201
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Liu TY, Huang HH, Wheeler D, Xu Y, Wells JA, Song YS, Wiita AP. Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics. Cell Syst 2017; 4:636-644.e9. [PMID: 28578850 DOI: 10.1016/j.cels.2017.05.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/17/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
Abstract
Ribosome profiling is a widespread tool for studying translational dynamics in human cells. Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis. Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomics. We focus on multiple myeloma cells exposed to bortezomib, a first-line chemotherapy and proteasome inhibitor. In the absence of drug effects, we found that direct measurement of protein synthesis by pSILAC correlated well with indirect measurement of synthesis from ribosome footprint density. This correlation, however, broke down under bortezomib-induced stress. By developing a statistical model integrating longitudinal proteomic and mRNA-sequencing measurements, we found that proteomics could directly detect global alterations in translational rate caused by bortezomib; these changes are not detectable by ribosomal profiling alone. Further, by incorporating pSILAC data into a gene expression model, we predict cell-stress specific proteome remodeling events. These results demonstrate that pSILAC provides an important complement to ribosome profiling in measuring proteome dynamics.
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Affiliation(s)
- Tzu-Yu Liu
- Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA; Departments of Mathematics and Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hector H Huang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Diamond Wheeler
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yichen Xu
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA; Departments of Mathematics and Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA.
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202
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Zhdanov AV, Andreev DE, Baranov PV, Papkovsky DB. Low energy costs of F1Fo ATP synthase reversal in colon carcinoma cells deficient in mitochondrial complex IV. Free Radic Biol Med 2017; 106:184-195. [PMID: 28189850 DOI: 10.1016/j.freeradbiomed.2017.02.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/08/2017] [Accepted: 02/08/2017] [Indexed: 10/20/2022]
Abstract
Mitochondrial polarisation is paramount for a variety of cellular functions. Under ischemia, mitochondrial membrane potential (ΔΨm) and proton gradient (ΔpH) are maintained via a reversal of mitochondrial F1Fo ATP synthase (mATPase), which can rapidly deplete ATP and drive cells into energy crisis. We found that under normal conditions in cells with disassembled cytochrome c oxidase complex (COX-deficient HCT116), mATPase maintains ΔΨm at levels only 15-20% lower than in WT cells, and for this utilises relatively little ATP. For a small energy expenditure, mATPase enables mitochondrial ΔpH, protein import, Ca2+ turnover, and supports free radical detoxication machinery enlarged to protect the cells from oxidative damage. Whereas in COX-deficient cells the main source of ATP is glycolysis, the ΔΨm is still maintained upon inhibition of the adenine nucleotide translocators with bongkrekic acid and carboxyatractyloside, indicating that the role of ANTs is redundant, and matrix substrate level phosphorylation alone or in cooperation with ATP-Mg/Pi carriers can continuously support the mATPase activity. Intriguingly, we found that mitochondrial complex III is active, and it contributes not only to free radical production, but also to ΔΨm maintenance and energy budget of COX-deficient cells. Overall, this study demonstrates that F1Fo ATP synthase can support general mitochondrial and cellular functions, working in extremely efficient 'energy saving' reverse mode and flexibly recruiting free radical detoxication and ATP producing / transporting pathways.
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Affiliation(s)
- Alexander V Zhdanov
- School of Biochemistry & Cell Biology, University College Cork, Cork, Ireland.
| | - Dmitry E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel V Baranov
- School of Biochemistry & Cell Biology, University College Cork, Cork, Ireland
| | - Dmitri B Papkovsky
- School of Biochemistry & Cell Biology, University College Cork, Cork, Ireland
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203
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Terenin IM, Smirnova VV, Andreev DE, Dmitriev SE, Shatsky IN. A researcher's guide to the galaxy of IRESs. Cell Mol Life Sci 2017; 74:1431-1455. [PMID: 27853833 PMCID: PMC11107752 DOI: 10.1007/s00018-016-2409-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/01/2016] [Accepted: 11/02/2016] [Indexed: 12/25/2022]
Abstract
The idea of internal initiation is frequently exploited to explain the peculiar translation properties or unusual features of some eukaryotic mRNAs. In this review, we summarize the methods and arguments most commonly used to address cases of translation governed by internal ribosome entry sites (IRESs). Frequent mistakes are revealed. We explain why "cap-independent" does not readily mean "IRES-dependent" and why the presence of a long and highly structured 5' untranslated region (5'UTR) or translation under stress conditions cannot be regarded as an argument for appealing to internal initiation. We carefully describe the known pitfalls and limitations of the bicistronic assay and artefacts of some commercially available in vitro translation systems. We explain why plasmid DNA transfection should not be used in IRES studies and which control experiments are unavoidable if someone decides to use it anyway. Finally, we propose a workflow for the validation of IRES activity, including fast and simple experiments based on a single genetic construct with a sequence of interest.
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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, 119334, Russia.
| | - Victoria V Smirnova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Dmitri E Andreev
- 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, 119334, Russia
- Department of Biochemistry, 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.
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204
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Sajjanar B, Deb R, Raina SK, Pawar S, Brahmane MP, Nirmale AV, Kurade NP, Manjunathareddy GB, Bal SK, Singh NP. Untranslated regions (UTRs) orchestrate translation reprogramming in cellular stress responses. J Therm Biol 2017; 65:69-75. [DOI: 10.1016/j.jtherbio.2017.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 11/29/2022]
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205
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Gobet C, Naef F. Ribosome profiling and dynamic regulation of translation in mammals. Curr Opin Genet Dev 2017; 43:120-127. [PMID: 28363112 DOI: 10.1016/j.gde.2017.03.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 10/19/2022]
Abstract
Protein synthesis is an energy-demanding cellular process. Consequently, a well-timed, fine-tuned and plastic regulation of translation is needed to adjust and maintain cell states under dynamically changing environments. Genome-wide monitoring of translation was recently facilitated by ribosome profiling, which uncovered key features of translation regulation. In this review, we summarize recent ribosome profiling studies in mammals providing novel insight in dynamic translation regulation, notably related to circadian rhythms, diurnal feeding/fasting cycles, cell cycle progression, stress responses, and tRNA landscapes. In particular, recent results show that regulating translation initiation and elongation represent important mechanisms used in mammalian cells to rapidly modulate protein expression in dynamically changing environments.
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Affiliation(s)
- Cédric Gobet
- The Institute of Bioengineering (IBI), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Switzerland
| | - Felix Naef
- The Institute of Bioengineering (IBI), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Switzerland.
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206
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Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain. PLoS Biol 2017; 15:e2001882. [PMID: 28323820 PMCID: PMC5360235 DOI: 10.1371/journal.pbio.2001882] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/22/2017] [Indexed: 01/12/2023] Open
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a key role in regulating the levels of plasma low-density lipoprotein cholesterol (LDL-C). Here, we demonstrate that the compound PF-06446846 inhibits translation of PCSK9 by inducing the ribosome to stall around codon 34, mediated by the sequence of the nascent chain within the exit tunnel. We further show that PF-06446846 reduces plasma PCSK9 and total cholesterol levels in rats following oral dosing. Using ribosome profiling, we demonstrate that PF-06446846 is highly selective for the inhibition of PCSK9 translation. The mechanism of action employed by PF-06446846 reveals a previously unexpected tunability of the human ribosome that allows small molecules to specifically block translation of individual transcripts. Many disease-mediating proteins have proven difficult to target with traditional small-molecule pharmaceuticals. In this paper, we report that a small molecule, PF-06446846, directly inhibits translation of one such protein, proprotein convertase subtilisin/kexin type 9 (PCSK9), by acting on the translating human ribosome. PF-06446846 causes the translating ribosome to stall soon after translating the PCSK9 signal sequence. We further show that PF-06446846 activity is dependent on the amino acid sequence of the nascent chain inside the ribosome exit tunnel. In a rat safety study, we observe decreases in plasma PCSK9, total cholesterol, and low-density lipoprotein (LDL) cholesterol. Using mass spectrometry in cell culture and ribosome profiling, we demonstrate that despite acting on the ribosome, which synthesizes every protein in the cell, PF-06446846 displays a high level of selectivity for PCSK9. This unexpected potential for small molecules to selectively inhibit the human ribosome opens the possibility for future development of small molecules targeting disease-mediating proteins that were previously thought to be undruggable.
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207
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Translation complex profile sequencing to study the in vivo dynamics of mRNA–ribosome interactions during translation initiation, elongation and termination. Nat Protoc 2017; 12:697-731. [DOI: 10.1038/nprot.2016.189] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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208
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Abstract
As obligate parasites, viruses strictly depend on host cell translation for the production of new progeny, yet infected cells also synthesize antiviral proteins to limit virus infection. Modulation of host cell translation therefore represents a frequent strategy by which viruses optimize their replication and spread. Here we sought to define how host cell translation is regulated during infection of human cells with dengue virus (DENV) and Zika virus (ZIKV), two positive-strand RNA flaviviruses. Polysome profiling and analysis of de novo protein synthesis revealed that flavivirus infection causes potent repression of host cell translation, while synthesis of viral proteins remains efficient. Selective repression of host cell translation was mediated by the DENV polyprotein at the level of translation initiation. In addition, DENV and ZIKV infection suppressed host cell stress responses such as the formation of stress granules and phosphorylation of the translation initiation factor eIF2α (α subunit of eukaryotic initiation factor 2). Mechanistic analyses revealed that translation repression was uncoupled from the disruption of stress granule formation and eIF2α signaling. Rather, DENV infection induced p38-Mnk1 signaling that resulted in the phosphorylation of the eukaryotic translation initiation factor eIF4E and was essential for the efficient production of virus particles. Together, these results identify the uncoupling of translation suppression from the cellular stress responses as a conserved strategy by which flaviviruses ensure efficient replication in human cells. For efficient production of new progeny, viruses need to balance their dependency on the host cell translation machinery with potentially adverse effects of antiviral proteins produced by the infected cell. To achieve this, many viruses evolved mechanisms to manipulate host cell translation. Here we find that infection of human cells with two major human pathogens, dengue virus (DENV) and Zika virus (ZIKV), leads to the potent repression of host cell translation initiation, while the synthesis of viral protein remains unaffected. Unlike other RNA viruses, these flaviviruses concomitantly suppress host cell stress responses, thereby uncoupling translation suppression from stress granule formation. We identified that the p38-Mnk1 cascade regulating phosphorylation of eIF4E is a target of DENV infection and plays an important role in virus production. Our results define several molecular interfaces by which flaviviruses hijack host cell translation and interfere with stress responses to optimize the production of new virus particles.
