1
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Rafnsdottir S, Jang K, Halldorsdottir ST, Vinod M, Tomasdottir A, Möller K, Halldorsdottir K, Reynisdottir T, Atladottir LH, Allison KE, Ostacolo K, He J, Zhang L, Northington FJ, Magnusdottir E, Chavez-Valdez R, Anderson KJ, Bjornsson HT. SMYD5 is a regulator of the mild hypothermia response. Cell Rep 2024; 43:114554. [PMID: 39083378 DOI: 10.1016/j.celrep.2024.114554] [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: 04/18/2024] [Revised: 06/24/2024] [Accepted: 07/12/2024] [Indexed: 08/02/2024] Open
Abstract
The mild hypothermia response (MHR) maintains organismal homeostasis during cold exposure and is thought to be critical for the neuroprotection documented with therapeutic hypothermia. To date, little is known about the transcriptional regulation of the MHR. We utilize a forward CRISPR-Cas9 mutagenesis screen to identify the histone lysine methyltransferase SMYD5 as a regulator of the MHR. SMYD5 represses the key MHR gene SP1 at euthermia. This repression correlates with temperature-dependent levels of histone H3 lysine 26 trimethylation (H3K36me3) at the SP1 locus and globally, indicating that the mammalian MHR is regulated at the level of histone modifications. We have identified 37 additional SMYD5-regulated temperature-dependent genes, suggesting a broader MHR-related role for SMYD5. Our study provides an example of how histone modifications integrate environmental cues into the genetic circuitry of mammalian cells and provides insights that may yield therapeutic avenues for neuroprotection after catastrophic events.
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Affiliation(s)
- Salvor Rafnsdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kijin Jang
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Sara Tholl Halldorsdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Meghna Vinod
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Arnhildur Tomasdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Katrin Möller
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Katrin Halldorsdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Tinna Reynisdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Laufey Halla Atladottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Kevin Ostacolo
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland; Department of Genetics and Molecular Medicine, Landspitali University Hospital, Reykjavik, Iceland
| | - Jin He
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East Lansing, MI, USA
| | - Li Zhang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Frances J Northington
- Division of Neonatology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Neuroscience Intensive Care Nursery Program, Johns Hopkins University, Baltimore, MD, USA
| | - Erna Magnusdottir
- Department of Biomedical Science and Department of Anatomy, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Raul Chavez-Valdez
- Division of Neonatology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Neuroscience Intensive Care Nursery Program, Johns Hopkins University, Baltimore, MD, USA
| | - Kimberley Jade Anderson
- Department of Genetics and Molecular Medicine, Landspitali University Hospital, Reykjavik, Iceland
| | - Hans Tomas Bjornsson
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland; McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA; Department of Genetics and Molecular Medicine, Landspitali University Hospital, Reykjavik, Iceland.
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2
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Rafnsdottir S, Jang K, Halldorsdottir ST, Vinod M, Tomasdottir A, Möller K, Halldorsdottir K, Reynisdottir T, Atladottir LH, Allison KE, Ostacolo K, He J, Zhang L, Northington FJ, Magnusdottir E, Chavez-Valdez R, Anderson KJ, Bjornsson HT. SMYD5 is a regulator of the mild hypothermia response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.11.540170. [PMID: 37333301 PMCID: PMC10274674 DOI: 10.1101/2023.05.11.540170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The mild hypothermia response (MHR) maintains organismal homeostasis during cold exposure and is thought to be critical for the neuroprotection documented with therapeutic hypothermia. To date, little is known about the transcriptional regulation of the MHR. We utilize a forward CRISPR-Cas9 mutagenesis screen to identify the histone lysine methyltransferase SMYD5 as a regulator of the MHR. SMYD5 represses the key MHR gene SP1 at euthermia. This repression correlates with temperature-dependent levels of H3K36me3 at the SP1-locus and globally, indicating that the mammalian MHR is regulated at the level of histone modifications. We have identified 37 additional SMYD5 regulated temperature-dependent genes, suggesting a broader MHR-related role for SMYD5. Our study provides an example of how histone modifications integrate environmental cues into the genetic circuitry of mammalian cells and provides insights that may yield therapeutic avenues for neuroprotection after catastrophic events.
