAb, present in breast cancer but not in normal mammary epithelial cells, contains three upstream open reading frames (uORFs) in its 5′UTR and is translationally repressed. Comparable tandem uORFs are characteristically seen in mRNAs whose translational efficiency paradoxically increases when the overall translation rate is decreased due to phosphorylation of eukaryotic translation initiation factor 2 α (eIF2α). Here we show fish oil derived eicosopanthenoic acid (EPA) that induces eIF2α phosphorylation translationally up-regulates the expression of BRCA1 in human breast cancer cells. We demonstrate further that a diet rich in EPA strongly induces expression of BRCA1 in human breast cancer xenografts.
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Affiliation(s)
- Bertal H Aktas
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Selen Peker
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA.,Ankara University Biotechnology Institute, Ankara, Turkey
| | - Sophia Merajver
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jose A Halperin
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
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21
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Abstract
ATP-binding cassette 50 (ABC50; also known as ABCF1) binds to eukaryotic initiation factor 2 (eIF2) and is required for efficient translation initiation. An essential step of this process is accurate recognition and selection of the initiation codon. It is widely accepted that the presence and movement of eIF1, eIF1A and eIF5 are key factors in modulating the stringency of start-site selection, which normally requires an AUG codon in an appropriate sequence context. In the present study, we show that expression of ABC50 mutants, which cannot hydrolyse ATP, decreases general translation and relaxes the discrimination against the use of non-AUG codons at translation start sites. These mutants do not appear to alter the association of key initiation factors to 40S subunits. The stringency of start-site selection can be restored through overexpression of eIF1, consistent with the role of that factor in enhancing stringency. The present study indicates that interfering with the function of ABC50 influences the accuracy of initiation codon selection.
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22
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Dubiez E, Aleksandrov A, Lazennec-Schurdevin C, Mechulam Y, Schmitt E. Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2. Nucleic Acids Res 2015; 43:2946-57. [PMID: 25690901 PMCID: PMC4357699 DOI: 10.1093/nar/gkv053] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Eukaryotic and archaeal translation initiation processes involve a heterotrimeric GTPase e/aIF2 crucial for accuracy of start codon selection. In eukaryotes, the GTPase activity of eIF2 is assisted by a GTPase-activating protein (GAP), eIF5. In archaea, orthologs of eIF5 are not found and aIF2 GTPase activity is thought to be non-assisted. However, no in vitro GTPase activity of the archaeal factor has been reported to date. Here, we show that aIF2 significantly hydrolyses GTP in vitro. Within aIF2γ, H97, corresponding to the catalytic histidine found in other translational GTPases, and D19, from the GKT loop, both participate in this activity. Several high-resolution crystal structures were determined to get insight into GTP hydrolysis by aIF2γ. In particular, a crystal structure of the H97A mutant was obtained in the presence of non-hydrolyzed GTP. This structure reveals the presence of a second magnesium ion bound to GTP and D19. Quantum chemical/molecular mechanical simulations support the idea that the second magnesium ion may assist GTP hydrolysis by helping to neutralize the developing negative charge in the transition state. These results are discussed in light of the absence of an identified GAP in archaea to assist GTP hydrolysis on aIF2.
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Affiliation(s)
- Etienne Dubiez
- Laboratoire de Biochimie, Unité Mixte de Recherche 7654, Ecole Polytechnique, Centre National de la Recherche Scientifique, F-91128 Palaiseau cedex, France
| | - Alexey Aleksandrov
- Laboratoire de Biochimie, Unité Mixte de Recherche 7654, Ecole Polytechnique, Centre National de la Recherche Scientifique, F-91128 Palaiseau cedex, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biochimie, Unité Mixte de Recherche 7654, Ecole Polytechnique, Centre National de la Recherche Scientifique, F-91128 Palaiseau cedex, France
| | - Yves Mechulam
- Laboratoire de Biochimie, Unité Mixte de Recherche 7654, Ecole Polytechnique, Centre National de la Recherche Scientifique, F-91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, Unité Mixte de Recherche 7654, Ecole Polytechnique, Centre National de la Recherche Scientifique, F-91128 Palaiseau cedex, France
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23
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Bavli-Kertselli I, Melamed D, Bar-Ziv L, Volf H, Arava Y. Overexpression of eukaryotic initiation factor 5 rescues the translational defect of tpk1w in a manner that necessitates a novel phosphorylation site. FEBS J 2014; 282:504-20. [PMID: 25417541 DOI: 10.1111/febs.13158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 11/11/2014] [Accepted: 11/20/2014] [Indexed: 02/04/2023]
Abstract
Cells respond to changes in their environment through mechanisms that often necessitate reprogramming of the translation machinery. The fastest and strongest of all tested responses is the translation inhibition observed following abrupt depletion of glucose from the media of yeast cells. The speed of the response suggests a post-translational modification of a key component of the translation machinery. This translation factor is as yet unknown. A cAMP-dependent protein kinase mutant yeast strain (tpk1(w)) that does not respond properly to glucose depletion and maintains translation was described previously. We hypothesized that the inability of tpk1(w) to arrest translation results from abnormal expression of key translation mediators. Genome-wide analysis of steady-state mRNA levels in tpk1(w) revealed underexpression of several candidates. Elevating the cellular levels of eukaryotic initiation factor (eIF) 5 by overexpression rescued the translational defect of tpk1(w). Restoring ribosomal dissociation by eIF5 necessitated an active GAP domain and multiple regions throughout this protein. Phosphoproteomics analysis of wild-type cells overexpressing eIF5 revealed increased phosphorylation in a novel site (Thr191) upon glucose depletion. Mutating this residue and introducing it into tpk1(w) abolished the ability of eIF5 to rescue the translational defect. Intriguingly, introducing this mutation into the wild-type strain did not hamper its translational response. We further show that Thr191 is phosphorylated in vitro by Casein Kinase II (CKII), and yeast cells with a mutated CKII have a reduced response to glucose depletion. These results implicate phosphorylation of eIF5 at Thr191 by CKII as one of the pathways for regulating translation upon glucose depletion.
