Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals

Mitochondrial stress activates a mitonuclear response to safeguard and repair mitochondrial function and to adapt cellular metabolism to stress. Using a multiomics approach in mammalian cells treated with four types of mitochondrial stressors, we identify activating transcription factor 4 (ATF4) as the main regulator of the stress response. Surprisingly, canonical mitochondrial unfolded protein response genes mediated by ATF5 are not activated. Instead, ATF4 activates the expression of cytoprotective genes, which reprogram cellular metabolism through activation of the integrated stress response (ISR). Mitochondrial stress promotes a local proteostatic response by reducing mitochondrial ribosomal proteins, inhibiting mitochondrial translation, and coupling the activation of the ISR with the attenuation of mitochondrial function. Through a trans–expression quantitative trait locus analysis, we provide genetic evidence supporting a role for Fh1 in the control of Atf4 expression in mammals. Using gene expression data from mice and humans with mitochondrial diseases, we show that the ATF4 pathway is activated in vivo upon mitochondrial stress. Our data illustrate the value of a multiomics approach to characterize complex cellular networks and provide a versatile resource to identify new regulators of mitochondrial-related diseases.

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hnRNP A1 Relocalization to the Stress Granules Reflects a Role in the Stress Response

Molecular and Cellular Biology ◽

10.1128/mcb.00224-06 ◽

2006 ◽

Vol 26 (15) ◽

pp. 5744-5758 ◽

Cited By ~ 194

Author(s):

Sonia Guil ◽

Jennifer C. Long ◽

Javier F. Cáceres

Keyword(s):

Stress Response ◽

Mammalian Cells ◽

Stress Granules ◽

Binding Activity ◽

Hnrnp A1 ◽

Mrna Metabolism ◽

Discrete Phase ◽

Cytoplasmic Accumulation ◽

Mrna Binding

ABSTRACT hnRNP A1 is a nucleocytoplasmic shuttling protein that is involved in many aspects of mRNA metabolism. We have previously shown that activation of the p38 stress-signaling pathway in mammalian cells results in both hyperphosphorylation and cytoplasmic accumulation of hnRNP A1, affecting alternative splicing regulation in vivo. Here we show that the stress-induced cytoplasmic accumulation of hnRNP A1 occurs in discrete phase-dense particles, the cytoplasmic stress granules (SGs). Interestingly, mRNA-binding activity is required for both phosphorylation of hnRNP A1 and localization to SGs. We also show that these effects are mediated by the Mnk1/2 protein kinases that act downstream of p38. Finally, depletion of hnRNP A1 affects the recovery of cells from stress, suggesting a physiologically significant role for hnRNP A1 in the stress response. Our data are consistent with a model whereby hnRNP A1 recruitment to SGs involves Mnk1/2-dependent phosphorylation of mRNA-bound hnRNP A1.

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Glutamyl-tRNAGln amidotransferase is essential for mammalian mitochondrial translation in vivo

Biochemical Journal ◽

10.1042/bj20131107 ◽

2014 ◽

Vol 460 (1) ◽

pp. 91-101 ◽

Cited By ~ 20

Author(s):

Lucía Echevarría ◽

Paula Clemente ◽

Rosana Hernández-Sierra ◽

María Esther Gallardo ◽

Miguel A. Fernández-Moreno ◽

...

Keyword(s):

Protein Synthesis ◽

Mammalian Cells ◽

Mitochondrial Protein ◽

Mitochondrial Protein Synthesis ◽

Indirect Pathway ◽

Mitochondrial Translation

We have demonstrated that in mitochondria of mammalian cells the aminoacylation of tRNAGln is produced by an indirect pathway involving the enzyme glutamyl-tRNAGln amidotransferase. Misaminoacylated Glu-tRNAGln is rejected from the ribosomes maintaining the fidelity of the mitochondrial protein synthesis.

