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Gerbaldo F, Sonder E, Fischer V, Frei S, Wang J, Gapp K, Robinson MD, Germain PL. On the identification of differentially-active transcription factors from ATAC-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583825. [PMID: 38496482 PMCID: PMC10942475 DOI: 10.1101/2024.03.06.583825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approaches for doing so. Here we benchmark several such methods using a combination of curated datasets with various forms of short-term perturbations on known TFs, as well as semi-simulations. We include both methods specifically designed for this type of data as well as some that can be repurposed for it. We also investigate variations to these methods, and identify three particularly promising approaches (chromVAR-limma with critical adjustments, monaLisa and a combination of GC smooth quantile normalization and multivariate modeling). We further investigate the specific use of nucleosome-free fragments, the combination of top methods, and the impact of technical variation. Finally, we illustrate the use of the top methods on a novel dataset to characterize the impact on DNA accessibility of TRAnscription Factor TArgeting Chimeras (TRAFTAC), which can deplete TFs - in our case NFkB - at the protein level.
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Affiliation(s)
- Felix Gerbaldo
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Systems Neuroscience, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Emanuel Sonder
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Systems Neuroscience, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
| | - Vincent Fischer
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Selina Frei
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Jiayi Wang
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Katharina Gapp
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
| | - Pierre-Luc Germain
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
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2
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Bhatter N, Dmitriev SE, Ivanov P. Cell death or survival: Insights into the role of mRNA translational control. Semin Cell Dev Biol 2024; 154:138-154. [PMID: 37357122 PMCID: PMC10695129 DOI: 10.1016/j.semcdb.2023.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
Cellular stress is an intrinsic part of cell physiology that underlines cell survival or death. The ability of mammalian cells to regulate global protein synthesis (aka translational control) represents a critical, yet underappreciated, layer of regulation during the stress response. Various cellular stress response pathways monitor conditions of cell growth and subsequently reshape the cellular translatome to optimize translational outputs. On the molecular level, such translational reprogramming involves an intricate network of interactions between translation machinery, RNA-binding proteins, mRNAs, and non-protein coding RNAs. In this review, we will discuss molecular mechanisms, signaling pathways, and targets of translational control that contribute to cellular adaptation to stress and to cell survival or death.
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Affiliation(s)
- Nupur Bhatter
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Harvard Initiative for RNA Medicine, Boston, Massachusetts, USA.
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3
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Makeeva DS, Riggs CL, Burakov AV, Ivanov PA, Kushchenko AS, Bykov DA, Popenko VI, Prassolov VS, Ivanov PV, Dmitriev SE. Relocalization of Translation Termination and Ribosome Recycling Factors to Stress Granules Coincides with Elevated Stop-Codon Readthrough and Reinitiation Rates upon Oxidative Stress. Cells 2023; 12:259. [PMID: 36672194 PMCID: PMC9856671 DOI: 10.3390/cells12020259] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Upon oxidative stress, mammalian cells rapidly reprogram their translation. This is accompanied by the formation of stress granules (SGs), cytoplasmic ribonucleoprotein condensates containing untranslated mRNA molecules, RNA-binding proteins, 40S ribosomal subunits, and a set of translation initiation factors. Here we show that arsenite-induced stress causes a dramatic increase in the stop-codon readthrough rate and significantly elevates translation reinitiation levels on uORF-containing and bicistronic mRNAs. We also report the recruitment of translation termination factors eRF1 and eRF3, as well as ribosome recycling and translation reinitiation factors ABCE1, eIF2D, MCT-1, and DENR to SGs upon arsenite treatment. Localization of these factors to SGs may contribute to a rapid resumption of mRNA translation after stress relief and SG disassembly. It may also suggest the presence of post-termination, recycling, or reinitiation complexes in SGs. This new layer of translational control under stress conditions, relying on the altered spatial distribution of translation factors between cellular compartments, is discussed.
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Affiliation(s)
- Desislava S. Makeeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Claire L. Riggs
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anton V. Burakov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Pavel A. Ivanov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Artem S. Kushchenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Dmitri A. Bykov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir I. Popenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir S. Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Pavel V. Ivanov
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sergey E. Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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4
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Bahamondes Lorca VA, Bastidas Mayorga BD, Tong L, Wu S. UVB-induced eIF2α phosphorylation in keratinocytes depends on decreased ATF4, GADD34 and CReP expression levels. Life Sci 2021; 286:120044. [PMID: 34637792 DOI: 10.1016/j.lfs.2021.120044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 02/05/2023]
Abstract
AIM To elucidate the mechanism behind the sustained high levels of phosphorylated eIF2α in HaCaT cells post-UVB. MAIN METHODS In this study, expression levels of the machinery involved in the dephosphorylation of eIF2α (GADD34, CReP and PP1), as well as the PERK-eIF2α-ATF4-CHOP, IRE1α/XBP1s and ATF6α signaling cascades, were analyzed by western blot and fluorescence microscope. KEY FINDINGS Our data showed that UVB induces the phosphorylation of eIF2α, which induces the translation of ATF4 and consequently the expression of CHOP and GADD34. Nevertheless, UVB also suppresses the translation of ATF4 and GADD34 in HaCaT cells via a p-eIF2α independent mechanism. Therefore, the lack of ATF4, GADD34 and CReP is responsible for the sustained phosphorylation of eIF2α. Finally, our data also showed that UVB selectively modifies PERK and downregulates ATF6α expression but does not induce activation of the IRE1α/XBP1s pathway in HaCaT cells. SIGNIFICANCE Novel mechanism to explain the prolonged phosphorylation of eIF2α post-UVB irradiation.
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Affiliation(s)
- Verónica A Bahamondes Lorca
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA; Departamento de Tecnología Médica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Bernardo D Bastidas Mayorga
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
| | - Lingying Tong
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA.
| | - Shiyong Wu
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA.
