1
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Ulfig A, Jakob U. Cellular oxidants and the proteostasis network: balance between activation and destruction. Trends Biochem Sci 2024:S0968-0004(24)00164-6. [PMID: 39168791 DOI: 10.1016/j.tibs.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/27/2024] [Accepted: 07/09/2024] [Indexed: 08/23/2024]
Abstract
Loss of protein homeostasis (proteostasis) is a common hallmark of aging and age-associated diseases. Considered as the guardian of proteostasis, the proteostasis network (PN) acts to preserve the functionality of proteins during their lifetime. However, its activity declines with age, leading to disease manifestation. While reactive oxygen species (ROS) were traditionally considered culprits in this process, recent research challenges this view. While harmful at high concentrations, moderate ROS levels protect the cell against age-mediated onset of proteotoxicity by activating molecular chaperones, stress response pathways, and autophagy. This review explores the nuanced roles of ROS in proteostasis and discusses the most recent findings regarding the redox regulation of the PN and its potential in extending healthspan and delaying age-related pathologies.
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Affiliation(s)
- Agnes Ulfig
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA; Biological Chemistry Department, University of Michigan Medical School, Ann Arbor, MI, USA.
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2
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Maduka AO, Manohar S, Foster MW, Silva GM. Localized K63 ubiquitin signaling is regulated by VCP/p97 during oxidative stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.598218. [PMID: 38948861 PMCID: PMC11213022 DOI: 10.1101/2024.06.20.598218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Under stress conditions, cells reprogram their molecular machineries to mitigate damage and promote survival. Ubiquitin signaling is globally increased during oxidative stress, controlling protein fate and supporting stress defenses at several subcellular compartments. However, the rules driving subcellular ubiquitin localization to promote these concerted response mechanisms remain understudied. Here, we show that K63-linked ubiquitin chains, known to promote proteasome-independent pathways, accumulate primarily in non-cytosolic compartments during oxidative stress induced by sodium arsenite in mammalian cells. Our subcellular ubiquitin proteomic analyses of non-cytosolic compartments expanded 10-fold the pool of proteins known to be ubiquitinated during arsenite stress (2,046) and revealed their involvement in pathways related to immune signaling and translation control. Moreover, subcellular proteome analyses revealed proteins that are recruited to non-cytosolic compartments under stress, including a significant enrichment of helper ubiquitin-binding adaptors of the ATPase VCP that processes ubiquitinated substrates for downstream signaling. We further show that VCP recruitment to non-cytosolic compartments under arsenite stress occurs in a ubiquitin-dependent manner mediated by its adaptor NPLOC4. Additionally, we show that VCP and NPLOC4 activities are critical to sustain low levels of non-cytosolic K63-linked ubiquitin chains, supporting a cyclical model of ubiquitin conjugation and removal that is disrupted by cellular exposure to reactive oxygen species. This work deepens our understanding of the role of localized ubiquitin and VCP signaling in the basic mechanisms of stress response and highlights new pathways and molecular players that are essential to reshape the composition and function of the human subcellular proteome under dynamic environments.
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Affiliation(s)
| | - Sandhya Manohar
- Institute for Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Matthew W. Foster
- Proteomics and Metabolomics Core Facility, Duke University, Durham, NC, 27708, USA
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3
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Delledonne A, Punturiero C, Ferrari C, Bernini F, Milanesi R, Bagnato A, Strillacci MG. Copy number variant scan in more than four thousand Holstein cows bred in Lombardy, Italy. PLoS One 2024; 19:e0303044. [PMID: 38771855 PMCID: PMC11108207 DOI: 10.1371/journal.pone.0303044] [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: 02/04/2024] [Accepted: 04/18/2024] [Indexed: 05/23/2024] Open
Abstract
Copy Number Variants (CNV) are modifications affecting the genome sequence of DNA, for instance, they can be duplications or deletions of a considerable number of base pairs (i.e., greater than 1000 bp and up to millions of bp). Their impact on the variation of the phenotypic traits has been widely demonstrated. In addition, CNVs are a class of markers useful to identify the genetic biodiversity among populations related to adaptation to the environment. The aim of this study was to detect CNVs in more than four thousand Holstein cows, using information derived by a genotyping done with the GGP (GeneSeek Genomic Profiler) bovine 100K SNP chip. To detect CNV the SVS 8.9 software was used, then CNV regions (CNVRs) were detected. A total of 123,814 CNVs (4,150 non redundant) were called and aggregated into 1,397 CNVRs. The PCA results obtained using the CNVs information, showed that there is some variability among animals. For many genes annotated within the CNVRs, the role in immune response is well known, as well as their association with important and economic traits object of selection in Holstein, such as milk production and quality, udder conformation and body morphology. Comparison with reference revealed unique CNVRs of the Holstein breed, and others in common with Jersey and Brown. The information regarding CNVs represents a valuable resource to understand how this class of markers may improve the accuracy in prediction of genomic value, nowadays solely based on SNPs markers.
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Affiliation(s)
- Andrea Delledonne
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, Lodi, Italy
| | - Chiara Punturiero
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, Lodi, Italy
| | - Carlotta Ferrari
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, Lodi, Italy
| | - Francesca Bernini
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, Lodi, Italy
| | - Raffaella Milanesi
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, Lodi, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, Lodi, Italy
| | - Maria G. Strillacci
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, Lodi, Italy
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4
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Miquel-Rio L, Sarriés-Serrano U, Sancho-Alonso M, Florensa-Zanuy E, Paz V, Ruiz-Bronchal E, Manashirov S, Campa L, Pilar-Cuéllar F, Bortolozzi A. ER stress in mouse serotonin neurons triggers a depressive phenotype alleviated by ketamine targeting eIF2α signaling. iScience 2024; 27:109787. [PMID: 38711453 PMCID: PMC11070602 DOI: 10.1016/j.isci.2024.109787] [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: 10/27/2023] [Revised: 02/19/2024] [Accepted: 04/16/2024] [Indexed: 05/08/2024] Open
Abstract
Depression is a devastating mood disorder that causes significant disability worldwide. Current knowledge of its pathophysiology remains modest and clear biological markers are lacking. Emerging evidence from human and animal models reveals persistent alterations in endoplasmic reticulum (ER) homeostasis, suggesting that ER stress-related signaling pathways may be targets for prevention and treatment. However, the neurobiological basis linking the pathways involved in depression-related ER stress remains unknown. Here, we report that an induced model of ER stress in mouse serotonin (5-HT) neurons is associated with reduced Egr1-dependent 5-HT cellular activity and 5-HT neurotransmission, resulting in neuroplasticity deficits in forebrain regions and a depressive-like phenotype. Ketamine administration engages downstream eIF2α signaling to trigger rapid neuroplasticity events that rescue the depressive-like effects. Collectively, these data identify ER stress in 5-HT neurons as a cellular pathway involved in the pathophysiology of depression and show that eIF2α is critical in eliciting ketamine's fast antidepressant effects.