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HRI coordinates translation necessary for protein homeostasis and mitochondrial function in erythropoiesis

eLife ◽

10.7554/elife.46976 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 17

Author(s):

Shuping Zhang ◽

Alejandra Macias-Garcia ◽

Jacob C Ulirsch ◽

Jason Velazquez ◽

Vincent L Butty ◽

...

Keyword(s):

Iron Deficiency ◽

Mitochondrial Function ◽

Ribosomal Proteins ◽

Target Genes ◽

Mitochondrial Protein ◽

Erythroid Differentiation ◽

Protein Translation ◽

Ribosome Profiling ◽

Underlying Mechanisms

Iron and heme play central roles in the production of red blood cells, but the underlying mechanisms remain incompletely understood. Heme-regulated eIF2α kinase (HRI) controls translation by phosphorylating eIF2α. Here, we investigate the global impact of iron, heme, and HRI on protein translation in vivo in murine primary erythroblasts using ribosome profiling. We validate the known role of HRI-mediated translational stimulation of integratedstressresponse mRNAs during iron deficiency in vivo. Moreover, we find that the translation of mRNAs encoding cytosolic and mitochondrial ribosomal proteins is substantially repressed by HRI during iron deficiency, causing a decrease in cytosolic and mitochondrial protein synthesis. The absence of HRI during iron deficiency elicits a prominent cytoplasmic unfolded protein response and impairs mitochondrial respiration. Importantly, ATF4 target genes are activated during iron deficiency to maintain mitochondrial function and to enable erythroid differentiation. We further identify GRB10 as a previously unappreciated regulator of terminal erythropoiesis.

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ATF4 helps mitochondria pass the stress test

The Journal of Cell Biology ◽

10.1083/jcb.201706026 ◽

2017 ◽

Vol 216 (7) ◽

pp. 1865-1865

Author(s):

Ben Short

Keyword(s):

Transcription Factor ◽

Stress Response ◽

Mammalian Cells ◽

Stress Test ◽

Mitochondrial Stress

The transcription factor ATF4 coordinates the mitochondrial stress response in mammalian cells.

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A conserved role of CBP/p300 in mitochondrial stress response and longevity

10.21203/rs.3.rs-86465/v1 ◽

2020 ◽

Author(s):

Terytty Yang Li ◽

Maroun Bou Sleiman ◽

Hao Li ◽

Arwen W. Gao ◽

Adrienne Mottis ◽

...

Keyword(s):

Stress Response ◽

Stress Responses ◽

Mammalian Cells ◽

Amyloid Β ◽

Human Populations ◽

Histone Demethylases ◽

Mitochondrial Stress ◽

Unfolded Protein ◽

Evolutionarily Conserved ◽

Protein Response

Abstract Organisms respond to mitochondrial stress by activating multiple defense pathways including the mitochondrial unfolded protein response (UPRmt). However, how different layers of UPRmt regulators are orchestrated to transcriptionally activate the stress responses remains largely unknown. Here we identified CBP-1, the worm ortholog of the mammalian acetyltransferases CBP/p300, as an essential regulator for UPRmt activation, as well as for mitochondrial stress-induced immune response, reduction of amyloid-β aggregation and lifespan extension in Caenorhabditis elegans. Mechanistically, CBP-1 acts downstream of histone demethylases, JMJD-1.2/JMJD-3.1, and upstream of UPRmt transcription factors including ATFS-1, to systematically induce a broad spectrum of UPRmt genes and execute multiple beneficial functions. In mouse and human populations, transcript levels of CBP/p300 positively correlate with UPRmt transcripts and longevity. Furthermore, CBP/p300 inhibition disrupts, while forced expression of p300 is sufficient to activate, the UPRmt in mammalian cells. These results highlight an evolutionarily conserved mechanism that determines mitochondrial stress response, and promotes health and longevity through CBP/p300.