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Affiliation(s)
- Ira Bavli-Kertselli
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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24
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Wang M, Kaufman RJ. The impact of the endoplasmic reticulum protein-folding environment on cancer development. Nat Rev Cancer 2014; 14:581-97. [PMID: 25145482 DOI: 10.1038/nrc3800] [Citation(s) in RCA: 776] [Impact Index Per Article: 77.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The endoplasmic reticulum (ER) is an essential organelle in eukaryotic cells for the storage and regulated release of calcium and as the entrance to the secretory pathway. Protein misfolding in the ER causes accumulation of misfolded proteins (ER stress) and activation of the unfolded protein response (UPR), which has evolved to maintain a productive ER protein-folding environment. Both ER stress and UPR activation are documented in many different human cancers. In this Review, we summarize the impact of ER stress and UPR activation on every aspect of cancer and discuss outstanding questions for which answers will pave the way for therapeutics.
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Affiliation(s)
- Miao Wang
- Degenerative Diseases Program, Center for Cancer Research, Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Rd, La Jolla, California 92037, USA
| | - Randal J Kaufman
- Degenerative Diseases Program, Center for Cancer Research, Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Rd, La Jolla, California 92037, USA
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25
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Saini AK, Nanda JS, Martin-Marcos P, Dong J, Zhang F, Bhardwaj M, Lorsch JR, Hinnebusch AG. Eukaryotic translation initiation factor eIF5 promotes the accuracy of start codon recognition by regulating Pi release and conformational transitions of the preinitiation complex. Nucleic Acids Res 2014; 42:9623-40. [PMID: 25114053 PMCID: PMC4150770 DOI: 10.1093/nar/gku653] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
eIF5 is the GTPase activating protein (GAP) for the eIF2 · GTP · Met-tRNAi (Met) ternary complex with a critical role in initiation codon selection. Previous work suggested that the eIF5 mutation G31R/SUI5 elevates initiation at UUG codons by increasing GAP function. Subsequent work implicated eIF5 in rearrangement of the preinitiation complex (PIC) from an open, scanning conformation to a closed state at AUG codons, from which Pi is released from eIF2 · GDP · Pi. To identify eIF5 functions crucial for accurate initiation, we investigated the consequences of G31R on GTP hydrolysis and Pi release, and the effects of intragenic G31R suppressors on these reactions, and on the partitioning of PICs between open and closed states. eIF5-G31R altered regulation of Pi release, accelerating it at UUG while decreasing it at AUG codons, consistent with its ability to stabilize the closed complex at UUG. Suppressor G62S mitigates both defects of G31R, accounting for its efficient suppression of UUG initiation in G31R,G62S cells; however suppressor M18V impairs GTP hydrolysis with little effect on PIC conformation. The strong defect in GTP hydrolysis conferred by M18V likely explains its broad suppression of Sui(-) mutations in numerous factors. We conclude that both of eIF5's functions, regulating Pi release and stabilizing the closed PIC conformation, contribute to stringent AUG selection in vivo.
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Affiliation(s)
- Adesh K Saini
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jagpreet S Nanda
- Shoolini University of Biotechnology and Management Sciences, Department of Biotechnology, Bajhol, Solan, Himachal Pradesh 173229, India
| | - Pilar Martin-Marcos
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jinsheng Dong
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Fan Zhang
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Monika Bhardwaj
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jon R Lorsch
- Shoolini University of Biotechnology and Management Sciences, Department of Biotechnology, Bajhol, Solan, Himachal Pradesh 173229, India
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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26
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Abstract
Translation initiation plays a critical role in the regulation of cell growth and tumorigenesis. We report here that inhibiting translation initiation through induction of eIF2α phosphorylation by small-molecular-weight compounds restricts the availability of the eIF2·GTP·Met-tRNAi ternary complex and abrogates the proliferation of cancer cells in vitro and tumor growth in vivo. Restricting the availability of the ternary complex preferentially down-regulates the expression of growth-promoting proteins and up-regulates the expression of ER stress response genes in cancer cells as well as in tumors excised from either animal models of human cancer or cancer patients. These findings provide the first direct evidence for translational control of gene-specific expression by small molecules in vivo and indicate that translation initiation factors are bona fide targets for development of mechanism-specific anti-cancer agents.