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Miles RR, Amin PH, Diaz MB, Misra J, Aukerman E, Das A, Ghosh N, Guith T, Knierman MD, Roy S, Spandau DF, Wek RC. The eIF2 kinase GCN2 directs keratinocyte collective cell migration during wound healing via coordination of reactive oxygen species and amino acids. J Biol Chem 2021; 297:101257. [PMID: 34597669 PMCID: PMC8554533 DOI: 10.1016/j.jbc.2021.101257] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/25/2022] Open
Abstract
Healing of cutaneous wounds requires the collective migration of epithelial keratinocytes to seal the wound bed from the environment. However, the signaling events that coordinate this collective migration are unclear. In this report, we address the role of phosphorylation of eukaryotic initiation factor 2 (eIF2) and attendant gene expression during wound healing. Wounding of human keratinocyte monolayers in vitro led to the rapid activation of the eIF2 kinase GCN2. We determined that deletion or pharmacological inhibition of GCN2 significantly delayed collective cell migration and wound closure. Global transcriptomic, biochemical, and cellular analyses indicated that GCN2 is necessary for maintenance of intracellular free amino acids, particularly cysteine, as well as coordination of RAC1-GTP-driven reactive oxygen species (ROS) generation, lamellipodia formation, and focal adhesion dynamics following keratinocyte wounding. In vivo experiments using mice deficient for GCN2 validated the role of the eIF2 kinase during wound healing in intact skin. These results indicate that GCN2 is critical for appropriate induction of collective cell migration and plays a critical role in coordinating the re-epithelialization of cutaneous wounds.
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Affiliation(s)
- Rebecca R Miles
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Parth H Amin
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Miguel Barriera Diaz
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jagannath Misra
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Erica Aukerman
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Amitava Das
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana, USA; Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Nandini Ghosh
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana, USA; Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Tanner Guith
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana, USA; Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Michael D Knierman
- Laboratory for Experimental Medicine, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Sashwati Roy
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana, USA; Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Dan F Spandau
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, Indiana, USA.
| | - Ronald C Wek
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
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6
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Jolles B, Jean-Jean O. Poly(A) tail degradation in human cells: ATF4 mRNA as a model for biphasic deadenylation. Biochimie 2021; 185:128-134. [PMID: 33775689 DOI: 10.1016/j.biochi.2021.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]
Abstract
Eukaryotic mRNA deadenylation is generally considered as a two-step process in which the PAN2-PAN3 complex initiates the poly(A) tail degradation while, in the second step, the CCR4-NOT complex completes deadenylation, leading to decapping and degradation of the mRNA body. However, the mechanism of the biphasic poly(A) tail deadenylation remains enigmatic in several points such as the timing of the switch between the two steps, the role of translation termination and the mRNAs population involved. Here, we have studied the deadenylation of endogenous mRNAs in human cells depleted in either PAN3 or translation termination factor eRF3. Among the mRNAs tested, we found that only the endogenous ATF4 mRNA meets the biphasic model for deadenylation and that eRF3 prevents the shortening of its poly(A) tail. For the other mRNAs, the poor effect of PAN3 depletion on their poly(A) tail shortening questions the mode of their deadenylation. It is possible that these mRNAs experience a single step deadenylation process. Alternatively, we propose that a very short initial deadenylation by PAN2-PAN3 is followed by a rapid transition to the second phase involving CCR4-NOT complex. These differences in the timing of the transition from one deadenylation step to the other could explain the difficulties encountered in the generalization of the biphasic deadenylation model.
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Affiliation(s)
- Béatrice Jolles
- Sorbonne Université, Institute of Biology Paris-Seine, IBPS, CNRS, Biological Adaptation and Ageing, B2A, F, 75005, Paris, France
| | - Olivier Jean-Jean
- Sorbonne Université, Institute of Biology Paris-Seine, IBPS, CNRS, Biological Adaptation and Ageing, B2A, F, 75005, Paris, France.
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7
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Zaky DA, Wadie W, Eldehna WM, El Kerdawy AM, Abdallah DM, El Abhar HS. Modulation of endoplasmic reticulum stress response in gut-origin encephalopathy: Impact of vascular endothelial growth factor receptor-2 manipulation. Life Sci 2020; 252:117654. [PMID: 32277979 DOI: 10.1016/j.lfs.2020.117654] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/09/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Septic encephalopathy, the most frequent complication of sepsis, is orchestrated by a complex interplay of signals that leads to high mortality rates among intensive care unit patients. However, the role of the vascular endothelial growth factor receptor-2 (VEGFR2) in endoplasmic reticulum stress response (ERSR), during septic encephalopathy, is still elusive. AIM This study was aimed to examine the effect of an in-house designed/synthesized VEGFR2 antagonist, named WAG4S, on septic encephalopathy using cecal ligation and perforation (CLP). MAIN METHODS Rats were intraperitoneally injected with WAG-4S (1 mg/kg/d) for 7 days post-CLP. KEY FINDINGS In septic animals, VEGFR2 antagonism declined the expression of cortical p-VEGFR2 and p-mammalian target of rapamycin complex-1 (p-mTORC1). It also worsened the behavioral and histopathological alterations beyond CLP. However, and contrary to CLP, WAG-4S decreased the p-protein kinase R-like ER kinase (p-PERK) and eukaryotic initiation factor-2α (p-eIF2α) expression. Moreover, VEGFR2 blockade upregulated the mRNA expression of activating transcription factor-4 (ATF4), binding immunoglobulin protein/glucose-regulated protein-78 (Bip/GRP78), growth arrest and DNA damage-34 (GADD34) and spliced X-box binding protein-1 (XBP1s) above CLP. Similarly, it boosted inositol requiring enzyme-1α (IRE1α) activation and redox imbalance. In the same context, WAG-4S augmented the protein levels of CLP-induced ERSR apoptotic markers, namely C/EBP homologous protein (CHOP/GADD153), c-jun N-terminal kinase (JNK) and caspase-3. SIGNIFICANCE In conclusion, the PERK/eIF2α axis inhibition, during septic encephalopathy, is VEGFR2-independent, whereas the activated IRE1α/XBP1s/CHOP/JNK/caspase-3 cue promotes the ERSR execution module through VEGFR2 inhibition. This has turned VEGFR2 into a potential therapeutic target for ameliorating such an ailment.