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209
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Artcibasova AV, Korzinkin MB, Sorokin MI, Shegay PV, Zhavoronkov AA, Gaifullin N, Alekseev BY, Vorobyev NV, Kuzmin DV, Kaprin АD, Borisov NM, Buzdin AA. MiRImpact, a new bioinformatic method using complete microRNA expression profiles to assess their overall influence on the activity of intracellular molecular pathways. Cell Cycle 2016; 15:689-98. [PMID: 27027999 PMCID: PMC4845938 DOI: 10.1080/15384101.2016.1147633] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
MicroRNAs (miRs) are short noncoding RNA molecules that regulate expression of target mRNAs. Many published sources provide information about miRs and their targets. However, bioinformatic tools elucidating higher level impact of the established total miR profiles, are still largely missing. Recently, we developed a method termed OncoFinder enabling quantification of the activities of intracellular molecular pathways basing on gene expression data. Here we propose a new technique, MiRImpact, which enables to link miR expression data with its estimated outcome on the regulation of molecular pathways, like signaling, metabolic, cytoskeleton rearrangement, and DNA repair pathways. MiRImpact uses OncoFinder rationale for pathway activity calculations, with the major distinctions that (i) it deals with the concentrations of miRs - known regulators of gene products participating in molecular pathways, and (ii) miRs are considered as negative regulators of target molecules, if other is not specified. MiRImpact operates with 2 types of databases: for molecular targets of miRs and for gene products participating in molecular pathways. We applied MiRImpact to compare regulation of human bladder cancer-specific signaling pathways at the levels of mRNA and miR expression. We took 2 most complete alternative databases of experimentally validated miR targets – miRTarBase and DianaTarBase, and an OncoFinder database featuring 2725 gene products and 271 signaling pathways. We showed that the impact of miRs is orthogonal to pathway regulation at the mRNA level, which stresses the importance of studying posttranscriptional regulation of gene expression. We also report characteristic set of miR and mRNA regulation features linked with bladder cancer.
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Affiliation(s)
- Alina V Artcibasova
- a Pathway Pharmaceuticals , Wan Chai , Hong Kong, Hong Kong SAR.,b Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | | | - Maksim I Sorokin
- a Pathway Pharmaceuticals , Wan Chai , Hong Kong, Hong Kong SAR.,c First Oncology Research and Advisory Center , Moscow , Russia
| | - Peter V Shegay
- d P.A. Herzen Moscow Oncological Research Institute , Moscow , Russia
| | - Alex A Zhavoronkov
- b Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | - Nurshat Gaifullin
- e Moscow State University, Faculty of Fundamental Medicine , Moscow , Russia
| | - Boris Y Alekseev
- d P.A. Herzen Moscow Oncological Research Institute , Moscow , Russia
| | | | - Denis V Kuzmin
- f Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia
| | - Аndrey D Kaprin
- d P.A. Herzen Moscow Oncological Research Institute , Moscow , Russia
| | - Nikolay M Borisov
- g National Research Centre "Kurchatov Institute," Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies , Moscow , Russia
| | - Anton A Buzdin
- b Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia.,f Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia.,g National Research Centre "Kurchatov Institute," Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies , Moscow , Russia
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210
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Rittiner JE, Caffall ZF, Hernández-Martinez R, Sanderson SM, Pearson JL, Tsukayama KK, Liu AY, Xiao C, Tracy S, Shipman MK, Hickey P, Johnson J, Scott B, Stacy M, Saunders-Pullman R, Bressman S, Simonyan K, Sharma N, Ozelius LJ, Cirulli ET, Calakos N. Functional Genomic Analyses of Mendelian and Sporadic Disease Identify Impaired eIF2α Signaling as a Generalizable Mechanism for Dystonia. Neuron 2016; 92:1238-1251. [PMID: 27939583 DOI: 10.1016/j.neuron.2016.11.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/27/2016] [Accepted: 11/04/2016] [Indexed: 01/09/2023]
Abstract
Dystonia is a brain disorder causing involuntary, often painful movements. Apart from a role for dopamine deficiency in some forms, the cellular mechanisms underlying most dystonias are currently unknown. Here, we discover a role for deficient eIF2α signaling in DYT1 dystonia, a rare inherited generalized form, through a genome-wide RNAi screen. Subsequent experiments including patient-derived cells and a mouse model support both a pathogenic role and therapeutic potential for eIF2α pathway perturbations. We further find genetic and functional evidence supporting similar pathway impairment in patients with sporadic cervical dystonia, due to rare coding variation in the eIF2α effector ATF4. Considering also that another dystonia, DYT16, involves a gene upstream of the eIF2α pathway, these results mechanistically link multiple forms of dystonia and put forth a new overall cellular mechanism for dystonia pathogenesis, impairment of eIF2α signaling, a pathway known for its roles in cellular stress responses and synaptic plasticity.
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Affiliation(s)
| | | | | | | | - James L Pearson
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA; Department of RNAi Screening Facility, Duke University, Durham, NC 27708, USA
| | | | - Anna Y Liu
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Changrui Xiao
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Samantha Tracy
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | | | - Patrick Hickey
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Julia Johnson
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Burton Scott
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Mark Stacy
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Rachel Saunders-Pullman
- Department of Neurology, Mount Sinai Beth Israel Medical Center, New York, NY 10003, USA; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Susan Bressman
- Department of Neurology, Mount Sinai Beth Israel Medical Center, New York, NY 10003, USA; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristina Simonyan
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nutan Sharma
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Laurie J Ozelius
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth T Cirulli
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA; Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC 27708, USA
| | - Nicole Calakos
- Department of Neurology, Duke University, Durham, NC 27708, USA; Department of Neurobiology, Duke University, Durham, NC 27708, USA.
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211
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Andreev DE, O'Connor PBF, Loughran G, Dmitriev SE, Baranov PV, Shatsky IN. Insights into the mechanisms of eukaryotic translation gained with ribosome profiling. Nucleic Acids Res 2016; 45:513-526. [PMID: 27923997 PMCID: PMC5314775 DOI: 10.1093/nar/gkw1190] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/31/2016] [Accepted: 11/18/2016] [Indexed: 12/29/2022] Open
Abstract
The development of Ribosome Profiling (RiboSeq) has revolutionized functional genomics. RiboSeq is based on capturing and sequencing of the mRNA fragments enclosed within the translating ribosome and it thereby provides a ‘snapshot’ of ribosome positions at the transcriptome wide level. Although the method is predominantly used for analysis of differential gene expression and discovery of novel translated ORFs, the RiboSeq data can also be a rich source of information about molecular mechanisms of polypeptide synthesis and translational control. This review will focus on how recent findings made with RiboSeq have revealed important details of the molecular mechanisms of translation in eukaryotes. These include mRNA translation sensitivity to drugs affecting translation initiation and elongation, the roles of upstream ORFs in response to stress, the dynamics of elongation and termination as well as details of intrinsic ribosome behavior on the mRNA after translation termination. As the RiboSeq method is still at a relatively early stage we will also discuss the implications of RiboSeq artifacts on data interpretation.
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Affiliation(s)
- Dmitry E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | | | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
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212
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Akulich KA, Andreev DE, Terenin IM, Smirnova VV, Anisimova AS, Makeeva DS, Arkhipova VI, Stolboushkina EA, Garber MB, Prokofjeva MM, Spirin PV, Prassolov VS, Shatsky IN, Dmitriev SE. Four translation initiation pathways employed by the leaderless mRNA in eukaryotes. Sci Rep 2016; 6:37905. [PMID: 27892500 PMCID: PMC5124965 DOI: 10.1038/srep37905] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/02/2016] [Indexed: 01/09/2023] Open
Abstract
mRNAs lacking 5′ untranslated regions (leaderless mRNAs) are molecular relics of an ancient translation initiation pathway. Nevertheless, they still represent a significant portion of transcriptome in some taxons, including a number of eukaryotic species. In bacteria and archaea, the leaderless mRNAs can bind non-dissociated 70 S ribosomes and initiate translation without protein initiation factors involved. Here we use the Fleeting mRNA Transfection technique (FLERT) to show that translation of a leaderless reporter mRNA is resistant to conditions when eIF2 and eIF4F, two key eukaryotic translation initiation factors, are inactivated in mammalian cells. We report an unconventional translation initiation pathway utilized by the leaderless mRNA in vitro, in addition to the previously described 80S-, eIF2-, or eIF2D-mediated modes. This mechanism is a bacterial-like eIF5B/IF2-assisted initiation that has only been reported for hepatitis C virus-like internal ribosome entry sites (IRESs). Therefore, the leaderless mRNA is able to take any of four different translation initiation pathways in eukaryotes.
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Affiliation(s)
- Kseniya A Akulich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Dmitry E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ilya M Terenin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Victoria V Smirnova
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Aleksandra S Anisimova
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Desislava S Makeeva
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Valentina I Arkhipova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Elena A Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Maria B Garber
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Maria M Prokofjeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Pavel V Spirin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Vladimir S Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Sergey E Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.,Department of Biochemistry, Biological Faculty, Lomonosov Moscow State University, Moscow, 119991, Russia
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213
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The ribosome-engaged landscape of alternative splicing. Nat Struct Mol Biol 2016; 23:1117-1123. [PMID: 27820807 DOI: 10.1038/nsmb.3317] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/06/2016] [Indexed: 02/07/2023]
Abstract
High-throughput RNA sequencing (RNA-seq) has revealed an enormous complexity of alternative splicing (AS) across diverse cell and tissue types. However, it is currently unknown to what extent repertoires of splice-variant transcripts are translated into protein products. Here, we surveyed AS events engaged by the ribosome. Notably, at least 75% of human exon-skipping events detected in transcripts with medium-to-high abundance in RNA-seq data were also detected in ribosome profiling data. Furthermore, relatively small subsets of functionally related splice variants are engaged by ribosomes at levels that do not reflect their absolute abundance, thus indicating a role for AS in modulating translational output. This mode of regulation is associated with control of the mammalian cell cycle. Our results thus suggest that a major fraction of splice variants is translated and that specific cellular functions including cell-cycle control are subject to AS-dependent modulation of translation output.