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27
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Abstract
In eukaryotes, the translation initiation codon is generally identified by the scanning mechanism, wherein every triplet in the messenger RNA leader is inspected for complementarity to the anticodon of methionyl initiator transfer RNA (Met-tRNAi). Binding of Met-tRNAi to the small (40S) ribosomal subunit, in a ternary complex (TC) with eIF2-GTP, is stimulated by eukaryotic initiation factor 1 (eIF1), eIF1A, eIF3, and eIF5, and the resulting preinitiation complex (PIC) joins the 5' end of mRNA preactivated by eIF4F and poly(A)-binding protein. RNA helicases remove secondary structures that impede ribosome attachment and subsequent scanning. Hydrolysis of eIF2-bound GTP is stimulated by eIF5 in the scanning PIC, but completion of the reaction is impeded at non-AUG triplets. Although eIF1 and eIF1A promote scanning, eIF1 and possibly the C-terminal tail of eIF1A must be displaced from the P decoding site to permit base-pairing between Met-tRNAi and the AUG codon, as well as to allow subsequent phosphate release from eIF2-GDP. A second GTPase, eIF5B, catalyzes the joining of the 60S subunit to produce an 80S initiation complex that is competent for elongation.
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Affiliation(s)
- Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892;
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28
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Barth-Baus D, Bhasker CR, Zoll W, Merrick WC. Influence of translation factor activities on start site selection in six different mRNAs. ACTA ACUST UNITED AC 2013; 1:e24419. [PMID: 26824019 PMCID: PMC4718060 DOI: 10.4161/trla.24419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/21/2013] [Accepted: 03/22/2013] [Indexed: 11/19/2022]
Abstract
Current literature using biochemical assays, structural analyses and genetic manipulations has reported that the key factors associated with the faithful matching of the initiator met-tRNA to the start codon AUG are eIF1, eIF1A and eIF5. However, these findings were in each case based upon the utilization of a single mRNA, perhaps with variations. In an effort to evaluate this general finding, we tested six different mRNAs. Our results confirm that these three proteins are important for start site selection. However, two additional findings would not have been predicted. The first is that eIF1 plays a major role in selecting against start codons that are in close proximity to the 5′ end of the mRNA (i.e., less than 21 nucleotides). Second, the addition of eIF5B had nearly the same affect as the addition of eIF5. This is unexpected given the different roles that eIF5 and eIF5B have been proposed to play in the 80S initiation pathway. Finally, although many of the mRNAs appear to respond qualitatively in a similar manner, the quantitative differences noted suggest that there is still some mRNA specific character to our findings. This character may be the length of the 5′ UTR, involvement of an IRES element, secondary structure either 5′ or 3′ of the start codon or specific sequence/structure elements that interact with RNA binding proteins or the ribosome.
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Affiliation(s)
- Daine Barth-Baus
- Department of Biochemistry; School of Medicine; Case Western Reserve University; Cleveland, OH USA
| | | | - Wendy Zoll
- Biology Department; Montgomery County Community College; Blue Bell, PA USA
| | - William C Merrick
- Department of Biochemistry; School of Medicine; Case Western Reserve University; Cleveland, OH USA
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29
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Valásek LS. 'Ribozoomin'--translation initiation from the perspective of the ribosome-bound eukaryotic initiation factors (eIFs). Curr Protein Pept Sci 2013; 13:305-30. [PMID: 22708493 PMCID: PMC3434475 DOI: 10.2174/138920312801619385] [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: 02/12/2011] [Revised: 01/16/2012] [Accepted: 02/16/2012] [Indexed: 02/05/2023]
Abstract
Protein synthesis is a fundamental biological mechanism bringing the DNA-encoded genetic information into
life by its translation into molecular effectors - proteins. The initiation phase of translation is one of the key points of gene
regulation in eukaryotes, playing a role in processes from neuronal function to development. Indeed, the importance of the
study of protein synthesis is increasing with the growing list of genetic diseases caused by mutations that affect mRNA
translation. To grasp how this regulation is achieved or altered in the latter case, we must first understand the molecular
details of all underlying processes of the translational cycle with the main focus put on its initiation. In this review I discuss
recent advances in our comprehension of the molecular basis of particular initiation reactions set into the context of
how and where individual eIFs bind to the small ribosomal subunit in the pre-initiation complex. I also summarize our
current knowledge on how eukaryotic initiation factor eIF3 controls gene expression in the gene-specific manner via reinitiation.
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Affiliation(s)
- Leos Shivaya Valásek
- Laboratory of Eukaryotic Gene Regulation, Institute of Microbiology AS CR, Prague, Czech Republic.
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30
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Nanda JS, Saini AK, Muñoz AM, Hinnebusch AG, Lorsch JR. Coordinated movements of eukaryotic translation initiation factors eIF1, eIF1A, and eIF5 trigger phosphate release from eIF2 in response to start codon recognition by the ribosomal preinitiation complex. J Biol Chem 2013; 288:5316-29. [PMID: 23293029 PMCID: PMC3581429 DOI: 10.1074/jbc.m112.440693] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/04/2013] [Indexed: 11/06/2022] Open
Abstract
Accurate recognition of the start codon in an mRNA by the eukaryotic translation preinitiation complex (PIC) is essential for proper gene expression. The process is mediated by eukaryotic translation initiation factors (eIFs) in conjunction with the 40 S ribosomal subunit and (initiator) tRNA(i). Here, we provide evidence that the C-terminal tail (CTT) of eIF1A, which we previously implicated in start codon recognition, moves closer to the N-terminal domain of eIF5 when the PIC encounters an AUG codon. Importantly, this movement is coupled to dissociation of eIF1 from the PIC, a critical event in start codon recognition, and is dependent on the scanning enhancer elements in the eIF1A CTT. The data further indicate that eIF1 dissociation must be accompanied by the movement of the eIF1A CTT toward eIF5 in order to trigger release of phosphate from eIF2, which converts the latter to its GDP-bound state. Our results also suggest that release of eIF1 from the PIC and movement of the CTT of eIF1A are triggered by the same event, most likely accommodation of tRNA(i) in the P site of the 40 S subunit driven by base pairing between the start codon in the mRNA and the anticodon in tRNA(i). Finally, we show that the C-terminal domain of eIF5 is responsible for the factor's activity in antagonizing eIF1 binding to the PIC. Together, our data provide a more complete picture of the chain of molecular events that is triggered when the scanning PIC encounters an AUG start codon in the mRNA.
