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Skeparnias I, Bou-Nader C, Anastasakis DG, Fan L, Wang YX, Hafner M, Zhang J. Structural basis of MALAT1 RNA maturation and mascRNA biogenesis. Nat Struct Mol Biol 2024:10.1038/s41594-024-01340-4. [PMID: 38956168 DOI: 10.1038/s41594-024-01340-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 05/29/2024] [Indexed: 07/04/2024]
Abstract
The metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) long noncoding RNA (lncRNA) has key roles in regulating transcription, splicing, tumorigenesis, etc. Its maturation and stabilization require precise processing by RNase P, which simultaneously initiates the biogenesis of a 3' cytoplasmic MALAT1-associated small cytoplasmic RNA (mascRNA). mascRNA was proposed to fold into a transfer RNA (tRNA)-like secondary structure but lacks eight conserved linking residues required by the canonical tRNA fold. Here we report crystal structures of human mascRNA before and after processing, which reveal an ultracompact, quasi-tRNA-like structure. Despite lacking all linker residues, mascRNA faithfully recreates the characteristic 'elbow' feature of tRNAs to recruit RNase P and ElaC homolog protein 2 (ELAC2) for processing, which exhibit distinct substrate specificities. Rotation and repositioning of the D-stem and anticodon regions preclude mascRNA from aminoacylation, avoiding interference with translation. Therefore, a class of metazoan lncRNA loci uses a previously unrecognized, unusually streamlined quasi-tRNA architecture to recruit select tRNA-processing enzymes while excluding others to drive bespoke RNA biogenesis, processing and maturation.
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Affiliation(s)
- Ilias Skeparnias
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Dimitrios G Anastasakis
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-Ray Scattering Core Facility of National Cancer Institute, Frederick, MD, USA
| | - Yun-Xing Wang
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-Ray Scattering Core Facility of National Cancer Institute, Frederick, MD, USA
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
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2
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Gibbs VJ, Lin YH, Ghuge AA, Anderson RA, Schiemann AH, Conaglen L, Sansom BJM, da Silva RC, Sattlegger E. GCN2 in Viral Defence and the Subversive Tactics Employed by Viruses. J Mol Biol 2024; 436:168594. [PMID: 38724002 DOI: 10.1016/j.jmb.2024.168594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/01/2024] [Accepted: 05/01/2024] [Indexed: 06/10/2024]
Abstract
The recent SARS-CoV-2 pandemic and associated COVID19 disease illustrates the important role of viral defence mechanisms in ensuring survival and recovery of the host or patient. Viruses absolutely depend on the host's protein synthesis machinery to replicate, meaning that impeding translation is a powerful way to counteract viruses. One major approach used by cells to obstruct protein synthesis is to phosphorylate the alpha subunit of eukaryotic translation initiation factor 2 (eIF2α). Mammals possess four different eIF2α-kinases: PKR, HRI, PEK/PERK, and GCN2. While PKR is currently considered the principal eIF2α-kinase involved in viral defence, the other eIF2α-kinases have also been found to play significant roles. Unsurprisingly, viruses have developed mechanisms to counteract the actions of eIF2α-kinases, or even to exploit them to their benefit. While some of these virulence factors are specific to one eIF2α-kinase, such as GCN2, others target all eIF2α-kinases. This review critically evaluates the current knowledge of viral mechanisms targeting the eIF2α-kinase GCN2. A detailed and in-depth understanding of the molecular mechanisms by which viruses evade host defence mechanisms will help to inform the development of powerful anti-viral measures.
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Affiliation(s)
- Victoria J Gibbs
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Yu H Lin
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Aditi A Ghuge
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Reuben A Anderson
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Anja H Schiemann
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Layla Conaglen
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Bianca J M Sansom
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Richard C da Silva
- School of Natural Sciences, Massey University, Auckland, New Zealand; Genome Biology and Epigenetics, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Evelyn Sattlegger
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand; School of Natural Sciences, Massey University, Auckland, New Zealand; Maurice Wilkins Centre for Molecular BioDiscovery, Palmerston North, New Zealand.
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3
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Li X, Yang Y, Bai X, Wang X, Tan H, Chen Y, Zhu Y, Liu Q, Wu MN, Li Y. A brain-derived insulin signal encodes protein satiety for nutrient-specific feeding inhibition. Cell Rep 2024; 43:114282. [PMID: 38795342 PMCID: PMC11220824 DOI: 10.1016/j.celrep.2024.114282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 04/08/2024] [Accepted: 05/10/2024] [Indexed: 05/27/2024] Open
Abstract
The suppressive effect of insulin on food intake has been documented for decades. However, whether insulin signals can encode a certain type of nutrients to regulate nutrient-specific feeding behavior remains elusive. Here, we show that in female Drosophila, a pair of dopaminergic neurons, tritocerebrum 1-dopaminergic neurons (T1-DANs), are directly activated by a protein-intake-induced insulin signal from insulin-producing cells (IPCs). Intriguingly, opto-activating IPCs elicits feeding inhibition for both protein and sugar, while silencing T1-DANs blocks this inhibition only for protein food. Elevating insulin signaling in T1-DANs or opto-activating these neurons is sufficient to mimic protein satiety. Furthermore, this signal is conveyed to local neurons of the protocerebral bridge (PB-LNs) and specifically suppresses protein intake. Therefore, our findings reveal that a brain-derived insulin signal encodes protein satiety and suppresses feeding behavior in a nutrient-specific manner, shedding light on the functional specificity of brain insulin signals in regulating behaviors.
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Affiliation(s)
- Xiaoyu Li
- Institute of Biophysics, State Key Laboratory of Brain and Cognitive Science, Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yang
- Institute of Biophysics, State Key Laboratory of Brain and Cognitive Science, Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaobing Bai
- Institute of Biophysics, State Key Laboratory of Brain and Cognitive Science, Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish Center for Education and Research, Beijing 100190, China
| | - Xiaotong Wang
- Institute of Biophysics, State Key Laboratory of Brain and Cognitive Science, Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Houqi Tan
- Institute of Biophysics, State Key Laboratory of Brain and Cognitive Science, Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanbo Chen
- Institute of Biophysics, State Key Laboratory of Brain and Cognitive Science, Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Zhu
- Institute of Biophysics, State Key Laboratory of Brain and Cognitive Science, Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish Center for Education and Research, Beijing 100190, China
| | - Qili Liu
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mark N Wu
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yan Li
- Institute of Biophysics, State Key Laboratory of Brain and Cognitive Science, Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish Center for Education and Research, Beijing 100190, China.
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4
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Li L, Yang L, Zhang L, He F, Xia Z, Xiang B. Multi-omic analysis reveals that Bacillus licheniformis enhances pekin ducks growth performance via lipid metabolism regulation. Front Pharmacol 2024; 15:1412231. [PMID: 38933681 PMCID: PMC11201536 DOI: 10.3389/fphar.2024.1412231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 05/13/2024] [Indexed: 06/28/2024] Open
Abstract
Introduction: Bacillus licheniformis (B.licheniformis) was widely used in poultry feeds. However, it is still unclear about how B.licheniformis regulates the growth and development of Pekin ducks. Methods: The experiment was designed to clarify the effect and molecular mechanism of B. licheniformis on the lipid metabolism and developmental growth of Pekin ducks through multiomics analysis, including transcriptomic and metabolomic analyses. Results: The results showed that compared with the control group, the addition of 400 mg/kg B. licheniformis could significantly increase the body weight of Pekin ducks and the content of triglyceride (p < 0.05), at the same time, the addition of B. licheniformis could affect the lipid metabolism of liver in Pekin ducks, and the addition of 400 mg/kg B. licheniformis could significantly increase the content of lipoprotein lipase in liver of Pekin ducks. Transcriptomic analysis revealed that the addition of B. licheniformis primarily impacted fatty acid and glutathione, amino acid metabolism, fatty acid degradation, as well as biosynthesis and elongation of unsaturated fatty acids. Metabolomic analysis indicated that B. licheniformis primarily affected the regulation of glycerol phospholipids, fatty acids, and glycerol metabolites. Multiomics analysis demonstrated that the addition of B. licheniformis to the diet of Pekin ducks enhanced the regulation of enzymes involved in fat synthesis via the PPAR signaling pathway, actively participating in fat synthesis and fatty acid transport. Discussion: We found that B. licheniformis effectively influences fat content and lipid metabolism by modulating lipid metabolism-associated enzymes in the liver. Ultimately, this study contributes to our understanding of how B. licheniformis can improve the growth performance of Pekin ducks, particularly in terms of fat deposition, thereby providing a theoretical foundation for its practical application. Conclusion: B. licheniformis can increase the regulation of enzymes related to fat synthesis through PPAR signal pathway, and actively participate in liver fat synthesis and fatty acid transport, thus changing the lipid metabolism of Pekin ducks, mainly in the regulation of glycerol phospholipids, fatty acids and glycerol lipid metabolites.
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Affiliation(s)
- Lei Li
- College of Animal Veterinary Medicine, Yunnan Agricultural University, Kunming, China
- College of Animal Veterinary Medicine, China Agricultural University, Beijing, China
| | - Liangyu Yang
- College of Animal Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Limei Zhang
- College of Animal Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Fengping He
- College of Animal Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Zhaofei Xia
- College of Animal Veterinary Medicine, China Agricultural University, Beijing, China
| | - Bin Xiang
- College of Animal Veterinary Medicine, Yunnan Agricultural University, Kunming, China
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5
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Yin JZ, Keszei AFA, Houliston S, Filandr F, Beenstock J, Daou S, Kitaygorodsky J, Schriemer DC, Mazhab-Jafari MT, Gingras AC, Sicheri F. The HisRS-like domain of GCN2 is a pseudoenzyme that can bind uncharged tRNA. Structure 2024; 32:795-811.e6. [PMID: 38531363 DOI: 10.1016/j.str.2024.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 01/09/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
GCN2 is a stress response kinase that phosphorylates the translation initiation factor eIF2α to inhibit general protein synthesis when activated by uncharged tRNA and stalled ribosomes. The presence of a HisRS-like domain in GCN2, normally associated with tRNA aminoacylation, led to the hypothesis that eIF2α kinase activity is regulated by the direct binding of this domain to uncharged tRNA. Here we solved the structure of the HisRS-like domain in the context of full-length GCN2 by cryoEM. Structure and function analysis shows the HisRS-like domain of GCN2 has lost histidine and ATP binding but retains tRNA binding abilities. Hydrogen deuterium exchange mass spectrometry, site-directed mutagenesis and computational docking experiments support a tRNA binding model that is partially shifted from that employed by bona fide HisRS enzymes. These results demonstrate that the HisRS-like domain of GCN2 is a pseudoenzyme and advance our understanding of GCN2 regulation and function.
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Affiliation(s)
- Jay Z Yin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alexander F A Keszei
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Frantisek Filandr
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jonah Beenstock
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Salima Daou
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Julia Kitaygorodsky
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mohammad T Mazhab-Jafari
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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6
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Malnassy G, Ziolkowski L, Macleod KF, Oakes SA. The Integrated Stress Response in Pancreatic Development, Tissue Homeostasis, and Cancer. Gastroenterology 2024:S0016-5085(24)04931-X. [PMID: 38768690 DOI: 10.1053/j.gastro.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/06/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024]
Abstract
Present in all eukaryotic cells, the integrated stress response (ISR) is a highly coordinated signaling network that controls cellular behavior, metabolism, and survival in response to diverse stresses. The ISR is initiated when any 1 of 3 stress-sensing kinases (protein kinase R-like endoplasmic reticulum kinase [PERK], general control non-derepressible 2 [GCN2], double-stranded RNA-dependent protein kinase [PKR], heme-regulated eukaryotic translation initiation factor 2α kinase [HRI]) becomes activated to phosphorylate the protein translation initiation factor eukaryotic translation initiation factor 2α (eIF2α), shifting gene expression toward a comprehensive rewiring of cellular machinery to promote adaptation. Although the ISR has been shown to play an important role in the homeostasis of multiple tissues, evidence suggests that it is particularly crucial for the development and ongoing health of the pancreas. Among the most synthetically dynamic tissues in the body, the exocrine and endocrine pancreas relies heavily on the ISR to rapidly adjust cell function to meet the metabolic demands of the organism. The hardwiring of the ISR into normal pancreatic functions and adaptation to stress may explain why it is a commonly used pro-oncogenic and therapy-resistance mechanism in pancreatic ductal adenocarcinoma and pancreatic neuroendocrine tumors. Here we review what is known about the key roles that the ISR plays in the development, homeostasis, and neoplasia of the pancreas.
