The eIF2α/ATF4 pathway is essential for stress-induced autophagy gene expression

In response to different environmental stresses, eIF2α phosphorylation represses global translation coincident with preferential translation of ATF4, a master regulator controlling the transcription of key genes essential for adaptative functions. Here, we establish that the eIF2α/ATF4 pathway directs an autophagy gene transcriptional program in response to amino acid starvation or endoplasmic reticulum stress. The eIF2α-kinases GCN2 and PERK and the transcription factors ATF4 and CHOP are also required to increase the transcription of a set of genes implicated in the formation, elongation and function of the autophagosome. We also identify three classes of autophagy genes according to their dependence on ATF4 and CHOP and the binding of these factors to specific promoter cis elements. Furthermore, different combinations of CHOP and ATF4 bindings to target promoters allow the trigger of a differential transcriptional response according to the stress intensity. Overall, this study reveals a novel regulatory role of the eIF2α–ATF4 pathway in the fine-tuning of the autophagy gene transcription program in response to stresses.

[1]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[2]  C. Kraft,et al.  Mechanisms and regulation of autophagosome formation. , 2012, Current opinion in cell biology.

[3]  In Hye Lee,et al.  Atg7 Modulates p53 Activity to Regulate Cell Cycle and Survival During Metabolic Stress , 2012, Science.

[4]  Robert Clarke,et al.  Guidelines for the use and interpretation of assays for monitoring autophagy , 2012 .

[5]  Masaaki Komatsu,et al.  Autophagy: Renovation of Cells and Tissues , 2011, Cell.

[6]  J. Debnath,et al.  PERK Integrates Autophagy and Oxidative Stress Responses To Promote Survival during Extracellular Matrix Detachment , 2011, Molecular and Cellular Biology.

[7]  Z. Elazar,et al.  Biogenesis and cargo selectivity of autophagosomes. , 2011, Annual review of biochemistry.

[8]  T. Lamark,et al.  Selective autophagy mediated by autophagic adapter proteins , 2011, Autophagy.

[9]  S. S. Chen,et al.  Activation of the unfolded protein response and autophagy after hepatitis C virus infection suppresses innate antiviral immunity in vitro. , 2011, The Journal of clinical investigation.

[10]  V. Carraro,et al.  Amino Acid Availability Controls TRB3 Transcription in Liver through the GCN2/eIF2α/ATF4 Pathway , 2010, PloS one.

[11]  G. Kroemer,et al.  Autophagy and the integrated stress response. , 2010, Molecular cell.

[12]  N. Mizushima,et al.  Physiological role of autophagy as an intracellular recycling system: with an emphasis on nutrient metabolism. , 2010, Seminars in cell & developmental biology.

[13]  A. Harris,et al.  Regulation of autophagy by ATF4 in response to severe hypoxia , 2010, Oncogene.

[14]  V. Carraro,et al.  Molecular mechanisms involved in the adaptation to amino acid limitation in mammals. , 2010, Biochimie.

[15]  Jiangbin Ye,et al.  The GCN2‐ATF4 pathway is critical for tumour cell survival and proliferation in response to nutrient deprivation , 2010, The EMBO journal.

[16]  M. Hatzoglou,et al.  Molecular Symbiosis of CHOP and C/EBPβ Isoform LIP Contributes to Endoplasmic Reticulum Stress-Induced Apoptosis , 2010, Molecular and Cellular Biology.

[17]  Chang Hwa Jung,et al.  mTOR regulation of autophagy , 2010, FEBS letters.

[18]  N. Mizushima,et al.  Methods in Mammalian Autophagy Research , 2010, Cell.

[19]  Philippe Lambin,et al.  The unfolded protein response protects human tumor cells during hypoxia through regulation of the autophagy genes MAP1LC3B and ATG5. , 2010, The Journal of clinical investigation.

[20]  A. Harris,et al.  Role of ATF4 in regulation of autophagy and resistance to drugs and hypoxia , 2009, Cell cycle.

[21]  N. Su,et al.  ATF4-dependent transcription mediates signaling of amino acid limitation , 2009, Trends in Endocrinology & Metabolism.

[22]  A. Maurin,et al.  Amino acids as regulators of gene expression in mammals: Molecular mechanisms , 2009, BioFactors.

