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Plasticity of the mammalian integrated stress response

. 2025 May ; 641 (8065) : 1319-1328. [epub] 20250326

Language English Country Great Britain, England Media print-electronic

Document type Journal Article

Grant support
T34 GM137792 NIGMS NIH HHS - United States
R01 DK053307 NIDDK NIH HHS - United States
Z01 AG000511 Intramural NIH HHS - United States
R01 CA230453 NCI NIH HHS - United States
R37 DK060596 NIDDK NIH HHS - United States
P30 CA043703 NCI NIH HHS - United States
R35 NS116842 NINDS NIH HHS - United States
R01 CA259386 NCI NIH HHS - United States
R35 GM127089 NIGMS NIH HHS - United States
R01 DK060596 NIDDK NIH HHS - United States
R01 GM128981 NIGMS NIH HHS - United States
R01 GM148662 NIGMS NIH HHS - United States

Links

PubMed 40140574
PubMed Central PMC12119373
DOI 10.1038/s41586-025-08794-6
PII: 10.1038/s41586-025-08794-6
Knihovny.cz E-resources

An increased level of phosphorylation of eukaryotic translation initiation factor 2 subunit-α (eIF2α, encoded by EIF2S1; eIF2α-p) coupled with decreased guanine nucleotide exchange activity of eIF2B is a hallmark of the 'canonical' integrated stress response (c-ISR)1. It is unclear whether impaired eIF2B activity in human diseases including leukodystrophies2, which occurs in the absence of eIF2α-p induction, is synonymous with the c-ISR. Here we describe a mechanism triggered by decreased eIF2B activity, distinct from the c-ISR, which we term the split ISR (s-ISR). The s-ISR is characterized by translational and transcriptional programs that are different from those observed in the c-ISR. Opposite to the c-ISR, the s-ISR requires eIF4E-dependent translation of the upstream open reading frame 1 and subsequent stabilization of ATF4 mRNA. This is followed by altered expression of a subset of metabolic genes (for example, PCK2), resulting in metabolic rewiring required to maintain cellular bioenergetics when eIF2B activity is attenuated. Overall, these data demonstrate a plasticity of the mammalian ISR, whereby the loss of eIF2B activity in the absence of eIF2α-p induction activates the eIF4E-ATF4-PCK2 axis to maintain energy homeostasis.

Center for Gene Regulation in Health and Disease Cleveland State University Cleveland OH USA

College of Sciences and Health Profession King Saud bin Abdulaziz University for Health Sciences Jeddah Saudi Arabia

Department of Biochemistry Case Western Reserve University Cleveland OH USA

Department of Biochemistry McGill University Montreal Quebec Canada

Department of Biological Sciences Louisiana State University Baton Rouge LA USA

Department of Biology New York University New York NY USA

Department of Cell Biology and Molecular Genetics University of Maryland College Park MD USA

Department of Genetics and Genome Sciences Case Western Reserve University Cleveland OH USA

Department of Molecular Biology Institute of Biological Sciences Maria Curie Skłodowska University Lublin Poland

Department of Molecular Biophysics and Biochemistry Yale University New Haven CT USA

Department of Oncology Pathology Karolinska Institute Science of Life Laboratory Solna Sweden

Department of Pharmacology Case Western Reserve University Cleveland OH USA

Division of Clinical and Translational Research Department of Medicine Faculty of Medicine McGill University Montreal Quebec Canada

Gerald Bronfman Department of Oncology Faculty of Medicine McGill University Montreal Quebec Canada

Institute for Bioscience and Biotechnology Research University of Maryland Rockville MD USA

Institute for Glial Sciences Case Western Reserve University School of Medicine Cleveland OH USA

King Abdullah International Medical Research Center Jeddah Saudi Arabia

Laboratory of Genetics and Genomics National Institute of Aging Intramural Research Program NIH Baltimore MD USA

Laboratory of Regulation of Gene Expression Institute of Microbiology of the Czech Academy of Sciences Prague Czech Republic