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Affiliation(s)
- Jagpreet S. Nanda
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | - Adesh K. Saini
- the Laboratory of Gene Regulation and Development, Eunice K. Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892
| | - Antonio M. Muñoz
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | - Alan G. Hinnebusch
- the Laboratory of Gene Regulation and Development, Eunice K. Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892
| | - Jon R. Lorsch
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
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31
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van der Harst P, Zhang W, Mateo Leach I, Rendon A, Verweij N, Sehmi J, Paul DS, Elling U, Allayee H, Li X, Radhakrishnan A, Tan ST, Voss K, Weichenberger CX, Albers CA, Al-Hussani A, Asselbergs FW, Ciullo M, Danjou F, Dina C, Esko T, Evans DM, Franke L, Gögele M, Hartiala J, Hersch M, Holm H, Hottenga JJ, Kanoni S, Kleber ME, Lagou V, Langenberg C, Lopez LM, Lyytikäinen LP, Melander O, Murgia F, Nolte IM, O'Reilly PF, Padmanabhan S, Parsa A, Pirastu N, Porcu E, Portas L, Prokopenko I, Ried JS, Shin SY, Tang CS, Teumer A, Traglia M, Ulivi S, Westra HJ, Yang J, Zhao JH, Anni F, Abdellaoui A, Attwood A, Balkau B, Bandinelli S, Bastardot F, Benyamin B, Boehm BO, Cookson WO, Das D, de Bakker PIW, de Boer RA, de Geus EJC, de Moor MH, Dimitriou M, Domingues FS, Döring A, Engström G, Eyjolfsson GI, Ferrucci L, Fischer K, Galanello R, Garner SF, Genser B, Gibson QD, Girotto G, Gudbjartsson DF, Harris SE, Hartikainen AL, Hastie CE, Hedblad B, Illig T, Jolley J, Kähönen M, Kema IP, Kemp JP, Liang L, Lloyd-Jones H, Loos RJF, Meacham S, Medland SE, Meisinger C, Memari Y, Mihailov E, Miller K, Moffatt MF, Nauck M, Novatchkova M, Nutile T, Olafsson I, Onundarson PT, Parracciani D, Penninx BW, Perseu L, Piga A, Pistis G, Pouta A, Puc U, Raitakari O, Ring SM, Robino A, Ruggiero D, Ruokonen A, Saint-Pierre A, Sala C, Salumets A, Sambrook J, Schepers H, Schmidt CO, Silljé HHW, Sladek R, Smit JH, Starr JM, Stephens J, Sulem P, Tanaka T, Thorsteinsdottir U, Tragante V, van Gilst WH, van Pelt LJ, van Veldhuisen DJ, Völker U, Whitfield JB, Willemsen G, Winkelmann BR, Wirnsberger G, Algra A, Cucca F, d'Adamo AP, Danesh J, Deary IJ, Dominiczak AF, Elliott P, Fortina P, Froguel P, Gasparini P, Greinacher A, Hazen SL, Jarvelin MR, Khaw KT, Lehtimäki T, Maerz W, Martin NG, Metspalu A, Mitchell BD, Montgomery GW, Moore C, Navis G, Pirastu M, Pramstaller PP, Ramirez-Solis R, Schadt E, Scott J, Shuldiner AR, Smith GD, Smith JG, Snieder H, Sorice R, Spector TD, Stefansson K, Stumvoll M, Tang WHW, Toniolo D, Tönjes A, Visscher PM, Vollenweider P, Wareham NJ, Wolffenbuttel BHR, Boomsma DI, Beckmann JS, Dedoussis GV, Deloukas P, Ferreira MA, Sanna S, Uda M, Hicks AA, Penninger JM, Gieger C, Kooner JS, Ouwehand WH, Soranzo N, Chambers JC. Seventy-five genetic loci influencing the human red blood cell. Nature 2012; 492:369-75. [PMID: 23222517 PMCID: PMC3623669 DOI: 10.1038/nature11677] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 10/15/2012] [Indexed: 11/09/2022]
Abstract
Anaemia is a chief determinant of global ill health, contributing to cognitive impairment, growth retardation and impaired physical capacity. To understand further the genetic factors influencing red blood cells, we carried out a genome-wide association study of haemoglobin concentration and related parameters in up to 135,367 individuals. Here we identify 75 independent genetic loci associated with one or more red blood cell phenotypes at P < 10(-8), which together explain 4-9% of the phenotypic variance per trait. Using expression quantitative trait loci and bioinformatic strategies, we identify 121 candidate genes enriched in functions relevant to red blood cell biology. The candidate genes are expressed preferentially in red blood cell precursors, and 43 have haematopoietic phenotypes in Mus musculus or Drosophila melanogaster. Through open-chromatin and coding-variant analyses we identify potential causal genetic variants at 41 loci. Our findings provide extensive new insights into genetic mechanisms and biological pathways controlling red blood cell formation and function.