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Affiliation(s)
- Greg Malnassy
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Leah Ziolkowski
- The Ben May Department for Cancer Research, University of Chicago, Chicago, Illinoi; Committee on Molecular Metabolism and Nutrition, University of Chicago, Chicago, Illinois
| | - Kay F Macleod
- The Ben May Department for Cancer Research, University of Chicago, Chicago, Illinoi; Committee on Molecular Metabolism and Nutrition, University of Chicago, Chicago, Illinois; Committee on Cancer Biology, University of Chicago, Chicago, Illinois.
| | - Scott A Oakes
- Department of Pathology, University of Chicago, Chicago, Illinois; Committee on Molecular Metabolism and Nutrition, University of Chicago, Chicago, Illinois; Committee on Cancer Biology, University of Chicago, Chicago, Illinois.
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7
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Boon NJ, Oliveira RA, Körner PR, Kochavi A, Mertens S, Malka Y, Voogd R, van der Horst SEM, Huismans MA, Smabers LP, Draper JM, Wessels LFA, Haahr P, Roodhart JML, Schumacher TNM, Snippert HJ, Agami R, Brummelkamp TR. DNA damage induces p53-independent apoptosis through ribosome stalling. Science 2024; 384:785-792. [PMID: 38753784 DOI: 10.1126/science.adh7950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/11/2024] [Indexed: 05/18/2024]
Abstract
In response to excessive DNA damage, human cells can activate p53 to induce apoptosis. Cells lacking p53 can still undergo apoptosis upon DNA damage, yet the responsible pathways are unknown. We observed that p53-independent apoptosis in response to DNA damage coincided with translation inhibition, which was characterized by ribosome stalling on rare leucine-encoding UUA codons and globally curtailed translation initiation. A genetic screen identified the transfer RNAse SLFN11 and the kinase GCN2 as factors required for UUA stalling and global translation inhibition, respectively. Stalled ribosomes activated a ribotoxic stress signal conveyed by the ribosome sensor ZAKα to the apoptosis machinery. These results provide an explanation for the frequent inactivation of SLFN11 in chemotherapy-unresponsive tumors and highlight ribosome stalling as a signaling event affecting cell fate in response to DNA damage.
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Affiliation(s)
- Nicolaas J Boon
- Oncode Institute, Utrecht, Netherlands
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Rafaela A Oliveira
- Oncode Institute, Utrecht, Netherlands
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Pierré-René Körner
- Oncode Institute, Utrecht, Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Adva Kochavi
- Oncode Institute, Utrecht, Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sander Mertens
- Oncode Institute, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Yuval Malka
- Oncode Institute, Utrecht, Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Rhianne Voogd
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Suzanne E M van der Horst
- Oncode Institute, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Maarten A Huismans
- Oncode Institute, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Lidwien P Smabers
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jonne M Draper
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Lodewyk F A Wessels
- Oncode Institute, Utrecht, Netherlands
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Peter Haahr
- Oncode Institute, Utrecht, Netherlands
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
- Center for Gene Expression, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeanine M L Roodhart
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Ton N M Schumacher
- Oncode Institute, Utrecht, Netherlands
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Hugo J Snippert
- Oncode Institute, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Reuven Agami
- Oncode Institute, Utrecht, Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Thijn R Brummelkamp
- Oncode Institute, Utrecht, Netherlands
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
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8
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Nanjaraj Urs AN, Lasehinde V, Kim L, McDonald E, Yan LL, Zaher HS. Inability to rescue stalled ribosomes results in overactivation of the integrated stress response. J Biol Chem 2024; 300:107290. [PMID: 38636664 PMCID: PMC11106528 DOI: 10.1016/j.jbc.2024.107290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
Endogenous and exogenous chemical agents are known to compromise the integrity of RNA and cause ribosome stalling and collisions. Recent studies have shown that collided ribosomes serve as sensors for multiple processes, including ribosome quality control (RQC) and the integrated stress response (ISR). Since RQC and the ISR have distinct downstream consequences, it is of great importance that organisms activate the appropriate process. We previously showed that RQC is robustly activated in response to collisions and suppresses the ISR activation. However, the molecular mechanics behind this apparent competition were not immediately clear. Here we show that Hel2 does not physically compete with factors of the ISR, but instead its ribosomal-protein ubiquitination activity, and downstream resolution of collided ribosomes, is responsible for suppressing the ISR. Introducing a mutation in the RING domain of Hel2-which inhibits its ubiquitination activity and downstream RQC but imparts higher affinity of the factor for collided ribosomes-resulted in increased activation of the ISR upon MMS-induced alkylation stress. Similarly, mutating Hel2's lysine targets in uS10, which is responsible for RQC activation, resulted in increased Gcn4 target induction. Remarkably, the entire process of RQC appears to be limited by the action of Hel2, as the overexpression of this one factor dramatically suppressed the activation of the ISR. Collectively, our data suggest that cells evolved Hel2 to bind collided ribosomes with a relatively high affinity but kept its concentration relatively low, ensuring that it gets exhausted under stress conditions that cannot be resolved by quality control processes.
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Affiliation(s)
| | - Victor Lasehinde
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA
| | - Lucas Kim
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA
| | - Elesa McDonald
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA
| | - Liewei L Yan
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA.
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9
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Solorio-Kirpichyan K, Fan X, Golovenko D, Korostelev AA, Yan N, Korennykh A. Cryo-EM Structure of HRSL Domain Reveals Activating Crossed Helices at the Core of GCN2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.591037. [PMID: 38712127 PMCID: PMC11071503 DOI: 10.1101/2024.04.24.591037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
GCN2 is a conserved receptor kinase activating the Integrated Stress Response (ISR) in eukaryotic cells. The ISR kinases detect accumulation of stress molecules and reprogram translation from basal tasks to preferred production of cytoprotective proteins. GCN2 stands out evolutionarily among all protein kinases due to the presence of a h istidyl t R NA s ynthetase-like (HRSL) domain, which arises only in GCN2 and is located next to the kinase domain. How HRSL contributes to GCN2 signaling remains unknown. Here we report a 3.2 Å cryo-EM structure of HRSL from thermotolerant yeast Kluyveromyces marxianus . This structure shows a constitutive symmetrical homodimer featuring a compact helical-bundle structure at the junction between HRSL and kinase domains, in the core of the receptor. Mutagenesis demonstrates that this junction structure activates GCN2 and indicates that our cryo-EM structure captures the active signaling state of HRSL. Based on these results, we put forward a GCN2 regulation mechanism, where HRSL drives the formation of activated kinase dimers. Remaining domains of GCN2 have the opposite role and in the absence of stress they help keep GCN2 basally inactive. This autoinhibitory activity is relieved upon stress ligand binding. We propose that the opposing action of HRSL and additional GCN2 domains thus yields a regulated ISR receptor. Significance statement Regulation of protein synthesis (translation) is a central mechanism by which eukaryotic cells adapt to stressful conditions. In starving cells, this translational adaptation is achieved via the receptor kinase GCN2, which stays inactive under normal conditions, but is switched on under stress. The molecular mechanism of GCN2 switching is not well understood due to the presence of a structurally and biochemically uncharacterized h istidyl t R NA s ynthetase-like domain (HRSL) at the core of GCN2. Here we use single-particle cryo-EM and biochemistry to elucidate the structure and function of HRSL. We identify a structure at the kinase/HRSL interface, which forms crossed helices and helps position GCN2 kinase domains for activation. These data clarify the molecular mechanism of GCN2 regulation.
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10
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Thomson CG, Aicher TD, Cheng W, Du H, Dudgeon C, Li AH, Li B, Lightcap E, Luo D, Mulvihill M, Pan P, Rahemtulla BF, Rigby AC, Sherborne B, Sood S, Surguladze D, Talbot EPA, Tameire F, Taylor S, Wang Y, Wojnarowicz P, Xiao F, Ramurthy S. Discovery of HC-7366: An Orally Bioavailable and Efficacious GCN2 Kinase Activator. J Med Chem 2024; 67:5259-5271. [PMID: 38530741 DOI: 10.1021/acs.jmedchem.3c02384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
A series of activators of GCN2 (general control nonderepressible 2) kinase have been developed, leading to HC-7366, which has entered the clinic as an antitumor therapy. Optimization resulted in improved permeability compared to that of the original indazole hinge binding scaffold, while maintaining potency at GCN2 and selectivity over PERK (protein kinase RNA-like endoplasmic reticulum kinase). The improved ADME properties of this series led to robust in vivo compound exposure in both rats and mice, allowing HC-7366 to be dosed in xenograft models, demonstrating that activation of the GCN2 pathway by this compound leads to tumor growth inhibition.
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Affiliation(s)
- Christopher G Thomson
- Integrated Drug Discovery Services, Pharmaron UK Ltd., West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire EN11 9FH, U.K
| | - Thomas D Aicher
- Department of Chemistry, Lycera Corporation, Ann Arbor, Michigan 48103, United States
| | - Weiwei Cheng
- Pharmaron Beijing, Company Ltd., No. 6, TaiHe Road, BDA, Beijing 100176, China
| | - Hongwen Du
- Pharmaron Beijing, Company Ltd., No. 6, TaiHe Road, BDA, Beijing 100176, China
| | - Crissy Dudgeon
- HiberCell Inc., 619 West 54th Street, New York, New York 10019, United States
| | - An-Hu Li
- HiberCell Inc., 619 West 54th Street, New York, New York 10019, United States
| | - Baozhong Li
- Pharmaron Beijing, Company Ltd., No. 6, TaiHe Road, BDA, Beijing 100176, China
| | - Eric Lightcap
- HiberCell Inc., 619 West 54th Street, New York, New York 10019, United States
| | - Diheng Luo
- Pharmaron Xi'an, Company Ltd., No. 1, 12th Fengcheng Road, Xi'an 710018, China
| | - Mark Mulvihill
- HiberCell Inc., 619 West 54th Street, New York, New York 10019, United States
| | - Pengwei Pan
- Pharmaron Beijing, Company Ltd., No. 6, TaiHe Road, BDA, Beijing 100176, China
| | - Benjamin F Rahemtulla
- Integrated Drug Discovery Services, Pharmaron UK Ltd., West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire EN11 9FH, U.K
| | - Alan C Rigby
- HiberCell Inc., 619 West 54th Street, New York, New York 10019, United States
| | - Bradley Sherborne
- Integrated Drug Discovery Services, Pharmaron UK Ltd., West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire EN11 9FH, U.K
| | - Sanjeev Sood
- Preformulation and Preclinical Services, Pharmaron UK Ltd., West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire EN11 9FH, U.K
| | - David Surguladze
- HiberCell Inc., 619 West 54th Street, New York, New York 10019, United States
| | - Eric P A Talbot
- Integrated Drug Discovery Services, Pharmaron UK Ltd., West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire EN11 9FH, U.K
| | - Feven Tameire
- HiberCell Inc., 619 West 54th Street, New York, New York 10019, United States
| | - Simon Taylor
- Integrated Drug Discovery Services, Pharmaron UK Ltd., West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire EN11 9FH, U.K
| | - Yi Wang
- Pharmaron Beijing, Company Ltd., No. 6, TaiHe Road, BDA, Beijing 100176, China
| | - Paulina Wojnarowicz
- HiberCell Inc., 619 West 54th Street, New York, New York 10019, United States
| | - Fenfen Xiao
- Pharmaron Xi'an, Company Ltd., No. 1, 12th Fengcheng Road, Xi'an 710018, China
| | - Savithri Ramurthy
- HiberCell Inc., 619 West 54th Street, New York, New York 10019, United States
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11
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Shanmugam R, Anderson R, Schiemann AH, Sattlegger E. Evidence that Xrn1 is in complex with Gcn1, and is required for full levels of eIF2α phosphorylation. Biochem J 2024; 481:481-498. [PMID: 38440860 PMCID: PMC11088878 DOI: 10.1042/bcj20220531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/04/2024] [Accepted: 03/05/2024] [Indexed: 03/06/2024]
Abstract
The protein kinase Gcn2 and its effector protein Gcn1 are part of the general amino acid control signalling (GAAC) pathway best known in yeast for its function in maintaining amino acid homeostasis. Under amino acid limitation, Gcn2 becomes activated, subsequently increasing the levels of phosphorylated eIF2α (eIF2α-P). This leads to the increased translation of transcriptional regulators, such as Gcn4 in yeast and ATF4 in mammals, and subsequent re-programming of the cell's gene transcription profile, thereby allowing cells to cope with starvation. Xrn1 is involved in RNA decay, quality control and processing. We found that Xrn1 co-precipitates Gcn1 and Gcn2, suggesting that these three proteins are in the same complex. Growth under starvation conditions was dependent on Xrn1 but not on Xrn1-ribosome association, and this correlated with reduced eIF2α-P levels. Constitutively active Gcn2 leads to a growth defect due to eIF2α-hyperphosphorylation, and we found that this phenotype was independent of Xrn1, suggesting that xrn1 deletion does not enhance eIF2α de-phosphorylation. Our study provides evidence that Xrn1 is required for efficient Gcn2 activation, directly or indirectly. Thus, we have uncovered a potential new link between RNA metabolism and the GAAC.