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Affiliation(s)
- Doaa A Zaky
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Kasr El-Aini street, Cairo, P.O. Box 11562, Egypt.
| | - Walaa Wadie
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Kasr El-Aini street, Cairo, P.O. Box 11562, Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, P.O. Box 33516, Egypt
| | - Ahmed M El Kerdawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini street, Cairo, P.O. Box 11562, Egypt
| | - Dalaal M Abdallah
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Kasr El-Aini street, Cairo, P.O. Box 11562, Egypt
| | - Hanan S El Abhar
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Kasr El-Aini street, Cairo, P.O. Box 11562, Egypt; Department of Pharmacology & Toxicology, Faculty of Pharmaceutical Sciences and Pharmaceutical Industries, Future University in Egypt, Cairo, P.O. Box 11835, Egypt
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8
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Schwenzer H, Jühling F, Chu A, Pallett LJ, Baumert TF, Maini M, Fassati A. Oxidative Stress Triggers Selective tRNA Retrograde Transport in Human Cells during the Integrated Stress Response. Cell Rep 2020; 26:3416-3428.e5. [PMID: 30893612 PMCID: PMC6426654 DOI: 10.1016/j.celrep.2019.02.077] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/04/2019] [Accepted: 02/20/2019] [Indexed: 01/05/2023] Open
Abstract
In eukaryotes, tRNAs are transcribed in the nucleus and exported to the cytosol, where they deliver amino acids to ribosomes for protein translation. This nuclear-cytoplasmic movement was believed to be unidirectional. However, active shuttling of tRNAs, named tRNA retrograde transport, between the cytosol and nucleus has been discovered. This pathway is conserved in eukaryotes, suggesting a fundamental function; however, little is known about its role in human cells. Here we report that, in human cells, oxidative stress triggers tRNA retrograde transport, which is rapid, reversible, and selective for certain tRNA species, mostly with shorter 3′ ends. Retrograde transport of tRNASeC, which promotes translation of selenoproteins required to maintain homeostatic redox levels in cells, is highly efficient. tRNA retrograde transport is regulated by the integrated stress response pathway via the PERK-REDD1-mTOR axis. Thus, we propose that tRNA retrograde transport is part of the cellular response to oxidative stress. Oxidative stress triggers nuclear import of cytoplasmic tRNAs Import is selective for certain tRNAs Import requires activation of the unfolded protein response and inhibition of mTOR via REDD1 tRNA nuclear import is a component of the integrated stress response
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Affiliation(s)
- Hagen Schwenzer
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK
| | - Frank Jühling
- INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 2 Université de Strasbourg, 67000 Strasbourg, France
| | - Alexander Chu
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK
| | - Laura J Pallett
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK
| | - Thomas F Baumert
- INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 2 Université de Strasbourg, 67000 Strasbourg, France; Nouvel Hôpital Civil, Institut Hospitalo-Universitaire, 67000 Strasbourg, France
| | - Mala Maini
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK
| | - Ariberto Fassati
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK.
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9
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Aliouat A, Hatin I, Bertin P, François P, Stierlé V, Namy O, Salhi S, Jean-Jean O. Divergent effects of translation termination factor eRF3A and nonsense-mediated mRNA decay factor UPF1 on the expression of uORF carrying mRNAs and ribosome protein genes. RNA Biol 2019; 17:227-239. [PMID: 31619139 PMCID: PMC6973328 DOI: 10.1080/15476286.2019.1674595] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In addition to its role in translation termination, eRF3A has been implicated in the nonsense-mediated mRNA decay (NMD) pathway through its interaction with UPF1. NMD is a RNA quality control mechanism, which detects and degrades aberrant mRNAs as well as some normal transcripts including those that harbour upstream open reading frames in their 5ʹ leader sequence. In this study, we used RNA-sequencing and ribosome profiling to perform a genome wide analysis of the effect of either eRF3A or UPF1 depletion in human cells. Our bioinformatics analyses allow to delineate the features of the transcripts controlled by eRF3A and UPF1 and to compare the effect of each of these factors on gene expression. We find that eRF3A and UPF1 have very different impacts on the human transcriptome, less than 250 transcripts being targeted by both factors. We show that eRF3A depletion globally derepresses the expression of mRNAs containing translated uORFs while UPF1 knockdown derepresses only the mRNAs harbouring uORFs with an AUG codon in an optimal context for translation initiation. Finally, we also find that eRF3A and UPF1 have opposite effects on ribosome protein gene expression. Together, our results provide important elements for understanding the impact of translation termination and NMD on the human transcriptome and reveal novel determinants of ribosome biogenesis regulation.
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Affiliation(s)
- Affaf Aliouat
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Isabelle Hatin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Pierre Bertin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Pauline François
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Vérène Stierlé
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Samia Salhi
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Olivier Jean-Jean
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
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10
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Zhang DG, Cheng J, Tai ZP, Luo Z. Identification of five genes in endoplasmic reticulum (ER) stress-apoptosis pathways in yellow catfish Pelteobagrus fulvidraco and their transcriptional responses to dietary lipid levels. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:1117-1127. [PMID: 30847627 DOI: 10.1007/s10695-019-00627-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
The activating transcription factor 4 (ATF4), DNA damage-inducible transcript 3 (DDIT3), growth arrest, and DNA damage-inducible protein 34 (GADD34), endoplasmic reticulum oxidoreductin 1α (ERO1α), and tumor necrosis factor receptor associated factor 2 (TRAF2) cDNAs were first characterized from yellow catfish Pelteobagrus fulvidraco. Compared to corresponding genes of mammals, all of these proteins shared similar conserved domains. Their mRNAs were widely expressed in various tissues, but at variable levels. Dietary lipid levels did not significantly influence ATF4 mRNA expression. mRNA expression of DDIT3 and GADD34 was highest for fish fed the low-lipid diets and lowest for fish fed middle-lipid diets. The mRNA levels of ERO1α and TRAF2 declined with increasing dietary lipid levels. For the first time, we characterized the full-length cDNA sequences of ATF4, DDIT3, GADD34, ERO1α, and TRAF2 and determined their tissue expression profiles and transcriptional responses to dietary lipid levels, which would contribute to our exploration into their biological functions, and providing new insights on relations between ER stress and lipid metabolism in fish.
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Affiliation(s)
- Dian-Guang Zhang
- Fishery College, Huazhong Agricultural University, Wuhan, 43000, China
| | - Jie Cheng
- Fishery College, Huazhong Agricultural University, Wuhan, 43000, China
| | - Zhi-Peng Tai
- Fishery College, Huazhong Agricultural University, Wuhan, 43000, China
| | - Zhi Luo
- Fishery College, Huazhong Agricultural University, Wuhan, 43000, China.