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214
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Kozel C, Thompson B, Hustak S, Moore C, Nakashima A, Singh CR, Reid M, Cox C, Papadopoulos E, Luna RE, Anderson A, Tagami H, Hiraishi H, Slone EA, Yoshino KI, Asano M, Gillaspie S, Nietfeld J, Perchellet JP, Rothenburg S, Masai H, Wagner G, Beeser A, Kikkawa U, Fleming SD, Asano K. Overexpression of eIF5 or its protein mimic 5MP perturbs eIF2 function and induces ATF4 translation through delayed re-initiation. Nucleic Acids Res 2016; 44:8704-8713. [PMID: 27325740 PMCID: PMC5062967 DOI: 10.1093/nar/gkw559] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/07/2016] [Accepted: 06/10/2016] [Indexed: 11/14/2022] Open
Abstract
ATF4 is a pro-oncogenic transcription factor whose translation is activated by eIF2 phosphorylation through delayed re-initiation involving two uORFs in the mRNA leader. However, in yeast, the effect of eIF2 phosphorylation can be mimicked by eIF5 overexpression, which turns eIF5 into translational inhibitor, thereby promoting translation of GCN4, the yeast ATF4 equivalent. Furthermore, regulatory protein termed eIF5-mimic protein (5MP) can bind eIF2 and inhibit general translation. Here, we show that 5MP1 overexpression in human cells leads to strong formation of 5MP1:eIF2 complex, nearly comparable to that of eIF5:eIF2 complex produced by eIF5 overexpression. Overexpression of eIF5, 5MP1 and 5MP2, the second human paralog, promotes ATF4 expression in certain types of human cells including fibrosarcoma. 5MP overexpression also induces ATF4 expression in Drosophila The knockdown of 5MP1 in fibrosarcoma attenuates ATF4 expression and its tumor formation on nude mice. Since 5MP2 is overproduced in salivary mucoepidermoid carcinoma, we propose that overexpression of eIF5 and 5MP induces translation of ATF4 and potentially other genes with uORFs in their mRNA leaders through delayed re-initiation, thereby enhancing the survival of normal and cancer cells under stress conditions.
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Affiliation(s)
- Caitlin Kozel
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Brytteny Thompson
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Samantha Hustak
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Chelsea Moore
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Akio Nakashima
- Biosignal Research Center, Kobe University, Kobe 657-8501, Japan
| | - Chingakham Ranjit Singh
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Megan Reid
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Christian Cox
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Evangelos Papadopoulos
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Rafael E Luna
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Abbey Anderson
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Hideaki Tagami
- Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan
| | - Hiroyuki Hiraishi
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Emily Archer Slone
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Ken-Ichi Yoshino
- Biosignal Research Center, Kobe University, Kobe 657-8501, Japan
| | - Masayo Asano
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Sarah Gillaspie
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Jerome Nietfeld
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Jean-Pierre Perchellet
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Stefan Rothenburg
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Hisao Masai
- Genome Dynamics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander Beeser
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Ushio Kikkawa
- Biosignal Research Center, Kobe University, Kobe 657-8501, Japan
| | - Sherry D Fleming
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Katsura Asano
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
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215
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Bal NV, Susorov D, Chesnokova E, Kasianov A, Mikhailova T, Alkalaeva E, Balaban PM, Kolosov P. Upstream Open Reading Frames Located in the Leader of Protein Kinase Mζ mRNA Regulate Its Translation. Front Mol Neurosci 2016; 9:103. [PMID: 27790092 PMCID: PMC5061749 DOI: 10.3389/fnmol.2016.00103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/30/2016] [Indexed: 12/17/2022] Open
Abstract
For protein synthesis that occurs locally in dendrites, the translational control mechanisms are much more important for neuronal functioning than the transcription levels. Here, we show that uORFs (upstream open reading frames) in the 5′ untranslated region (5′UTR) play a critical role in regulation of the translation of protein kinase Mζ (PKMζ). Elimination of these uORFs activates translation of the reporter protein in vitro and in primary cultures of rat hippocampal neurons. Using cell-free translation systems, we demonstrate that translational initiation complexes are formed only on uORFs. Further, we address the mechanism of translational repression of PKMζ translation, by uORFs. We observed an increase in translation of the reporter protein under the control of PKMζ leader in neuronal culture during non-specific activation by picrotoxin. We also show that such a mechanism is similar to the mechanism seen in cell stress, as application of sodium arsenite to neuron cultures induced translation of mRNA carrying PKMζ 5′UTR similarly to picrotoxin activation. Therefore, we suppose that phosphorylation of eIF2a, like in cell stress, is a main regulator of PKMζ translation. Altogether, our findings considerably extend our understanding of the role of uORF in regulation of PKMζ translation in activated neurons, important at early stages of LTP.
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Affiliation(s)
- Natalia V Bal
- Cellular Neurobiology of Learning Laboratory, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences Moscow, Russia
| | - Denis Susorov
- Laboratory of Mechanisms and Control of Translation, Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia; Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State UniversityMoscow, Russia
| | - Ekaterina Chesnokova
- Cellular Neurobiology of Learning Laboratory, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences Moscow, Russia
| | - Artem Kasianov
- Laboratory of System Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences Moscow, Russia
| | - Tatiana Mikhailova
- Laboratory of Mechanisms and Control of Translation, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia
| | - Elena Alkalaeva
- Laboratory of Mechanisms and Control of Translation, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia
| | - Pavel M Balaban
- Cellular Neurobiology of Learning Laboratory, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences Moscow, Russia
| | - Peter Kolosov
- Cellular Neurobiology of Learning Laboratory, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences Moscow, Russia
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216
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O'Connor PBF, Andreev DE, Baranov PV. Comparative survey of the relative impact of mRNA features on local ribosome profiling read density. Nat Commun 2016; 7:12915. [PMID: 27698342 PMCID: PMC5059445 DOI: 10.1038/ncomms12915] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 08/16/2016] [Indexed: 12/20/2022] Open
Abstract
Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise. We illustrate how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally. We show that a few parameters extracted with RUST are sufficient for predicting experimental densities with high accuracy. Importantly the application of RUST to 30 publicly available Ribo-seq data sets revealed a substantial variation in sequence determinants of ribosome footprint frequencies, questioning the reliability of Ribo-seq as an accurate representation of local ribosome densities without prior quality control. This emphasizes our incomplete understanding of how protocol parameters affect ribosome footprint densities. Ribosome profiling data can suffer from uneven coverage which hampers estimation of elongation rates. Connor et al. present an enhanced data smoothing method for Ribo-seq data and highlight significant variability in sequence determinants of ribosome density in publicly available data sets.
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Affiliation(s)
| | - Dmitry E Andreev
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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217
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Golovko A, Kojukhov A, Guan BJ, Morpurgo B, Merrick WC, Mazumder B, Hatzoglou M, Komar AA. The eIF2A knockout mouse. Cell Cycle 2016; 15:3115-3120. [PMID: 27686860 DOI: 10.1080/15384101.2016.1237324] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Eukaryotic initiation factor 2A (eIF2A) is a 65-kDa protein that was first identified in the early 1970s as a factor capable of stimulating initiator methionyl-tRNAi (Met-tRNAMeti) binding to 40S ribosomal subunits in vitro. However, in contrast to the eIF2, which stimulates Met-tRNAMeti binding to 40S ribosomal subunits in a GTP-dependent manner, eIF2A didn't reveal any GTP-dependence, but instead was found to direct binding of the Met-tRNAMeti to 40S ribosomal subunits in a codon-dependent manner. eIF2A appears to be highly conserved across eukaryotic species, suggesting conservation of function in evolution. The yeast Saccharomyces cerevisae eIF2A null mutant revealed no apparent phenotype, however, it was found that in yeast eIF2A functions as a suppressor of internal ribosome entry site (IRES)-mediated translation. It was thus suggested that eIF2A my act by impinging on the expression of specific mRNAs. Subsequent studies in mammalian cell systems implicated eIF2A in non-canonical (non-AUG-dependent) translation initiation events involving near cognate UUG and CUG codons. Yet, the role of eIF2A in cellular functions remains largely enigmatic. As a first step toward characterization of the eIF2A function in mammalian systems in vivo, we have obtained homozygous eIF2A-total knockout (KO) mice, in which a gene trap cassette was inserted between eIF2A exons 1 and 2 disrupting expression of all exons downstream of the insertion. The KO mice strain is viable and to date displays no apparent phenotype. We believe that the eIF2A KO mice strain will serve as a valuable tool for researchers studying non-canonical initiation of translation in vivo.