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Affiliation(s)
- Renuka Shanmugam
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Reuben Anderson
- School of Natural Sciences, Massey University, Auckland, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Anja H. Schiemann
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Evelyn Sattlegger
- School of Natural Sciences, Massey University, Auckland, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Maurice Wilkins Centre for Molecular BioDiscovery, Massey University, Palmerston North, New Zealand
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12
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Ryoo HD. The integrated stress response in metabolic adaptation. J Biol Chem 2024; 300:107151. [PMID: 38462161 PMCID: PMC10998230 DOI: 10.1016/j.jbc.2024.107151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/28/2024] [Accepted: 03/03/2024] [Indexed: 03/12/2024] Open
Abstract
The integrated stress response (ISR) refers to signaling pathways initiated by stress-activated eIF2α kinases. Distinct eIF2α kinases respond to different stress signals, including amino acid deprivation and mitochondrial stress. Such stress-induced eIF2α phosphorylation attenuates general mRNA translation and, at the same time, stimulates the preferential translation of specific downstream factors to orchestrate an adaptive gene expression program. In recent years, there have been significant new advances in our understanding of ISR during metabolic stress adaptation. Here, I discuss those advances, reviewing among others the ISR activation mechanisms in response to amino acid deprivation and mitochondrial stress. In addition, I review how ISR regulates the amino acid metabolic pathways and how changes in the ISR impact the physiology and pathology of various disease models.
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Affiliation(s)
- Hyung Don Ryoo
- Department of Cell Biology, New York University Grossman School of Medicine, New York, New York, USA.
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13
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Mariner BL, Rodriguez AS, Heath OC, McCormick MA. Induction of proteasomal activity in mammalian cells by lifespan-extending tRNA synthetase inhibitors. GeroScience 2024; 46:1755-1773. [PMID: 37749371 PMCID: PMC10828360 DOI: 10.1007/s11357-023-00938-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
We have recently shown that multiple tRNA synthetase inhibitors can greatly increase lifespan in multiple models by acting through the conserved transcription factor ATF4. Here, we show that these compounds, and several others of the same class, can greatly upregulate mammalian ATF4 in cells in vitro, in a dose dependent manner. Further, RNASeq analysis of these cells pointed toward changes in protein turnover. In subsequent experiments here we show that multiple tRNA synthetase inhibitors can greatly upregulate activity of the ubiquitin proteasome system (UPS) in cells in an ATF4-dependent manner. The UPS plays an important role in the turnover of many damaged or dysfunctional proteins in an organism. Increasing UPS activity has been shown to enhance the survival of Huntington's disease cell models, but there are few known pharmacological enhancers of the UPS. Additionally, we see separate ATF4 dependent upregulation of macroautophagy upon treatment with tRNA synthetase inhibitors. Protein degradation is an essential cellular process linked to many important human diseases of aging such as Alzheimer's disease and Huntington's disease. These drugs' ability to enhance proteostasis more broadly could have wide-ranging implications in the treatment of important age-related neurodegenerative diseases.
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Affiliation(s)
- Blaise L Mariner
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, Albuquerque, NM, 87131, USA
| | - Antonio S Rodriguez
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Olivia C Heath
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Mark A McCormick
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, Albuquerque, NM, 87131, USA.
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14
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Grmai L, Michaca M, Lackner E, Nampoothiri V P N, Vasudevan D. Integrated stress response signaling acts as a metabolic sensor in fat tissues to regulate oocyte maturation and ovulation. Cell Rep 2024; 43:113863. [PMID: 38457339 DOI: 10.1016/j.celrep.2024.113863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 11/23/2023] [Accepted: 02/08/2024] [Indexed: 03/10/2024] Open
Abstract
Reproduction is an energy-intensive process requiring systemic coordination. However, the inter-organ signaling mechanisms that relay nutrient status to modulate reproductive output are poorly understood. Here, we use Drosophila melanogaster as a model to establish the integrated stress response (ISR) transcription factor, Atf4, as a fat tissue metabolic sensor that instructs oogenesis. We demonstrate that Atf4 regulates lipase activity to mediate yolk lipoprotein synthesis in the fat body. Depletion of Atf4 in the fat body also blunts oogenesis recovery after amino acid deprivation and re-feeding, suggestive of a nutrient-sensing role for Atf4. We also discovered that Atf4 promotes secretion of a fat-body-derived neuropeptide, CNMamide, which modulates neural circuits that promote egg-laying behavior (ovulation). Thus, we posit that ISR signaling in fat tissue acts as a "metabolic sensor" that instructs female reproduction-directly by impacting yolk lipoprotein production and follicle maturation and systemically by regulating ovulation.
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Affiliation(s)
- Lydia Grmai
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, USA
| | - Manuel Michaca
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Emily Lackner
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Deepika Vasudevan
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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15
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Inada T, Beckmann R. Mechanisms of Translation-coupled Quality Control. J Mol Biol 2024; 436:168496. [PMID: 38365086 DOI: 10.1016/j.jmb.2024.168496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
Stalling of ribosomes engaged in protein synthesis can lead to significant defects in the function of newly synthesized proteins and thereby impair protein homeostasis. Consequently, partially synthesized polypeptides resulting from translation stalling are recognized and eliminated by several quality control mechanisms. First, if translation elongation reactions are halted prematurely, a quality control mechanism called ribosome-associated quality control (RQC) initiates the ubiquitination of the nascent polypeptide chain and subsequent proteasomal degradation. Additionally, when ribosomes with defective codon recognition or peptide-bond formation stall during translation, a quality control mechanism known as non-functional ribosomal RNA decay (NRD) leads to the degradation of malfunctioning ribosomes. In both of these quality control mechanisms, E3 ubiquitin ligases selectively recognize ribosomes in distinct translation-stalling states and ubiquitinate specific ribosomal proteins. Significant efforts have been devoted to characterize E3 ubiquitin ligase sensing of ribosome 'collision' or 'stalling' and subsequent ribosome is rescued. This article provides an overview of our current understanding of the molecular mechanisms and physiological functions of ribosome dynamics control and quality control of abnormal translation.
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Affiliation(s)
- Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku, Tokyo 108-8639, Japan.
| | - Roland Beckmann
- Gene Center and Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany.
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16
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Padhiar NH, Katneni U, Komar AA, Motorin Y, Kimchi-Sarfaty C. Advances in methods for tRNA sequencing and quantification. Trends Genet 2024; 40:276-290. [PMID: 38123442 DOI: 10.1016/j.tig.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/23/2023]
Abstract
In the past decade tRNA sequencing (tRNA-seq) has attracted considerable attention as an important tool for the development of novel approaches to quantify highly modified tRNA species and to propel tRNA research aimed at understanding the cellular physiology and disease and development of tRNA-based therapeutics. Many methods are available to quantify tRNA abundance while accounting for modifications and tRNA charging/acylation. Advances in both library preparation methods and bioinformatic workflows have enabled developments in next-generation sequencing (NGS) workflows. Other approaches forgo NGS applications in favor of hybridization-based approaches. In this review we provide a brief comparative overview of various tRNA quantification approaches, focusing on the advantages and disadvantages of these methods, which together facilitate reliable tRNA quantification.
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Affiliation(s)
- Nigam H Padhiar
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Upendra Katneni
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Anton A Komar
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - Yuri Motorin
- CNRS-Université de Lorraine, UAR 2008, IBSLor UMR 7365 IMoPA, Nancy, France.
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
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17
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Misra J, Carlson KR, Spandau DF, Wek RC. Multiple mechanisms activate GCN2 eIF2 kinase in response to diverse stress conditions. Nucleic Acids Res 2024; 52:1830-1846. [PMID: 38281137 PMCID: PMC10899773 DOI: 10.1093/nar/gkae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024] Open
Abstract
Diverse environmental insults induce the integrated stress response (ISR), which features eIF2 phosphorylation and translational control that serves to restore protein homeostasis. The eIF2 kinase GCN2 is a first responder in the ISR that is activated by amino acid depletion and other stresses not directly related to nutrients. Two mechanisms are suggested to trigger an ordered process of GCN2 activation during stress: GCN2 monitoring stress via accumulating uncharged tRNAs or by stalled and colliding ribosomes. Our results suggest that while ribosomal collisions are indeed essential for GCN2 activation in response to translational elongation inhibitors, conditions that trigger deacylation of tRNAs activate GCN2 via its direct association with affected tRNAs. Both mechanisms require the GCN2 regulatory domain related to histidyl tRNA synthetases. GCN2 activation by UV irradiation features lowered amino acids and increased uncharged tRNAs and UV-induced ribosome collisions are suggested to be dispensable. We conclude that there are multiple mechanisms that activate GCN2 during diverse stresses.
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Affiliation(s)
- Jagannath Misra
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4067 Indianapolis, Indiana 46202, USA
| | - Kenneth R Carlson
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4067 Indianapolis, Indiana 46202, USA
| | - Dan F Spandau
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4067 Indianapolis, Indiana 46202, USA
- Department of Dermatology, Indiana University School of Medicine, 635 Barnhill Drive, MS4067 Indianapolis, Indiana 46202, USA
- Richard L. Roudebush Veterans Administration Medical Center, Indiana University School of Medicine, 635 Barnhill Drive, MS4067 Indianapolis, Indiana 46202, USA
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4067 Indianapolis, Indiana 46202, USA
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18
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Williams TD, Rousseau A. Translation regulation in response to stress. FEBS J 2024. [PMID: 38308808 DOI: 10.1111/febs.17076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024]
Abstract
Cell stresses occur in a wide variety of settings: in disease, during industrial processes, and as part of normal day-to-day rhythms. Adaptation to these stresses requires cells to alter their proteome. Cells modify the proteins they synthesize to aid proteome adaptation. Changes in both mRNA transcription and translation contribute to altered protein synthesis. Here, we discuss the changes in translational mechanisms that occur following the onset of stress, and the impact these have on stress adaptation.
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Affiliation(s)
- Thomas D Williams
- MRC-PPU, School of Life Sciences, University of Dundee, UK
- Sir William Dunn School of Pathology, University of Oxford, UK
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19
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Yoo JS. Cellular Stress Responses against Coronavirus Infection: A Means of the Innate Antiviral Defense. J Microbiol Biotechnol 2024; 34:1-9. [PMID: 37674398 PMCID: PMC10840489 DOI: 10.4014/jmb.2307.07038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/20/2023] [Accepted: 09/06/2023] [Indexed: 09/08/2023]
Abstract
Cellular stress responses are crucial for maintaining cellular homeostasis. Stress granules (SGs), activated by eIF2α kinases in response to various stimuli, play a pivotal role in dealing with diverse stress conditions. Viral infection, as one kind of cellular stress, triggers specific cellular programs aimed at overcoming virus-induced stresses. Recent studies have revealed that virus-derived stress responses are tightly linked to the host's antiviral innate immunity. Virus infection-induced SGs act as platforms for antiviral sensors, facilitating the initiation of protective antiviral responses called "antiviral stress granules" (avSGs). However, many viruses, including coronaviruses, have evolved strategies to suppress avSG formation, thereby counteracting the host's immune responses. This review discusses the intricate relationship between cellular stress responses and antiviral innate immunity, with a specific focus on coronaviruses. Furthermore, the diverse mechanisms employed by viruses to counteract avSGs are described.
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Affiliation(s)
- Ji-Seung Yoo
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
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20
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Zhang J. Recognition of the tRNA structure: Everything everywhere but not all at once. Cell Chem Biol 2024; 31:36-52. [PMID: 38159570 PMCID: PMC10843564 DOI: 10.1016/j.chembiol.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/02/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
tRNAs are among the most abundant and essential biomolecules in cells. These spontaneously folding, extensively structured yet conformationally flexible anionic polymers literally bridge the worlds of RNAs and proteins, and serve as Rosetta stones that decipher and interpret the genetic code. Their ubiquitous presence, functional irreplaceability, and privileged access to cellular compartments and ribosomes render them prime targets for both endogenous regulation and exogenous manipulation. There is essentially no part of the tRNA that is not touched by another interaction partner, either as programmed or imposed by an external adversary. Recent progresses in genetic, biochemical, and structural analyses of the tRNA interactome produced a wealth of new knowledge into their interaction networks, regulatory functions, and molecular interfaces. In this review, I describe and illustrate the general principles of tRNA recognition by proteins and other RNAs, and discuss the underlying molecular mechanisms that deliver affinity, specificity, and functional competency.