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11
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Translation termination-dependent deadenylation of MYC mRNA in human cells. Oncotarget 2018; 9:26171-26182. [PMID: 29899850 PMCID: PMC5995228 DOI: 10.18632/oncotarget.25459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 05/08/2018] [Indexed: 11/25/2022] Open
Abstract
The earliest step in the mRNA degradation process is deadenylation, a progressive shortening of the mRNA poly(A) tail by deadenylases. The question of when deadenylation takes place remains open. MYC mRNA is one of the rare examples for which it was proposed a shortening of the poly(A) tail during ongoing translation. In this study, we analyzed the poly(A) tail length distribution of various mRNAs, including MYC mRNA. The mRNAs were isolated from the polysomal fractions of polysome profiling experiments and analyzed using ligase-mediated poly(A) test analysis. We show that, for all the mRNAs tested with the only exception of MYC, the poly(A) tail length distribution does not change in accordance with the number of ribosomes carried by the mRNA. Conversely, for MYC mRNA, we observed a poly(A) tail length decrease in the fractions containing the largest polysomes. Because the fractions with the highest number of ribosomes are also those for which translation termination is more frequent, we analyzed the poly(A) tail length distribution in polysomal fractions of cells depleted in translation termination factor eRF3. Our results show that the shortening of MYC mRNA poly(A) tail is alleviated by the silencing of translation termination factor eRF3. These findings suggest that MYC mRNA is co-translationally deadenylated and that the deadenylation process requires translation termination to proceed.
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12
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Allen JE, Kline CLB, Prabhu VV, Wagner J, Ishizawa J, Madhukar N, Lev A, Baumeister M, Zhou L, Lulla A, Stogniew M, Schalop L, Benes C, Kaufman HL, Pottorf RS, Nallaganchu BR, Olson GL, Al-Mulla F, Duvic M, Wu GS, Dicker DT, Talekar MK, Lim B, Elemento O, Oster W, Bertino J, Flaherty K, Wang ML, Borthakur G, Andreeff M, Stein M, El-Deiry WS. Discovery and clinical introduction of first-in-class imipridone ONC201. Oncotarget 2018; 7:74380-74392. [PMID: 27602582 PMCID: PMC5342060 DOI: 10.18632/oncotarget.11814] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 08/30/2016] [Indexed: 12/20/2022] Open
Abstract
ONC201 is the founding member of a novel class of anti-cancer compounds called imipridones that is currently in Phase II clinical trials in multiple advanced cancers. Since the discovery of ONC201 as a p53-independent inducer of TRAIL gene transcription, preclinical studies have determined that ONC201 has anti-proliferative and pro-apoptotic effects against a broad range of tumor cells but not normal cells. The mechanism of action of ONC201 involves engagement of PERK-independent activation of the integrated stress response, leading to tumor upregulation of DR5 and dual Akt/ERK inactivation, and consequent Foxo3a activation leading to upregulation of the death ligand TRAIL. ONC201 is orally active with infrequent dosing in animals models, causes sustained pharmacodynamic effects, and is not genotoxic. The first-in-human clinical trial of ONC201 in advanced aggressive refractory solid tumors confirmed that ONC201 is exceptionally well-tolerated and established the recommended phase II dose of 625 mg administered orally every three weeks defined by drug exposure comparable to efficacious levels in preclinical models. Clinical trials are evaluating the single agent efficacy of ONC201 in multiple solid tumors and hematological malignancies and exploring alternative dosing regimens. In addition, chemical analogs that have shown promise in other oncology indications are in pre-clinical development. In summary, the imipridone family that comprises ONC201 and its chemical analogs represent a new class of anti-cancer therapy with a unique mechanism of action being translated in ongoing clinical trials.
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Affiliation(s)
| | | | | | | | - Jo Ishizawa
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Avital Lev
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | - Lanlan Zhou
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | | | | | - Cyril Benes
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | | | | | - Gary L Olson
- Provid Pharmaceuticals, Monmouth Junction, NJ, USA
| | | | - Madeleine Duvic
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Mala K Talekar
- The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bora Lim
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Joseph Bertino
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Keith Flaherty
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Michael L Wang
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Mark Stein
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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13
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Adjibade P, Grenier St-Sauveur V, Bergeman J, Huot ME, Khandjian EW, Mazroui R. DDX3 regulates endoplasmic reticulum stress-induced ATF4 expression. Sci Rep 2017; 7:13832. [PMID: 29062139 PMCID: PMC5653821 DOI: 10.1038/s41598-017-14262-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 10/06/2017] [Indexed: 12/26/2022] Open
Abstract
Accumulation of unfolded and potentially toxic proteins in the endoplasmic reticulum (ER) activates a cell stress adaptive response, which involves a reprogramming of general gene expression. ATF4 is a master stress-induced transcription factor that orchestrates gene expression in cells treated with various ER stress inducers including those used to treat cancers. ER stress-induced ATF4 expression occurs mainly at the translational level involving the activity of the phosphorylated (P) translation initiation factor (eIF) eIF2α. While it is well established that under ER stress PeIF2α drives ATF4 expression through a specialised mode of translation re-initiation, factors (e.g. RNA-binding proteins and specific eIFs) involved in PeIF2α-mediated ATF4 translation remain unknown. Here we identified the RNA-binding protein named DDX3 as a promotor of ATF4 expression in cancer cells treated with sorafenib, an ER stress inducer used as a chemotherapeutic. Depletion experiments showed that DDX3 is required for PeIF2α-mediated ATF4 expression. Luciferase and polyribosomes assays showed that DDX3 drives ER stress-induced ATF4 mRNA expression at the translational level. Protein-interaction assays showed that DDX3 binds the eIF4F complex, which we found to be required for ER stress-induced ATF4 expression. This study thus showed that PeIF2α-mediated ATF4 mRNA translation requires DDX3 as a part of the eIF4F complex.