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Affiliation(s)
- Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands.
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32
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Hinnebusch AG, Lorsch JR. The mechanism of eukaryotic translation initiation: new insights and challenges. Cold Spring Harb Perspect Biol 2012; 4:cshperspect.a011544. [PMID: 22815232 DOI: 10.1101/cshperspect.a011544] [Citation(s) in RCA: 340] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Translation initiation in eukaryotes is a highly regulated and complex stage of gene expression. It requires the action of at least 12 initiation factors, many of which are known to be the targets of regulatory pathways. Here we review our current understanding of the molecular mechanics of eukaryotic translation initiation, focusing on recent breakthroughs from in vitro and in vivo studies. We also identify important unanswered questions that will require new ideas and techniques to solve.
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Affiliation(s)
- Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
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33
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Aitken CE, Lorsch JR. A mechanistic overview of translation initiation in eukaryotes. Nat Struct Mol Biol 2012; 19:568-76. [PMID: 22664984 DOI: 10.1038/nsmb.2303] [Citation(s) in RCA: 290] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Translation initiation in eukaryotes is a complex and highly regulated process requiring the action of at least 12 protein factors. The pathway is distinguished by the formation of a pre-initiation complex that recruits the 5' end of the mRNA and scans along it to locate the start codon. During the past decade, a combination of genetics, biochemistry and structural studies has begun to illuminate key molecular events in this critical phase of gene expression. Here, we outline our current understanding of eukaryotic translation initiation and discuss important outstanding challenges.
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Affiliation(s)
- Colin Echeverría Aitken
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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34
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Pavitt GD, Ron D. New insights into translational regulation in the endoplasmic reticulum unfolded protein response. Cold Spring Harb Perspect Biol 2012; 4:cshperspect.a012278. [PMID: 22535228 DOI: 10.1101/cshperspect.a012278] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Homeostasis of the protein-folding environment in the endoplasmic reticulum (ER) is maintained by signal transduction pathways that collectively constitute an unfolded protein response (UPR). These affect bulk protein synthesis and thereby the levels of ER stress, but also culminate in regulated expression of specific mRNAs, such as that encoding the transcription factor ATF4. Mechanisms linking eukaryotic initiation factor 2 (eIF2) phosphorylation to control of unfolded protein load in the ER were elucidated more than 10 years ago, but recent work has highlighted the diversity of processes that impinge on eIF2 activity and revealed that there are multiple mechanisms by which changes in eIF2 activity can modulate the translation of individual mRNAs. In addition, the potential for affecting this step of translation initiation pharmacologically is becoming clearer. Furthermore, it is now clear that another strand of the UPR, controlled by the endoribonuclease inositol-requiring enzyme 1 (IRE1), also affects rates of protein synthesis in stressed cells and that its effector function, mediated by the transcription factor X-box-binding protein 1 (XBP1), is subject to important mRNA-specific translational regulation. These new insights into the convergence of translational control and the UPR will be reviewed here.
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Affiliation(s)
- Graham D Pavitt
- Faculty of Life Sciences, University of Manchester, United Kingdom.
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35
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Fields PA, Cox KM, Karch KR. Latitudinal Variation in Protein Expression After Heat Stress in the Salt Marsh Mussel Geukensia demissa. Integr Comp Biol 2012; 52:636-47. [DOI: 10.1093/icb/ics086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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36
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Loughran G, Sachs MS, Atkins JF, Ivanov IP. Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5. Nucleic Acids Res 2012; 40:2898-906. [PMID: 22156057 PMCID: PMC3326321 DOI: 10.1093/nar/gkr1192] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 11/14/2011] [Accepted: 11/15/2011] [Indexed: 12/26/2022] Open
Abstract
An AUG in an optimal nucleotide context is the preferred translation initiation site in eukaryotic cells. Interactions among translation initiation factors, including eIF1 and eIF5, govern start codon selection. Experiments described here showed that high intracellular eIF5 levels reduced the stringency of start codon selection in human cells. In contrast, high intracellular eIF1 levels increased stringency. High levels of eIF5 induced translation of inhibitory upstream open reading frames (uORFs) in eIF5 mRNA that initiate with AUG codons in conserved poor contexts. This resulted in reduced translation from the downstream eIF5 start codon, indicating that eIF5 autoregulates its own synthesis. As with eIF1, which is also autoregulated through translation initiation, features contributing to eIF5 autoregulation show deep evolutionary conservation. The results obtained provide the basis for a model in which auto- and cross-regulation of eIF5 and eIF1 translation establish a regulatory feedback loop that would stabilize the stringency of start codon selection.