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Affiliation(s)
- Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
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21
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Stryapunina I, Itoe MA, Trinh Q, Vidoudez C, Du E, Mendoza L, Hulai O, Kauffman J, Carew J, Shaw WR, Catteruccia F. Precise coordination between nutrient transporters ensures fertility in the malaria mosquito Anopheles gambiae. PLoS Genet 2024; 20:e1011145. [PMID: 38285728 PMCID: PMC10852252 DOI: 10.1371/journal.pgen.1011145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 02/08/2024] [Accepted: 01/20/2024] [Indexed: 01/31/2024] Open
Abstract
Females from many mosquito species feed on blood to acquire nutrients for egg development. The oogenetic cycle has been characterized in the arboviral vector Aedes aegypti, where after a bloodmeal, the lipid transporter lipophorin (Lp) shuttles lipids from the midgut and fat body to the ovaries, and a yolk precursor protein, vitellogenin (Vg), is deposited into the oocyte by receptor-mediated endocytosis. Our understanding of how the roles of these two nutrient transporters are mutually coordinated is however limited in this and other mosquito species. Here, we demonstrate that in the malaria mosquito Anopheles gambiae, Lp and Vg are reciprocally regulated in a timely manner to optimize egg development and ensure fertility. Defective lipid transport via Lp knockdown triggers abortive ovarian follicle development, leading to misregulation of Vg and aberrant yolk granules. Conversely, depletion of Vg causes an upregulation of Lp in the fat body in a manner that appears to be at least partially dependent on target of rapamycin (TOR) signaling, resulting in excess lipid accumulation in the developing follicles. Embryos deposited by Vg-depleted mothers are completely inviable, and are arrested early during development, likely due to severely reduced amino acid levels and protein synthesis. Our findings demonstrate that the mutual regulation of these two nutrient transporters is essential to safeguard fertility by ensuring correct nutrient balance in the developing oocyte, and validate Vg and Lp as two potential candidates for mosquito control.
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Affiliation(s)
- Iryna Stryapunina
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Maurice A. Itoe
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Queenie Trinh
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Charles Vidoudez
- Harvard Center for Mass Spectrometry, Cambridge, Massachusetts, United States of America
| | - Esrah Du
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Lydia Mendoza
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Oleksandr Hulai
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Jamie Kauffman
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - John Carew
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - W. Robert Shaw
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Flaminia Catteruccia
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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22
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Rong Y, Darnell AM, Sapp KM, Vander Heiden MG, Spencer SL. Cells use multiple mechanisms for cell-cycle arrest upon withdrawal of individual amino acids. Cell Rep 2023; 42:113539. [PMID: 38070134 PMCID: PMC11238304 DOI: 10.1016/j.celrep.2023.113539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/29/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023] Open
Abstract
Amino acids are required for cell growth and proliferation, but it remains unclear when and how amino acid availability impinges on the proliferation-quiescence decision. Here, we used time-lapse microscopy and single-cell tracking of cyclin-dependent kinase 2 (CDK2) activity to assess the response of individual cells to withdrawal of single amino acids and found strikingly different cell-cycle effects depending on the amino acid. For example, upon leucine withdrawal, MCF10A cells complete two cell cycles and then enter a CDK2-low quiescence, whereas lysine withdrawal causes immediate cell-cycle stalling. Methionine withdrawal triggers a restriction point phenotype similar to serum starvation or Mek inhibition: upon methionine withdrawal, cells complete their current cell cycle and enter a CDK2-low quiescence after mitosis. Modulation of restriction point regulators p21/p27 or cyclin D1 enables short-term rescue of proliferation under methionine and leucine withdrawal, and to a lesser extent lysine withdrawal, revealing a checkpoint connecting nutrient signaling to cell-cycle entry.
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Affiliation(s)
- Yao Rong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kiera M Sapp
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute, Cambridge, MA 02139, USA
| | - Sabrina L Spencer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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23
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Boone M, Zappa F. Signaling plasticity in the integrated stress response. Front Cell Dev Biol 2023; 11:1271141. [PMID: 38143923 PMCID: PMC10740175 DOI: 10.3389/fcell.2023.1271141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/29/2023] [Indexed: 12/26/2023] Open
Abstract
The Integrated Stress Response (ISR) is an essential homeostatic signaling network that controls the cell's biosynthetic capacity. Four ISR sensor kinases detect multiple stressors and relay this information to downstream effectors by phosphorylating a common node: the alpha subunit of the eukaryotic initiation factor eIF2. As a result, general protein synthesis is repressed while select transcripts are preferentially translated, thus remodeling the proteome and transcriptome. Mounting evidence supports a view of the ISR as a dynamic signaling network with multiple modulators and feedback regulatory features that vary across cell and tissue types. Here, we discuss updated views on ISR sensor kinase mechanisms, how the subcellular localization of ISR components impacts signaling, and highlight ISR signaling differences across cells and tissues. Finally, we consider crosstalk between the ISR and other signaling pathways as a determinant of cell health.
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24
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Ge MK, Zhang C, Zhang N, He P, Cai HY, Li S, Wu S, Chu XL, Zhang YX, Ma HM, Xia L, Yang S, Yu JX, Yao SY, Zhou XL, Su B, Chen GQ, Shen SM. The tRNA-GCN2-FBXO22-axis-mediated mTOR ubiquitination senses amino acid insufficiency. Cell Metab 2023; 35:2216-2230.e8. [PMID: 37979583 DOI: 10.1016/j.cmet.2023.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 07/26/2023] [Accepted: 10/26/2023] [Indexed: 11/20/2023]
Abstract
Mammalian target of rapamycin complex 1 (mTORC1) monitors cellular amino acid changes for function, but the molecular mediators of this process remain to be fully defined. Here, we report that depletion of cellular amino acids, either alone or in combination, leads to the ubiquitination of mTOR, which inhibits mTORC1 kinase activity by preventing substrate recruitment. Mechanistically, amino acid depletion causes accumulation of uncharged tRNAs, thereby stimulating GCN2 to phosphorylate FBXO22, which in turn accrues in the cytoplasm and ubiquitinates mTOR at Lys2066 in a K27-linked manner. Accordingly, mutation of mTOR Lys2066 abolished mTOR ubiquitination in response to amino acid depletion, rendering mTOR insensitive to amino acid starvation both in vitro and in vivo. Collectively, these data reveal a novel mechanism of amino acid sensing by mTORC1 via a previously unknown GCN2-FBXO22-mTOR pathway that is uniquely controlled by uncharged tRNAs.
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Affiliation(s)
- Meng-Kai Ge
- Institute of Aging & Tissue Regeneration, State Key Laboratory of Systems Medicine for Cancer and Stress and Cancer Research Unit of Chinese Academy of Medical Sciences (No. 2019RU043), Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200127, China; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Cheng Zhang
- Institute of Aging & Tissue Regeneration, State Key Laboratory of Systems Medicine for Cancer and Stress and Cancer Research Unit of Chinese Academy of Medical Sciences (No. 2019RU043), Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200127, China
| | - Na Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Ping He
- Institute of Aging & Tissue Regeneration, State Key Laboratory of Systems Medicine for Cancer and Stress and Cancer Research Unit of Chinese Academy of Medical Sciences (No. 2019RU043), Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200127, China
| | - Hai-Yan Cai
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Song Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, SJTU-SM, Shanghai 200025, China
| | - Shuai Wu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Xi-Li Chu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Yu-Xue Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Hong-Ming Ma
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Li Xia
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Shuo Yang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Jian-Xiu Yu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Shi-Ying Yao
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bing Su
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, SJTU-SM, Shanghai 200025, China.
| | - Guo-Qiang Chen
- Institute of Aging & Tissue Regeneration, State Key Laboratory of Systems Medicine for Cancer and Stress and Cancer Research Unit of Chinese Academy of Medical Sciences (No. 2019RU043), Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200127, China; Hainan Academy of Medical Sciences, Hainan Medical University, Hainan 571199, China.
| | - Shao-Ming Shen
- Institute of Aging & Tissue Regeneration, State Key Laboratory of Systems Medicine for Cancer and Stress and Cancer Research Unit of Chinese Academy of Medical Sciences (No. 2019RU043), Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200127, China; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China.
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25
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Kuhle B, Chen Q, Schimmel P. tRNA renovatio: Rebirth through fragmentation. Mol Cell 2023; 83:3953-3971. [PMID: 37802077 PMCID: PMC10841463 DOI: 10.1016/j.molcel.2023.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023]
Abstract
tRNA function is based on unique structures that enable mRNA decoding using anticodon trinucleotides. These structures interact with specific aminoacyl-tRNA synthetases and ribosomes using 3D shape and sequence signatures. Beyond translation, tRNAs serve as versatile signaling molecules interacting with other RNAs and proteins. Through evolutionary processes, tRNA fragmentation emerges as not merely random degradation but an act of recreation, generating specific shorter molecules called tRNA-derived small RNAs (tsRNAs). These tsRNAs exploit their linear sequences and newly arranged 3D structures for unexpected biological functions, epitomizing the tRNA "renovatio" (from Latin, meaning renewal, renovation, and rebirth). Emerging methods to uncover full tRNA/tsRNA sequences and modifications, combined with techniques to study RNA structures and to integrate AI-powered predictions, will enable comprehensive investigations of tRNA fragmentation products and new interaction potentials in relation to their biological functions. We anticipate that these directions will herald a new era for understanding biological complexity and advancing pharmaceutical engineering.
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Affiliation(s)
- Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA; Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Qi Chen
- Molecular Medicine Program, Department of Human Genetics, and Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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26
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Iyer KV, Müller M, Tittel LS, Winz ML. Molecular Highway Patrol for Ribosome Collisions. Chembiochem 2023; 24:e202300264. [PMID: 37382189 DOI: 10.1002/cbic.202300264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
During translation, messenger RNAs (mRNAs) are decoded by ribosomes which can stall for various reasons. These include chemical damage, codon composition, starvation, or translation inhibition. Trailing ribosomes can collide with stalled ribosomes, potentially leading to dysfunctional or toxic proteins. Such aberrant proteins can form aggregates and favor diseases, especially neurodegeneration. To prevent this, both eukaryotes and bacteria have evolved different pathways to remove faulty nascent peptides, mRNAs and defective ribosomes from the collided complex. In eukaryotes, ubiquitin ligases play central roles in triggering downstream responses and several complexes have been characterized that split affected ribosomes and facilitate degradation of the various components. As collided ribosomes signal translation stress to affected cells, in eukaryotes additional stress response pathways are triggered when collisions are sensed. These pathways inhibit translation and modulate cell survival and immune responses. Here, we summarize the current state of knowledge about rescue and stress response pathways triggered by ribosome collisions.
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Affiliation(s)
- Kaushik Viswanathan Iyer
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Max Müller
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Lena Sophie Tittel
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Marie-Luise Winz
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
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27
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Sniegowski T, Rajasekaran D, Sennoune SR, Sunitha S, Chen F, Fokar M, Kshirsagar S, Reddy PH, Korac K, Mahmud Syed M, Sharker T, Ganapathy V, Bhutia YD. Amino acid transporter SLC38A5 is a tumor promoter and a novel therapeutic target for pancreatic cancer. Sci Rep 2023; 13:16863. [PMID: 37803043 PMCID: PMC10558479 DOI: 10.1038/s41598-023-43983-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/01/2023] [Indexed: 10/08/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) cells have a great demand for nutrients in the form of sugars, amino acids, and lipids. Particularly, amino acids are critical for cancer growth and, as intermediates, connect glucose, lipid and nucleotide metabolism. PDAC cells meet these requirements by upregulating selective amino acid transporters. Here we show that SLC38A5 (SN2/SNAT5), a neutral amino acid transporter is highly upregulated and functional in PDAC cells. Using CRISPR/Cas9-mediated knockout of SLC38A5, we show its tumor promoting role in an in vitro cell line model as well as in a subcutaneous xenograft mouse model. Using metabolomics and RNA sequencing, we show significant reduction in many amino acid substrates of SLC38A5 as well as OXPHOS inactivation in response to SLC38A5 deletion. Experimental validation demonstrates inhibition of mTORC1, glycolysis and mitochondrial respiration in KO cells, suggesting a serious metabolic crisis associated with SLC38A5 deletion. Since many SLC38A5 substrates are activators of mTORC1 as well as TCA cycle intermediates/precursors, we speculate amino acid insufficiency as a possible link between SLC38A5 deletion and inactivation of mTORC1, glycolysis and mitochondrial respiration, and the underlying mechanism for PDAC attenuation. Overall, we show that SLC38A5 promotes PDAC, thereby identifying a novel, hitherto unknown, therapeutic target for PDAC.