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Affiliation(s)
- Pauline Adjibade
- Centre de recherche en cancérologie. Centre de recherche du CHU de Québec. Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Université Laval, Québec, PQ, Canada
| | - Valérie Grenier St-Sauveur
- Centre de recherche en cancérologie. Centre de recherche du CHU de Québec. Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Université Laval, Québec, PQ, Canada.,Complexe de diagnostic et d'épidémiosurveillance vétérinaires du Québec (CDEVQ) Université de Montréal, Montréal, Canada
| | - Jonathan Bergeman
- Centre de recherche en cancérologie. Centre de recherche du CHU de Québec. Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Université Laval, Québec, PQ, Canada
| | - Marc-Etienne Huot
- Centre de recherche en cancérologie. Centre de recherche du CHU de Québec. Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Université Laval, Québec, PQ, Canada
| | - Edouard W Khandjian
- Centre de Recherche, Institut universitaire en santé mentale de Québec. Département de psychiatrie et de neurosciences, Faculté de médecine, Université Laval, Québec, PQ, Canada
| | - Rachid Mazroui
- Centre de recherche en cancérologie. Centre de recherche du CHU de Québec. Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Université Laval, Québec, PQ, Canada.
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14
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Huang K, Qi G, Sun Z, Liu X, Xu X, Wang H, Wu Z, Wan Y, Hu C. Ctenopharyngodon idella IRF2 and ATF4 down-regulate the transcriptional level of PRKRA. FISH & SHELLFISH IMMUNOLOGY 2017; 64:155-164. [PMID: 28263879 DOI: 10.1016/j.fsi.2017.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 06/06/2023]
Abstract
PRKRA (interferon-inducible double-stranded RNA-dependent protein kinase activator A) is a protective protein which regulates the adaptation of cells to ER stress and virus-stimulated signaling pathways by activating PKR. In the present study, a grass carp (Ctenopharyngodon idella) PRKRA full-length cDNA (named CiPRKRA, KT891991) was cloned and identified. The full-length cDNA is comprised of a 5' UTR (36 bp), a 3' UTR (350 bp) and the longest ORF (882 bp) encoding a polypeptide of 293 amino acids. The deduced amino acid sequence of CiPRKRA contains three typical dsRNA binding motifs (dsRBM). Phylogenetic tree analysis revealed a closer evolutionary relationship of CiPRKRA with other fish PRKRA, especially with Danio rerio PRKRA. qRT-PCR showed that CiPRKRA was significantly up-regulated after stimulation with tunicamycin (Tm) and Poly I:C in C. idella kidney (CIK) cells. To further study its transcriptional regulation, the partial promoter sequence of CiPRKRA (1463 bp) containing one ISRE and one CARE was cloned by Tail-PCR. Subsequently, grass carp IRF2 (CiIRF2) and ATF4 (CiATF4) were expressed in Escherichia coli BL21 and purified by affinity chromatography with the Ni-NTA His-Bind Resin. In vitro, both CiIRF2 and CiATF4 bound to CiPRKRA promoter with high affinity by gel mobility shift assays, revealing that IRF2 and ATF4 might be potential transcriptional regulatory factors for CiPRKRA. Dual-luciferase reporter assays were applied to further investigate the transcriptional regulation of CiPRKRA in vivo. Recombinant plasmid of pGL3-PRKRAPro was constructed and transiently co-transfected into CIK cells with pcDNA3.1-CiIRF2 and pcDNA3.1-CiATF4, respectively. The results showed that both CiIRF2 and CiATF4 significantly decreased the luciferase activity of pGL3-PRKRAPro, suggesting that they play a negative role in CiPRKRA transcription.
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Affiliation(s)
- Keyi Huang
- College of Life Science, Key Lab of Aquatic Resources and Utilization of Jiangxi Province, Nanchang University, Nanchang 330031, China
| | - Guoqin Qi
- College of Life Science, Key Lab of Aquatic Resources and Utilization of Jiangxi Province, Nanchang University, Nanchang 330031, China
| | - Zhicheng Sun
- College of Life Science, Key Lab of Aquatic Resources and Utilization of Jiangxi Province, Nanchang University, Nanchang 330031, China
| | - Xiancheng Liu
- College of Life Science, Key Lab of Aquatic Resources and Utilization of Jiangxi Province, Nanchang University, Nanchang 330031, China
| | - Xiaowen Xu
- College of Life Science, Key Lab of Aquatic Resources and Utilization of Jiangxi Province, Nanchang University, Nanchang 330031, China
| | - Haizhou Wang
- College of Life Science, Key Lab of Aquatic Resources and Utilization of Jiangxi Province, Nanchang University, Nanchang 330031, China
| | - Zhen Wu
- College of Life Science, Key Lab of Aquatic Resources and Utilization of Jiangxi Province, Nanchang University, Nanchang 330031, China
| | - Yiqi Wan
- College of Life Science, Key Lab of Aquatic Resources and Utilization of Jiangxi Province, Nanchang University, Nanchang 330031, China
| | - Chengyu Hu
- College of Life Science, Key Lab of Aquatic Resources and Utilization of Jiangxi Province, Nanchang University, Nanchang 330031, China.
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15
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Dominick G, Bowman J, Li X, Miller RA, Garcia GG. mTOR regulates the expression of DNA damage response enzymes in long-lived Snell dwarf, GHRKO, and PAPPA-KO mice. Aging Cell 2017; 16:52-60. [PMID: 27618784 PMCID: PMC5242303 DOI: 10.1111/acel.12525] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2016] [Indexed: 01/05/2023] Open
Abstract
Studies of the mTOR pathway have prompted speculation that diminished mTOR complex‐1 (mTORC1) function may be involved in controlling the aging process. Our previous studies have shown diminished mTORC1 activity in tissues of three long‐lived mutant mice: Snell dwarf mice, growth hormone receptor gene disrupted mice (GHRKO), and in this article, mice deficient in the pregnancy‐associated protein‐A (PAPPA‐KO). The ways in which lower mTOR signals slow aging and age‐related diseases are, however, not well characterized. Here, we show that Snell, GHKRO, and PAPPA‐KO mice express high levels of two proteins involved in DNA repair, O‐6‐methylguanine‐DNA methyltransferase (MGMT) and N‐myc downstream‐regulated gene 1 (NDRG1). Furthermore, we report that lowering mTOR enhances MGMT and NDRG1 protein expression via post‐transcriptional mechanisms. We show that the CCR4‐NOT complex, a post‐transcriptional regulator of gene expression, is downstream of the mTORC1 pathway and may be responsible for the upregulation of MGMT and NDRG1 in all three varieties of long‐lived mice. Our data thus suggest a novel link between DNA repair and mTOR signaling via post‐transcriptional regulation involving specific alteration in the CCR4‐NOT complex, whose modulation could control multiple aspects of the aging process.