Lady Davis Institute for Medical Research Sir Mortimer B Davis Jewish General Hospital Montreal Quebec Canada

See more in PubMed

Costa-Mattioli, M. & Walter, P. The integrated stress response: from mechanism to disease. Science368, eaat5314 (2020). PubMed PMC

Abbink, T. E. M. et al. Vanishing white matter: deregulated integrated stress response as therapy target. Ann. Clin. Transl. Neurol.6, 1407–1422 (2019). PubMed PMC

Advani, V. M. & Ivanov, P. Translational control under stress: reshaping the translatome. Bioessays41, e1900009 (2019). PubMed PMC

Wang, X. & Proud, C. G. The role of eIF2 phosphorylation in cell and organismal physiology: new roles for well-known actors. Biochem. J.479, 1059–1082 (2022). PubMed

Dever, T. E., Ivanov, I. P. & Hinnebusch, A. G. Translational regulation by uORFs and start codon selection stringency. Genes Dev.37, 474–489 (2023). PubMed PMC

Guan, B. J. et al. A unique ISR program determines cellular responses to chronic stress. Mol. Cell68, 885–900 (2017). PubMed PMC

Novoa, I. et al. Stress-induced gene expression requires programmed recovery from translational repression. EMBO J.22, 1180–1187 (2003). PubMed PMC

Mahe, M., Rios-Fuller, T., Katsara, O. & Schneider, R. J. Non-canonical mRNA translation initiation in cell stress and cancer. NAR Cancer6, zcae026 (2024). PubMed PMC

Lu, P. D., Harding, H. P. & Ron, D. Translation reinitiation at alternative open reading frames regulates gene expression in an integrated stress response. J. Cell Biol.167, 27–33 (2004). PubMed PMC

Vattem, K. M. & Wek, R. C. Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells. Proc. Natl Acad. Sci. USA101, 11269–11274 (2004). PubMed PMC

Smirnova, A. M. et al. Stem-loop-induced ribosome queuing in the uORF2/ATF4 overlap fine-tunes stress-induced human ATF4 translational control. Cell Rep.43, 113976 (2024). PubMed PMC

Riggs, C. L., Kedersha, N., Ivanov, P. & Anderson, P. Mammalian stress granules and P bodies at a glance. J. Cell Sci.133, jcs242487 (2020). PubMed PMC

Mukhopadhyay, S., Amodeo, M. E. & Lee, A. S. Y. eIF3d controls the persistent integrated stress response. Mol. Cell83, 3303–3313 (2023). PubMed PMC

Watatani, Y. et al. Stress-induced translation of ATF5 mRNA is regulated by the 5′-untranslated region. J. Biol. Chem.283, 2543–2553 (2008). PubMed

Lee, Y. Y., Cevallos, R. C. & Jan, E. An upstream open reading frame regulates translation of GADD34 during cellular stresses that induce eIF2α phosphorylation. J. Biol. Chem.284, 6661–6673 (2009). PubMed PMC

Palam, L. R., Baird, T. D. & Wek, R. C. Phosphorylation of eIF2 facilitates ribosomal bypass of an inhibitory upstream ORF to enhance CHOP translation. J. Biol. Chem.286, 10939–10949 (2011). PubMed PMC

Gandin, V. et al. mTORC1 and CK2 coordinate ternary and eIF4F complex assembly. Nat. Commun.7, 11127 (2016). PubMed PMC

Gandin, V. et al. Polysome fractionation and analysis of mammalian translatomes on a genome-wide scale. J. Vis. Exp.10.3791/51455 (2014). PubMed PMC

Oertlin, C. et al. Generally applicable transcriptome-wide analysis of translation using anota2seq. Nucleic Acids Res.47, e70 (2019). PubMed PMC

Han, J. et al. ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death. Nat. Cell Biol.15, 481–490 (2013). PubMed PMC