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Affiliation(s)
- Andrei Golovko
- a Texas A&M Institute for Genomic Medicine , College Station , TX , USA
| | - Artyom Kojukhov
- b Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, Cleveland State University , Cleveland , OH , USA
| | - Bo-Jhih Guan
- c Department of Genetics and Genome Sciences , Case Western Reserve University , Cleveland , OH , USA
| | - Benjamin Morpurgo
- a Texas A&M Institute for Genomic Medicine , College Station , TX , USA
| | - William C Merrick
- d Department of Biochemistry , School of Medicine, Case Western Reserve University , Cleveland , OH , USA
| | - Barsanjit Mazumder
- b Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, Cleveland State University , Cleveland , OH , USA
| | - Maria Hatzoglou
- c Department of Genetics and Genome Sciences , Case Western Reserve University , Cleveland , OH , USA
| | - Anton A Komar
- b Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, Cleveland State University , Cleveland , OH , USA.,d Department of Biochemistry , School of Medicine, Case Western Reserve University , Cleveland , OH , USA.,e The Center for Gene Regulation in Health and Disease, Cleveland State University , Cleveland , OH , USA
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218
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Gerashchenko MV, Gladyshev VN. Ribonuclease selection for ribosome profiling. Nucleic Acids Res 2016; 45:e6. [PMID: 27638886 PMCID: PMC5314788 DOI: 10.1093/nar/gkw822] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/14/2016] [Accepted: 09/06/2016] [Indexed: 11/14/2022] Open
Abstract
Ribosome profiling has emerged as a powerful method to assess global gene translation, but methodological and analytical challenges often lead to inconsistencies across labs and model organisms. A critical issue in ribosome profiling is nuclease treatment of ribosome-mRNA complexes, as it is important to ensure both stability of ribosomal particles and complete conversion of polysomes to monosomes. We performed comparative ribosome profiling in yeast and mice with various ribonucleases including I, A, S7 and T1, characterized their cutting preferences, trinucleotide periodicity patterns and coverage similarities across coding sequences, and showed that they yield comparable estimations of gene expression when ribosome integrity is not compromised. However, ribosome coverage patterns of individual transcripts had little in common between the ribonucleases. We further examined their potency at converting polysomes to monosomes across other commonly used model organisms, including bacteria, nematodes and fruit flies. In some cases, ribonuclease treatment completely degraded ribosome populations. Ribonuclease T1 was the only enzyme that preserved ribosomal integrity while thoroughly converting polysomes to monosomes in all examined species. This study provides a guide for ribonuclease selection in ribosome profiling experiments across most common model systems.
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Affiliation(s)
- Maxim V Gerashchenko
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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219
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The rules and impact of nonsense-mediated mRNA decay in human cancers. Nat Genet 2016; 48:1112-8. [PMID: 27618451 PMCID: PMC5045715 DOI: 10.1038/ng.3664] [Citation(s) in RCA: 339] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 08/11/2016] [Indexed: 12/19/2022]
Abstract
Premature termination codons (PTCs) cause a large proportion of inherited human genetic diseases. PTC-containing transcripts can be degraded by an mRNA surveillance pathway termed nonsense-mediated mRNA decay (NMD). However, the efficiency of NMD varies; it is inefficient when a PTC is located downstream of the last exon junction complex (EJC). We used matched exome and transcriptome data from 9,769 human tumors to systematically elucidate the rules of NMD targeting in human cells. An integrated model incorporating multiple rules beyond the canonical EJC model explains approximately three-quarters of the non-random variance in NMD efficiency across thousands of PTCs. We also show that dosage compensation may mask the effects of NMD. Applying the NMD model identifies signatures of both positive and negative selection on NMD-triggering mutations in human tumors and provides a classification of tumor suppressor genes.
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220
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Curran JA, Weiss B. What Is the Impact of mRNA 5' TL Heterogeneity on Translational Start Site Selection and the Mammalian Cellular Phenotype? Front Genet 2016; 7:156. [PMID: 27630668 PMCID: PMC5005323 DOI: 10.3389/fgene.2016.00156] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/16/2016] [Indexed: 12/23/2022] Open
Abstract
A major determinant in the efficiency of ribosome loading onto mRNAs is the 5′ TL (transcript leader or 5′ UTR). In addition, elements within this region also impact on start site selection demonstrating that it can modulate the protein readout at both quantitative and qualitative levels. With the increasing wealth of data generated by the mining of the mammalian transcriptome, it has become evident that a genes 5′ TL is not homogeneous but actually exhibits significant heterogeneity. This arises due to the utilization of alternative promoters, and is further compounded by significant variability with regards to the precise transcriptional start sites of each (not to mention alternative splicing). Consequently, the transcript for a protein coding gene is not a unique mRNA, but in-fact a complexed quasi-species of variants whose composition may respond to the changing physiological environment of the cell. Here we examine the potential impact of these events with regards to the protein readout.
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Affiliation(s)
- Joseph A Curran
- Department of Microbiology and Molecular Medicine, Medical School, University of GenevaGeneva, Switzerland; Institute of Genetics and Genomics of Geneva, University of GenevaGeneva, Switzerland
| | - Benjamin Weiss
- Department of Microbiology and Molecular Medicine, Medical School, University of Geneva Geneva, Switzerland
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221
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Response of Three Different Viruses to Interferon Priming and Dithiothreitol Treatment of Avian Cells. J Virol 2016; 90:8328-40. [PMID: 27440902 DOI: 10.1128/jvi.01175-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 06/30/2016] [Indexed: 02/05/2023] Open
Abstract
UNLABELLED We have previously shown that the replication of avian reovirus (ARV) in chicken cells is much more resistant to interferon (IFN) than the replication of vesicular stomatitis virus (VSV) or vaccinia virus (VV). In this study, we have investigated the role that the double-stranded RNA (dsRNA)-activated protein kinase (PKR) plays in the sensitivity of these three viruses toward the antiviral action of chicken interferon. Our data suggest that while interferon priming of avian cells blocks vaccinia virus replication by promoting PKR activation, the replication of vesicular stomatitis virus appears to be blocked at a pretranslational step. Our data further suggest that the replication of avian reovirus in chicken cells is quite resistant to interferon priming because this virus uses strategies to downregulate PKR activation and also because translation of avian reovirus mRNAs is more resistant to phosphorylation of the alpha subunit of initiation factor eIF2 than translation of their cellular counterparts. Our results further reveal that the avian reovirus protein sigmaA is able to prevent PKR activation and that this function is dependent on its double-stranded RNA-binding activity. Finally, this study demonstrates that vaccinia virus and avian reovirus, but not vesicular stomatitis virus, express/induce factors that counteract the ability of dithiothreitol to promote eIF2 phosphorylation. Our data demonstrate that each of the three different viruses used in this study elicits distinct responses to interferon and to dithiothreitol-induced eIF2 phosphorylation when infecting avian cells. IMPORTANCE Type I interferons constitute the first barrier of defense against viral infections, and one of the best characterized antiviral strategies is mediated by the double-stranded RNA-activated protein kinase R (PKR). The results of this study revealed that IFN priming of avian cells has little effect on avian reovirus (ARV) replication but drastically diminishes the replication of vaccinia virus (VV) and vesicular stomatitis virus (VSV) by PKR-dependent and -independent mechanisms, respectively. Our data also demonstrate that the dsRNA-binding ability of ARV protein sigmaA plays a key role in the resistance of ARV toward IFN by preventing PKR activation. Our findings will contribute to improve the current understanding of the interaction of viruses with the host's innate immune system. Finally, it would be of interest to uncover the mechanisms that allow avian reovirus transcripts to be efficiently translated under conditions (moderate eIF2 phosphorylation) that block the synthesis of cellular proteins.
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222
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Abstract
Ribosome profiling has emerged as a technique for measuring translation comprehensively and quantitatively by deep sequencing of ribosome-protected mRNA fragments. By identifying the precise positions of ribosomes, footprinting experiments have unveiled key insights into the composition and regulation of the expressed proteome, including delineating potentially functional micropeptides, revealing pervasive translation on cytosolic RNAs, and identifying differences in elongation rates driven by codon usage or other factors. This Primer looks at important experimental and analytical concerns for executing ribosome profiling experiments and surveys recent examples where the approach was developed to explore protein biogenesis and homeostasis.
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223
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Bercovich-Kinori A, Tai J, Gelbart IA, Shitrit A, Ben-Moshe S, Drori Y, Itzkovitz S, Mandelboim M, Stern-Ginossar N. A systematic view on influenza induced host shutoff. eLife 2016; 5. [PMID: 27525483 PMCID: PMC5028189 DOI: 10.7554/elife.18311] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/14/2016] [Indexed: 12/25/2022] Open
Abstract
Host shutoff is a common strategy used by viruses to repress cellular mRNA translation and concomitantly allow the efficient translation of viral mRNAs. Here we use RNA-sequencing and ribosome profiling to explore the mechanisms that are being utilized by the Influenza A virus (IAV) to induce host shutoff. We show that viral transcripts are not preferentially translated and instead the decline in cellular protein synthesis is mediated by viral takeover on the mRNA pool. Our measurements also uncover strong variability in the levels of cellular transcripts reduction, revealing that short transcripts are less affected by IAV. Interestingly, these mRNAs that are refractory to IAV infection are enriched in cell maintenance processes such as oxidative phosphorylation. Furthermore, we show that the continuous oxidative phosphorylation activity is important for viral propagation. Our results advance our understanding of IAV-induced shutoff, and suggest a mechanism that facilitates the translation of genes with important housekeeping functions. DOI:http://dx.doi.org/10.7554/eLife.18311.001 Proteins carry out diverse activities in our cells. These proteins are constantly being built according to accurate instructions, which are encoded on molecules named messenger RNAs (mRNAs for short). The process of converting the instructions into proteins is called translation. Viruses infect host cells and take over the cellular machinery that is responsible for translation. This causes the cell to produce viral proteins at the expense of host proteins – a process called host shutoff. As a result, viral proteins take over the cell and the infection accelerates. There are two main strategies used by viruses to co-opt the cell’s translation machinery: either host mRNAs are destroyed, or the machines that read mRNA molecules are manipulated to read only the viral instructions. Most viruses appear to dedicate themselves to using just one of these strategies. However, evidence suggests that the Influenza A virus uses both strategies to induce host shutoff. To investigate the extent to which each of the shutoff strategies is used by the Influenza A virus, Bercovich-Kinori, Tai et al. have studied infected human lung cells. This revealed that the virus primarily reduces the amount of host mRNA in the cells to take over the mRNA pool. The host mRNAs were affected by the infection to different extents. For example, the mRNAs that coded for proteins that perform important roles for the virus, such as produce energy, were not affected by the virus. A future challenge is to find out exactly how the Influenza A virus distinguishes between different cellular mRNAs. This knowledge may help to develop new treatments for flu. DOI:http://dx.doi.org/10.7554/eLife.18311.002
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Affiliation(s)
- Adi Bercovich-Kinori
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Julie Tai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Idit Anna Gelbart
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alina Shitrit
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shani Ben-Moshe
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaron Drori
- Central Virology Laboratory, Chaim Sheba Medical Center, Ministry of Health, Rehovot, Israel.,Department of Epidemiology and Preventive Medicine, Tel-Aviv University, Tel-Aviv, Israel.,School of Public Health, Tel-Aviv University, Tel-Aviv, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Chaim Sheba Medical Center, Ministry of Health, Rehovot, Israel.,Department of Epidemiology and Preventive Medicine, Tel-Aviv University, Tel-Aviv, Israel.,School of Public Health, Tel-Aviv University, Tel-Aviv, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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224
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Cabrera-Quio LE, Herberg S, Pauli A. Decoding sORF translation - from small proteins to gene regulation. RNA Biol 2016; 13:1051-1059. [PMID: 27653973 DOI: 10.1080/15476286.2016.1218589] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Translation is best known as the fundamental mechanism by which the ribosome converts a sequence of nucleotides into a string of amino acids. Extensive research over many years has elucidated the key principles of translation, and the majority of translated regions were thought to be known. The recent discovery of wide-spread translation outside of annotated protein-coding open reading frames (ORFs) came therefore as a surprise, raising the intriguing possibility that these newly discovered translated regions might have unrecognized protein-coding or gene-regulatory functions. Here, we highlight recent findings that provide evidence that some of these newly discovered translated short ORFs (sORFs) encode functional, previously missed small proteins, while others have regulatory roles. Based on known examples we will also speculate about putative additional roles and the potentially much wider impact that these translated regions might have on cellular homeostasis and gene regulation.