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Affiliation(s)
- Graham Dominick
- Department of Molecular, Cellular, and Developmental Biology; University of Michigan College of Literature, Science and the Arts; Ann Arbor MI USA
| | - Jacqueline Bowman
- Department of Molecular, Cellular, and Developmental Biology; University of Michigan College of Literature, Science and the Arts; Ann Arbor MI USA
| | - Xinna Li
- Department of Pathology; University of Michigan School of Medicine; Ann Arbor MI USA
| | - Richard A. Miller
- Department of Pathology; University of Michigan School of Medicine; Ann Arbor MI USA
- University of Michigan Geriatrics Center; Ann Arbor MI USA
| | - Gonzalo G. Garcia
- Department of Pathology; University of Michigan School of Medicine; Ann Arbor MI USA
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16
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Galimberti V, Kinor N, Shav-Tal Y, Biggiogera M, Brüning A. The stress-inducible transcription factor ATF4 accumulates at specific rRNA-processing nucleolar regions after proteasome inhibition. Eur J Cell Biol 2016; 95:389-400. [PMID: 27567537 DOI: 10.1016/j.ejcb.2016.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/10/2016] [Accepted: 08/18/2016] [Indexed: 10/21/2022] Open
Abstract
Functional protein homeostasis is essential for the maintenance of normal cellular physiology, cell growth, and cell survival. Proteasome inhibition in cancer cells can disturb protein homeostasis in such a way that synthetic proteasome inhibitors like bortezomib may selectively kill myeloma cells. Solid cancer cells appear to respond less to bortezomib which may in part be due to a rescue mechanism of the unfolded protein response/endoplasmic reticulum stress mechanism which leads to a temporary shutdown of protein biosynthesis at the translational level. Here we show that proteasome inhibition by bortezomib may also interfere with general protein biosynthesis already at the stage of nucleolar ribosome biogenesis. Ultrastructural analysis revealed not only that bortezomib induces conspicuous changes in cytoplasmic morphology but also pronounced morphological changes of the nucleolar ultrastructure, associated with an accumulation of the transcription factor ATF4 at nucleolar sites. Stress-induced intra-nucleolar ATF4 accumulation was observed in cancer cells in a dose and time dependent manner and ultrastructural studies revealed that ATF4 is preferentially localized inside the dense fibrillar and granular component of nucleoli. Furthermore, bortezomib affected not only the number of nucleoli, but also the volume and distribution of nucleolar components. The localization of ATF4 in the granular component of nucleoli together with its association with nascent RNA transcripts in cells undergoing proteotoxic cell stress could suggest a new function for ATF4 in cell stress management.
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Affiliation(s)
- Valentina Galimberti
- Department of Biology and Biotechnology, Laboratory of Biology and Neurobiology, University of Pavia, Pavia, Italy
| | - Noa Kinor
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Marco Biggiogera
- Department of Biology and Biotechnology, Laboratory of Biology and Neurobiology, University of Pavia, Pavia, Italy
| | - Ansgar Brüning
- Molecular Biology Laboratory, Dept. of OB/GYN, Ludwig-Maximilians-University, Munich, Germany.
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17
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Nutrient shortage triggers the hexosamine biosynthetic pathway via the GCN2-ATF4 signalling pathway. Sci Rep 2016; 6:27278. [PMID: 27255611 PMCID: PMC4891703 DOI: 10.1038/srep27278] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/17/2016] [Indexed: 12/22/2022] Open
Abstract
The hexosamine biosynthetic pathway (HBP) is a nutrient-sensing metabolic pathway that produces the activated amino sugar UDP-N-acetylglucosamine, a critical substrate for protein glycosylation. Despite its biological significance, little is known about the regulation of HBP flux during nutrient limitation. Here, we report that amino acid or glucose shortage increase GFAT1 production, the first and rate-limiting enzyme of the HBP. GFAT1 is a transcriptional target of the activating transcription factor 4 (ATF4) induced by the GCN2-eIF2α signalling pathway. The increased production of GFAT1 stimulates HBP flux and results in an increase in O-linked β-N-acetylglucosamine protein modifications. Taken together, these findings demonstrate that ATF4 provides a link between nutritional stress and the HBP for the regulation of the O-GlcNAcylation-dependent cellular signalling.
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18
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mTORC1 and CK2 coordinate ternary and eIF4F complex assembly. Nat Commun 2016; 7:11127. [PMID: 27040916 PMCID: PMC4822005 DOI: 10.1038/ncomms11127] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 02/23/2016] [Indexed: 02/02/2023] Open
Abstract
Ternary complex (TC) and eIF4F complex assembly are the two major rate-limiting steps in translation initiation regulated by eIF2α phosphorylation and the mTOR/4E-BP pathway, respectively. How TC and eIF4F assembly are coordinated, however, remains largely unknown. We show that mTOR suppresses translation of mRNAs activated under short-term stress wherein TC recycling is attenuated by eIF2α phosphorylation. During acute nutrient or growth factor stimulation, mTORC1 induces eIF2β phosphorylation and recruitment of NCK1 to eIF2, decreases eIF2α phosphorylation and bolsters TC recycling. Accordingly, eIF2β mediates the effect of mTORC1 on protein synthesis and proliferation. In addition, we demonstrate a formerly undocumented role for CK2 in regulation of translation initiation, whereby CK2 stimulates phosphorylation of eIF2β and simultaneously bolsters eIF4F complex assembly via the mTORC1/4E-BP pathway. These findings imply a previously unrecognized mode of translation regulation, whereby mTORC1 and CK2 coordinate TC and eIF4F complex assembly to stimulate cell proliferation. Ternary complex (TC) and eIF4F complex assembly are rate-limiting steps in translation initiation that are regulated by eIF2α phosphorylation and the mTOR/4E-BP pathway. Here the authors show that the protein kinases mTORC1 and CK2 coordinate TC and eIF4F complex assembly through eIF2β to stimulate cell proliferation.