Fogli, A. et al. Decreased guanine nucleotide exchange factor activity in eIF2B-mutated patients. Eur. J. Hum. Genet.12, 561–566 (2004). PubMed

Hanson, F. M., Hodgson, R. E., de Oliveira, M. I. R., Allen, K. E. & Campbell, S. G. Regulation and function of elF2B in neurological and metabolic disorders. Biosci. Rep.42, BSR20211699 (2022). PubMed PMC

Bugiani, M., Vuong, C., Breur, M. & van der Knaap, M. S. Vanishing white matter: a leukodystrophy due to astrocytic dysfunction. Brain Pathol.28, 408–421 (2018). PubMed PMC

Wong, Y. L. et al. eIF2B activator prevents neurological defects caused by a chronic integrated stress response. eLife8, e42940 (2019). PubMed PMC

Bugiani, M. et al. Defective glial maturation in vanishing white matter disease. J. Neuropathol. Exp. Neurol.70, 69–82 (2011). PubMed PMC

Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol.15, 550 (2014). PubMed PMC

Deverman, B. E. & Patterson, P. H. Exogenous leukemia inhibitory factor stimulates oligodendrocyte progenitor cell proliferation and enhances hippocampal remyelination. J. Neurosci.32, 2100–2109 (2012). PubMed PMC

Seenappa, V., Joshi, M. B. & Satyamoorthy, K. Intricate regulation of phosphoenolpyruvate carboxykinase (PEPCK) isoforms in normal physiology and disease. Curr. Mol. Med.19, 247–272 (2019). PubMed

Calvo, S. E., Clauser, K. R. & Mootha, V. K. MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. Nucleic Acids Res.44, D1251–D1257 (2016). PubMed PMC

Yu, S., Meng, S., Xiang, M. & Ma, H. Phosphoenolpyruvate carboxykinase in cell metabolism: roles and mechanisms beyond gluconeogenesis. Mol. Metab.53, 101257 (2021). PubMed PMC

Mendez-Lucas, A., Hyrossova, P., Novellasdemunt, L., Vinals, F. & Perales, J. C. Mitochondrial phosphoenolpyruvate carboxykinase (PEPCK-M) is a pro-survival, endoplasmic reticulum (ER) stress response gene involved in tumor cell adaptation to nutrient availability. J. Biol. Chem.289, 22090–22102 (2014). PubMed PMC

Vincent, E. E. et al. Mitochondrial phosphoenolpyruvate carboxykinase regulates metabolic adaptation and enables glucose-independent tumor growth. Mol. Cell60, 195–207 (2015). PubMed

Park, Y., Reyna-Neyra, A., Philippe, L. & Thoreen, C. C. mTORC1 balances cellular amino acid supply with demand for protein synthesis through post-transcriptional control of ATF4. Cell Rep.19, 1083–1090 (2017). PubMed PMC

Dey, S. et al. Both transcriptional regulation and translational control of ATF4 are central to the integrated stress response. J. Biol. Chem.285, 33165–33174 (2010). PubMed PMC

Kim, Y. K. & Maquat, L. E. UPFront and center in RNA decay: UPF1 in nonsense-mediated mRNA decay and beyond. RNA25, 407–422 (2019). PubMed PMC

Boyce, M. et al. A selective inhibitor of eIF2α dephosphorylation protects cells from ER stress. Science307, 935–939 (2005). PubMed

Soto-Rifo, R. et al. DEAD-box protein DDX3 associates with eIF4F to promote translation of selected mRNAs. EMBO J.31, 3745–3756 (2012). PubMed PMC

Lamper, A. M., Fleming, R. H., Ladd, K. M. & Lee, A. S. Y. A phosphorylation-regulated eIF3d translation switch mediates cellular adaptation to metabolic stress. Science370, 853–856 (2020). PubMed

Fang, X. et al. Phosphorylation and inactivation of glycogen synthase kinase 3 by protein kinase A. Proc. Natl Acad. Sci. USA97, 11960–11965 (2000). PubMed PMC