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Affiliation(s)
- Tyler Sniegowski
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Devaraja Rajasekaran
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Souad R Sennoune
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Sukumaran Sunitha
- Center for Biotechnology & Genomics, Texas Tech University, Lubbock, TX, 79409, USA
| | - Fang Chen
- Center for Biotechnology & Genomics, Texas Tech University, Lubbock, TX, 79409, USA
| | - Mohamed Fokar
- Center for Biotechnology & Genomics, Texas Tech University, Lubbock, TX, 79409, USA
| | - Sudhir Kshirsagar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Ksenija Korac
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Mosharaf Mahmud Syed
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Tanima Sharker
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Vadivel Ganapathy
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Yangzom D Bhutia
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.
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28
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Loxha L, Ibrahim NK, Stasche AS, Cinar B, Dolgner T, Niessen J, Schreek S, Fehlhaber B, Forster M, Stanulla M, Hinze L. GSK3α Regulates Temporally Dynamic Changes in Ribosomal Proteins upon Amino Acid Starvation in Cancer Cells. Int J Mol Sci 2023; 24:13260. [PMID: 37686063 PMCID: PMC10488213 DOI: 10.3390/ijms241713260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Amino acid availability is crucial for cancer cells' survivability. Leukemia and colorectal cancer cells have been shown to resist asparagine depletion by utilizing GSK3-dependent proteasomal degradation, termed the Wnt-dependent stabilization of proteins (Wnt/STOP), to replenish their amino acid pool. The inhibition of GSK3α halts the sourcing of amino acids, which subsequently leads to cancer cell vulnerability toward asparaginase therapy. However, resistance toward GSK3α-mediated protein breakdown can occur, whose underlying mechanism is poorly understood. Here, we set out to define the mechanisms driving dependence toward this degradation machinery upon asparagine starvation in cancer cells. We show the independence of known stress response pathways including the integrated stress response mediated with GCN2. Additionally, we demonstrate the independence of changes in cell cycle progression and expression levels of the asparagine-synthesizing enzyme ASNS. Instead, RNA sequencing revealed that GSK3α inhibition and asparagine starvation leads to the temporally dynamic downregulation of distinct ribosomal proteins, which have been shown to display anti-proliferative functions. Using a CRISPR/Cas9 viability screen, we demonstrate that the downregulation of these specific ribosomal proteins can rescue cell death upon GSK3α inhibition and asparagine starvation. Thus, our findings suggest the vital role of the previously unrecognized regulation of ribosomal proteins in bridging GSK3α activity and tolerance of asparagine starvation.
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Affiliation(s)
- Lorent Loxha
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Nurul Khalida Ibrahim
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Anna Sophie Stasche
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Büsra Cinar
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Tim Dolgner
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Julia Niessen
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Sabine Schreek
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Beate Fehlhaber
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Michael Forster
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany;
| | - Martin Stanulla
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Laura Hinze
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
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29
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Lamichhane PP, Samir P. Cellular Stress: Modulator of Regulated Cell Death. BIOLOGY 2023; 12:1172. [PMID: 37759572 PMCID: PMC10525759 DOI: 10.3390/biology12091172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023]
Abstract
Cellular stress response activates a complex program of an adaptive response called integrated stress response (ISR) that can allow a cell to survive in the presence of stressors. ISR reprograms gene expression to increase the transcription and translation of stress response genes while repressing the translation of most proteins to reduce the metabolic burden. In some cases, ISR activation can lead to the assembly of a cytoplasmic membraneless compartment called stress granules (SGs). ISR and SGs can inhibit apoptosis, pyroptosis, and necroptosis, suggesting that they guard against uncontrolled regulated cell death (RCD) to promote organismal homeostasis. However, ISR and SGs also allow cancer cells to survive in stressful environments, including hypoxia and during chemotherapy. Therefore, there is a great need to understand the molecular mechanism of the crosstalk between ISR and RCD. This is an active area of research and is expected to be relevant to a range of human diseases. In this review, we provided an overview of the interplay between different cellular stress responses and RCD pathways and their modulation in health and disease.
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Affiliation(s)
| | - Parimal Samir
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
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30
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Wek RC, Anthony TG, Staschke KA. Surviving and Adapting to Stress: Translational Control and the Integrated Stress Response. Antioxid Redox Signal 2023; 39:351-373. [PMID: 36943285 PMCID: PMC10443206 DOI: 10.1089/ars.2022.0123] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/23/2023]
Abstract
Significance: Organisms adapt to changing environments by engaging cellular stress response pathways that serve to restore proteostasis and enhance survival. A primary adaptive mechanism is the integrated stress response (ISR), which features phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2). Four eIF2α kinases respond to different stresses, enabling cells to rapidly control translation to optimize management of resources and reprogram gene expression for stress adaptation. Phosphorylation of eIF2 blocks its guanine nucleotide exchange factor, eIF2B, thus lowering the levels of eIF2 bound to GTP that is required to deliver initiator transfer RNA (tRNA) to ribosomes. While bulk messenger RNA (mRNA) translation can be sharply lowered by heightened phosphorylation of eIF2α, there are other gene transcripts whose translation is unchanged or preferentially translated. Among the preferentially translated genes is ATF4, which directs transcription of adaptive genes in the ISR. Recent Advances and Critical Issues: This review focuses on how eIF2α kinases function as first responders of stress, the mechanisms by which eIF2α phosphorylation and other stress signals regulate the exchange activity of eIF2B, and the processes by which the ISR triggers differential mRNA translation. To illustrate the synergy between stress pathways, we describe the mechanisms and functional significance of communication between the ISR and another key regulator of translation, mammalian/mechanistic target of rapamycin complex 1 (mTORC1), during acute and chronic amino acid insufficiency. Finally, we discuss the pathological conditions that stem from aberrant regulation of the ISR, as well as therapeutic strategies targeting the ISR to alleviate disease. Future Directions: Important topics for future ISR research are strategies for modulating this stress pathway in disease conditions and drug development, molecular processes for differential translation and the coordinate regulation of GCN2 and other stress pathways during physiological and pathological conditions. Antioxid. Redox Signal. 39, 351-373.
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Affiliation(s)
- Ronald C. Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, USA
| | - Tracy G. Anthony
- Department of Nutritional Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Kirk A. Staschke
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, USA
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31
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Jones JA, Wei N, Cui H, Shi Y, Fu G, Rauniyar N, Shapiro R, Morodomi Y, Berenst N, Dumitru CD, Kanaji S, Yates JR, Kanaji T, Yang XL. Nuclear translocation of an aminoacyl-tRNA synthetase may mediate a chronic "integrated stress response". Cell Rep 2023; 42:112632. [PMID: 37314928 PMCID: PMC10592355 DOI: 10.1016/j.celrep.2023.112632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 04/24/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
Various stress conditions are signaled through phosphorylation of translation initiation factor eukaryotic initiation factor 2α (eIF2α) to inhibit global translation while selectively activating transcription factor ATF4 to aid cell survival and recovery. However, this integrated stress response is acute and cannot resolve lasting stress. Here, we report that tyrosyl-tRNA synthetase (TyrRS), a member of the aminoacyl-tRNA synthetase family that responds to diverse stress conditions through cytosol-nucleus translocation to activate stress-response genes, also inhibits global translation. However, it occurs at a later stage than eIF2α/ATF4 and mammalian target of rapamycin (mTOR) responses. Excluding TyrRS from the nucleus over-activates translation and increases apoptosis in cells under prolonged oxidative stress. Nuclear TyrRS transcriptionally represses translation genes by recruiting TRIM28 and/or NuRD complex. We propose that TyrRS, possibly along with other family members, can sense a variety of stress signals through intrinsic properties of this enzyme and strategically located nuclear localization signal and integrate them by nucleus translocation to effect protective responses against chronic stress.
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Affiliation(s)
- Julia A Jones
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Na Wei
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Haissi Cui
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yi Shi
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Guangsen Fu
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Navin Rauniyar
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan Shapiro
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yosuke Morodomi
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nadine Berenst
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Calin Dan Dumitru
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sachiko Kanaji
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Taisuke Kanaji
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiang-Lei Yang
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.
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32
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Liang Z, Jin C, Bai H, Liang G, Su X, Wang D, Yao J. Low rumen degradable starch promotes the growth performance of goats by increasing protein synthesis in skeletal muscle via the AMPK-mTOR pathway. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2023; 13:1-8. [PMID: 36873600 PMCID: PMC9981809 DOI: 10.1016/j.aninu.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/22/2022] [Accepted: 10/04/2022] [Indexed: 11/18/2022]
Abstract
Since starch digestion in the small intestine provides more energy than digestion in the rumen of ruminants, reducing dietary rumen degradable starch (RDS) content is beneficial for improving energy utilization of starch in ruminants. The present study tested whether the reduction of rumen degradable starch by restricting dietary corn processing for growing goats could improve growth performance, and further investigated the possible underlying mechanism. In this study, twenty-four 12-wk-old goats were selected and randomly allocated to receive either a high RDS diet (HRDS, crushed corn-based concentrate, the mean of particle sizes of corn grain = 1.64 mm, n = 12) or a low RDS diet (LRDS, non-processed corn-based concentrate, the mean of particle sizes of corn grain >8 mm, n = 12). Growth performance, carcass traits, plasma biochemical indices, gene expression of glucose and amino acid transporters, and protein expression of the AMPK-mTOR pathway were measured. Compared to the HRDS, LRDS tended to increase the average daily gain (ADG, P = 0.054) and decreased the feed-to-gain ratio (F/G, P < 0.05). Furthermore, LRDS increased the net lean tissue rate (P < 0.01), protein content (P < 0.05) and total free amino acids (P < 0.05) in the biceps femoris (BF) muscle of goats. LRDS increased the glucose concentration (P < 0.01), but reduced total amino acid concentration (P < 0.05) and tended to reduce blood urea nitrogen (BUN) concentration (P = 0.062) in plasma of goats. The mRNA expression of insulin receptors (INSR), glucose transporter 4 (GLUT4), L-type amino acid transporter 1 (LAT1) and 4F2 heavy chain (4F2hc) in BF muscle, and sodium-glucose cotransporters 1 (SGLT1) and glucose transporter 2 (GLUT2) in the small intestine were significantly increased (P < 0.05) in LRDS goats. LRDS also led to marked activation of p70-S6 kinase (S6K) (P < 0.05), but lower activation of AMP-activated protein kinase (AMPK) (P < 0.05) and eukaryotic initiation factor 2α (P < 0.01). Our findings suggested that reducing the content of dietary RDS enhanced postruminal starch digestion and increased plasma glucose, thereby improving amino acid utilization and promoting protein synthesis in the skeletal muscle of goats via the AMPK-mTOR pathway. These changes may contribute to improvement in growth performance and carcass traits in LRDS goats.
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Affiliation(s)
- Ziqi Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chunjia Jin
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hanxun Bai
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Gaofeng Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiaodong Su
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Dangdang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
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33
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Lee LMY, Lin ZQ, Zheng LX, Tu YF, So YH, Zheng XH, Feng TJ, Wang XY, Wong WT, Leung YC. Lysine Deprivation Suppresses Adipogenesis in 3T3-L1 Cells: A Transcriptome Analysis. Int J Mol Sci 2023; 24:ijms24119402. [PMID: 37298352 DOI: 10.3390/ijms24119402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Growing evidence proves that amino acid restriction can reverse obesity by reducing adipose tissue mass. Amino acids are not only the building blocks of proteins but also serve as signaling molecules in multiple biological pathways. The study of adipocytes' response to amino acid level changes is crucial. It has been reported that a low concentration of lysine suppresses lipid accumulation and transcription of several adipogenic genes in 3T3-L1 preadipocytes. However, the detailed lysine-deprivation-induced cellular transcriptomic changes and the altered pathways have yet to be fully studied. Here, using 3T3-L1 cells, we performed RNA sequencing on undifferentiated and differentiated cells, and differentiated cells under a lysine-free environment, and the data were subjected to KEGG enrichment. We found that the differentiation process of 3T3-L1 cells to adipocytes required the large-scale upregulation of metabolic pathways, mainly on the mitochondrial TCA cycle, oxidative phosphorylation, and downregulation of the lysosomal pathway. Single amino acid lysine depletion suppressed differentiation dose dependently. It disrupted the metabolism of cellular amino acids, which could be partially reflected in the changes in amino acid levels in the culture medium. It inhibited the mitochondria respiratory chain and upregulated the lysosomal pathway, which are essential for adipocyte differentiation. We also noticed that cellular interleukin 6 (IL6) expression and medium IL6 level were dramatically increased, which was one of the targets for suppressing adipogenesis induced by lysine depletion. Moreover, we showed that the depletion of some essential amino acids such as methionine and cystine could induce similar phenomena. This suggests that individual amino acid deprivation may share some common pathways. This descriptive study dissects the pathways for adipogenesis and how the cellular transcriptome was altered under lysine depletion.