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19
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Kline CLB, Van den Heuvel APJ, Allen JE, Prabhu VV, Dicker DT, El-Deiry WS. ONC201 kills solid tumor cells by triggering an integrated stress response dependent on ATF4 activation by specific eIF2α kinases. Sci Signal 2016; 9:ra18. [PMID: 26884600 DOI: 10.1126/scisignal.aac4374] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
ONC201 (also called TIC10) is a small molecule that inactivates the cell proliferation- and cell survival-promoting kinases Akt and ERK and induces cell death through the proapoptotic protein TRAIL. ONC201 is currently in early-phase clinical testing for various malignancies. We found through gene expression and protein analyses that ONC201 triggered an increase in TRAIL abundance and cell death through an integrated stress response (ISR) involving the transcription factor ATF4, the transactivator CHOP, and the TRAIL receptor DR5. ATF4 was not activated in ONC201-resistant cancer cells, and in ONC201-sensitive cells, knockdown of ATF4 or CHOP partially abrogated ONC201-induced cytotoxicity and diminished the ONC201-stimulated increase in DR5 abundance. The activation of ATF4 in response to ONC201 required the kinases HRI and PKR, which phosphorylate and activate the translation initiation factor eIF2α. ONC201 rapidly triggered cell cycle arrest, which was associated with decreased abundance of cyclin D1, decreased activity of the kinase complex mTORC1, and dephosphorylation of the retinoblastoma (Rb) protein. The abundance of X-linked inhibitor of apoptosis protein (XIAP) negatively correlated with the extent of apoptosis in response to ONC201. These effects of ONC201 were independent of whether cancer cells had normal or mutant p53. Thus, ONC201 induces cell death through the coordinated induction of TRAIL by an ISR pathway.
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Affiliation(s)
- C Leah B Kline
- Hematology/Oncology Division and Penn State Hershey Cancer Institute, Penn State College of Medicine, Hershey, PA 17033, USA. Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Department of Hematology/Oncology and Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - A Pieter J Van den Heuvel
- Hematology/Oncology Division and Penn State Hershey Cancer Institute, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Joshua E Allen
- Hematology/Oncology Division and Penn State Hershey Cancer Institute, Penn State College of Medicine, Hershey, PA 17033, USA. Oncoceutics Inc., Hummelstown, PA 17036, USA
| | - Varun V Prabhu
- Hematology/Oncology Division and Penn State Hershey Cancer Institute, Penn State College of Medicine, Hershey, PA 17033, USA. Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Department of Hematology/Oncology and Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - David T Dicker
- Hematology/Oncology Division and Penn State Hershey Cancer Institute, Penn State College of Medicine, Hershey, PA 17033, USA. Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Department of Hematology/Oncology and Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Wafik S El-Deiry
- Hematology/Oncology Division and Penn State Hershey Cancer Institute, Penn State College of Medicine, Hershey, PA 17033, USA. Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Department of Hematology/Oncology and Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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20
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Chung BY, Hardcastle TJ, Jones JD, Irigoyen N, Firth AE, Baulcombe DC, Brierley I. The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis. RNA (NEW YORK, N.Y.) 2015; 21:1731-45. [PMID: 26286745 PMCID: PMC4574750 DOI: 10.1261/rna.052548.115] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/23/2015] [Indexed: 05/19/2023]
Abstract
Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. Here we describe a modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and utility. The protocol, applicable to diverse organisms, including organelles, is based largely on previously published profiling methodologies, but uses duplex-specific nuclease (DSN) as a convenient, species-independent way to reduce rRNA contamination. We show that DSN-based depletion compares favorably with other commonly used rRNA depletion strategies and introduces little bias. The profiling protocol typically produces high levels of triplet periodicity, facilitating the detection of coding sequences, including upstream, downstream, and overlapping open reading frames (ORFs) and an alternative ribosome conformation evident during termination of protein synthesis. In addition, we provide a software package that presents a set of methods for parsing ribosomal profiling data from multiple samples, aligning reads to coding sequences, inferring alternative ORFs, and plotting average and transcript-specific aspects of the data. Methods are also provided for extracting the data in a form suitable for differential analysis of translation and translational efficiency.
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Affiliation(s)
- Betty Y Chung
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Joshua D Jones
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
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21
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Tsalikis J, Tattoli I, Ling A, Sorbara MT, Croitoru DO, Philpott DJ, Girardin SE. Intracellular Bacterial Pathogens Trigger the Formation of U Small Nuclear RNA Bodies (U Bodies) through Metabolic Stress Induction. J Biol Chem 2015; 290:20904-20918. [PMID: 26134566 DOI: 10.1074/jbc.m115.659466] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 12/30/2022] Open
Abstract
Invasive bacterial pathogens induce an amino acid starvation (AAS) response in infected host cells that controls host defense in part by promoting autophagy. However, whether AAS has additional significant effects on the host response to intracellular bacteria remains poorly characterized. Here we showed that Shigella, Salmonella, and Listeria interfere with spliceosomal U snRNA maturation in the cytosol. Bacterial infection resulted in the rerouting of U snRNAs and their cytoplasmic escort, the survival motor neuron (SMN) complex, to processing bodies, thus forming U snRNA bodies (U bodies). This process likely contributes to the decline in the cytosolic levels of U snRNAs and of the SMN complex proteins SMN and DDX20 that we observed in infected cells. U body formation was triggered by membrane damage in infected cells and was associated with the induction of metabolic stresses, such as AAS or endoplasmic reticulum stress. Mechanistically, targeting of U snRNAs to U bodies was regulated by translation initiation inhibition and the ATF4/ATF3 pathway, and U bodies rapidly disappeared upon removal of the stress, suggesting that their accumulation represented an adaptive response to metabolic stress. Importantly, this process likely contributed to shape the host response to invasive bacteria because down-regulation of DDX20 expression using short hairpin RNA (shRNA) amplified ATF3- and NF-κB-dependent signaling. Together, these results identify a critical role for metabolic stress and invasive bacterial pathogens in U body formation and suggest that this process contributes to host defense.
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Affiliation(s)
- Jessica Tsalikis
- Departments of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M6G 2T6, Canada
| | - Ivan Tattoli
- Departments of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M6G 2T6, Canada; Departments of Immunology, University of Toronto, Toronto M6G 2T6, Canada
| | - Arthur Ling
- Departments of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M6G 2T6, Canada
| | - Matthew T Sorbara
- Departments of Immunology, University of Toronto, Toronto M6G 2T6, Canada
| | - David O Croitoru
- Departments of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M6G 2T6, Canada
| | - Dana J Philpott
- Departments of Immunology, University of Toronto, Toronto M6G 2T6, Canada
| | - Stephen E Girardin
- Departments of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M6G 2T6, Canada.