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Affiliation(s)
| | - Sarah Herberg
- a The Research Institute of Molecular Pathology, Vienna Biocenter (VBC) , Vienna , Austria
| | - Andrea Pauli
- a The Research Institute of Molecular Pathology, Vienna Biocenter (VBC) , Vienna , Austria
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225
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Young SK, Wek RC. Upstream Open Reading Frames Differentially Regulate Gene-specific Translation in the Integrated Stress Response. J Biol Chem 2016; 291:16927-35. [PMID: 27358398 DOI: 10.1074/jbc.r116.733899] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Translation regulation largely occurs during initiation, which features ribosome assembly onto mRNAs and selection of the translation start site. Short, upstream ORFs (uORFs) located in the 5'-leader of the mRNA can be selected for translation. Multiple transcripts associated with stress amelioration are preferentially translated through uORF-mediated mechanisms during activation of the integrated stress response (ISR) in which phosphorylation of the α subunit of eIF2 results in a coincident global reduction in translation initiation. This review presents key features of uORFs that serve to optimize translational control that is essential for regulation of cell fate in response to environmental stresses.
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Affiliation(s)
- Sara K Young
- From the Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5126
| | - Ronald C Wek
- From the Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5126
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226
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Hinnebusch AG, Ivanov IP, Sonenberg N. Translational control by 5'-untranslated regions of eukaryotic mRNAs. Science 2016; 352:1413-6. [PMID: 27313038 DOI: 10.1126/science.aad9868] [Citation(s) in RCA: 748] [Impact Index Per Article: 83.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The eukaryotic 5' untranslated region (UTR) is critical for ribosome recruitment to the messenger RNA (mRNA) and start codon choice and plays a major role in the control of translation efficiency and shaping the cellular proteome. The ribosomal initiation complex is assembled on the mRNA via a cap-dependent or cap-independent mechanism. We describe various mechanisms controlling ribosome scanning and initiation codon selection by 5' upstream open reading frames, translation initiation factors, and primary and secondary structures of the 5'UTR, including particular sequence motifs. We also discuss translational control via phosphorylation of eukaryotic initiation factor 2, which is implicated in learning and memory, neurodegenerative diseases, and cancer.
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Affiliation(s)
- Alan G Hinnebusch
- Group on Cell Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivaylo P Ivanov
- Group on Cell Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.
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227
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Gamil AAA, Xu C, Mutoloki S, Evensen Ø. PKR Activation Favors Infectious Pancreatic Necrosis Virus Replication in Infected Cells. Viruses 2016; 8:v8060173. [PMID: 27338445 PMCID: PMC4926193 DOI: 10.3390/v8060173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/31/2016] [Accepted: 06/03/2016] [Indexed: 01/17/2023] Open
Abstract
The double-stranded RNA-activated protein kinase R (PKR) is a Type I interferon (IFN) stimulated gene that has important biological and immunological functions. In viral infections, in general, PKR inhibits or promotes viral replication, but PKR-IPNV interaction has not been previously studied. We investigated the involvement of PKR during infectious pancreatic necrosis virus (IPNV) infection using a custom-made rabbit antiserum and the PKR inhibitor C16. Reactivity of the antiserum to PKR in CHSE-214 cells was confirmed after IFNα treatment giving an increased protein level. IPNV infection alone did not give increased PKR levels by Western blot, while pre-treatment with PKR inhibitor before IPNV infection gave decreased eukaryotic initiation factor 2-alpha (eIF2α) phosphorylation. This suggests that PKR, despite not being upregulated, is involved in eIF2α phosphorylation during IPNV infection. PKR inhibitor pre-treatment resulted in decreased virus titers, extra- and intracellularly, concomitant with reduction of cells with compromised membranes in IPNV-permissive cell lines. These findings suggest that IPNV uses PKR activation to promote virus replication in infected cells.
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Affiliation(s)
- Amr A A Gamil
- Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 8146 Dep., 0033 Oslo, Norway.
| | - Cheng Xu
- Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 8146 Dep., 0033 Oslo, Norway.
| | - Stephen Mutoloki
- Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 8146 Dep., 0033 Oslo, Norway.
| | - Øystein Evensen
- Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 8146 Dep., 0033 Oslo, Norway.
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228
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Complementary Roles of GADD34- and CReP-Containing Eukaryotic Initiation Factor 2α Phosphatases during the Unfolded Protein Response. Mol Cell Biol 2016; 36:1868-80. [PMID: 27161320 DOI: 10.1128/mcb.00190-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 04/27/2016] [Indexed: 02/02/2023] Open
Abstract
Phosphorylation of eukaryotic initiation factor 2α (eIF2α) controls transcriptome-wide changes in mRNA translation in stressed cells. While phosphorylated eIF2α (P-eIF2α) attenuates global protein synthesis, mRNAs encoding stress proteins are more efficiently translated. Two eIF2α phosphatases, containing GADD34 and CReP, catalyze P-eIF2α dephosphorylation. The current view of GADD34, whose transcription is stress induced, is that it functions in a feedback loop to resolve cell stress. In contrast, CReP, which is constitutively expressed, controls basal P-eIF2α levels in unstressed cells. Our studies show that GADD34 drives substantial changes in mRNA translation in unstressed cells, particularly targeting the secretome. Following activation of the unfolded protein response (UPR), rapid translation of GADD34 mRNA occurs and GADD34 is essential for UPR progression. In the absence of GADD34, eIF2α phosphorylation is persistently enhanced and the UPR translational program is significantly attenuated. This "stalled" UPR is relieved by the subsequent activation of compensatory mechanisms that include AKT-mediated suppression of PKR-like kinase (PERK) and increased expression of CReP mRNA, partially restoring protein synthesis. Our studies highlight the coordinate regulation of UPR by the GADD34- and CReP-containing eIF2α phosphatases to control cell viability.
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229
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Steffen KK, Dillin A. A Ribosomal Perspective on Proteostasis and Aging. Cell Metab 2016; 23:1004-1012. [PMID: 27304502 DOI: 10.1016/j.cmet.2016.05.013] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/23/2016] [Accepted: 05/26/2016] [Indexed: 12/31/2022]
Abstract
As the first and most direct process influencing the proteostasis capacity of a cell, regulation of translation influences lifespan across taxa. Here we highlight some of the newly discovered means by which translational regulation affects cellular proteostasis, with a focus on mechanisms that may ultimately impinge upon the aging process.
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Affiliation(s)
- Kristan K Steffen
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew Dillin
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720, USA.
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230
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Tzani I, Ivanov IP, Andreev DE, Dmitriev RI, Dean KA, Baranov PV, Atkins JF, Loughran G. Systematic analysis of the PTEN 5' leader identifies a major AUU initiated proteoform. Open Biol 2016; 6:rsob.150203. [PMID: 27249819 PMCID: PMC4892431 DOI: 10.1098/rsob.150203] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/26/2016] [Indexed: 12/22/2022] Open
Abstract
Abundant evidence for translation within the 5' leaders of many human genes is rapidly emerging, especially, because of the advent of ribosome profiling. In most cases, it is believed that the act of translation rather than the encoded peptide is important. However, the wealth of available sequencing data in recent years allows phylogenetic detection of sequences within 5' leaders that have emerged under coding constraint and therefore allow for the prediction of functional 5' leader translation. Using this approach, we previously predicted a CUG-initiated, 173 amino acid N-terminal extension to the human tumour suppressor PTEN. Here, a systematic experimental analysis of translation events in the PTEN 5' leader identifies at least two additional non-AUG-initiated PTEN proteoforms that are expressed in most human cell lines tested. The most abundant extended PTEN proteoform initiates at a conserved AUU codon and extends the canonical AUG-initiated PTEN by 146 amino acids. All N-terminally extended PTEN proteoforms tested retain the ability to downregulate the PI3K pathway. We also provide evidence for the translation of two conserved AUG-initiated upstream open reading frames within the PTEN 5' leader that control the ratio of PTEN proteoforms.