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Affiliation(s)
- Leo Man-Yuen Lee
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- Lo Ka Chung Research Centre for Natural Anti-Cancer Drug Development and State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- School of Biomedical Science, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong, China
| | - Zhi-Qiang Lin
- School of Biomedical Science, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong, China
| | - Lu-Xi Zheng
- School of Biomedical Science, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong, China
| | - Yi-Fan Tu
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- Lo Ka Chung Research Centre for Natural Anti-Cancer Drug Development and State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, New Territory, Hong Kong, China
| | - Yik-Hing So
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- Lo Ka Chung Research Centre for Natural Anti-Cancer Drug Development and State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Xiu-Hua Zheng
- School of Biomedical Science, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong, China
| | - Tie-Jun Feng
- School of Biomedical Science, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong, China
| | - Xi-Yue Wang
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen 518000, China
| | - Wai-Ting Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yun-Chung Leung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- Lo Ka Chung Research Centre for Natural Anti-Cancer Drug Development and State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
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34
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Hurtig JE, van Hoof A. An unknown essential function of tRNA splicing endonuclease is linked to the integrated stress response and intron debranching. Genetics 2023; 224:iyad044. [PMID: 36943791 PMCID: PMC10213494 DOI: 10.1093/genetics/iyad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 10/31/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
tRNA splicing endonuclease (TSEN) has a well-characterized role in transfer RNA (tRNA) splicing but also other functions. For yeast TSEN, these other functions include degradation of a subset of mRNAs that encode mitochondrial proteins and an unknown essential function. In this study, we use yeast genetics to characterize the unknown tRNA-independent function(s) of TSEN. Using a high-copy suppressor screen, we found that sen2 mutants can be suppressed by overexpression of SEN54. This effect was seen both for tRNA-dependent and tRNA-independent functions indicating that SEN54 is a general suppressor of sen2, likely through structural stabilization. A spontaneous suppressor screen identified mutations in the intron-debranching enzyme, Dbr1, as tRNA splicing-independent suppressors. Transcriptome analysis showed that sen2 mutation activates the Gcn4 stress response. These Gcn4 target transcripts decreased considerably in the sen2 dbr1 double mutant. We propose that Dbr1 and TSEN may compete for a shared substrate, which TSEN normally processes into an essential RNA, while Dbr1 initiates its degradation. These data provide further insight into the essential function(s) of TSEN. Importantly, single amino acid mutations in TSEN cause the generally fatal neuronal disease pontocerebellar hypoplasia (PCH). The mechanism by which defects in TSEN cause this disease is unknown, and our results reveal new possible mechanisms.
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Affiliation(s)
- Jennifer E Hurtig
- Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ambro van Hoof
- Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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35
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Gupta R, Hinnebusch AG. Differential requirements for P stalk components in activating yeast protein kinase Gcn2 by stalled ribosomes during stress. Proc Natl Acad Sci U S A 2023; 120:e2300521120. [PMID: 37043534 PMCID: PMC10120022 DOI: 10.1073/pnas.2300521120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/13/2023] [Indexed: 04/13/2023] Open
Abstract
The General Amino Acid Control is a conserved response to amino acid starvation involving activation of protein kinase Gcn2, which phosphorylates eukaryotic initiation factor 2 (eIF2α) with attendant inhibition of global protein synthesis and increased translation of yeast transcriptional activator GCN4. Gcn2 can be activated by either amino acid starvation or conditions that stall elongating ribosomes without reducing aminoacylation of tRNA, but it is unclear whether distinct molecular mechanisms operate in these two circumstances. We identified three regimes that activate Gcn2 in yeast cells by starvation-independent (SI) ribosome-stalling: treatment with tigecycline, eliminating the sole gene encoding tRNAArgUCC, and depletion of translation termination factor eRF1. We further demonstrated requirements for the tRNA- and ribosome-binding domains of Gcn2, the positive effector proteins Gcn1/Gcn20, and the tethering of at least one of two distinct P1/P2 heterodimers to the uL10 subunit of the ribosomal P stalk, for detectable activation by SI-ribosome stalling. Remarkably, no tethered P1/P2 proteins were required for strong Gcn2 activation elicited by starvation for histidine or branched-chain amino acids isoleucine/valine. These results indicate that Gcn2 activation has different requirements for the P stalk depending on how ribosomes are stalled. We propose that accumulation of deacylated tRNAs in amino acid-starved cells can functionally substitute for the P stalk in binding to the histidyl-tRNA synthetase-like domain of Gcn2 for eIF2α kinase activation by ribosomes stalled with A sites devoid of the eEF1A∙GTP∙aminoacyl-tRNA ternary complex.
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Affiliation(s)
- Ritu Gupta
- Section on Nutrient Control of Gene Expression, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD20892
| | - Alan G. Hinnebusch
- Section on Nutrient Control of Gene Expression, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD20892
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36
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Carlson KR, Georgiadis MM, Tameire F, Staschke KA, Wek RC. Activation of Gcn2 by small molecules designed to be inhibitors. J Biol Chem 2023; 299:104595. [PMID: 36898579 PMCID: PMC10124904 DOI: 10.1016/j.jbc.2023.104595] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/06/2023] [Indexed: 03/10/2023] Open
Abstract
The integrated stress response (ISR) is an important mechanism by which cells confer protection against environmental stresses. Central to the ISR is a collection of related protein kinases that monitor stress conditions, such as Gcn2 (EIF2AK4) that recognizes nutrient limitations, inducing phosphorylation of eukaryotic translation initiation factor 2 (eIF2). Gcn2 phosphorylation of eIF2 lowers bulk protein synthesis, conserving energy and nutrients, coincident with preferential translation of stress-adaptive gene transcripts, such as that encoding the Atf4 transcriptional regulator. While Gcn2 is central for cell protection to nutrient stress and its depletion in humans leads to pulmonary disorders, Gcn2 can also contribute to the progression of cancers and facilitate neurological disorders during chronic stress. Consequently, specific ATP-competitive inhibitors of Gcn2 protein kinase have been developed. In this study, we report that one such Gcn2 inhibitor, Gcn2iB, can activate Gcn2, and we probe the mechanism by which this activation occurs. Low concentrations of Gcn2iB increase Gcn2 phosphorylation of eIF2 and enhance Atf4 expression and activity. Of importance, Gcn2iB can activate Gcn2 mutants devoid of functional regulatory domains or with certain kinase domain substitutions derived from Gcn2-deficient human patients. Other ATP-competitive inhibitors can also activate Gcn2, although there are differences in their mechanisms of activation. These results provide a cautionary note about the pharmacodynamics of eIF2 kinase inhibitors in therapeutic applications. Compounds designed to be kinase inhibitors that instead directly activate Gcn2, even loss of function variants, may provide tools to alleviate deficiencies in Gcn2 and other regulators of the ISR.
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Affiliation(s)
- Kenneth R Carlson
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, USA
| | | | - Kirk A Staschke
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, USA
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, USA.
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37
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Santos-Ribeiro D, Lecocq M, de Beukelaer M, Verleden S, Bouzin C, Ambroise J, Dorfmuller P, Yakoub Y, Huaux F, Quarck R, Karmouty-Quintana H, Ghigna MR, Bignard J, Nadaud S, Soubrier F, Horman S, Perros F, Godinas L, Pilette C. Disruption of GCN2 Pathway Aggravates Vascular and Parenchymal Remodeling during Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2023; 68:326-338. [PMID: 36476191 DOI: 10.1165/rcmb.2021-0541oc] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pulmonary fibrosis (PF) and pulmonary hypertension (PH) are chronic diseases of the pulmonary parenchyma and circulation, respectively, which may coexist, but underlying mechanisms remain elusive. Mutations in the GCN2 (general control nonderepressible 2) gene (EIF2AK4 [eukaryotic translation initiation factor 2 alpha kinase 4]) were recently associated with pulmonary veno-occlusive disease. The aim of this study is to explore the involvement of the GCN2/eIF2α (eukaryotic initiation factor 2α) pathway in the development of PH during PF, in both human disease and in a laboratory animal model. Lung tissue from patients with PF with or without PH was collected at the time of lung transplantation, and control tissue was obtained from tumor resection surgery. Experimental lung disease was induced in either male wild-type or EIF2AK4-mutated Sprague-Dawley rats, randomly receiving a single intratracheal instillation of bleomycin or saline. Hemodynamic studies and organ collection were performed 3 weeks after instillation. Only significant results (P < 0.05) are presented. In PF lung tissue, GCN2 protein expression was decreased compared with control tissue. GCN2 expression was reduced in CD31+ endothelial cells. In line with human data, GCN2 protein expression was decreased in the lung of bleomycin rats compared with saline. EIF2AK4-mutated rats treated with bleomycin showed increased parenchymal fibrosis (hydroxyproline concentrations) and vascular remodeling (media wall thickness) as well as increased right ventricular systolic pressure compared with wild-type animals. Our data show that GCN2 is dysregulated in both humans and in an animal model of combined PF and PH. The possibility of a causative implication of GCN2 dysregulation in PF and/or PH development should be further studied.
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Affiliation(s)
| | | | | | - Stijn Verleden
- Laboratory of Respiratory Diseases & Thoracic Surgery, Department of Chronic Diseases and Metabolism, and
| | | | | | - Peter Dorfmuller
- Department of Pathology, University of Giessen and Marburg Lung Center, Justus-Liebig University Giessen, German Center for Lung Research, Giessen, Germany
| | - Yousef Yakoub
- Louvain Center for Toxicology and Applied Pharmacology, and
| | - François Huaux
- Louvain Center for Toxicology and Applied Pharmacology, and
| | - Rozenn Quarck
- Clinical Department of Respiratory Diseases, University Hospitals - University of Leuven, Leuven, Belgium
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology and.,Division of Critical Care and.,Division of Pulmonary and Sleep Medicine, Department of Internal Medicine, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Maria-Rosa Ghigna
- Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,Département de Pathologie and.,INSERM UMR_S 999, Hôpital Marie Lannelongue, Le Plessis-Robinson, France
| | | | - Sophie Nadaud
- UMR_S 1166-ICAN, INSERM, Sorbonne Université, Paris, France
| | | | - Sandrine Horman
- Cardiovascular Research Unit, Institute of Experimental and Clinical Research, Catholic University of Louvain, Brussels, Belgium
| | - Frederic Perros
- Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,INSERM UMR_S 999, Hôpital Marie Lannelongue, Le Plessis-Robinson, France.,Assistance Publique-Hôpitaux de Paris, Centre de Référence de l'Hypertension Pulmonaire, Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital Bicêtre, Le Kremlin-Bicêtre, France.,Laboratoire CarMeN, UMR INSERM U1060/INRA U1397, Université Claude Bernard Lyon1, Pierre-Bénite and Bron, France; and
| | - Laurent Godinas
- Clinical Department of Respiratory Diseases, University Hospitals - University of Leuven, Leuven, Belgium
| | - Charles Pilette
- Pneumology, ENT and Dermatology.,Département de Pneumologie, Cliniques Universitaires St-Luc, Brussels, Belgium
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38
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Grmai L, Michaca M, Lackner E, Nampoothiri V P N, Vasudevan D. Integrated Stress Response signaling acts as a metabolic sensor in fat tissues to regulate oocyte maturation and ovulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530289. [PMID: 36909541 PMCID: PMC10002630 DOI: 10.1101/2023.02.27.530289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Reproduction is an energy-intensive process requiring systemic coordination. However, the inter-organ signaling mechanisms that relay nutrient status to modulate reproductive output are poorly understood. Here, we use Drosophila melanogaster as a model to establish the Integrated Stress response (ISR) transcription factor, Atf4, as a fat tissue metabolic sensor which instructs oogenesis. We demonstrate that Atf4 regulates the lipase Brummer to mediate yolk lipoprotein synthesis in the fat body. Depletion of Atf4 in the fat body also blunts oogenesis recovery after amino acid deprivation and re-feeding, suggestive of a nutrient sensing role for Atf4. We also discovered that Atf4 promotes secretion of a fat body-derived neuropeptide, CNMamide, which modulates neural circuits that promote egg-laying behavior (ovulation). Thus, we posit that ISR signaling in fat tissue acts as a "metabolic sensor" that instructs female reproduction: directly, by impacting yolk lipoprotein production and follicle maturation, and systemically, by regulating ovulation.