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Affiliation(s)
- Lluis Miquel-Rio
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain
- Systems Neuropharmacology Research Group, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
- Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
- University of Barcelona (UB), 08036 Barcelona, Spain
| | - Unai Sarriés-Serrano
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain
- Systems Neuropharmacology Research Group, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
- Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
- University of the Basque Country UPV/EHU, E-48940 Leioa, Bizkaia, Spain
| | - María Sancho-Alonso
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain
- Systems Neuropharmacology Research Group, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
- Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
| | - Eva Florensa-Zanuy
- Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
- Department of Molecular and Cellular Signaling, Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria-CSIC, 39011 Santander, Spain
| | - Verónica Paz
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain
- Systems Neuropharmacology Research Group, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
- Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
| | - Esther Ruiz-Bronchal
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain
- Systems Neuropharmacology Research Group, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
- Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
| | - Sharon Manashirov
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain
- Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
- miCure Therapeutics LTD., Tel-Aviv 6423902, Israel
| | - Leticia Campa
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain
- Systems Neuropharmacology Research Group, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
- Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
| | - Fuencisla Pilar-Cuéllar
- Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
- Department of Molecular and Cellular Signaling, Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria-CSIC, 39011 Santander, Spain
| | - Analia Bortolozzi
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain
- Systems Neuropharmacology Research Group, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
- Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
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5
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Sakurai Y, Oba E, Honda A, Tanaka H, Takano H, Akita H. The stress-responsive cytotoxic effect of diesel exhaust particles on lymphatic endothelial cells. Sci Rep 2024; 14:10503. [PMID: 38714844 PMCID: PMC11076499 DOI: 10.1038/s41598-024-61255-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
Diesel exhaust particles (DEPs) are very small (typically < 0.2 μm) fragments that have become major air pollutants. DEPs are comprised of a carbonaceous core surrounded by organic compounds such as polycyclic aromatic hydrocarbons (PAHs) and nitro-PAHs. Inhaled DEPs reach the deepest sites in the respiratory system where they could induce respiratory/cardiovascular dysfunction. Additionally, a previous study has revealed that a portion of inhaled DEPs often activate immune cells and subsequently induce somatic inflammation. Moreover, DEPs are known to localize in lymph nodes. Therefore, in this study we explored the effect of DEPs on the lymphatic endothelial cells (LECs) that are a constituent of the walls of lymph nodes. DEP exposure induced cell death in a reactive oxygen species (ROS)-dependent manner. Following exposure to DEPs, next-generation sequence (NGS) analysis identified an upregulation of the integrated stress response (ISR) pathway and cell death cascades. Both the soluble and insoluble components of DEPs generated intracellular ROS. Three-dimensional Raman imaging revealed that DEPs are taken up by LECs, which suggests internalized DEP cores produce ROS, as well as soluble DEP components. However, significant cell death pathways such as apoptosis, necroptosis, ferroptosis, pyroptosis, and parthanatos seem unlikely to be involved in DEP-induced cell death in LECs. This study clarifies how DEPs invading the body might affect the lymphatic system through the induction of cell death in LECs.
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Affiliation(s)
- Yu Sakurai
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Eiki Oba
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Akiko Honda
- Graduate School of Engineering, Kyoto University, Kyoto, 615-8530, Japan
| | - Hiroki Tanaka
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Hirohisa Takano
- Institute for International Academic Research, Kyoto University of Advanced Science, Kyoto, 621-8555, Japan
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, 615-8530, Japan
| | - Hidetaka Akita
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan.
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6
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Barros GC, Guerrero S, Silva GM. The central role of translation elongation in response to stress. Biochem Soc Trans 2023; 51:959-969. [PMID: 37318088 PMCID: PMC11160351 DOI: 10.1042/bst20220584] [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: 02/06/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
Protein synthesis is essential to support homeostasis, and thus, must be highly regulated during cellular response to harmful environments. All stages of translation are susceptible to regulation under stress, however, the mechanisms involved in translation regulation beyond initiation have only begun to be elucidated. Methodological advances enabled critical discoveries on the control of translation elongation, highlighting its important role in translation repression and the synthesis of stress-response proteins. In this article, we discuss recent findings on mechanisms of elongation control mediated by ribosome pausing and collisions and the availability of tRNAs and elongation factors. We also discuss how elongation intersects with distinct modes of translation control, further supporting cellular viability and gene expression reprogramming. Finally, we highlight how several of these pathways are reversibly regulated, emphasizing the dynamics of translation control during stress-response progression. A comprehensive understanding of translation regulation under stress will produce fundamental knowledge of protein dynamics while opening new avenues and strategies to overcome dysregulated protein production and cellular sensitivity to stress.
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Affiliation(s)
| | | | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, NC, USA
- Lead contact
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7
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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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8
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Salimi K, Alvandi M, Saberi Pirouz M, Rakhshan K, Howatson G. Regulating eEF2 and eEF2K in skeletal muscle by exercise. Arch Physiol Biochem 2023:1-12. [PMID: 36633938 DOI: 10.1080/13813455.2023.2164898] [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: 06/16/2022] [Revised: 12/15/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023]
Abstract
Skeletal muscle is a flexible and adaptable tissue that strongly responds to exercise training. The skeletal muscle responds to exercise by increasing muscle protein synthesis (MPS) when energy is available. One of protein synthesis's major rate-limiting and critical regulatory steps is the translation elongation pathway. The process of translation elongation in skeletal muscle is highly regulated. It requires elongation factors that are intensely affected by various physiological stimuli such as exercise and the total available energy of cells. Studies have shown that exercise involves the elongation pathway by numerous signalling pathways. Since the elongation pathway, has been far less studied than the other translation steps, its comprehensive prospect and quantitative understanding remain in the dark. This study highlights the current understanding of the effect of exercise training on the translation elongation pathway focussing on the molecular factors affecting the pathway, including Ca2+, AMPK, PKA, mTORC1/P70S6K, MAPKs, and myostatin. We further discussed the mode and volume of exercise training intervention on the translation elongation pathway.What is the topic of this review? This review summarises the impacts of exercise training on the translation elongation pathway in skeletal muscle focussing on eEF2 and eEF2K.What advances does it highlight? This review highlights mechanisms and factors that profoundly influence the translation elongation pathway and argues that exercise might modulate the response. This review also combines the experimental observations focussing on the regulation of translation elongation during and after exercise. The findings widen our horizon to the notion of mechanisms involved in muscle protein synthesis (MPS) through translation elongation response to exercise training.