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Regulation of polyamine biosynthesis by antizyme and some recent developments relating the induction of polyamine biosynthesis to cell growth

Bioscience Reports ◽

10.1007/bf01119588 ◽

1985 ◽

Vol 5 (3) ◽

pp. 189-204 ◽

Cited By ~ 36

Author(s):

E. S. Canellakis ◽

D. A. Kyriakidis ◽

C. A. Rinehart ◽

S.-C. Huang ◽

C. Panagiotidis ◽

...

Keyword(s):

Ornithine Decarboxylase ◽

Mammalian Cells ◽

Ribosomal Proteins ◽

Physiological Role ◽

Arginine Decarboxylase ◽

Cell Of Origin ◽

Polyamine Biosynthesis ◽

Recent Developments

This review considers the role of antizyme, of amino acids and of protein synthesis in the regulation of polyamine biosynthesis.The ornithine decarboxylase of eukaryotic ceils and of Escherichia coli coli can be non-competitively inhibited by proteins, termed antizymes, which are induced by di-and poly- amines. Some antizymes have been purified to homogeneity and have been shown to be structurally unique to the cell of origin. Yet, the E. coli antizyme and the rat liver antizyme cross react and inhibit each other's biosynthetic decarboxylases. These results indicate that aspects of the control of polyamine biosynthesis have been highly conserved throughout evolution.Evidence for the physiological role of the antizyme in mammalian cells rests upon its identification in normal uninduced cells, upon the inverse relationship that exists between antizyme and ornithine decarboxylase as well as upon the existence of the complex of ornithine decarboxylase and antizyme in vivo. Furthermore, the antizyme has been shown to be highly specific; its Keq for ornithine decarboxylase is 1.4 × 1011 M-1. In addition, mammalian ceils contain an anti-antizyme, a protein that specifically binds to the antizyme of an ornithine decarboxylase-antizyme complex and liberates free ornithine decarboxylase from the complex. In B. coli, in which polyamine biosynthesis is mediated both by ornithine decarboxylase and by arginine decarboxylase, three proteins (one acidic and two basic) have been purified, each of which inhibits both these enzymes. They do not inhibit the biodegradative ornithine and arginine decarboxylases nor lysine decarboxylase. The two basic inhibitors have been shown to correspond to the ribosomal proteins S20/L26 and L34, respectively. The relationship of the acidic antizyme to other known B. coli proteins remains to be determined.

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Inhibition of mitochondrial translation overcomes venetoclax resistance in AML through activation of the integrated stress response

Science Translational Medicine ◽

10.1126/scitranslmed.aax2863 ◽

2019 ◽

Vol 11 (516) ◽

pp. eaax2863 ◽

Cited By ~ 26

Author(s):

David Sharon ◽

Severine Cathelin ◽

Sara Mirali ◽

Justin M. Di Trani ◽

David J. Yanofsky ◽

...

Keyword(s):

Stress Response ◽

Single Agent ◽

Mitochondrial Protein ◽

B Cell Lymphoma ◽

Atp Depletion ◽

Integrated Stress Response ◽

Mitochondrial Translation ◽

A Genome

Venetoclax is a specific B cell lymphoma 2 (BCL-2) inhibitor with promising activity against acute myeloid leukemia (AML), but its clinical efficacy as a single agent or in combination with hypomethylating agents (HMAs), such as azacitidine, is hampered by intrinsic and acquired resistance. Here, we performed a genome-wide CRISPR knockout screen and found that inactivation of genes involved in mitochondrial translation restored sensitivity to venetoclax in resistant AML cells. Pharmacologic inhibition of mitochondrial protein synthesis with antibiotics that target the ribosome, including tedizolid and doxycycline, effectively overcame venetoclax resistance. Mechanistic studies showed that both tedizolid and venetoclax suppressed mitochondrial respiration, with the latter demonstrating inhibitory activity against complex I [nicotinamide adenine dinucleotide plus hydrogen (NADH) dehydrogenase] of the electron transport chain (ETC). The drugs cooperated to activate a heightened integrated stress response (ISR), which, in turn, suppressed glycolytic capacity, resulting in adenosine triphosphate (ATP) depletion and subsequent cell death. Combination treatment with tedizolid and venetoclax was superior to either agent alone in reducing leukemic burden in mice engrafted with treatment-resistant human AML. The addition of tedizolid to azacitidine and venetoclax further enhanced the killing of resistant AML cells in vitro and in vivo. Our findings demonstrate that inhibition of mitochondrial translation is an effective approach to overcoming venetoclax resistance and provide a rationale for combining tedizolid, azacitidine, and venetoclax as a triplet therapy for AML.