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39
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Kenski JCN, Huang X, Vredevoogd DW, de Bruijn B, Traets JJH, Ibáñez-Molero S, Schieven SM, van Vliet A, Krijgsman O, Kuilman T, Pozniak J, Loayza-Puch F, Terry AM, Müller J, Logtenberg MEW, de Bruijn M, Levy P, Körner PR, Goding CR, Schumacher TN, Marine JC, Agami R, Peeper DS. An adverse tumor-protective effect of IDO1 inhibition. Cell Rep Med 2023; 4:100941. [PMID: 36812891 PMCID: PMC9975322 DOI: 10.1016/j.xcrm.2023.100941] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 11/19/2022] [Accepted: 01/20/2023] [Indexed: 02/23/2023]
Abstract
By restoring tryptophan, indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors aim to reactivate anti-tumor T cells. However, a phase III trial assessing their clinical benefit failed, prompting us to revisit the role of IDO1 in tumor cells under T cell attack. We show here that IDO1 inhibition leads to an adverse protection of melanoma cells to T cell-derived interferon-gamma (IFNγ). RNA sequencing and ribosome profiling shows that IFNγ shuts down general protein translation, which is reversed by IDO1 inhibition. Impaired translation is accompanied by an amino acid deprivation-dependent stress response driving activating transcription factor-4 (ATF4)high/microphtalmia-associated transcription factor (MITF)low transcriptomic signatures, also in patient melanomas. Single-cell sequencing analysis reveals that MITF downregulation upon immune checkpoint blockade treatment predicts improved patient outcome. Conversely, MITF restoration in cultured melanoma cells causes T cell resistance. These results highlight the critical role of tryptophan and MITF in the melanoma response to T cell-derived IFNγ and uncover an unexpected negative consequence of IDO1 inhibition.
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Affiliation(s)
- Juliana C N Kenski
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Xinyao Huang
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - David W Vredevoogd
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Beaunelle de Bruijn
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joleen J H Traets
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Sofía Ibáñez-Molero
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Sebastiaan M Schieven
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alex van Vliet
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Thomas Kuilman
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joanna Pozniak
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Fabricio Loayza-Puch
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alexandra M Terry
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Judith Müller
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Meike E W Logtenberg
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Marjolein de Bruijn
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pierre Levy
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pierre-René Körner
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, OX OX3 7DQ, UK
| | - Ton N Schumacher
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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40
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Zhao C, Guo H, Hou Y, Lei T, Wei D, Zhao Y. Multiple Roles of the Stress Sensor GCN2 in Immune Cells. Int J Mol Sci 2023; 24:ijms24054285. [PMID: 36901714 PMCID: PMC10002013 DOI: 10.3390/ijms24054285] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
The serine/threonine-protein kinase general control nonderepressible 2 (GCN2) is a well-known stress sensor that responds to amino acid starvation and other stresses, making it critical to the maintenance of cellular and organismal homeostasis. More than 20 years of research has revealed the molecular structure/complex, inducers/regulators, intracellular signaling pathways and bio-functions of GCN2 in various biological processes, across an organism's lifespan, and in many diseases. Accumulated studies have demonstrated that the GCN2 kinase is also closely involved in the immune system and in various immune-related diseases, such as GCN2 acts as an important regulatory molecule to control macrophage functional polarization and CD4+ T cell subset differentiation. Herein, we comprehensively summarize the biological functions of GCN2 and discuss its roles in the immune system, including innate and adaptive immune cells. We also discuss the antagonism of GCN2 and mTOR pathways in immune cells. A better understanding of GCN2's functions and signaling pathways in the immune system under physiological, stressful, and pathological situations will be beneficial to the development of potential therapies for many immune-relevant diseases.
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Affiliation(s)
- Chenxu Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Han Guo
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangxiao Hou
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Lei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Wei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Correspondence: ; Tel.: +86-10-64807302
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41
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Sabbarini IM, Reif D, McQuown AJ, Nelliat AR, Prince J, Membreno BS, Wu CCC, Murray AW, Denic V. Zinc-finger protein Zpr1 is a bespoke chaperone essential for eEF1A biogenesis. Mol Cell 2023; 83:252-265.e13. [PMID: 36630955 PMCID: PMC10016025 DOI: 10.1016/j.molcel.2022.12.012] [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: 10/30/2022] [Revised: 11/15/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023]
Abstract
The conserved regulon of heat shock factor 1 in budding yeast contains chaperones for general protein folding as well as zinc-finger protein Zpr1, whose essential role in archaea and eukaryotes remains unknown. Here, we show that Zpr1 depletion causes acute proteotoxicity driven by biosynthesis of misfolded eukaryotic translation elongation factor 1A (eEF1A). Prolonged Zpr1 depletion leads to eEF1A insufficiency, thereby inducing the integrated stress response and inhibiting protein synthesis. Strikingly, we show by using two distinct biochemical reconstitution approaches that Zpr1 enables eEF1A to achieve a conformational state resistant to protease digestion. Lastly, we use a ColabFold model of the Zpr1-eEF1A complex to reveal a folding mechanism mediated by the Zpr1's zinc-finger and alpha-helical hairpin structures. Our work uncovers the long-sought-after function of Zpr1 as a bespoke chaperone tailored to the biogenesis of one of the most abundant proteins in the cell.
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Affiliation(s)
- Ibrahim M Sabbarini
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dvir Reif
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander J McQuown
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Anjali R Nelliat
- Graduate Program in Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey Prince
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Britnie Santiago Membreno
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Colin Chih-Chien Wu
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vladimir Denic
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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Li Q, Hoppe T. Role of amino acid metabolism in mitochondrial homeostasis. Front Cell Dev Biol 2023; 11:1127618. [PMID: 36923249 PMCID: PMC10008872 DOI: 10.3389/fcell.2023.1127618] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/16/2023] [Indexed: 03/03/2023] Open
Abstract
Mitochondria are central hubs for energy production, metabolism and cellular signal transduction in eukaryotic cells. Maintenance of mitochondrial homeostasis is important for cellular function and survival. In particular, cellular metabolic state is in constant communication with mitochondrial homeostasis. One of the most important metabolic processes that provide energy in the cell is amino acid metabolism. Almost all of the 20 amino acids that serve as the building blocks of proteins are produced or degraded in the mitochondria. The synthesis of the amino acids aspartate and arginine depends on the activity of the respiratory chain, which is essential for cell proliferation. The degradation of branched-chain amino acids mainly occurs in the mitochondrial matrix, contributing to energy metabolism, mitochondrial biogenesis, as well as protein quality control in both mitochondria and cytosol. Dietary supplementation or restriction of amino acids in worms, flies and mice modulates lifespan and health, which has been associated with changes in mitochondrial biogenesis, antioxidant response, as well as the activity of tricarboxylic acid cycle and respiratory chain. Consequently, impaired amino acid metabolism has been associated with both primary mitochondrial diseases and diseases with mitochondrial dysfunction such as cancer. Here, we present recent observations on the crosstalk between amino acid metabolism and mitochondrial homeostasis, summarise the underlying molecular mechanisms to date, and discuss their role in cellular functions and organismal physiology.
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Affiliation(s)
- Qiaochu Li
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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Waad Sadiq Z, Brioli A, Al-Abdulla R, Çetin G, Schütt J, Murua Escobar H, Krüger E, Ebstein F. Immunogenic cell death triggered by impaired deubiquitination in multiple myeloma relies on dysregulated type I interferon signaling. Front Immunol 2023; 14:982720. [PMID: 36936919 PMCID: PMC10018035 DOI: 10.3389/fimmu.2023.982720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction Proteasome inhibition is first line therapy in multiple myeloma (MM). The immunological potential of cell death triggered by defects of the ubiquitin-proteasome system (UPS) and subsequent perturbations of protein homeostasis is, however, less well defined. Methods In this paper, we applied the protein homeostasis disruptors bortezomib (BTZ), ONX0914, RA190 and PR619 to various MM cell lines and primary patient samples to investigate their ability to induce immunogenic cell death (ICD). Results Our data show that while BTZ treatment triggers sterile type I interferon (IFN) responses, exposure of the cells to ONX0914 or RA190 was mostly immunologically silent. Interestingly, inhibition of protein de-ubiquitination by PR619 was associated with the acquisition of a strong type I IFN gene signature which relied on key components of the unfolded protein and integrated stress responses including inositol-requiring enzyme 1 (IRE1), protein kinase R (PKR) and general control nonderepressible 2 (GCN2). The immunological relevance of blocking de-ubiquitination in MM was further reflected by the ability of PR619-induced apoptotic cells to facilitate dendritic cell (DC) maturation via type I IFN-dependent mechanisms. Conclusion Altogether, our findings identify de-ubiquitination inhibition as a promising strategy for inducing ICD of MM to expand current available treatments.
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Affiliation(s)
- Zeinab Waad Sadiq
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany
| | - Annamaria Brioli
- Klinik und Poliklinik für Innere Medizin C, Universitätsmedizin Greifswald, Greifswald, Germany
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Ruba Al-Abdulla
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany
| | - Gonca Çetin
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany
| | - Jacqueline Schütt
- Klinik und Poliklinik für Innere Medizin C, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Hugo Murua Escobar
- Department of Medicine, Clinic III, Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, Rostock, Germany
| | - Elke Krüger
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany
| | - Frédéric Ebstein
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany
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Ranea-Robles P, Pavlova NN, Bender A, Pereyra AS, Ellis JM, Stauffer B, Yu C, Thompson CB, Argmann C, Puchowicz M, Houten SM. A mitochondrial long-chain fatty acid oxidation defect leads to transfer RNA uncharging and activation of the integrated stress response in the mouse heart. Cardiovasc Res 2022; 118:3198-3210. [PMID: 35388887 PMCID: PMC9799058 DOI: 10.1093/cvr/cvac050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 03/08/2022] [Accepted: 03/23/2022] [Indexed: 01/25/2023] Open
Abstract
AIMS Cardiomyopathy and arrhythmias can be severe presentations in patients with inherited defects of mitochondrial long-chain fatty acid β-oxidation (FAO). The pathophysiological mechanisms that underlie these cardiac abnormalities remain largely unknown. We investigated the molecular adaptations to a FAO deficiency in the heart using the long-chain acyl-CoA dehydrogenase (LCAD) knockout (KO) mouse model. METHODS AND RESULTS We observed enrichment of amino acid metabolic pathways and of ATF4 target genes among the upregulated genes in the LCAD KO heart transcriptome. We also found a prominent activation of the eIF2α/ATF4 axis at the protein level that was independent of the feeding status, in addition to a reduction of cardiac protein synthesis during a short period of food withdrawal. These findings are consistent with an activation of the integrated stress response (ISR) in the LCAD KO mouse heart. Notably, charging of several transfer RNAs (tRNAs), such as tRNAGln was decreased in LCAD KO hearts, reflecting a reduced availability of cardiac amino acids, in particular, glutamine. We replicated the activation of the ISR in the hearts of mice with muscle-specific deletion of carnitine palmitoyltransferase 2. CONCLUSIONS Our results show that perturbations in amino acid metabolism caused by long-chain FAO deficiency impact cardiac metabolic signalling, in particular the ISR. These results may serve as a foundation for investigating the role of the ISR in the cardiac pathology associated with long-chain FAO defects.Translational Perspective: The heart relies mainly on mitochondrial fatty acid β-oxidation (FAO) for its high energy requirements. The heart disease observed in patients with a genetic defect in this pathway highlights the importance of FAO for cardiac health. We show that the consequences of a FAO defect extend beyond cardiac energy homeostasis and include amino acid metabolism and associated signalling pathways such as the integrated stress response.