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Affiliation(s)
- Gary Loughran
- BioSciences Institute, University College Cork, Ireland, Department of Biology, Texas A&M University, College Station, TX 77843 and Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Matthew S. Sachs
- BioSciences Institute, University College Cork, Ireland, Department of Biology, Texas A&M University, College Station, TX 77843 and Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - John F. Atkins
- BioSciences Institute, University College Cork, Ireland, Department of Biology, Texas A&M University, College Station, TX 77843 and Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Ivaylo P. Ivanov
- BioSciences Institute, University College Cork, Ireland, Department of Biology, Texas A&M University, College Station, TX 77843 and Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
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37
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Satpati P, Simonson T. Conformational selection through electrostatics: Free energy simulations of GTP and GDP binding to archaeal initiation factor 2. Proteins 2012; 80:1264-82. [PMID: 22275120 DOI: 10.1002/prot.24023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 11/29/2011] [Accepted: 12/13/2011] [Indexed: 11/05/2022]
Abstract
Archaeal Initiation Factor 2 is a GTPase involved in protein biosynthesis. In its GTP-bound, "ON" conformation, it binds an initiator tRNA and carries it to the ribosome. In its GDP-bound, "OFF" conformation, it dissociates from tRNA. To understand the specific binding of GTP and GDP and their dependence on the conformational state, molecular dynamics free energy simulations were performed. The ON state specificity was predicted to be weak, with a GTP/GDP binding free energy difference of -1 kcal/mol, favoring GTP. The OFF state specificity is larger, 4 kcal/mol, favoring GDP. The overall effects result from a competition among many interactions in several complexes. To interpret them, we use a simpler, dielectric continuum model. Several effects are robust with respect to the model details. Both nucleotides have a net negative charge, so that removing them from solvent into the binding pocket carries a desolvation penalty, which is large for the ON state, and strongly disfavors GTP binding compared to GDP. Short-range interactions between the additional GTP phosphate group and ionized sidechains in the binding pocket offset most, but not all of the desolvation penalty; more distant groups also contribute significantly, and the switch 1 loop only slightly. The desolvation penalty is lower for the more open, wetter OFF state, and the GTP/GDP difference much smaller. Short-range interactions in the binding pocket and with more distant groups again make a significant contribution. Overall, the simulations help explain how conformational selection is achieved with a single phosphate group.
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Affiliation(s)
- Priyadarshi Satpati
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
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38
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Molecular mechanism of scanning and start codon selection in eukaryotes. Microbiol Mol Biol Rev 2012; 75:434-67, first page of table of contents. [PMID: 21885680 DOI: 10.1128/mmbr.00008-11] [Citation(s) in RCA: 281] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The correct translation of mRNA depends critically on the ability to initiate at the right AUG codon. For most mRNAs in eukaryotic cells, this is accomplished by the scanning mechanism, wherein the small (40S) ribosomal subunit attaches to the 5' end of the mRNA and then inspects the leader base by base for an AUG in a suitable context, using complementarity with the anticodon of methionyl initiator tRNA (Met-tRNAiMet) as the key means of identifying AUG. Over the past decade, a combination of yeast genetics, biochemical analysis in reconstituted systems, and structural biology has enabled great progress in deciphering the mechanism of ribosomal scanning. A robust molecular model now exists, describing the roles of initiation factors, notably eukaryotic initiation factor 1 (eIF1) and eIF1A, in stabilizing an "open" conformation of the 40S subunit with Met-tRNAiMet bound in a low-affinity state conducive to scanning and in triggering rearrangement into a "closed" conformation incompatible with scanning, which features Met-tRNAiMet more tightly bound to the "P" site and base paired with AUG. It has also emerged that multiple DEAD-box RNA helicases participate in producing a single-stranded "landing pad" for the 40S subunit and in removing the secondary structure to enable the mRNA to traverse the 40S mRNA-binding channel in the single-stranded form for base-by-base inspection in the P site.
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Yoo H, Yoo JK, Lee J, Lee DR, Ko JJ, Oh SH, Choo YK, Kim JK. The hsa-miR-5787 represses cellular growth by targeting eukaryotic translation initiation factor 5 (eIF5) in fibroblasts. Biochem Biophys Res Commun 2011; 415:567-72. [PMID: 22062548 DOI: 10.1016/j.bbrc.2011.10.103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 10/22/2011] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate diverse biological processes. We cloned novel small RNA from human mesenchymal stem cells (hMSCs) and termed microRNA-5787 (hsa-miR-5787) that met the criteria for a miRNA. The level of miR-5787 was elevated in senescent fibroblasts. Based on the target prediction algorithm and results that were obtained, we find that eukaryotic translation initiation factor 5 (eIF5) is a target of miR-5787. Similar to the over-expression of miR-5787, we showed that repression of eIF5 in fibroblasts negatively affected cell growth. Therefore, we propose that the miR-5787 represses cell growth, in part, by targeting eIF5.
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Affiliation(s)
- Hanna Yoo
- Department of Pharmacy, College of Pharmacy, CHA University, 222 Yatap-Dong, Bundang-Gu, Seongnam-Si, Republic of Korea
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40
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Lorsch JR, Dever TE. Molecular view of 43 S complex formation and start site selection in eukaryotic translation initiation. J Biol Chem 2010; 285:21203-7. [PMID: 20444698 PMCID: PMC2898419 DOI: 10.1074/jbc.r110.119743] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A central step to high fidelity protein synthesis is selection of the proper start codon. Recent structural, biochemical, and genetic analyses have provided molecular insights into the coordinated activities of the initiation factors in start codon selection. A molecular model is emerging in which start codon recognition is linked to dynamic reorganization of factors on the ribosome and structural changes in the ribosome itself.