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Affiliation(s)
- Ioanna Tzani
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ivaylo P Ivanov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dmitri E Andreev
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ruslan I Dmitriev
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Kellie A Dean
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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231
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Chew GL, Pauli A, Schier AF. Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish. Nat Commun 2016; 7:11663. [PMID: 27216465 PMCID: PMC4890304 DOI: 10.1038/ncomms11663] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 04/18/2016] [Indexed: 02/07/2023] Open
Abstract
Upstream open reading frames (uORFs) are ubiquitous repressive genetic elements in vertebrate mRNAs. While much is known about the regulation of individual genes by their uORFs, the range of uORF-mediated translational repression in vertebrate genomes is largely unexplored. Moreover, it is unclear whether the repressive effects of uORFs are conserved across species. To address these questions, we analyse transcript sequences and ribosome profiling data from human, mouse and zebrafish. We find that uORFs are depleted near coding sequences (CDSes) and have initiation contexts that diminish their translation. Linear modelling reveals that sequence features at both uORFs and CDSes modulate the translation of CDSes. Moreover, the ratio of translation over 5′ leaders and CDSes is conserved between human and mouse, and correlates with the number of uORFs. These observations suggest that the prevalence of vertebrate uORFs may be explained by their conserved role in repressing CDS translation. Upstream open reading frames (uORFs) can repress gene expression. Here, Guo-Liang Chew and colleagues use bioinformatics approaches to show that conservation of uORF-mediated translational repression is mediated by sequence features in human, mouse and zebrafish genomes.
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Affiliation(s)
- Guo-Liang Chew
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Andrea Pauli
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA.,FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts 02138, USA
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232
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Zhang L, Hapon MB, Goyeneche AA, Srinivasan R, Gamarra-Luques CD, Callegari EA, Drappeau DD, Terpstra EJ, Pan B, Knapp JR, Chien J, Wang X, Eyster KM, Telleria CM. Mifepristone increases mRNA translation rate, triggers the unfolded protein response, increases autophagic flux, and kills ovarian cancer cells in combination with proteasome or lysosome inhibitors. Mol Oncol 2016; 10:1099-117. [PMID: 27233943 DOI: 10.1016/j.molonc.2016.05.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/25/2016] [Accepted: 05/11/2016] [Indexed: 12/12/2022] Open
Abstract
The synthetic steroid mifepristone blocks the growth of ovarian cancer cells, yet the mechanism driving such effect is not entirely understood. Unbiased genomic and proteomic screenings using ovarian cancer cell lines of different genetic backgrounds and sensitivities to platinum led to the identification of two key genes upregulated by mifepristone and involved in the unfolded protein response (UPR): the master chaperone of the endoplasmic reticulum (ER), glucose regulated protein (GRP) of 78 kDa, and the CCAAT/enhancer binding protein homologous transcription factor (CHOP). GRP78 and CHOP were upregulated by mifepristone in ovarian cancer cells regardless of p53 status and platinum sensitivity. Further studies revealed that the three UPR-associated pathways, PERK, IRE1α, and ATF6, were activated by mifepristone. Also, the synthetic steroid acutely increased mRNA translation rate, which, if prevented, abrogated the splicing of XBP1 mRNA, a non-translatable readout of IRE1α activation. Moreover, mifepristone increased LC3-II levels due to increased autophagic flux. When the autophagic-lysosomal pathway was inhibited with chloroquine, mifepristone was lethal to the cells. Lastly, doses of proteasome inhibitors that are inadequate to block the activity of the proteasomes, caused cell death when combined with mifepristone; this phenotype was accompanied by accumulation of poly-ubiquitinated proteins denoting proteasome inhibition. The stimulation by mifepristone of ER stress and autophagic flux offers a therapeutic opportunity for utilizing this compound to sensitize ovarian cancer cells to proteasome or lysosome inhibitors.
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Affiliation(s)
- Lei Zhang
- Division of Basic Biomedical Sciences, Sanford School of Medicine of The University of South Dakota, Vermillion, SD 57069, USA
| | - Maria B Hapon
- Division of Basic Biomedical Sciences, Sanford School of Medicine of The University of South Dakota, Vermillion, SD 57069, USA
| | - Alicia A Goyeneche
- Division of Basic Biomedical Sciences, Sanford School of Medicine of The University of South Dakota, Vermillion, SD 57069, USA; Department of Pathology, Faculty of Medicine, McGill University, Montreal, QC H3A 2B4, Canada
| | - Rekha Srinivasan
- Division of Basic Biomedical Sciences, Sanford School of Medicine of The University of South Dakota, Vermillion, SD 57069, USA
| | - Carlos D Gamarra-Luques
- Division of Basic Biomedical Sciences, Sanford School of Medicine of The University of South Dakota, Vermillion, SD 57069, USA
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences, Sanford School of Medicine of The University of South Dakota, Vermillion, SD 57069, USA
| | - Donis D Drappeau
- Division of Basic Biomedical Sciences, Sanford School of Medicine of The University of South Dakota, Vermillion, SD 57069, USA
| | - Erin J Terpstra
- Division of Basic Biomedical Sciences, Sanford School of Medicine of The University of South Dakota, Vermillion, SD 57069, USA
| | - Bo Pan
- Division of Basic Biomedical Sciences, Sanford School of Medicine of The University of South Dakota, Vermillion, SD 57069, USA
| | - Jennifer R Knapp
- Kansas Intellectual and Development Disabilities Research Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jeremy Chien
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Xuejun Wang
- Division of Basic Biomedical Sciences, Sanford School of Medicine of The University of South Dakota, Vermillion, SD 57069, USA
| | - Kathleen M Eyster
- Division of Basic Biomedical Sciences, Sanford School of Medicine of The University of South Dakota, Vermillion, SD 57069, USA
| | - Carlos M Telleria
- Division of Basic Biomedical Sciences, Sanford School of Medicine of The University of South Dakota, Vermillion, SD 57069, USA; Department of Pathology, Faculty of Medicine, McGill University, Montreal, QC H3A 2B4, Canada.
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233
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Diament A, Tuller T. Estimation of ribosome profiling performance and reproducibility at various levels of resolution. Biol Direct 2016; 11:24. [PMID: 27160013 PMCID: PMC4862193 DOI: 10.1186/s13062-016-0127-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/29/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Ribosome profiling (or Ribo-seq) is currently the most popular methodology for studying translation; it has been employed in recent years to decipher various fundamental gene expression regulation aspects. The main promise of the approach is its ability to detect ribosome densities over an entire transcriptome in high resolution of single codons. Indeed, dozens of ribo-seq studies have included results related to local ribosome densities in different parts of the transcript; nevertheless, the performance of Ribo-seq has yet to be quantitatively evaluated and reported in a large-scale multi-organismal and multi-protocol study of currently available datasets. RESULTS Here we provide the first objective evaluation of Ribo-seq at the resolution of a single nucleotide(s) using clear, interpretable measures, based on the analysis of 15 experiments, 6 organisms, and a total of 612, 961 transcripts. Our major conclusion is that the ability to infer signals of ribosomal densities at nucleotide scale is considerably lower than previously thought, as signals at this level are not reproduced well in experimental replicates. In addition, we provide various quantitative measures that connect the expected error rate with Ribo-seq analysis resolution. CONCLUSIONS The analysis of Ribo-seq data at the resolution of codons and nucleotides provides a challenging task, calls for task-specific statistical methods and further protocol improvements. We believe that our results are important for every researcher studying translation and specifically for researchers analyzing data generated by the Ribo-seq approach. REVIEWERS This article was reviewed by Dmitrij Frishman, Eugene Koonin and Frank Eisenhaber.
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Affiliation(s)
- Alon Diament
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Tamir Tuller
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv-Yafo, Israel. .,The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv-Yafo, Israel.
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234
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Wang C, Han B, Zhou R, Zhuang X. Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells. Cell 2016; 165:990-1001. [PMID: 27153499 PMCID: PMC4905760 DOI: 10.1016/j.cell.2016.04.040] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/07/2016] [Accepted: 04/15/2016] [Indexed: 10/21/2022]
Abstract
Translation is under tight spatial and temporal controls to ensure protein production in the right time and place in cells. Methods that allow real-time, high-resolution visualization of translation in live cells are essential for understanding the spatiotemporal dynamics of translation regulation. Based on multivalent fluorescence amplification of the nascent polypeptide signal, we develop a method to image translation on individual mRNA molecules in real time in live cells, allowing direct visualization of translation events at the translation sites. Using this approach, we monitor transient changes of translation dynamics in responses to environmental stresses, capture distinct mobilities of individual polysomes in different subcellular compartments, and detect 3' UTR-dependent local translation and active transport of polysomes in dendrites of primary neurons.
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Affiliation(s)
- Chong Wang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Boran Han
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Ruobo Zhou
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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235
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Abstract
The past several years have seen dramatic leaps in our understanding of how gene expression is rewired at the translation level during tumorigenesis to support the transformed phenotype. This work has been driven by an explosion in technological advances and is revealing previously unimagined regulatory mechanisms that dictate functional expression of the cancer genome. In this Review we discuss emerging trends and exciting new discoveries that reveal how this translational circuitry contributes to specific aspects of tumorigenesis and cancer cell function, with a particular focus on recent insights into the role of translational control in the adaptive response to oncogenic stress conditions.
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Affiliation(s)
- Morgan L Truitt
- Department of Urology, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94158, USA
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94158, USA
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236
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Fields AP, Rodriguez EH, Jovanovic M, Stern-Ginossar N, Haas BJ, Mertins P, Raychowdhury R, Hacohen N, Carr SA, Ingolia NT, Regev A, Weissman JS. A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation. Mol Cell 2016; 60:816-827. [PMID: 26638175 PMCID: PMC4720255 DOI: 10.1016/j.molcel.2015.11.013] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/08/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
Abstract
A fundamental goal of genomics is to identify the complete set of expressed proteins. Automated annotation strategies rely on assumptions about protein-coding sequences (CDSs), e.g., they are conserved, do not overlap, and exceed a minimum length. However, an increasing number of newly discovered proteins violate these rules. Here we present an experimental and analytical framework, based on ribosome profiling and linear regression, for systematic identification and quantification of translation. Application of this approach to lipopolysaccharide-stimulated mouse dendritic cells and HCMV-infected human fibroblasts identifies thousands of novel CDSs, including micropeptides and variants of known proteins, that bear the hallmarks of canonical translation and exhibit translation levels and dynamics comparable to that of annotated CDSs. Remarkably, many translation events are identified in both mouse and human cells even when the peptide sequence is not conserved. Our work thus reveals an unexpected complexity to mammalian translation suited to provide both conserved regulatory or protein-based functions.