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Affiliation(s)
- Kia Salimi
- Department of Exercise Physiology, Faculty of Sport and Exercise Sciences, University of Tehran, Tehran, Iran
| | - Masoomeh Alvandi
- Department of Biological Science in Sport and Health, University of Shahid Beheshti, Tehran, Iran
| | - Mahdi Saberi Pirouz
- Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Kamran Rakhshan
- Department of Medical Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Electrophysiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Glyn Howatson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Water Research Group, North West University, Potchefstroom, South Africa
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9
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PARP1 Activation Controls Stress Granule Assembly after Oxidative Stress and DNA Damage. Cells 2022; 11:cells11233932. [PMID: 36497190 PMCID: PMC9740212 DOI: 10.3390/cells11233932] [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: 10/28/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
DNA damage causes PARP1 activation in the nucleus to set up the machinery responsible for the DNA damage response. Here, we report that, in contrast to cytoplasmic PARPs, the synthesis of poly(ADP-ribose) by PARP1 opposes the formation of cytoplasmic mRNA-rich granules after arsenite exposure by reducing polysome dissociation. However, when mRNA-rich granules are pre-formed, whether in the cytoplasm or nucleus, PARP1 activation positively regulates their assembly, though without additional recruitment of poly(ADP-ribose) in stress granules. In addition, PARP1 promotes the formation of TDP-43- and FUS-rich granules in the cytoplasm, two RNA-binding proteins which form neuronal cytoplasmic inclusions observed in certain neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Together, the results therefore reveal a dual role of PARP1 activation which, on the one hand, prevents the early stage of stress granule assembly and, on the other hand, enables the persistence of cytoplasmic mRNA-rich granules in cells which may be detrimental in aging neurons.
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10
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Caulier A, Jankovsky N, Gautier EF, El Nemer W, Guitton C, Ouled-Haddou H, Guillonneau F, Mayeux P, Salnot V, Bruce J, Picard V, Garçon L. Red blood cell proteomics reveal remnant protein biosynthesis and folding pathways in PIEZO1-related hereditary xerocytosis. Front Physiol 2022; 13:960291. [PMID: 36531183 PMCID: PMC9751340 DOI: 10.3389/fphys.2022.960291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/21/2022] [Indexed: 11/25/2023] Open
Abstract
Hereditary xerocytosis is a dominant red cell membrane disorder characterized by an increased leak of potassium from the inside to outside the red blood cell membrane, associated with loss of water leading to red cell dehydration and chronic hemolysis. 90% of cases are related to heterozygous gain of function mutations in PIEZO1, encoding a mechanotransductor that translates a mechanical stimulus into a biological signaling. Data are still required to understand better PIEZO1-HX pathophysiology. Recent studies identified proteomics as an accurate and high-input tool to study erythroid progenitors and circulating red cell physiology. Here, we isolated red blood cells from 5 controls and 5 HX patients carrying an identified and pathogenic PIEZO1 mutation and performed a comparative deep proteomic analysis. A total of 603 proteins were identified among which 56 were differentially expressed (40 over expressed and 16 under expressed) between controls and HX with a homogenous expression profile within each group. We observed relevant modifications in the protein expression profile related to PIEZO1 mutations, identifying two main "knots". The first contained both proteins of the chaperonin containing TCP1 complex involved in the assembly of unfolded proteins, and proteins involved in translation. The second contained proteins involved in ubiquitination. Deregulation of proteins involved in protein biosynthesis was also observed in in vitro-produced reticulocytes after Yoda1 exposure. Thus, our work identifies significant changes in the protein content of PIEZO1-HX erythrocytes, revealing a "PIEZO1 signature" and identifying potentially targetable pathways in this disease characterized by a heterogeneous clinical expression and contra-indication of splenectomy.
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Affiliation(s)
- Alexis Caulier
- HEMATIM, CURS, Amiens and Laboratoire d’Hématologie, CHU Amiens, UPJV, Amiens, France
| | - Nicolas Jankovsky
- HEMATIM, CURS, Amiens and Laboratoire d’Hématologie, CHU Amiens, UPJV, Amiens, France
| | - Emilie Fleur Gautier
- 3P5 Proteom’IC, Institut Cochin, INSERM, CNRS, Université Paris Cité, Paris, France
- Institut Imagine-INSERM U1163, Necker Hospital, University of Paris, Paris, France
- Laboratoire d’excellence GR-Ex, Paris, France
| | | | - Corinne Guitton
- Laboratoire d’Hématologie et Filière MCGRE, CHU Bicêtre, Le Kremlin-Bicêtre, France
| | - Hakim Ouled-Haddou
- HEMATIM, CURS, Amiens and Laboratoire d’Hématologie, CHU Amiens, UPJV, Amiens, France
| | - François Guillonneau
- 3P5 Proteom’IC, Institut Cochin, INSERM, CNRS, Université Paris Cité, Paris, France
| | - Patrick Mayeux
- 3P5 Proteom’IC, Institut Cochin, INSERM, CNRS, Université Paris Cité, Paris, France
| | - Virginie Salnot
- 3P5 Proteom’IC, Institut Cochin, INSERM, CNRS, Université Paris Cité, Paris, France
| | - Johanna Bruce
- 3P5 Proteom’IC, Institut Cochin, INSERM, CNRS, Université Paris Cité, Paris, France
| | - Véronique Picard
- Laboratoire d’Hématologie et Filière MCGRE, CHU Bicêtre, Le Kremlin-Bicêtre, France
- Laboratoire d’Hématologie, Faculté de Pharmacie, Université Paris Saclay, Amiens, France
| | - Loïc Garçon
- HEMATIM, CURS, Amiens and Laboratoire d’Hématologie, CHU Amiens, UPJV, Amiens, France
- INSERM U1134, INTS, Paris, France
- Laboratoire d’Hématologie et Filière MCGRE, CHU Bicêtre, Le Kremlin-Bicêtre, France
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11
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Lokdarshi A, von Arnim AG. Review: Emerging roles of the signaling network of the protein kinase GCN2 in the plant stress response. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 320:111280. [PMID: 35643606 PMCID: PMC9197246 DOI: 10.1016/j.plantsci.2022.111280] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/07/2022] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
The pan-eukaryotic protein kinase GCN2 (General Control Nonderepressible2) regulates the translation of mRNAs in response to external and metabolic conditions. Although GCN2 and its substrate, translation initiation factor 2 (eIF2) α, and several partner proteins are substantially conserved in plants, this kinase has assumed novel functions in plants, including in innate immunity and retrograde signaling between the chloroplast and cytosol. How exactly some of the biochemical paradigms of the GCN2 system have diverged in the green plant lineage is only partially resolved. Specifically, conflicting data underscore and cast doubt on whether GCN2 regulates amino acid biosynthesis; also whether phosphorylation of eIF2α can in fact repress global translation or activate mRNA specific translation via upstream open reading frames; and whether GCN2 is controlled in vivo by the level of uncharged tRNA. This review examines the status of research on the eIF2α kinase, GCN2, its function in the response to xenobiotics, pathogens, and abiotic stress conditions, and its rather tenuous role in the translational control of mRNAs.