[23]  V. Carraro,et al.  Amino acid limitation regulates the expression of genes involved in several specific biological processes through GCN2‐dependent and GCN2‐independent pathways , 2009, The FEBS journal.

[24]  N. Su,et al.  C/EBP Homology Protein (CHOP) Interacts with Activating Transcription Factor 4 (ATF4) and Negatively Regulates the Stress-dependent Induction of the Asparagine Synthetase Gene* , 2008, Journal of Biological Chemistry.

[25]  J. Andersen,et al.  Ordered Organelle Degradation during Starvation-induced Autophagy*S , 2008, Molecular & Cellular Proteomics.

[26]  M. Schröder.  Endoplasmic reticulum stress responses , 2008, Cellular and Molecular Life Sciences.

[27]  Daniel J. Klionsky,et al.  Autophagy fights disease through cellular self-digestion , 2008, Nature.

[28]  John L Cleveland,et al.  Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes , 2008, Autophagy.

[29]  Guido Kroemer,et al.  Autophagy in the Pathogenesis of Disease , 2008, Cell.

[30]  A. Goldberg,et al.  FoxO3 coordinately activates protein degradation by the autophagic/lysosomal and proteasomal pathways in atrophying muscle cells. , 2007, Cell metabolism.

[31]  A. Goldberg,et al.  FoxO3 controls autophagy in skeletal muscle in vivo. , 2007, Cell metabolism.

[32]  N. Mizushima,et al.  Autophagy: process and function. , 2007, Genes & development.

[33]  R. Wek,et al.  Translational control and the unfolded protein response. , 2007, Antioxidants & redox signaling.

[34]  Guido Kroemer,et al.  Self-eating and self-killing: crosstalk between autophagy and apoptosis , 2007, Nature Reviews Molecular Cell Biology.

[35]  G. Bjørkøy,et al.  p62/SQSTM1 Binds Directly to Atg8/LC3 to Facilitate Degradation of Ubiquitinated Protein Aggregates by Autophagy* , 2007, Journal of Biological Chemistry.

[36]  D. Stolz,et al.  Linking of autophagy to ubiquitin-proteasome system is important for the regulation of endoplasmic reticulum stress and cell viability. , 2007, The American journal of pathology.

[37]  N. Jones,et al.  ATF2 is required for amino acid-regulated transcription by orchestrating specific histone acetylation , 2007, Nucleic acids research.

[38]  F. Urano,et al.  Autophagy Is Activated for Cell Survival after Endoplasmic ReticulumStress , 2006, Molecular and Cellular Biology.

[39]  T. Anthony,et al.  Coping with stress: eIF2 kinases and translational control. , 2006, Biochemical Society transactions.

[40]  G. Bjørkøy,et al.  p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death , 2005, The Journal of cell biology.

[41]  R. Deberardinis,et al.  Autophagy in metazoans: cell survival in the land of plenty , 2005, Nature Reviews Molecular Cell Biology.

[42]  H. Hayashi,et al.  TRB3, a novel ER stress‐inducible gene, is induced via ATF4–CHOP pathway and is involved in cell death , 2005, The EMBO journal.

[43]  Yuan-Xiang Pan,et al.  Amino Acid Deprivation Induces the Transcription Rate of the Human Asparagine Synthetase Gene through a Timed Program of Expression and Promoter Binding of Nutrient-responsive Basic Region/Leucine Zipper Transcription Factors as Well as Localized Histone Acetylation* , 2004, Journal of Biological Chemistry.

[44]  D. Ron,et al.  Translation reinitiation at alternative open reading frames regulates gene expression in an integrated stress response , 2004, The Journal of cell biology.

[45]  N. Krishna,et al.  Sequestosome 1/p62 Is a Polyubiquitin Chain Binding Protein Involved in Ubiquitin Proteasome Degradation , 2004, Molecular and Cellular Biology.

[46]  R. Wek,et al.  Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[47]  V. Carraro,et al.  Induction of CHOP Expression by Amino Acid Limitation Requires Both ATF4 Expression and ATF2 Phosphorylation* , 2004, Journal of Biological Chemistry.

[48]  S. Emr,et al.  A unified nomenclature for yeast autophagy-related genes. , 2003, Developmental cell.

[49]  R. Paules,et al.  An integrated stress response regulates amino acid metabolism and resistance to oxidative stress. , 2003, Molecular cell.