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Fan Q, Mao H, Wu C, Liu Y, Hu Y, Zhong B, Mi Y, Hu C. ATF4 (activating transcription factor 4) from grass carp (Ctenopharyngodon idella) modulates the transcription initiation of GRP78 and GRP94 in CIK cells. FISH & SHELLFISH IMMUNOLOGY 2014; 38:140-148. [PMID: 24636856 DOI: 10.1016/j.fsi.2014.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 02/24/2014] [Accepted: 03/07/2014] [Indexed: 06/03/2023]
Abstract
GRP78 and GRP94, belong to GRP (glucose-regulated protein) family of endoplasmatic reticulum (ER) chaperone superfamily, are essential for cell survival under ER stress. ATF4 is a protective protein which regulates the adaptation of cells to ER stress by modulating the transcription of UPR (Unfolded Protein Response) target genes, including GRP78 and GRP94. To understand the molecular mechanism of ATF4 modulates the transcription initiation of CiGRP78 and CiGRP94, we cloned ATF4 ORF cDNA sequences (CiATF4) by homologous cloning techniques. The expression trend of CiATF4 was similar to CiGRP78 and CiGRP94 did under 37 °C thermal stress, namely, the expression of CiATF4 was up-regulated twice at 2 h post-thermal stress and at 18 h post recovery from thermal stress. In this paper, CiATF4 was expressed in BL21 Escherichia coli, and the expressed protein was purified by affinity chromatography with the Ni-NTA His-Bind Resin. On the basis of the cloned CiGRP78 and CiGRP94 cDNA in our laboratory previously, we cloned their promoter sequences by genomic walking approach. In vitro, gel mobility shift assays revealed that CiATF4 could bind to CiGRP78 and CiGRP94 promoter with high affinity. Subsequently, the recombinant plasmid of pGL3-CiGRPs and pcDNA3.1-CiATF4 were constructed and transiently co-transfected into Ctenopharyngodon idella kidney (CIK) cells. The impact of CiATF4 on CiGRP promoter sequences were measured by luciferase assays. These results demonstrated that CiATF4 could activate the transcription of CiGRP78 and CiGRP94. What's more, for better understanding the molecular mechanism of CiATF4 modulate the transcription initiation of CiGRP, three mutant fragments of CiGRP78 promoter recombinant plasmids (called CARE-mut/LUC, CRE1-mut/LUC and CRE2-mut/LUC) were constructed and transiently co-transfected with CiATF4 into CIK cells. The results indicated that CRE or CARE elements were the regulatory element for transcription initiation of CiGRP78. Between them, CRE element would play more important role in it.
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Affiliation(s)
- Qidi Fan
- Department of Bioscience, College of Life Science and Food Engineering, Nanchang University, Nanchang 330031, China
| | - Huiling Mao
- Department of Bioscience, College of Life Science and Food Engineering, Nanchang University, Nanchang 330031, China
| | - Chuxin Wu
- Nanchang Teachers College, Nanchang 330103, China
| | - Yong Liu
- Department of Bioscience, College of Life Science and Food Engineering, Nanchang University, Nanchang 330031, China
| | - Yousheng Hu
- Department of Bioscience, College of Life Science and Food Engineering, Nanchang University, Nanchang 330031, China
| | - Bin Zhong
- Department of Bioscience, College of Life Science and Food Engineering, Nanchang University, Nanchang 330031, China
| | - Yichuan Mi
- Department of Bioscience, College of Life Science and Food Engineering, Nanchang University, Nanchang 330031, China
| | - Chengyu Hu
- Department of Bioscience, College of Life Science and Food Engineering, Nanchang University, Nanchang 330031, China.
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23
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Tsalikis J, Croitoru DO, Philpott DJ, Girardin SE. Nutrient sensing and metabolic stress pathways in innate immunity. Cell Microbiol 2013; 15:1632-41. [PMID: 23834352 DOI: 10.1111/cmi.12165] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/25/2013] [Accepted: 07/01/2013] [Indexed: 01/13/2023]
Abstract
Cells monitor nutrient availability through several highly conserved pathways that include the mTOR signalling axis regulated by AKT/PI3K, HIF and AMPK, as well as the GCN2/eIF2α integrated stress response pathway that provides cellular adaptation to amino acid starvation. Recent evidence has identified a critical interplay between these nutrient sensing pathways and innate immunity to bacterial pathogens, viruses and parasites. These observations suggest that, in addition to the well-characterized pro-inflammatory signalling mediated by pattern recognition molecules, a metabolic stress programme contributes to shape the global response to pathogens.
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Affiliation(s)
- Jessica Tsalikis
- Department of Laboratory Medicine and Pathobiologyy, University of Toronto, Toronto, M5S 1A8, Canada
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Chan CP, Kok KH, Tang HMV, Wong CM, Jin DY. Internal ribosome entry site-mediated translational regulation of ATF4 splice variant in mammalian unfolded protein response. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2165-75. [PMID: 23665047 DOI: 10.1016/j.bbamcr.2013.05.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 04/30/2013] [Accepted: 05/02/2013] [Indexed: 02/04/2023]
Abstract
Activating transcription factor 4 (ATF4) is a master regulator of genes involved in unfolded protein response (UPR) and its translation is regulated through reinitiation at upstream open reading frames. Here, we demonstrate internal ribosome entry site (IRES)-mediated translation of an alternatively spliced variant of human ATF4. This variant that contains four upstream open reading frames in the 5' leader region was expressed in leukocytes and other tissues. mRNA and protein expression of this variant was activated in the UPR. Its translation was neither inhibited by steric hindrance nor affected by eIF4G1 inactivation, indicating a cap-independent and IRES-dependent mechanism not mediated by ribosome scanning-reinitiation. The IRES activity mapped to a highly structured region that partially overlaps with the third and fourth open reading frames was unlikely attributed to cryptic promoter or splicing, but was activated by PERK-induced eIF2α phosphorylation. Taken together, our findings reveal a new mechanism for translational regulation of ATF4 in mammalian UPR.
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Affiliation(s)
- Ching-Ping Chan
- Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong
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