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Affiliation(s)
- Ansul Lokdarshi
- Department of Biology, Valdosta State University, Valdosta, GA 31698, USA.
| | - Albrecht G von Arnim
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-1939, USA; UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-1939, USA.
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Hernández-Elvira M, Sunnerhagen P. Post-transcriptional regulation during stress. FEMS Yeast Res 2022; 22:6585650. [PMID: 35561747 PMCID: PMC9246287 DOI: 10.1093/femsyr/foac025] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/25/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022] Open
Abstract
To remain competitive, cells exposed to stress of varying duration, rapidity of onset, and intensity, have to balance their expenditure on growth and proliferation versus stress protection. To a large degree dependent on the time scale of stress exposure, the different levels of gene expression control: transcriptional, post-transcriptional and post-translational, will be engaged in stress responses. The post-transcriptional level is appropriate for minute-scale responses to transient stress, and for recovery upon return to normal conditions. The turnover rate, translational activity, covalent modifications, and subcellular localisation of RNA species are regulated under stress by multiple cellular pathways. The interplay between these pathways is required to achieve the appropriate signalling intensity and prevent undue triggering of stress-activated pathways at low stress levels, avoid overshoot, and down-regulate the response in a timely fashion. As much of our understanding of post-transcriptional regulation has been gained in yeast, this review is written with a yeast bias, but attempts to generalise to other eukaryotes. It summarises aspects of how post-transcriptional events in eukaryotes mitigate short-term environmental stresses, and how different pathways interact to optimise the stress response under shifting external conditions.
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Affiliation(s)
- Mariana Hernández-Elvira
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, P.O. Box 462, S-405 30 Göteborg, Sweden
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, P.O. Box 462, S-405 30 Göteborg, Sweden
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Guzikowski AR, Harvey AT, Zhang J, Zhu S, Begovich K, Cohn MH, Wilhelm JE, Zid BM. Differential translation elongation directs protein synthesis in response to acute glucose deprivation in yeast. RNA Biol 2022; 19:636-649. [PMID: 35491906 PMCID: PMC9067459 DOI: 10.1080/15476286.2022.2065784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Protein synthesis is energetically expensive and its rate is influenced by factors such as cell type and environment. Suppression of translation is a canonical response to stressful changes in the cellular environment. In particular, inhibition of the initiation step of translation has been highlighted as the key control step in stress-induced translational suppression as mechanisms that quickly suppress initiation are well-conserved. However, cells have evolved complex regulatory means to control translation apart from initiation. Here, we examine the role of the elongation step of translation in yeast subjected to acute glucose deprivation. The use of ribosome profiling and in vivo reporter assays demonstrated elongation rates slow progressively following glucose removal. We observed that ribosome distribution broadly shifts towards the downstream ends of transcripts after both acute and gradual glucose deprivation but not in response to other stressors. Additionally, on assessed mRNAs, a correlation existed between ribosome occupancy and protein production pre-stress but was lost after stress. These results indicate that stress-induced elongation regulation causes ribosomes to slow down and build up on a considerable proportion of the transcriptome in response to glucose withdrawal. Finally, we report ribosomes that built up along transcripts are competent to resume elongation and complete protein synthesis after readdition of glucose to starved cells. This suggests that yeast has evolved mechanisms to slow translation elongation in response to glucose starvation which do not preclude continuation of protein production from those ribosomes, thereby averting a need for new initiation events to take place to synthesize proteins. Abbreviations: AUG: start codon, bp: base pair(s), CDS: coding sequence, CHX: cycloheximide, eEF2: eukaryotic elongation factor 2, LTM: lactimidomycin, nt: nucleotide, PGK1: 3-phosphoglycerate kinase, ribosomal biogenesis: ribi, RO: ribosome occupancy, RPF: ribosome protected fragment, TE: translational efficiency
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Affiliation(s)
- Anna R. Guzikowski
- Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Alex T. Harvey
- Department of Chemistry & Biochemistry, University of California, San Diego, CA, USA
| | - Jingxiao Zhang
- Department of Chemistry & Biochemistry, University of California, San Diego, CA, USA
| | - Shihui Zhu
- Department of Chemistry & Biochemistry, University of California, San Diego, CA, USA
| | - Kyle Begovich
- Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Molly H. Cohn
- Department of Chemistry & Biochemistry, University of California, San Diego, CA, USA
| | - James E. Wilhelm
- Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Brian M. Zid
- Department of Chemistry & Biochemistry, University of California, San Diego, CA, USA
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14
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The CAR-mRNA Interaction Surface Is a Zipper Extension of the Ribosome A Site. Int J Mol Sci 2022; 23:ijms23031417. [PMID: 35163343 PMCID: PMC8835751 DOI: 10.3390/ijms23031417] [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: 12/30/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/10/2022] Open
Abstract
The ribosome CAR interaction surface behaves as an extension of the decoding center A site and has H-bond interactions with the +1 codon, which is next in line to enter the A site. Through molecular dynamic simulations, we investigated the codon sequence specificity of this CAR–mRNA interaction and discovered a strong preference for GCN codons, suggesting that there may be a sequence-dependent layer of translational regulation dependent on the CAR interaction surface. Dissection of the CAR–mRNA interaction through nucleotide substitution experiments showed that the first nucleotide of the +1 codon dominates over the second nucleotide position, consistent with an energetically favorable zipper-like activity that emanates from the A site through the CAR–mRNA interface. Moreover, the CAR/+1 codon interaction is affected by the identity of nucleotide 3 of +1 GCN codons, which influences the stacking of G and C. Clustering analysis suggests that the A-site decoding center adopts different neighborhood substates that depend on the identity of the +1 codon.