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Affiliation(s)
- Pablo Ranea-Robles
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Natalya N Pavlova
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Aaron Bender
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Andrea S Pereyra
- Brody School of Medicine at East Carolina University, Department of Physiology, and East Carolina Diabetes and Obesity Institute, Greenville, NC 27858, USA
| | - Jessica M Ellis
- Brody School of Medicine at East Carolina University, Department of Physiology, and East Carolina Diabetes and Obesity Institute, Greenville, NC 27858, USA
| | - Brandon Stauffer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
- Mount Sinai Genomics, Inc, Stamford, CT 06902, USA
| | - Chunli Yu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
- Mount Sinai Genomics, Inc, Stamford, CT 06902, USA
| | - Craig B Thompson
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Michelle Puchowicz
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
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Castillo KD, Wu C, Ding Z, Lopez-Garcia OK, Rowlinson E, Sachs MS, Bell-Pedersen D. A circadian clock translational control mechanism targets specific mRNAs to cytoplasmic messenger ribonucleoprotein granules. Cell Rep 2022; 41:111879. [PMID: 36577368 PMCID: PMC10241597 DOI: 10.1016/j.celrep.2022.111879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 09/13/2022] [Accepted: 12/04/2022] [Indexed: 12/29/2022] Open
Abstract
Phosphorylation of Neurospora crassa eukaryotic initiation factor 2 α (eIF2α), a conserved translation initiation factor, is clock controlled. To determine the impact of rhythmic eIF2α phosphorylation on translation, we performed temporal ribosome profiling and RNA sequencing (RNA-seq) in wild-type (WT), clock mutant Δfrq, eIF2α kinase mutant Δcpc-3, and constitutively active cpc-3c cells. About 14% of mRNAs are rhythmically translated in WT cells, and translation rhythms for ∼30% of these mRNAs, which we named circadian translation-initiation-controlled genes (cTICs), are dependent on the clock and CPC-3. Most cTICs are expressed from arrhythmic mRNAs and contain a P-body (PB) localization motif in their 5' leader sequence. Deletion of SNR-1, a component of cytoplasmic messenger ribonucleoprotein granules (cmRNPgs) that include PBs and stress granules (SGs), and the PB motif on one of the cTIC mRNAs, zip-1, significantly alters zip-1 rhythmic translation. These results reveal that the clock regulates rhythmic translation of specific mRNAs through rhythmic eIF2α activity and cmRNPg metabolism.
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Affiliation(s)
- Kathrina D Castillo
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Zhaolan Ding
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Emma Rowlinson
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Deborah Bell-Pedersen
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA.
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The antitumor activity of a novel GCN2 inhibitor in head and neck squamous cell carcinoma cell lines. Transl Oncol 2022; 27:101592. [PMID: 36436443 PMCID: PMC9694079 DOI: 10.1016/j.tranon.2022.101592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 11/03/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND General control nonderepressible 2 (GCN2) senses amino acid deprivation and activates activating transcription factor 4 (ATF4), which regulates many adaptive genes. We evaluated the impact of AST-0513, a novel GCN2 inhibitor, on the GCN2-ATF4 pathway. Additionally, we evaluated the antitumor effects of AST-0513 in amino acid deprivation in head and neck squamous cell carcinoma (HNSCC) cell lines. METHODS GCN2 expression in HNSCC patient tissues was measured by immunohistochemistry. Five HNSCC cell lines (SNU-1041, SNU-1066, SNU-1076, Detroit-562, FaDu) grown under amino acid deprivation conditions, were treated with AST-0513. After AST-0513 treatment, cell proliferation was measured by CCK-8 assay. Flow cytometry was used to evaluate apoptosis and cell cycle phase. In addition, immunoblotting was performed to evaluate the effect of AST-0513 on the GCN2-ATF4 pathway, cell cycle arrest, and apoptosis. RESULTS We demonstrated that GCN2 was highly expressed in HNSCC patient tissues. AST-0513 inhibited the GCN2-ATF4 pathway in all five HNSCC cell lines. Inhibiting the GCN2-ATF4 pathway during amino acid deprivation reduced HNSCC cell proliferation and prevented adaptation to nutrient stress. Moreover, AST-0513 treatment led to p21 and Cyclin B1 accumulation and G2/M phase cycle arrest. Also, apoptosis was increased, consistent with increased bax expression, increased bcl-xL phosphorylation, and decreased bcl-2 expression. CONCLUSION A novel GCN2 inhibitor, AST-0513, inhibited the GCN2-ATF4 pathway and has antitumor activity that inhibits proliferation and promotes cell cycle arrest and apoptosis. Considering the high expression of GCN2 in HNSCC patients, these results suggest the potential role of GCN2 inhibitor for the treatment of HNSCC.
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Kulkarni A, Muralidharan C, May SC, Tersey SA, Mirmira RG. Inside the β Cell: Molecular Stress Response Pathways in Diabetes Pathogenesis. Endocrinology 2022; 164:6783239. [PMID: 36317483 PMCID: PMC9667558 DOI: 10.1210/endocr/bqac184] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Indexed: 11/05/2022]
Abstract
The pathogeneses of the 2 major forms of diabetes, type 1 and type 2, differ with respect to their major molecular insults (loss of immune tolerance and onset of tissue insulin resistance, respectively). However, evidence suggests that dysfunction and/or death of insulin-producing β-cells is common to virtually all forms of diabetes. Although the mechanisms underlying β-cell dysfunction remain incompletely characterized, recent years have witnessed major advances in our understanding of the molecular pathways that contribute to the demise of the β-cell. Cellular and environmental factors contribute to β-cell dysfunction/loss through the activation of molecular pathways that exacerbate endoplasmic reticulum stress, the integrated stress response, oxidative stress, and impaired autophagy. Whereas many of these stress responsive pathways are interconnected, their individual contributions to glucose homeostasis and β-cell health have been elucidated through the development and interrogation of animal models. In these studies, genetic models and pharmacological compounds have enabled the identification of genes and proteins specifically involved in β-cell dysfunction during diabetes pathogenesis. Here, we review the critical stress response pathways that are activated in β cells in the context of the animal models.
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Affiliation(s)
| | | | - Sarah C May
- Kovler Diabetes Center and Department of Medicine, The University of Chicago, Chicago, Illinois 60637, USA
| | - Sarah A Tersey
- Kovler Diabetes Center and Department of Medicine, The University of Chicago, Chicago, Illinois 60637, USA
| | - Raghavendra G Mirmira
- Correspondence: Raghavendra G. Mirmira, MD, PhD, Kovler Diabetes Center and Department of Medicine, The University of Chicago, 900 E 57th St, KCBD 8132, Chicago, IL 60637, USA.
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Pinch M, Muka T, Kandel Y, Lamsal M, Martinez N, Teixeira M, Boudko DY, Hansen IA. General control nonderepressible 1 interacts with cationic amino acid transporter 1 and affects Aedes aegypti fecundity. Parasit Vectors 2022; 15:383. [PMID: 36271393 PMCID: PMC9587632 DOI: 10.1186/s13071-022-05461-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/27/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The amino acid transporter protein cationic amino acid transporter 1 (CAT1) is part of the nutrient sensor in the fat body of mosquitoes. A member of the SLC7 family of cationic amino acid transporters, it is paramount for the detection of elevated amino acid levels in the mosquito hemolymph after a blood meal and the subsequent changes in gene expression in the fat body. METHODS We performed a re-annotation of Aedes aegypti cationic amino acid transporters (CATs) and selected the C-terminal tail of CAT1 to perform a yeast two-hybrid screen to identify putative interactors of this protein. One interesting interacting protein we identified was general control nonderepressible 1 (GCN1). We determined the expression pattern of GCN1 in several adult organs and structures using qRT-PCR and western blots. Finally, we knocked down GCN1 using double-stranded RNA and identified changes in downstream signaling intermediates and the effects of knockdown on vitellogenesis and fecundity. RESULTS In a screen for Ae. aegypti CAT1-interacting proteins we identified GCN1 as a putative interactor. GCN1 is highly expressed in the ovaries and fat body of the mosquito. We provide evidence that eukaryotic translation initiation factor 2 subunit alpha (eIF2α) phosphorylation changed during vitellogenesis and that RNA interference knockdown of GCN1 in whole mosquitoes reduced egg clutch sizes of treated mosquitoes relative to controls. CONCLUSIONS Aedes aegypti CAT1 and GCN1 are likely interacting partners and GCN1 is likely necessary for proper egg development. Our data suggest that GCN1 is part of a nutrient sensor mechanism in various mosquito tissues involved in vitellogenesis.
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Affiliation(s)
- Matthew Pinch
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Theodore Muka
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Yashoda Kandel
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Mahesh Lamsal
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Nathan Martinez
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | | | | | - Immo A Hansen
- Department of Biology, New Mexico State University, Las Cruces, NM, USA.
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Brüggenthies JB, Fiore A, Russier M, Bitsina C, Brötzmann J, Kordes S, Menninger S, Wolf A, Conti E, Eickhoff JE, Murray PJ. A cell-based chemical-genetic screen for amino acid stress response inhibitors reveals torins reverse stress kinase GCN2 signaling. J Biol Chem 2022; 298:102629. [PMID: 36273589 PMCID: PMC9668732 DOI: 10.1016/j.jbc.2022.102629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
mTORC1 and GCN2 are serine/threonine kinases that control how cells adapt to amino acid availability. mTORC1 responds to amino acids to promote translation and cell growth while GCN2 senses limiting amino acids to hinder translation via eIF2α phosphorylation. GCN2 is an appealing target for cancer therapies because malignant cells can harness the GCN2 pathway to temper the rate of translation during rapid amino acid consumption. To isolate new GCN2 inhibitors, we created cell-based, amino acid limitation reporters via genetic manipulation of Ddit3 (encoding the transcription factor CHOP). CHOP is strongly induced by limiting amino acids and in this context, GCN2-dependent. Using leucine starvation as a model for essential amino acid sensing, we unexpectedly discovered ATP-competitive PI3 kinase-related kinase inhibitors, including ATR and mTOR inhibitors like torins, completely reversed GCN2 activation in a time-dependent way. Mechanistically, via inhibiting mTORC1-dependent translation, torins increased intracellular leucine, which was sufficient to reverse GCN2 activation and the downstream integrated stress response including stress-induced transcriptional factor ATF4 expression. Strikingly, we found that general translation inhibitors mirrored the effects of torins. Therefore, we propose that mTOR kinase inhibitors concurrently inhibit different branches of amino acid sensing by a dual mechanism involving direct inhibition of mTOR and indirect suppression of GCN2 that are connected by effects on the translation machinery. Collectively, our results highlight distinct ways of regulating GCN2 activity.
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Affiliation(s)
| | | | - Marion Russier
- Max Planck Institute for Biochemistry, Martinsried, Germany
| | | | | | | | | | | | - Elena Conti
- Max Planck Institute for Biochemistry, Martinsried, Germany
| | | | - Peter J. Murray
- Max Planck Institute for Biochemistry, Martinsried, Germany,For correspondence: Peter J. Murray
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50
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Urano Y, Osaki S, Chiba R, Noguchi N. Integrated stress response is involved in the 24(S)-hydroxycholesterol-induced unconventional cell death mechanism. Cell Death Dis 2022; 8:406. [PMID: 36195595 PMCID: PMC9532424 DOI: 10.1038/s41420-022-01197-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 01/11/2023]
Abstract
Perturbation of proteostasis triggers the adaptive responses that contribute to the homeostatic pro-survival response, whereas disruption of proteostasis can ultimately lead to cell death. Brain-specific oxysterol-i.e., 24(S)-hydroxycholesterol (24S-OHC)-has been shown to cause cytotoxicity when esterified by acyl-CoA:cholesterol acyltransferase 1 (ACAT1) in the endoplasmic reticulum (ER). Here, we show that the accumulation of 24S-OHC esters caused phosphorylation of eukaryotic translation initiator factor 2α (eIF2α), dissociation of polysomes, and formation of stress granules (SG), resulting in robust downregulation of global protein de novo synthesis in human neuroblastoma SH-SY5Y cells. We also found that integrated stress response (ISR) activation through PERK and GCN2 activation induced by 24S-OHC treatment caused eIF2α phosphorylation. 24S-OHC-inducible SG formation and cell death were suppressed by inhibition of ISR. These results show that ACAT1-mediated 24S-OHC esterification induced ISR and formation of SG, which play crucial roles in 24S-OHC-inducible protein synthesis inhibition and unconventional cell death.
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Affiliation(s)
- Yasuomi Urano
- Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan.
| | - Shoya Osaki
- Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Ren Chiba
- Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Noriko Noguchi
- Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan.
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