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Affiliation(s)
- Jon R. Lorsch
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | - Thomas E. Dever
- the Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892
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41
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eIF5 has GDI activity necessary for translational control by eIF2 phosphorylation. Nature 2010; 465:378-81. [PMID: 20485439 PMCID: PMC2875157 DOI: 10.1038/nature09003] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 03/10/2010] [Indexed: 11/23/2022]
Abstract
In protein synthesis initiation, the eukaryotic translation initiation factor (eIF) 2 (a G protein) functions in its GTP-bound state to deliver initiator methionyl-tRNA (tRNAiMet) to the small ribosomal subunit and is necessary for protein synthesis in all cells1,2. Phosphorylation of eIF2 [eIF2(αP)] is critical for translational control in diverse settings including nutrient deprivation, viral infection and memory formation3,4,5. eIF5 functions in start site selection as a GTPase accelerating protein (GAP) for the eIF2•GTP•tRNAiMet ternary complex (TC) within the ribosome bound pre-initiation complex6,7,8. Here we define new regulatory functions of eIF5 in the recycling of eIF2 from its inactive eIF2•GDP state between successive rounds of translation initiation. Firstly we show that eIF5 stabilizes the binding of GDP to eIF2 and is therefore a bi-functional protein that acts as a GDP dissociation inhibitor (GDI). We find that this activity is independent of the GAP function and identify conserved residues within eIF5 that are necessary for this role. In addition we show that eIF5 is a critical component of the eIF2(αP) regulatory complex that inhibits the activity of the guanine-nucleotide exchange factor (GEF) eIF2B. Together our studies define a new step in the translation initiation pathway, one that is critical for normal translational controls.
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42
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Abstract
Recognition of the AUG start codon on mRNAs during translation initiation in eukaryotes occurs in a preinitiation complex that includes small ribosomal subunits and multiple translation initiation factors. The complexity of this process and the lack of appropriate tools have prevented its genetic study in multicellular organisms. Here we describe a genetic system in the nematode Caenorhabditis elegans to study how the AUG start codon is selected. We have generated a sensitive reporter assay that allows for the isolation of mutants with reduced fidelity to recognize the AUG start codon. Two mutants were identified to have dominant missense mutations in iftb-1, which encodes the beta-subunit of eIF2 (eIF2beta). Both mutations occur in a conserved region located outside of the C2-C2 zinc finger domain where yeast SUI3 mutations are localized in Saccharomyces cerevisiae eIF2beta. C. elegans iftb-1, as well as mutant eIF2betas carrying the equivalent SUI3 mutations, are able to initiate translation at non-AUG codons that retain two potential base-pairing interactions with the anticodon of the initiator methionyl tRNA. These analyses further support the critical role of eIF2beta in start codon selection, and two functional domains within eIF2beta are likely involved, one defined by our C. elegans mutants and the other by the yeast SUI3 mutants.
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Affiliation(s)
- Yinhua Zhang
- New England Biolabs, Ipswich, Massachusetts 01938
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43
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Fraser CS. The molecular basis of translational control. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 90:1-51. [PMID: 20374738 DOI: 10.1016/s1877-1173(09)90001-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Our current understanding of eukaryotic protein synthesis has emerged from many years of biochemical, genetic and biophysical approaches. Significant insight into the molecular details of the mechanism has been obtained, although there are clearly many aspects of the process that remain to be resolved. Importantly, our understanding of the mechanism has identified a number of key stages in the pathway that contribute to the regulation of general and gene-specific translation. Not surprisingly, translational control is now widely accepted to play a role in aspects of cell stress, growth, development, synaptic function, aging, and disease. This chapter reviews the mechanism of eukaryotic protein synthesis and its relevance to translational control.
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Affiliation(s)
- Christopher S Fraser
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, California 95616, USA
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44
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Balvay L, Soto Rifo R, Ricci EP, Decimo D, Ohlmann T. Structural and functional diversity of viral IRESes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:542-57. [PMID: 19632368 DOI: 10.1016/j.bbagrm.2009.07.005] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 07/17/2009] [Accepted: 07/19/2009] [Indexed: 01/06/2023]
Abstract
Some 20 years ago, the study of picornaviral RNA translation led to the characterization of an alternative mechanism of initiation by direct ribosome binding to the 5' UTR. By using a bicistronic vector, it was shown that the 5' UTR of the poliovirus (PV) or the Encephalomyelitis virus (EMCV) had the ability to bind the 43S preinitiation complex in a 5' and cap-independent manner. This is rendered possible by an RNA domain called IRES for Internal Ribosome Entry Site which enables efficient translation of an mRNA lacking a 5' cap structure. IRES elements have now been found in many different viral families where they often confer a selective advantage to allow ribosome recruitment under conditions where cap-dependent protein synthesis is severely repressed. In this review, we compare and contrast the structure and function of IRESes that are found within 4 distinct family of RNA positive stranded viruses which are the (i) Picornaviruses; (ii) Flaviviruses; (iii) Dicistroviruses; and (iv) Lentiviruses.
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Affiliation(s)
- Laurent Balvay
- Unité de Virologie Humaine, Ecole Normale Supérieure de Lyon, Lyon F-693643, France
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45
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Benelli D, Londei P. Begin at the beginning: evolution of translational initiation. Res Microbiol 2009; 160:493-501. [PMID: 19576983 DOI: 10.1016/j.resmic.2009.06.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 06/18/2009] [Accepted: 06/23/2009] [Indexed: 01/16/2023]
Abstract
Initiation of protein synthesis, entailing ribosomal recognition of the mRNA start codon and setting of the correct reading frame, is the rate-limiting step in translation and the main target of translation regulation in all modern cells. As efficient selection of the translation start site is vital for survival of extant cells, a mechanism for ensuring this may already have been in existence in the last universal common ancestor of present-day cells. This article reviews known features of the molecular machinery for initiation in the primary domains of life, Bacteria, Archaea and Eukarya, and attempts to identify conserved features that may be useful for reconstructing a model of the ancestral initiation apparatus.