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15
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Kumar GVN, Hoshitsuki K, Rathod S, Ramsey MJ, Kokai L, Kershaw EE, Xie W, Fernandez CA. Mechanistic studies of PEG-asparaginase-induced liver injury and hepatic steatosis in mice. Acta Pharm Sin B 2021; 11:3779-3790. [PMID: 35024306 PMCID: PMC8727916 DOI: 10.1016/j.apsb.2021.11.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 01/19/2023] Open
Abstract
PEGylated-l-asparaginase (PEG-ASNase) is a chemotherapeutic agent used to treat pediatric acute lymphoblastic leukemia (ALL). Its use is avoided in adults due to its high risk of liver injury including hepatic steatosis, with obesity and older age considered risk factors of the injury. Our study aims to elucidate the mechanism of PEG-ASNase-induced liver injury. Mice received 1500 U/kg of PEG-ASNase and were sacrificed 1, 3, 5, and 7 days after drug administration. Liver triglycerides were quantified, and plasma bilirubin, ALT, AST, and non-esterified fatty acids (NEFA) were measured. The mRNA and protein levels of genes involved in hepatic fatty acid synthesis, β-oxidation, very low-density lipoprotein (VLDL) secretion, and white adipose tissue (WAT) lipolysis were determined. Mice developed hepatic steatosis after PEG-ASNase, which associated with increases in bilirubin, ALT, and AST. The hepatic genes Ppara, Lcad/Mcad, Hadhb, Apob100, and Mttp were upregulated, and Srebp-1c and Fas were downregulated after PEG-ASNase. Increased plasma NEFA, WAT loss, and adipose tissue lipolysis were also observed after PEG-ASNase. Furthermore, we found that PEG-ASNase-induced liver injury was exacerbated in obese and aged mice, consistent with clinical studies of ASNase-induced liver injury. Our data suggest that PEG-ASNase-induced liver injury is due to drug-induced lipolysis and lipid redistribution to the liver.
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Affiliation(s)
- Gundala Venkata Naveen Kumar
- Department of Pharmaceutical Sciences and Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA 15261, USA
| | - Keito Hoshitsuki
- Department of Pharmaceutical Sciences and Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA 15261, USA
- Division of General Internal Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Sanjay Rathod
- Department of Pharmaceutical Sciences and Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA 15261, USA
| | - Manda J. Ramsey
- Department of Pharmaceutical Sciences and Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA 15261, USA
| | - Lauren Kokai
- Department of Plastic Surgery, University of Pittsburgh and the McGowan Institute for Regenerative Medicine, Pittsburgh, PA 15261, USA
| | - Erin E. Kershaw
- University of Pittsburgh, Division of Endocrinology, Department of Medicine, Pittsburgh, PA 15261, USA
| | - Wen Xie
- Department of Pharmaceutical Sciences and Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA 15261, USA
| | - Christian A. Fernandez
- Department of Pharmaceutical Sciences and Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA 15261, USA
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RNase Z Oxidative Degradation Impedes tRNA Maturation and is Involved in Streptococcal Translation Regulation in Response to Oxidative Stress. Microbiol Spectr 2021; 9:e0116721. [PMID: 34704809 PMCID: PMC8549757 DOI: 10.1128/spectrum.01167-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
When encountering oxidative stress, organisms selectively upregulate antioxidant genes and simultaneously suppress the translation of most other proteins. Eukaryotes employ multiple strategies to adjust translation at both the initiation and elongation stages; however, how prokaryotes modulate translation under oxidative stress remains unclear. Here, we report that upon hydrogen peroxide (H2O2) challenge, Streptococcus oligofermentans reduced translation via RNase Z (So-RNaseZ) oxidative degradation, thus hindering tRNA maturation. S. oligofermentans encodes all CCA-less tRNAs that require So-RNaseZ for 3′ end maturation. A combination of nonreducing SDS-PAGE and liquid chromatography/tandem mass spectrometry (LC/MS-MS) assays demonstrated that H2O2 oxidation induced Cys38-Cys149 disulfide linkages in recombinant So-RNaseZ protein, and serine substitution of Cys38 or Cys149 abolished these disulfide linkages. Consistently, redox Western blotting also determined intramolecular disulfide-linked So-RNaseZ in H2O2-treated S. oligofermentans cells. The disulfide-linked So-RNaseZ and monomer were both subject to proteolysis, whereas C149S mutation alleviated oxidative degradation of So-RNaseZ, suggesting that H2O2-mediated disulfide linkages substantially contributed to So-RNaseZ degradation. Accordingly, Northern blotting determined that tRNA precursor accumulation and mature tRNA species decrease in H2O2-treated S. oligofermentans. Moreover, reduced overall protein synthesis, as indicated by puromycin incorporation, and retarded growth of S. oligofermentans occurred in an H2O2 concentration-dependent manner. Overexpression of So-RNaseZ not only elevated tRNA precursor processing and protein synthesis but also partly rescued H2O2-suppressed S. oligofermentans growth. Moreover, So-RNaseZ oxidative degradation-mediated translation repression elevated S. oligofermentans survival under high H2O2 stress. Therefore, this work found that So-RNaseZ oxidative degradation-impeded tRNA maturation contributes to streptococcal translation repression and provides the oxidative stress adaptability for S. oligofermentans. IMPORTANCE Translation regulation is a common strategy used by organisms to reduce oxidative damage. Catalase-negative streptococci produce as well as tolerate high levels of H2O2. This work reports a novel translation regulation mechanism employed by Streptococcus oligofermentans in response to H2O2 challenge, in which the key tRNA endonuclease So-RNaseZ is oxidized to form Cys38-Cys149 disulfide linkages and both the disulfide-linked So-RNaseZ and monomers are subject to proteolysis; thus, tRNA maturation, protein translation, and growth are all suppressed. Notably, So-RNaseZ oxidative degradation-mediated translation repression offers oxidative adaptability to S. oligofermentans and enhances its survival against high H2O2 challenge. So-RNaseZ orthologs and H2O2-sensitive cysteines (Cys38 and Cys149) are widely distributed in Streptococcus and Lactococcus species genomes, which also encode all CCA-less tRNAs and lack catalase. Therefore, RNase Z oxidative degradation-based translation regulation could be widely employed by these lactic acid bacteria, including pathogenic streptococci, to cope with H2O2.