Welsh, G. I., Miller, C. M., Loughlin, A. J., Price, N. T. & Proud, C. G. Regulation of eukaryotic initiation factor eIF2B: glycogen synthase kinase-3 phosphorylates a conserved serine which undergoes dephosphorylation in response to insulin. FEBS Lett.421, 125–130 (1998). PubMed

Adjibade, P. et al. DDX3 regulates endoplasmic reticulum stress-induced ATF4 expression. Sci. Rep.7, 13832 (2017). PubMed PMC

Andreev, D. E. et al. Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes. Genome Biol.16, 90 (2015). PubMed PMC

Baird, T. D. et al. Selective mRNA translation during eIF2 phosphorylation induces expression of IBTKα. Mol. Biol. Cell25, 1686–1697 (2014). PubMed PMC

Kaspar, S. et al. Adaptation to mitochondrial stress requires CHOP-directed tuning of ISR. Sci. Adv.7, eabf0971 (2021). PubMed PMC

Merry, C. R. et al. Transcriptome-wide identification of mRNAs and lincRNAs associated with trastuzumab-resistance in HER2-positive breast cancer. Oncotarget7, 53230–53244 (2016). PubMed PMC

Elitt, M. S. et al. Chemical screening identifies enhancers of mutant oligodendrocyte survival and unmasks a distinct pathological phase in Pelizaeus-Merzbacher disease. Stem Cell Rep.11, 711–726 (2018). PubMed PMC

Lager, A. M. et al. Rapid functional genetics of the oligodendrocyte lineage using pluripotent stem cells. Nat. Commun.9, 3708 (2018). PubMed PMC

Najm, F. J. et al. Transcription factor-mediated reprogramming of fibroblasts to expandable, myelinogenic oligodendrocyte progenitor cells. Nat. Biotechnol.31, 426–433 (2013). PubMed PMC

Chen, C. W. et al. Adaptation to chronic ER stress enforces pancreatic beta-cell plasticity. Nat. Commun.13, 4621 (2022). PubMed PMC

Krokowski, D. et al. Stress-induced perturbations in intracellular amino acids reprogram mRNA translation in osmoadaptation independently of the ISR. Cell Rep.40, 111092 (2022). PubMed PMC

Dowling, R. J. et al. mTORC1-mediated cell proliferation, but not cell growth, controlled by the 4E-BPs. Science328, 1172–1176 (2010). PubMed PMC

Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods12, 357–360 (2015). PubMed PMC

Anders, S., Pyl, P. T. & Huber, W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics31, 166–169 (2015). PubMed PMC

Liao, Y., Smyth, G. K. & Shi, W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Res.47, e47 (2019). PubMed PMC

Oertlin, C., Watt, K., Ristau, J. & Larsson, O. Anota2seq analysis for transcriptome-wide studies of mRNA translation. Methods Mol. Biol.2418, 243–268 (2022). PubMed

Beissbarth, T. & Speed, T. P. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics20, 1464–1465 (2004). PubMed

Vlaski-Lafarge, M. et al. Bioenergetic changes underline plasticity of murine embryonic stem cells. Stem Cells37, 463–475 (2019). PubMed

Mookerjee, S. A., Gerencser, A. A., Nicholls, D. G. & Brand, M. D. Quantifying intracellular rates of glycolytic and oxidative ATP production and consumption using extracellular flux measurements. J. Biol. Chem.292, 7189–7207 (2017). PubMed PMC

Mookerjee, S. A., Nicholls, D. G. & Brand, M. D. Determining maximum glycolytic capacity using extracellular flux measurements. PLoS ONE11, e0152016 (2016). PubMed PMC

Mamer, O. et al. The complete targeted profile of the organic acid intermediates of the citric acid cycle using a single stable isotope dilution analysis, sodium borodeuteride reduction and selected ion monitoring GC/MS. Metabolomics9, 1019–1030 (2013). PubMed PMC

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