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Dynamic proteomics profiling of Legionella pneumophila infection unveils modulation of the host mitochondrial stress response pathway

10.1101/2020.05.19.105395 ◽

2020 ◽

Author(s):

Julia Noack ◽

David Jimenez-Morales ◽

Erica Stevenson ◽

Tom Moss ◽

Gwendolyn Jang ◽

...

Keyword(s):

Stress Response ◽

Host Cell ◽

Legionella Pneumophila ◽

Mammalian Cells ◽

Bacterial Pathogen ◽

Effector Proteins ◽

Mitochondrial Stress ◽

Cellular Targets ◽

Mitochondrial Proteome ◽

Cell Proteome

SUMMARYThe human pathogen Legionella pneumophila (L.p.) secretes ~330 bacterial effector proteins into the host cell which interfere with numerous cellular pathways and often regulate host cell proteins through post-translational modifications. However, the cellular targets and functions of most L.p. effectors are not known. In order to obtain a global overview of potential targets of these effectors, we analyzed the host cell proteome, ubiquitinome, and phosphoproteome during L.p. infection. Our analysis reveals dramatic spatiotemporal changes in the host cell proteome that are dependent on the secretion of bacterial effectors. Strikingly, we show that L.p. substantially reshapes the mitochondrial proteome and modulates mitochondrial stress response pathways such as the mitochondrial unfolded protein response (UPRmt). To our knowledge, this is the first evidence of manipulation of the UPRmt by a bacterial pathogen in mammalian cells. In addition, we have identified a previously uncharacterized L.p. effector that is targeted to host cell mitochondria and protects mitochondrial network integrity during mitochondrial stress.

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Historical perspective: phosphatidylserine and phosphatidylethanolamine from the 1800s to the present

The Journal of Lipid Research ◽

10.1194/jlr.r084004 ◽

2018 ◽

Vol 59 (6) ◽

pp. 923-944 ◽

Cited By ~ 20

Author(s):

Jean E. Vance

Keyword(s):

Mitochondrial Function ◽

Mammalian Cells ◽

Isotope Labeling ◽

Threshold Level ◽

Ether Lipids ◽

Membrane Contact Sites ◽

Outer Leaflet ◽

Physiological Processes ◽

Membrane Contact

This article provides a historical account of the discovery, chemistry, and biochemistry of two ubiquitous phosphoglycerolipids, phosphatidylserine (PS) and phosphatidylethanolamine (PE), including the ether lipids. In addition, the article describes the biosynthetic pathways for these phospholipids and how these pathways were elucidated. Several unique functions of PS and PE in mammalian cells in addition to their ability to define physical properties of membranes are discussed. For example, the translocation of PS from the inner to the outer leaflet of the plasma membrane of cells occurs during apoptosis and during some other specific physiological processes, and this translocation is responsible for profound life-or-death events. Moreover, mitochondrial function is severely impaired when the PE content of mitochondria is reduced below a threshold level. The discovery and implications of the existence of membrane contact sites between the endoplasmic reticulum and mitochondria and their relevance for PS and PE metabolism, as well as for mitochondrial function, are also discussed. Many of the recent advances in these fields are due to the use of isotope labeling for tracing biochemical pathways. In addition, techniques for disruption of specific genes in mice are now widely used and have provided major breakthroughs in understanding the roles and metabolism of PS and PE in vivo.

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