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Tamaddondoust RN, Wang Y, Jafarnejad SM, Graber TE, Alain T. The highs and lows of ionizing radiation and its effects on protein synthesis. Cell Signal 2021; 89:110169. [PMID: 34662715 DOI: 10.1016/j.cellsig.2021.110169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/19/2021] [Accepted: 10/06/2021] [Indexed: 11/03/2022]
Abstract
Ionizing radiation (IR) is a constant feature of our environment and one that can dramatically affect organismal health and development. Although the impacts of high-doses of IR on mammalian cells and systems have been broadly explored, there are still challenges in accurately quantifying biological responses to IR, especially in the low-dose range to which most individuals are exposed in their lifetime. The resulting uncertainty has led to the entrenchment of conservative radioprotection policies around the world. Thus, uncovering long-sought molecular mechanisms and tissue responses that are targeted by IR could lead to more informed policymaking and propose new therapeutic avenues for a variety of pathologies. One often overlooked target of IR is mRNA translation, a highly regulated cellular process that consumes more than 40% of the cell's energy. In response to environmental stimuli, regulation of mRNA translation allows for precise and rapid changes to the cellular proteome, and unsurprisingly high-dose of IR was shown to trigger a severe reprogramming of global protein synthesis allowing the cell to conserve energy by preventing the synthesis of unneeded proteins. Nonetheless, under these conditions, certain mRNAs encoding specific proteins are translationally favoured to produce the factors essential to repair the cell or send it down the path of no return through programmed cell death. Understanding the mechanisms controlling protein synthesis in response to varying doses of IR could provide novel insights into how this stress-mediated cellular adaptation is regulated and potentially uncover novel targets for radiosensitization or radioprotection. Here, we review the current literature on the effects of IR at both high- and low-dose on the mRNA translation machinery.
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Affiliation(s)
- Rosette Niloufar Tamaddondoust
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada; Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, Ontario, Canada.
| | - Yi Wang
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada; Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, Ontario, Canada
| | - Seyed Mehdi Jafarnejad
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Tyson E Graber
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Tommy Alain
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada.
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18
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Jiménez-Saucedo T, Berlanga JJ, Rodríguez-Gabriel M. Translational control of gene expression by eIF2 modulates proteostasis and extends lifespan. Aging (Albany NY) 2021; 13:10989-11009. [PMID: 33901016 PMCID: PMC8109070 DOI: 10.18632/aging.203018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/31/2021] [Indexed: 01/14/2023]
Abstract
Although the stress response in eukaryotes depends on early events triggered in cells by environmental insults, long-term processes such as aging are also affected. The loss of cellular proteostasis greatly impacts aging, which is regulated by the balancing of protein synthesis and degradation systems. As translation is the input event in proteostasis, we decided to study the role of translational activity on cell lifespan. Our hypothesis was that a reduction on translational activity or specific changes in translation may increase cellular longevity. Using mutant strains of Schizosaccharomyces pombe and various stress conditions, we showed that translational reduction caused by phosphorylation of eukaryotic translation initiation factor 2 (eIF2) during the exponential growth phase enhances chronological lifespan (CLS). Furthermore, through next-generation sequence analysis, we found eIF2α phosphorylation-dependent translational activation of some specific genes, especially those involved in autophagy. This fact, together with the observed regulation of autophagy, points to a conserved mechanism involving general and specific control of translation and autophagy as mediators of the role of eIF2α phosphorylation in aging.
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Affiliation(s)
- Tamara Jiménez-Saucedo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan José Berlanga
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel Rodríguez-Gabriel
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
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19
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James AM, Seal SE, Bailey AM, Foster GD. Viral inosine triphosphatase: A mysterious enzyme with typical activity, but an atypical function. MOLECULAR PLANT PATHOLOGY 2021; 22:382-389. [PMID: 33471956 PMCID: PMC7865087 DOI: 10.1111/mpp.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 05/03/2023]
Abstract
Plant viruses typically have highly condensed genomes, yet the plant-pathogenic viruses Cassava brown streak virus, Ugandan cassava brown streak virus, and Euphorbia ringspot virus are unusual in encoding an enzyme not yet found in any other virus, the "house-cleaning" enzyme inosine triphosphatase. Inosine triphosphatases (ITPases) are highly conserved enzymes that occur in all kingdoms of life and perform a house-cleaning function by hydrolysing the noncanonical nucleotide inosine triphosphate to inosine monophosphate. The ITPases encoded by cassava brown streak virus and Ugandan cassava brown streak virus have been characterized biochemically and are shown to have typical ITPase activity. However, their biological role in virus infection has yet to be elucidated. Here we review what is known of viral-encoded ITPases and speculate on potential roles in infection with the aim of generating a greater understanding of cassava brown streak viruses, a group of the world's most devastating viruses.
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Affiliation(s)
- Amy M. James
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
| | - Susan E. Seal
- Natural Resources Institute, Chatham MaritimeGillinghamUK
| | - Andy M. Bailey
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
| | - Gary D. Foster
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
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20
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Scopino K, Dalgarno C, Nachmanoff C, Krizanc D, Thayer KM, Weir MP. Arginine Methylation Regulates Ribosome CAR Function. Int J Mol Sci 2021; 22:ijms22031335. [PMID: 33572867 PMCID: PMC7866298 DOI: 10.3390/ijms22031335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/16/2022] Open
Abstract
The ribosome CAR interaction surface is hypothesized to provide a layer of translation regulation through hydrogen-bonding to the +1 mRNA codon that is next to enter the ribosome A site during translocation. The CAR surface consists of three residues, 16S/18S rRNA C1054, A1196 (E. coli 16S numbering), and R146 of yeast ribosomal protein Rps3. R146 can be methylated by the Sfm1 methyltransferase which is downregulated in stressed cells. Through molecular dynamics analysis, we show here that methylation of R146 compromises the integrity of CAR by reducing the cation-pi stacking of the R146 guanidinium group with A1196, leading to reduced CAR hydrogen-bonding with the +1 codon. We propose that ribosomes assembled under stressed conditions have unmethylated R146, resulting in elevated CAR/+1 codon interactions, which tunes translation levels in response to the altered cellular context.