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Affiliation(s)
- Alexander P Fields
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco and California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA
| | - Edwin H Rodriguez
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco and California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA
| | - Marko Jovanovic
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Brian J Haas
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Philipp Mertins
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Nir Hacohen
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Aviv Regev
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Jonathan S Weissman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco and California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA.
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237
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Ma J, Diedrich JK, Jungreis I, Donaldson C, Vaughan J, Kellis M, Yates JR, Saghatelian A. Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides. Anal Chem 2016; 88:3967-75. [PMID: 27010111 DOI: 10.1021/acs.analchem.6b00191] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Computational, genomic, and proteomic approaches have been used to discover nonannotated protein-coding small open reading frames (smORFs). Some novel smORFs have crucial biological roles in cells and organisms, which motivates the search for additional smORFs. Proteomic smORF discovery methods are advantageous because they detect smORF-encoded polypeptides (SEPs) to validate smORF translation and SEP stability. Because SEPs are shorter and less abundant than average proteins, SEP detection using proteomics faces unique challenges. Here, we optimize several steps in the SEP discovery workflow to improve SEP isolation and identification. These changes have led to the detection of several new human SEPs (novel human genes), improved confidence in the SEP assignments, and enabled quantification of SEPs under different cellular conditions. These improvements will allow faster detection and characterization of new SEPs and smORFs.
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Affiliation(s)
- Jiao Ma
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States.,Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology , 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jolene K Diedrich
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology , 10010 North Torrey Pines Road, La Jolla, California 92037, United States.,Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology , 32 Vassar Street, Cambridge, Massachusetts 02139, United States.,The Broad Institute of MIT and Harvard , 7 Cambridge Center, Cambridge, Massachusetts 02139, United States
| | - Cynthia Donaldson
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology , 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Joan Vaughan
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology , 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology , 32 Vassar Street, Cambridge, Massachusetts 02139, United States.,The Broad Institute of MIT and Harvard , 7 Cambridge Center, Cambridge, Massachusetts 02139, United States
| | - John R Yates
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology , 10010 North Torrey Pines Road, La Jolla, California 92037, United States.,Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alan Saghatelian
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology , 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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238
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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: 2.8] [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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239
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Johnstone TG, Bazzini AA, Giraldez AJ. Upstream ORFs are prevalent translational repressors in vertebrates. EMBO J 2016; 35:706-23. [PMID: 26896445 DOI: 10.15252/embj.201592759] [Citation(s) in RCA: 259] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 01/08/2016] [Indexed: 12/20/2022] Open
Abstract
Regulation of gene expression is fundamental in establishing cellular diversity and a target of natural selection. Untranslated mRNA regions (UTRs) are key mediators of post-transcriptional regulation. Previous studies have predicted thousands of ORFs in 5'UTRs, the vast majority of which have unknown function. Here, we present a systematic analysis of the translation and function of upstream open reading frames (uORFs) across vertebrates. Using high-resolution ribosome footprinting, we find that (i)uORFs are prevalent within vertebrate transcriptomes, (ii) the majority show signatures of active translation, and (iii)uORFs act as potent regulators of translation and RNA levels, with a similar magnitude to miRNAs. Reporter experiments reveal clear repression of downstream translation by uORFs/oORFs. uORF number, intercistronic distance, overlap with the CDS, and initiation context most strongly influence translation. Evolution has targeted these features to favor uORFs amenable to regulation over constitutively repressive uORFs/oORFs. Finally, we observe that the regulatory potential of uORFs on individual genes is conserved across species. These results provide insight into the regulatory code within mRNA leader sequences and their capacity to modulate translation across vertebrates.
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Affiliation(s)
- Timothy G Johnstone
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Ariel A Bazzini
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
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240
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Starck SR, Tsai JC, Chen K, Shodiya M, Wang L, Yahiro K, Martins-Green M, Shastri N, Walter P. Translation from the 5' untranslated region shapes the integrated stress response. Science 2016; 351:aad3867. [PMID: 26823435 DOI: 10.1126/science.aad3867] [Citation(s) in RCA: 274] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translated regions distinct from annotated coding sequences have emerged as essential elements of the proteome. This includes upstream open reading frames (uORFs) present in mRNAs controlled by the integrated stress response (ISR) that show "privileged" translation despite inhibited eukaryotic initiation factor 2-guanosine triphosphate-initiator methionyl transfer RNA (eIF2·GTP·Met-tRNA(i )(Met)). We developed tracing translation by T cells to directly measure the translation products of uORFs during the ISR. We identified signature translation events from uORFs in the 5' untranslated region of binding immunoglobulin protein (BiP) mRNA (also called heat shock 70-kilodalton protein 5 mRNA) that were not initiated at the start codon AUG. BiP expression during the ISR required both the alternative initiation factor eIF2A and non-AUG-initiated uORFs. We propose that persistent uORF translation, for a variety of chaperones, shelters select mRNAs from the ISR, while simultaneously generating peptides that could serve as major histocompatibility complex class I ligands, marking cells for recognition by the adaptive immune system.
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Affiliation(s)
- Shelley R Starck
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA. Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
| | - Jordan C Tsai
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA
| | - Keling Chen
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Michael Shodiya
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Lei Wang
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA 92521, USA
| | - Kinnosuke Yahiro
- Departments of Molecular Infectiology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Manuela Martins-Green
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA 92521, USA
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
| | - Peter Walter
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.
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241
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Sheshukova EV, Shindyapina AV, Komarova TV, Dorokhov YL. “Matreshka” genes with alternative reading frames. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416020149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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242
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Michel AM, Mullan JPA, Velayudhan V, O'Connor PBF, Donohue CA, Baranov PV. RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data. RNA Biol 2016; 13:316-9. [PMID: 26821742 PMCID: PMC4829337 DOI: 10.1080/15476286.2016.1141862] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ribosome profiling (ribo-seq) is a technique that uses high-throughput sequencing to reveal the exact locations and densities of translating ribosomes at the entire transcriptome level. The technique has become very popular since its inception in 2009. Yet experimentalists who generate ribo-seq data often have to rely on bioinformaticians to process and analyze their data. We present RiboGalaxy ( http://ribogalaxy.ucc.ie ), a freely available Galaxy-based web server for processing and analyzing ribosome profiling data with the visualization functionality provided by GWIPS-viz ( http://gwips.ucc.ie ). RiboGalaxy offers researchers a suite of tools specifically tailored for processing ribo-seq and corresponding mRNA-seq data. Researchers can take advantage of the published workflows which reduce the multi-step alignment process to a minimum of inputs from the user. Users can then explore their own aligned data as custom tracks in GWIPS-viz and compare their ribosome profiles to existing ribo-seq tracks from published studies. In addition, users can assess the quality of their ribo-seq data, determine the strength of the triplet periodicity signal, generate meta-gene ribosome profiles as well as analyze the relative impact of mRNA sequence features on local read density. RiboGalaxy is accompanied by extensive documentation and tips for helping users. In addition we provide a forum ( http://gwips.ucc.ie/Forum ) where we encourage users to post their questions and feedback to improve the overall RiboGalaxy service.
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Affiliation(s)
- Audrey M Michel
- a School of Biochemistry & Cell Biology, University College Cork , Cork , Ireland
| | - James P A Mullan
- a School of Biochemistry & Cell Biology, University College Cork , Cork , Ireland
| | | | - Patrick B F O'Connor
- a School of Biochemistry & Cell Biology, University College Cork , Cork , Ireland
| | - Claire A Donohue
- a School of Biochemistry & Cell Biology, University College Cork , Cork , Ireland
| | - Pavel V Baranov
- a School of Biochemistry & Cell Biology, University College Cork , Cork , Ireland
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243
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Mouilleron H, Delcourt V, Roucou X. Death of a dogma: eukaryotic mRNAs can code for more than one protein. Nucleic Acids Res 2016; 44:14-23. [PMID: 26578573 PMCID: PMC4705651 DOI: 10.1093/nar/gkv1218] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/13/2022] Open
Abstract
mRNAs carry the genetic information that is translated by ribosomes. The traditional view of a mature eukaryotic mRNA is a molecule with three main regions, the 5' UTR, the protein coding open reading frame (ORF) or coding sequence (CDS), and the 3' UTR. This concept assumes that ribosomes translate one ORF only, generally the longest one, and produce one protein. As a result, in the early days of genomics and bioinformatics, one CDS was associated with each protein-coding gene. This fundamental concept of a single CDS is being challenged by increasing experimental evidence indicating that annotated proteins are not the only proteins translated from mRNAs. In particular, mass spectrometry (MS)-based proteomics and ribosome profiling have detected productive translation of alternative open reading frames. In several cases, the alternative and annotated proteins interact. Thus, the expression of two or more proteins translated from the same mRNA may offer a mechanism to ensure the co-expression of proteins which have functional interactions. Translational mechanisms already described in eukaryotic cells indicate that the cellular machinery is able to translate different CDSs from a single viral or cellular mRNA. In addition to summarizing data showing that the protein coding potential of eukaryotic mRNAs has been underestimated, this review aims to challenge the single translated CDS dogma.