[50]  A. Reimold,et al.  Differences in the Molecular Mechanisms Involved in the Transcriptional Activation of the CHOP and Asparagine Synthetase Genes in Response to Amino Acid Deprivation or Activation of the Unfolded Protein Response* , 2002, The Journal of Biological Chemistry.

[51]  S. Kimball,et al.  The GCN2 eIF2α Kinase Is Required for Adaptation to Amino Acid Deprivation in Mice , 2002, Molecular and Cellular Biology.

[52]  M. Kilberg,et al.  ATF4 Is a Mediator of the Nutrient-sensing Response Pathway That Activates the Human Asparagine Synthetase Gene* , 2002, The Journal of Biological Chemistry.

[53]  D. Scheuner,et al.  Regulation of starvation- and virus-induced autophagy by the eIF2α kinase signaling pathway , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[54]  M. Schapira,et al.  Regulated translation initiation controls stress-induced gene expression in mammalian cells. , 2000, Molecular cell.

[55]  Pierre Fafournoux,et al.  Amino Acids Control Mammalian Gene Transcription: Activating Transcription Factor 2 Is Essential for the Amino Acid Responsiveness of the CHOP Promoter , 2000, Molecular and Cellular Biology.

[56]  F. Gachon,et al.  Molecular Interactions Involved in the Transactivation of the Human T-Cell Leukemia Virus Type 1 Promoter Mediated by Tax and CREB-2 (ATF-4) , 2000, Molecular and Cellular Biology.

[57]  R. Sood,et al.  A mammalian homologue of GCN2 protein kinase important for translational control by phosphorylation of eukaryotic initiation factor-2alpha. , 2000, Genetics.

[58]  D. Ron,et al.  Protein translation and folding are coupled by an endoplasmic-reticulum-resident kinase , 1999, Nature.

[59]  Heather Harding,et al.  CHOP-Dependent Stress-Inducible Expression of a Novel Form of Carbonic Anhydrase VI , 1999, Molecular and Cellular Biology.

[60]  H. Zinszner,et al.  Identification of novel stress‐induced genes downstream of chop , 1998, The EMBO journal.

[61]  Xiaozhong Wang,et al.  CHOP is implicated in programmed cell death in response to impaired function of the endoplasmic reticulum. , 1998, Genes & development.

[62]  D. Ron,et al.  Amino Acid Limitation Induces Expression of CHOP, a CCAAT/Enhancer Binding Protein-related Gene, at Both Transcriptional and Post-transcriptional Levels* , 1997, The Journal of Biological Chemistry.

[63]  I-Hsien Wu,et al.  Stress-induced binding of the transcriptional factor CHOP to a novel DNA control element , 1996, Molecular and cellular biology.

[64]  A. Meijer,et al.  Phosphorylation of Ribosomal Protein S6 Is Inhibitory for Autophagy in Isolated Rat Hepatocytes (*) , 1995, The Journal of Biological Chemistry.

[65]  D. Ron,et al.  CHOP, a novel developmentally regulated nuclear protein that dimerizes with transcription factors C/EBP and LAP and functions as a dominant-negative inhibitor of gene transcription. , 1992, Genes & development.

[66]  A. Hinnebusch,et al.  A quantitative model for translational control of the GCN4 gene of Saccharomyces cerevisiae. , 1991, The New biologist.

[67]  R. Baserga,et al.  Transcriptional activity of the human thymidine kinase gene determined by a method using the polymerase chain reaction and an intron-specific probe. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[68]  C. Schworer,et al.  Induction of autophagy by amino-acid deprivation in perfused rat liver , 1977, Nature.

[69]  G. Bjørkøy,et al.  Monitoring autophagic degradation of p62/SQSTM1. , 2009, Methods in enzymology.

[70]  Adrian L Harris,et al.  Activating transcription factor 4. , 2008, The international journal of biochemistry & cell biology.

[71]  R. Sood,et al.  A Mammalian Homologue of GCN 2 Protein Kinase Important for Translational Control by Phosphorylation of Eukaryotic Initiation Factor-2 a , 2000 .

[72]  A. Hinnebusch.  5 Mechanism and Regulation of Initiator Methionyl-tRNA Binding to Ribosomes , 2000 .

[73]  N. Sonenberg,et al.  Translational control of gene expression , 2000 .