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Affiliation(s)
- Kristen Scopino
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA; (K.S.); (C.D.); (C.N.)
| | - Carol Dalgarno
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA; (K.S.); (C.D.); (C.N.)
| | - Clara Nachmanoff
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA; (K.S.); (C.D.); (C.N.)
| | - Daniel Krizanc
- Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA; (D.K.); (K.M.T.)
- College of Integrative Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Kelly M. Thayer
- Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA; (D.K.); (K.M.T.)
- College of Integrative Sciences, Wesleyan University, Middletown, CT 06459, USA
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Michael P. Weir
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA; (K.S.); (C.D.); (C.N.)
- College of Integrative Sciences, Wesleyan University, Middletown, CT 06459, USA
- Correspondence:
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21
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Rubio A, Ghosh S, Mülleder M, Ralser M, Mata J. Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast. Nucleic Acids Res 2021; 49:383-399. [PMID: 33313903 PMCID: PMC7797079 DOI: 10.1093/nar/gkaa1180] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 11/13/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
Translational control is essential in response to stress. We investigated the translational programmes launched by the fission yeast Schizosaccharomyces pombe upon five environmental stresses. We also explored the contribution of defence pathways to these programmes: The Integrated Stress Response (ISR), which regulates translation initiation, and the stress-response MAPK pathway. We performed ribosome profiling of cells subjected to each stress, in wild type cells and in cells with the defence pathways inactivated. The transcription factor Fil1, a functional homologue of the yeast Gcn4 and the mammalian Atf4 proteins, was translationally upregulated and required for the response to most stresses. Moreover, many mRNAs encoding proteins required for ribosome biogenesis were translationally downregulated. Thus, several stresses trigger a universal translational response, including reduced ribosome production and a Fil1-mediated transcriptional programme. Surprisingly, ribosomes stalled on tryptophan codons upon oxidative stress, likely due to a decrease in charged tRNA-Tryptophan. Stalling caused ribosome accumulation upstream of tryptophan codons (ribosome queuing/collisions), demonstrating that stalled ribosomes affect translation elongation by other ribosomes. Consistently, tryptophan codon stalling led to reduced translation elongation and contributed to the ISR-mediated inhibition of initiation. We show that different stresses elicit common and specific translational responses, revealing a novel role in Tryptophan-tRNA availability.
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Affiliation(s)
- Angela Rubio
- Department of Biochemistry, University of Cambridge, UK
| | - Sanjay Ghosh
- Department of Biochemistry, University of Cambridge, UK
| | - Michael Mülleder
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Markus Ralser
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, UK
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22
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Terrey M, Adamson SI, Gibson AL, Deng T, Ishimura R, Chuang JH, Ackerman SL. GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis. eLife 2020; 9:e62731. [PMID: 33186095 PMCID: PMC7665888 DOI: 10.7554/elife.62731] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022] Open
Abstract
Ribosome-associated quality control pathways respond to defects in translational elongation to recycle arrested ribosomes and degrade aberrant polypeptides and mRNAs. Loss of a tRNA gene leads to ribosomal pausing that is resolved by the translational GTPase GTPBP2, and in its absence causes neuron death. Here, we show that loss of the homologous protein GTPBP1 during tRNA deficiency in the mouse brain also leads to codon-specific ribosome pausing and neurodegeneration, suggesting that these non-redundant GTPases function in the same pathway to mitigate ribosome pausing. As observed in Gtpbp2-/- mice (Ishimura et al., 2016), GCN2-mediated activation of the integrated stress response (ISR) was apparent in the Gtpbp1-/- brain. We observed decreased mTORC1 signaling which increased neuronal death, whereas ISR activation was neuroprotective. Our data demonstrate that GTPBP1 functions as an important quality control mechanism during translation elongation and suggest that translational signaling pathways intricately interact to regulate neuronal homeostasis during defective elongation.
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Affiliation(s)
- Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
- Graduate School of Biomedical Sciences and Engineering, University of MaineOronoUnited States
| | - Scott I Adamson
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Alana L Gibson
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Tianda Deng
- Division of Biological Sciences, Section of Molecular Biology, University of California, San DiegoSan DiegoUnited States
| | - Ryuta Ishimura
- The Jackson Laboratory for Mammalian GeneticsBar HarborUnited States
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
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Xie N, Zhang L, Gao W, Huang C, Huber PE, Zhou X, Li C, Shen G, Zou B. NAD + metabolism: pathophysiologic mechanisms and therapeutic potential. Signal Transduct Target Ther 2020; 5:227. [PMID: 33028824 PMCID: PMC7539288 DOI: 10.1038/s41392-020-00311-7] [Citation(s) in RCA: 372] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/04/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) and its metabolites function as critical regulators to maintain physiologic processes, enabling the plastic cells to adapt to environmental changes including nutrient perturbation, genotoxic factors, circadian disorder, infection, inflammation and xenobiotics. These effects are mainly achieved by the driving effect of NAD+ on metabolic pathways as enzyme cofactors transferring hydrogen in oxidation-reduction reactions. Besides, multiple NAD+-dependent enzymes are involved in physiology either by post-synthesis chemical modification of DNA, RNA and proteins, or releasing second messenger cyclic ADP-ribose (cADPR) and NAADP+. Prolonged disequilibrium of NAD+ metabolism disturbs the physiological functions, resulting in diseases including metabolic diseases, cancer, aging and neurodegeneration disorder. In this review, we summarize recent advances in our understanding of the molecular mechanisms of NAD+-regulated physiological responses to stresses, the contribution of NAD+ deficiency to various diseases via manipulating cellular communication networks and the potential new avenues for therapeutic intervention.
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Affiliation(s)
- Na Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Lu Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Wei Gao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Peter Ernst Huber
- CCU Molecular and Radiation Oncology, German Cancer Research Center; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Xiaobo Zhou
- First Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Changlong Li
- West China School of Basic Medical Sciences & Forensic Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Guobo Shen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
| | - Bingwen Zou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
- CCU Molecular and Radiation Oncology, German Cancer Research Center; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany.