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Affiliation(s)
- Hélène Mouilleron
- Department of biochemistry, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec, Canada
| | - Vivian Delcourt
- Department of biochemistry, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec, Canada Inserm U-1192, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), Université de Lille 1, Cité Scientifique, 59655 Villeneuve D'Ascq, France
| | - Xavier Roucou
- Department of biochemistry, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec, Canada
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244
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Detecting actively translated open reading frames in ribosome profiling data. Nat Methods 2015; 13:165-70. [PMID: 26657557 DOI: 10.1038/nmeth.3688] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/28/2015] [Indexed: 12/23/2022]
Abstract
RNA-sequencing protocols can quantify gene expression regulation from transcription to protein synthesis. Ribosome profiling (Ribo-seq) maps the positions of translating ribosomes over the entire transcriptome. We have developed RiboTaper (available at https://ohlerlab.mdc-berlin.de/software/), a rigorous statistical approach that identifies translated regions on the basis of the characteristic three-nucleotide periodicity of Ribo-seq data. We used RiboTaper with deep Ribo-seq data from HEK293 cells to derive an extensive map of translation that covered open reading frame (ORF) annotations for more than 11,000 protein-coding genes. We also found distinct ribosomal signatures for several hundred upstream ORFs and ORFs in annotated noncoding genes (ncORFs). Mass spectrometry data confirmed that RiboTaper achieved excellent coverage of the cellular proteome. Although dozens of novel peptide products were validated in this manner, few of the currently annotated long noncoding RNAs appeared to encode stable polypeptides. RiboTaper is a powerful method for comprehensive de novo identification of actively used ORFs from Ribo-seq data.
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245
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Reid DW, Shenolikar S, Nicchitta CV. Simple and inexpensive ribosome profiling analysis of mRNA translation. Methods 2015; 91:69-74. [PMID: 26164698 PMCID: PMC4684803 DOI: 10.1016/j.ymeth.2015.07.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/22/2015] [Accepted: 07/06/2015] [Indexed: 12/14/2022] Open
Abstract
The development and application of ribosome profiling has markedly advanced our understanding of ribosomes and mRNA translation. The experimental approach, which relies on deep sequencing of ribosome-protected mRNA fragments generated by treatment of polyribosomes with exogenous nucleases, provides a transcriptome-wide assessment of translation. The broad application of ribosome profiling has been slowed by the complexity and expense of the protocol. Here, we provide a simplified ribosome profiling method that uses micrococcal nuclease to generate ribosome footprints in crude cellular extracts, which are then purified simply by size selection via polyacrylamide gel electrophoresis. This simplification removes the laborious or expensive purification of ribosomes that has typically been used. This direct extraction method generates gene-level ribosome profiling data that are similar to a method that includes ribosome purification. This protocol should significantly ease the barrier to entry for research groups interested in employing ribosome profiling.
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Affiliation(s)
- David W Reid
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Graduate Medical School, Singapore 169857, Singapore.
| | - Shirish Shenolikar
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Graduate Medical School, Singapore 169857, Singapore; Programme in Neuroscience and Behavioral Disorders, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
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246
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Dieudonné FX, O'Connor PBF, Gubler-Jaquier P, Yasrebi H, Conne B, Nikolaev S, Antonarakis S, Baranov PV, Curran J. The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype. BMC Genomics 2015; 16:986. [PMID: 26589636 PMCID: PMC4654819 DOI: 10.1186/s12864-015-2179-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/31/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genetic program, as manifested as the cellular phenotype, is in large part dictated by the cell's protein composition. Since characterisation of the proteome remains technically laborious it is attractive to define the genetic expression profile using the transcriptome. However, the transcriptional landscape is complex and it is unclear as to what extent it reflects the ribosome associated mRNA population (the translatome). This is particularly pertinent for genes using multiple transcriptional start sites (TSS) generating mRNAs with heterogeneous 5' transcript leaders (5'TL). Furthermore, the relative abundance of the TSS gene variants is frequently cell-type specific. Indeed, promoter switches have been reported in pathologies such as cancer. The consequences of this 5'TL heterogeneity within the transcriptome for the translatome remain unresolved. This is not a moot point because the 5'TL plays a key role in regulating mRNA recruitment onto polysomes. RESULTS In this article, we have characterised both the transcriptome and translatome of the MCF7 (tumoural) and MCF10A (non-tumoural) cell lines. We identified ~550 genes exhibiting differential translation efficiency (TE). In itself, this is maybe not surprising. However, by focusing on genes exhibiting TSS heterogeneity we observed distinct differential promoter usage patterns in both the transcriptome and translatome. Only a minor fraction of these genes belonged to those exhibiting differential TE. Nonetheless, reporter assays demonstrated that the TSS variants impacted on the translational readout both quantitatively (the overall amount of protein expressed) and qualitatively (the nature of the proteins expressed). CONCLUSIONS The results point to considerable and distinct cell-specific 5'TL heterogeneity within both the transcriptome and translatome of the two cell lines analysed. This observation is in-line with the ribosome filter hypothesis which posits that the ribosomal machine can selectively filter information from within the transcriptome. As such it cautions against the simple extrapolation transcriptome → proteome. Furthermore, polysomal occupancy of specific gene 5'TL variants may also serve as novel disease biomarkers.
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Affiliation(s)
- Francois-Xavier Dieudonné
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | | | - Pascale Gubler-Jaquier
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Haleh Yasrebi
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Beatrice Conne
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland.,Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Sergey Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Stylianos Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,The Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Joseph Curran
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland. .,The Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland.
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247
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Ribosome profiling reveals the what, when, where and how of protein synthesis. Nat Rev Mol Cell Biol 2015; 16:651-64. [PMID: 26465719 DOI: 10.1038/nrm4069] [Citation(s) in RCA: 362] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Ribosome profiling, which involves the deep sequencing of ribosome-protected mRNA fragments, is a powerful tool for globally monitoring translation in vivo. The method has facilitated discovery of the regulation of gene expression underlying diverse and complex biological processes, of important aspects of the mechanism of protein synthesis, and even of new proteins, by providing a systematic approach for experimental annotation of coding regions. Here, we introduce the methodology of ribosome profiling and discuss examples in which this approach has been a key factor in guiding biological discovery, including its prominent role in identifying thousands of novel translated short open reading frames and alternative translation products.
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248
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Young SK, Willy JA, Wu C, Sachs MS, Wek RC. Ribosome Reinitiation Directs Gene-specific Translation and Regulates the Integrated Stress Response. J Biol Chem 2015; 290:28257-28271. [PMID: 26446796 DOI: 10.1074/jbc.m115.693184] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Indexed: 12/24/2022] Open
Abstract
In the integrated stress response, phosphorylation of eIF2α (eIF2α-P) reduces protein synthesis to conserve resources and facilitate preferential translation of transcripts that promote stress adaptation. Preferentially translated GADD34 (PPP1R15A) and constitutively expressed CReP (PPP1R15B) function to dephosphorylate eIF2α-P and restore protein synthesis. The 5'-leaders of GADD34 and CReP contain two upstream ORFs (uORFs). Using biochemical and genetic approaches we show that features of these uORFs are central for their differential expression. In the absence of stress, translation of an inhibitory uORF in GADD34 acts as a barrier that prevents reinitiation at the GADD34 coding region. Enhanced eIF2α-P during stress directs ribosome bypass of the uORF, facilitating translation of the GADD34 coding region. CReP expression occurs independent of eIF2α-P via an uORF that allows for translation reinitiation at the CReP coding region independent of stress. Importantly, alterations in the GADD34 uORF affect the status of eIF2α-P, translational control, and cell adaptation to stress. These results show that properties of uORFs that permit ribosome reinitiation are critical for directing gene-specific translational control in the integrated stress response.
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Affiliation(s)
- Sara K Young
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5126
| | - Jeffrey A Willy
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5126
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5126.
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249
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Legrand N, Jaquier-Gubler P, Curran J. The impact of the phosphomimetic eIF2αS/D on global translation, reinitiation and the integrated stress response is attenuated in N2a cells. Nucleic Acids Res 2015; 43:8392-404. [PMID: 26264663 PMCID: PMC4787802 DOI: 10.1093/nar/gkv827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/04/2015] [Indexed: 12/21/2022] Open
Abstract
A plethora of stresses trigger a rapid downregulation of protein synthesis. However, a fraction of mRNAs continue to be recruited onto polysomes and their protein products play a key role in deciding cell fate. These transcripts are characterized by the presence of uORFs within their 5' TL coupling protein expression to reinitiation. The translational brake arises due to the activation of a family of kinases targeting the α subunit of the trimolecular eIF2(αβγ) initiation factor. Phosphorylation of eIF2αSer51 inhibits ternary complex regeneration reducing the pool of 43S ribosomes. It is popular to mimic this event, and hence the integrated stress response (ISR), by the expression of the phosphomimetic eIF2αS51D. However, we report that whereas the ISR is reproduced by eIF2αS51D expression in human HEK293T cells this is not the case in N2a mouse neuroblastoma cells. With regards to translational downregulation, this arises due to the failure of the phosphomimetic protein to assemble an eIF2 complex with endogenous eIF2β/γ. This can be compensated for by the transient co-expression of all three subunits. Curiously, these conditions do not modulate reinitiation and consequently fail to trigger the ISR. This is the first demonstration that the inhibitory and reinitiation functions of eIF2αS/D can be separated.
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Affiliation(s)
- Noemie Legrand
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Switzerland
| | - Pascale Jaquier-Gubler
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Switzerland
| | - Joseph Curran
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Switzerland Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Switzerland
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250
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Abstract
Viral genomes harbor a variety of unusual translational phenomena that allow them to pack coding information more densely and evade host restriction mechanisms imposed by the cellular translational apparatus. Annotating translated sequences within these genomes thus poses particular challenges, but identifying the full complement of proteins encoded by a virus is critical for understanding its life cycle and defining the epitopes it presents for immune surveillance. Ribosome profiling is an emerging technique for global analysis of translation that offers direct and experimental annotation of viral genomes. Ribosome profiling has been applied to two herpesvirus genomes, those of human cytomegalovirus and Kaposi's sarcoma-associated herpesvirus, revealing translated sequences within presumptive long noncoding RNAs and identifying other micropeptides. Synthesis of these proteins has been confirmed by mass spectrometry and by identifying T cell responses following infection. Ribosome profiling in other viruses will likely expand further our understanding of viral gene regulation and the proteome.
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Affiliation(s)
- Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720;
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