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Affiliation(s)
- Dario Benelli
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Università di Roma Sapienza, Policlinico Umberto I, Viale Regina Elena 324, 00161 Roma, Italy
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46
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He C, Baba M, Klionsky DJ. Double duty of Atg9 self-association in autophagosome biogenesis. Autophagy 2009; 5:385-7. [PMID: 19182520 DOI: 10.4161/auto.5.3.7699] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The understanding of the membrane flow process during autophagosome formation is essential to illuminate the role of autophagy under various disease-causing conditions. Atg9 is the only identified integral membrane protein required for autophagosome formation, and it is thought to cycle between the membrane sources and the phagophore assembly site (PAS). Thus, Atg9 may play an important role as a membrane carrier. We report the self-interaction of Atg9 and generate an Atg9 mutant that is defective in this interaction. This mutation results in abnormal autophagy, due to altered phagophore formation as well as inefficient membrane delivery to the PAS. Based on our analyses, we discuss a model suggesting dual functions for the Atg9 complex: by reversibly binding to another Atg9 molecule, Atg9 can both promote lipid transport from the membrane origins to the PAS, and also help assemble an intact phagophore membrane.
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Affiliation(s)
- Congcong He
- Life Sciences Institute, and Departments of Molecular, Cellular and Developmental Biology and Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
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47
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Mechanism of ribosomal subunit joining during eukaryotic translation initiation. Biochem Soc Trans 2008; 36:653-7. [PMID: 18631135 DOI: 10.1042/bst0360653] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Decades of research have yielded significant insight into the mechanism by which a cell translates an mRNA into the encoded protein. However many of the molecular details of the process remain a mystery. Translation initiation is an important control point in gene expression, and misregulation can lead to diseases such as cancer. A better understanding of the mechanism of translation initiation is imperative for the development of novel therapeutic agents. Recently, a combination of genetic, biochemical and biophysical studies has begun to shed light on how, at a molecular level, the translational machinery initiates protein synthesis. In the present review, we briefly compare and contrast the initiation pathways utilized by bacteria, archaea and eukaryotes, and then focus on translation initiation in eukaryotes and recent advances in our understanding of the subunit joining step of the process.
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48
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Chung J, Kim TH. Integrin-dependent translational control: Implication in cancer progression. Microsc Res Tech 2008; 71:380-6. [PMID: 18300291 DOI: 10.1002/jemt.20566] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The importance of translational control in cancer progression has been underscored by a number of recent studies. However, little is known how cancer cells maintain their high efficiency of translation. Here, we summarize studies that support the role of integrins in translational control, especially at the initiation step, and discuss the various mechanisms by which integrins regulate the recruitment of translational machinery. This review also examines the hypothesis that integrins contribute to various aspects of cancer progression such as proliferation, survival, angiogenesis, and invasion through translational control.
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Affiliation(s)
- Jun Chung
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana 71130, USA.
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49
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Mitchell SF, Lorsch JR. Should I stay or should I go? Eukaryotic translation initiation factors 1 and 1A control start codon recognition. J Biol Chem 2008; 283:27345-27349. [PMID: 18593708 DOI: 10.1074/jbc.r800031200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Start codon selection is a key step in translation initiation as it sets the reading frame for decoding. Two eukaryotic initiation factors, eIF1 and eIF1A, are key actors in this process. Recent work has elucidated many details of the mechanisms these factors use to control start site selection. eIF1 prevents the irreversible GTP hydrolysis that commits the ribosome to initiation at a particular codon. eIF1A both promotes and inhibits commitment through the competing influences of its two unstructured termini. Both factors perform their tasks through a variety of interactions with other components of the initiation machinery, in many cases mediated by the unstructured regions of the two proteins.
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Affiliation(s)
- Sarah F Mitchell
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Jon R Lorsch
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205.
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50
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Paytubi S, Morrice NA, Boudeau J, Proud CG. The N-terminal region of ABC50 interacts with eukaryotic initiation factor eIF2 and is a target for regulatory phosphorylation by CK2. Biochem J 2007; 409:223-31. [PMID: 17894550 DOI: 10.1042/bj20070811] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
ABC50 is an ABC (ATP-binding cassette) protein which, unlike most ABC proteins, lacks membrane-spanning domains. ABC50 interacts with eIF2 (eukaryotic initiation factor 2), a protein that plays a key role in translation initiation and in its control, and in regulation of ribosomes. Here, we establish that the interaction of ABC50 with eIF2 involves features in the N-terminal domain of ABC50, the region of ABC50 that differs most markedly from other ABC proteins. This region also shows no apparent similarity to the eIF2-binding domains of other partners of eIF2. In contrast, the N-terminus of ABC50 cannot bind to ribosomes by itself, but it can in conjunction with one of the nucleotide-binding domains. We demonstrate that ABC50 is a phosphoprotein and is phosphorylated at two sites by CK2. These sites, Ser-109 and Ser-140, lie in the N-terminal part of ABC50 but are not required for the binding of ABC50 to eIF2. Expression of a mutant of ABC50 in which both sites are mutated to alanine markedly decreased the association of eIF2 with 80S ribosomal and polysomal fractions.
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Affiliation(s)
- Sonia Paytubi
- Division of Molecular Physiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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