- Department of Thoracic Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
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24
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Zhigailov AV, Alexandrova AM, Nizkorodova AS, Stanbekova GE, Kryldakov RV, Karpova OV, Polimbetova NS, Halford NG, Iskakov BK. Evidence That Phosphorylation of the α-Subunit of eIF2 Does Not Essentially Inhibit mRNA Translation in Wheat Germ Cell-Free System. FRONTIERS IN PLANT SCIENCE 2020; 11:936. [PMID: 32655610 PMCID: PMC7324750 DOI: 10.3389/fpls.2020.00936] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/09/2020] [Indexed: 05/30/2023]
Abstract
A mechanism based on reversible phosphorylation of the α-subunit of eukaryotic initiation factor 2 (eIF2α) has been confirmed as an important regulatory pathway for the inhibition of protein synthesis in mammalian and yeast cells, while plants constitute the significant exception. We studied the induction of TaeIF2α phosphorylation in germinated wheat (Triticum aestivum) embryos subjected to different adverse conditions. Data confirmed that formation of TaeIF2(αP) was not a general response, as no phosphorylation was observed under salt, oxidative, or heat stress. Nevertheless, treatment by salicylic acid, UV-light, cold shock and histidinol did induce phosphorylation of TaeIF2α of wheat as has been established previously for AteIF2α in Arabidopsis (Arabidopsis thaliana). The influence of TaeIF2α phosphorylation on translation of reporter mRNA with different 5'-untranslated regions (5'UTRs) was studied in wheat germ cell-free system (WG-CFS), in which TaeIF2α was first phosphorylated either by heterologous recombinant human protein kinase, HsPKR (activated by double-stranded (ds)RNA), or by endogenous protein kinase TaGCN2 (activated by histidinol). Pretreatment of WG-CFS with HsPKR in the presence of dsRNA or with histidinol resulted in intense phosphorylation of TaeIF2α; however, the translation levels of all tested mRNAs decreased by only 10-15% and remained relatively high. In addition, factor OceIF2 from rabbit (Oryctolagus cuniculus) bound GDP much more strongly than the homologous factor TaeIF2 from wheat germ. Furthermore, factor OceIF2B was able to stimulate guanine nucleotide exchange (GDP→GTP) on OceIF2 but had no effect on a similar exchange on TaeIF2. These results suggest that the mechanism of stress response via eIF2α phosphorylation is not identical in all eukaryotes, and further research is required to find and study in detail new plant-specific mechanisms that may inhibit overall protein synthesis in plants under stress.
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Affiliation(s)
- Andrey V. Zhigailov
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Science Committee, Ministry of Education and Science, Almaty, Kazakhstan
| | - Alena M. Alexandrova
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Science Committee, Ministry of Education and Science, Almaty, Kazakhstan
| | - Anna S. Nizkorodova
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Science Committee, Ministry of Education and Science, Almaty, Kazakhstan
| | - Gulshan E. Stanbekova
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Science Committee, Ministry of Education and Science, Almaty, Kazakhstan
| | - Ruslan V. Kryldakov
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Science Committee, Ministry of Education and Science, Almaty, Kazakhstan
- Institute of Plant Biology and Biotechnology, Science Committee, Ministry of Education and Science, Almaty, Kazakhstan
| | - Oxana V. Karpova
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Science Committee, Ministry of Education and Science, Almaty, Kazakhstan
| | - Nailya S. Polimbetova
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Science Committee, Ministry of Education and Science, Almaty, Kazakhstan
| | - Nigel G. Halford
- Plant Sciences Department, Rothamsted Research, Harpenden, United Kingdom
| | - Bulat K. Iskakov
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Science Committee, Ministry of Education and Science, Almaty, Kazakhstan
- Institute of Plant Biology and Biotechnology, Science Committee, Ministry of Education and Science, Almaty, Kazakhstan
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25
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Knight JRP, Garland G, Pöyry T, Mead E, Vlahov N, Sfakianos A, Grosso S, De-Lima-Hedayioglu F, Mallucci GR, von der Haar T, Smales CM, Sansom OJ, Willis AE. Control of translation elongation in health and disease. Dis Model Mech 2020; 13:dmm043208. [PMID: 32298235 PMCID: PMC7104864 DOI: 10.1242/dmm.043208] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Regulation of protein synthesis makes a major contribution to post-transcriptional control pathways. During disease, or under stress, cells initiate processes to reprogramme protein synthesis and thus orchestrate the appropriate cellular response. Recent data show that the elongation stage of protein synthesis is a key regulatory node for translational control in health and disease. There is a complex set of factors that individually affect the overall rate of elongation and, for the most part, these influence either transfer RNA (tRNA)- and eukaryotic elongation factor 1A (eEF1A)-dependent codon decoding, and/or elongation factor 2 (eEF2)-dependent ribosome translocation along the mRNA. Decoding speeds depend on the relative abundance of each tRNA, the cognate:near-cognate tRNA ratios and the degree of tRNA modification, whereas eEF2-dependent ribosome translocation is negatively regulated by phosphorylation on threonine-56 by eEF2 kinase. Additional factors that contribute to the control of the elongation rate include epigenetic modification of the mRNA, coding sequence variation and the expression of eIF5A, which stimulates peptide bond formation between proline residues. Importantly, dysregulation of elongation control is central to disease mechanisms in both tumorigenesis and neurodegeneration, making the individual key steps in this process attractive therapeutic targets. Here, we discuss the relative contribution of individual components of the translational apparatus (e.g. tRNAs, elongation factors and their modifiers) to the overall control of translation elongation and how their dysregulation contributes towards disease processes.
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Affiliation(s)
| | - Gavin Garland
- MRC Toxicology Unit, University of Cambridge, Lancaster Road, Leicester LE1 9HN, UK
| | - Tuija Pöyry
- MRC Toxicology Unit, University of Cambridge, Lancaster Road, Leicester LE1 9HN, UK
| | - Emma Mead
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Nikola Vlahov
- Beatson Institute for Cancer Research, Glasgow G61 1BD, UK
| | - Aristeidis Sfakianos
- MRC Toxicology Unit, University of Cambridge, Lancaster Road, Leicester LE1 9HN, UK
| | - Stefano Grosso
- MRC Toxicology Unit, University of Cambridge, Lancaster Road, Leicester LE1 9HN, UK
| | | | - Giovanna R Mallucci
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0XY, UK
| | | | - C Mark Smales
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Owen J Sansom
- Beatson Institute for Cancer Research, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Lancaster Road, Leicester LE1 9HN, UK
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