Plasticity of the mammalian integrated stress response
Status Publisher Language English Country Great Britain, England Media print-electronic
Document type Journal Article
Grant support
R35 GM127089
NIGMS NIH HHS - United States
PubMed
40140574
DOI
10.1038/s41586-025-08794-6
PII: 10.1038/s41586-025-08794-6
Knihovny.cz E-resources
- Publication type
- Journal Article MeSH
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
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 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
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
See more in PubMed
Costa-Mattioli, M. & Walter, P. The integrated stress response: from mechanism to disease. Science 368, eaat5314 (2020). PubMed DOI 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 DOI PMC
Advani, V. M. & Ivanov, P. Translational control under stress: reshaping the translatome. Bioessays 41, e1900009 (2019). PubMed DOI 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 DOI
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 DOI PMC
Guan, B. J. et al. A unique ISR program determines cellular responses to chronic stress. Mol. Cell 68, 885–900 (2017). PubMed DOI PMC
Novoa, I. et al. Stress-induced gene expression requires programmed recovery from translational repression. EMBO J. 22, 1180–1187 (2003). PubMed DOI PMC
Mahe, M., Rios-Fuller, T., Katsara, O. & Schneider, R. J. Non-canonical mRNA translation initiation in cell stress and cancer. NAR Cancer 6, zcae026 (2024). PubMed DOI 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 DOI PMC
Vattem, K. M. & Wek, R. C. Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells. Proc. Natl Acad. Sci. USA 101, 11269–11274 (2004). PubMed DOI 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 DOI 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 DOI PMC
Mukhopadhyay, S., Amodeo, M. E. & Lee, A. S. Y. eIF3d controls the persistent integrated stress response. Mol. Cell 83, 3303–3313 (2023). PubMed DOI 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 DOI
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 DOI 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 DOI PMC
Gandin, V. et al. mTORC1 and CK2 coordinate ternary and eIF4F complex assembly. Nat. Commun. 7, 11127 (2016). PubMed DOI PMC
Gandin, V. et al. Polysome fractionation and analysis of mammalian translatomes on a genome-wide scale. J. Vis. Exp. https://doi.org/10.3791/51455 (2014). PubMed DOI PMC
Oertlin, C. et al. Generally applicable transcriptome-wide analysis of translation using anota2seq. Nucleic Acids Res. 47, e70 (2019). PubMed DOI 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 DOI PMC
Fogli, A. et al. Decreased guanine nucleotide exchange factor activity in eIF2B-mutated patients. Eur. J. Hum. Genet. 12, 561–566 (2004). PubMed DOI
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 DOI 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 DOI PMC
Wong, Y. L. et al. eIF2B activator prevents neurological defects caused by a chronic integrated stress response. eLife 8, e42940 (2019). PubMed DOI PMC
Bugiani, M. et al. Defective glial maturation in vanishing white matter disease. J. Neuropathol. Exp. Neurol. 70, 69–82 (2011). PubMed DOI
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 DOI 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 DOI 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 DOI
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 DOI
Yu, S., Meng, S., Xiang, M. & Ma, H. Phosphoenolpyruvate carboxykinase in cell metabolism: roles and mechanisms beyond gluconeogenesis. Mol. Metab. 53, 101257 (2021). PubMed DOI 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 DOI PMC
Vincent, E. E. et al. Mitochondrial phosphoenolpyruvate carboxykinase regulates metabolic adaptation and enables glucose-independent tumor growth. Mol. Cell 60, 195–207 (2015). PubMed DOI
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 DOI 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 DOI PMC
Kim, Y. K. & Maquat, L. E. UPFront and center in RNA decay: UPF1 in nonsense-mediated mRNA decay and beyond. RNA 25, 407–422 (2019). PubMed DOI PMC
Boyce, M. et al. A selective inhibitor of eIF2α dephosphorylation protects cells from ER stress. Science 307, 935–939 (2005). PubMed DOI
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 DOI 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. Science 370, 853–856 (2020). PubMed DOI
Fang, X. et al. Phosphorylation and inactivation of glycogen synthase kinase 3 by protein kinase A. Proc. Natl Acad. Sci. USA 97, 11960–11965 (2000). PubMed DOI 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 DOI
Adjibade, P. et al. DDX3 regulates endoplasmic reticulum stress-induced ATF4 expression. Sci. Rep. 7, 13832 (2017). PubMed DOI 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 DOI PMC
Baird, T. D. et al. Selective mRNA translation during eIF2 phosphorylation induces expression of IBTKα. Mol. Biol. Cell 25, 1686–1697 (2014). PubMed DOI PMC
Kaspar, S. et al. Adaptation to mitochondrial stress requires CHOP-directed tuning of ISR. Sci. Adv. 7, eabf0971 (2021). PubMed DOI PMC
Merry, C. R. et al. Transcriptome-wide identification of mRNAs and lincRNAs associated with trastuzumab-resistance in HER2-positive breast cancer. Oncotarget 7, 53230–53244 (2016). PubMed DOI 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). DOI
Lager, A. M. et al. Rapid functional genetics of the oligodendrocyte lineage using pluripotent stem cells. Nat. Commun. 9, 3708 (2018). PubMed DOI 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 DOI PMC
Chen, C. W. et al. Adaptation to chronic ER stress enforces pancreatic beta-cell plasticity. Nat. Commun. 13, 4621 (2022). PubMed DOI 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 DOI PMC
Dowling, R. J. et al. mTORC1-mediated cell proliferation, but not cell growth, controlled by the 4E-BPs. Science 328, 1172–1176 (2010). PubMed DOI PMC
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015). PubMed DOI PMC
Anders, S., Pyl, P. T. & Huber, W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015). PubMed DOI
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 DOI 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 DOI
Beissbarth, T. & Speed, T. P. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20, 1464–1465 (2004). PubMed DOI
Vlaski-Lafarge, M. et al. Bioenergetic changes underline plasticity of murine embryonic stem cells. Stem Cells 37, 463–475 (2019). PubMed DOI
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 DOI PMC
Mookerjee, S. A., Nicholls, D. G. & Brand, M. D. Determining maximum glycolytic capacity using extracellular flux measurements. PLoS ONE 11, e0152016 (2016). PubMed DOI 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. Metabolomics 9, 1019–1030 (2013). PubMed DOI PMC