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Affiliation(s)
- Salvor Rafnsdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Kijin Jang
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Sara Tholl Halldorsdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Meghna Vinod
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Arnhildur Tomasdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Katrin Möller
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Katrin Halldorsdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Tinna Reynisdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Laufey Halla Atladottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | | | - Kevin Ostacolo
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
- Department of Genetics and Molecular Medicine, Landspitali University Hospital; Reykjavik, Iceland
| | - Jin He
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University; MI, USA
| | - Li Zhang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Frances J. Northington
- Division of Neonatology, Department of Pediatrics, Johns Hopkins University School of Medicine; Baltimore, MD, USA
- Neuroscience Intensive Care Nursery Program, Johns Hopkins University; Baltimore, MD, USA
| | - Erna Magnusdottir
- Department of Biomedical Science and Department of Anatomy, Faculty of Medicine, University of Iceland; Reykjavík, Iceland
| | - Raul Chavez-Valdez
- Division of Neonatology, Department of Pediatrics, Johns Hopkins University School of Medicine; Baltimore, MD, USA
- Neuroscience Intensive Care Nursery Program, Johns Hopkins University; Baltimore, MD, USA
| | - Kimberley Jade Anderson
- Department of Genetics and Molecular Medicine, Landspitali University Hospital; Reykjavik, Iceland
| | - Hans Tomas Bjornsson
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University; Baltimore, MD, USA
- Department of Genetics and Molecular Medicine, Landspitali University Hospital; Reykjavik, Iceland
- Lead contact
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3
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Kamata T, Yamada S, Sekijima T. Differential AMPK-mediated metabolic regulation observed in hibernation-style polymorphisms in Siberian chipmunks. Front Physiol 2023; 14:1220058. [PMID: 37664438 PMCID: PMC10468594 DOI: 10.3389/fphys.2023.1220058] [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: 05/10/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Hibernation is a unique physiological phenomenon allowing extreme hypothermia in endothermic mammals. Hypometabolism and hypothermia tolerance in hibernating animals have been investigated with particular interest; recently, studies of cultured cells and manipulation of the nervous system have made it possible to reproduce physiological states related to hypothermia induction. However, much remains unknown about the periodic regulation of hibernation. In particular, the physiological mechanisms facilitating the switch from an active state to a hibernation period, including behavioral changes and the acquisition of hypothermia tolerance remain to be elucidated. AMPK is a protein known to play a central role not only in feeding behavior but also in metabolic regulation in response to starvation. Our previous research has revealed that chipmunks activate AMPK in the brain during hibernation. However, whether AMPK is activated during winter in non-hibernating animals is unknown. Previous comparative studies between hibernating and non-hibernating animals have often been conducted between different species, consequently it has been impossible to account for the effects of phylogenetic differences. Our long-term monitoring of siberian chipmunks, has revealed intraspecific variation between those individuals that hibernate annually and those that never become hypothermic. Apparent differences were found between hibernating and non-hibernating types with seasonal changes in lifespan and blood HP levels. By comparing seasonal changes in AMPK activity between these polymorphisms, we clarified the relationship between hibernation and AMPK regulation. In hibernating types, phosphorylation of p-AMPK and p-ACC was enhanced throughout the brain during hibernation, indicating that AMPK-mediated metabolic regulation is activated. In non-hibernating types, AMPK and ACC were not seasonally activated. In addition, AMPK activation in the hypothalamus had already begun during high Tb before hibernation. Changes in AMPK activity in the brain during hibernation may be driven by circannual rhythms, suggesting a hibernation-regulatory mechanism involving AMPK activation independent of Tb. The differences in brain AMPK regulation between hibernators and non-hibernators revealed in this study were based on a single species thus did not involve phylogenetic differences, thereby supporting the importance of brain temperature-independent AMPK activation in regulating seasonal metabolism in hibernating animals.
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Affiliation(s)
- Taito Kamata
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Shintaro Yamada
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
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Perez-Pouchoulen M, Jaiyesimi A, Bardhi K, Waddell J, Banerjee A. Hypothermia increases cold-inducible protein expression and improves cerebellar-dependent learning after hypoxia ischemia in the neonatal rat. Pediatr Res 2023; 94:539-546. [PMID: 36810641 PMCID: PMC10403381 DOI: 10.1038/s41390-023-02535-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Hypoxic ischemic encephalopathy remains a significant cause of developmental disability.1,2 The standard of care for term infants is hypothermia, which has multifactorial effects.3-5 Therapeutic hypothermia upregulates the cold-inducible protein RNA binding motif 3 (RBM3) that is highly expressed in developing and proliferative regions of the brain.6,7 The neuroprotective effects of RBM3 in adults are mediated by its ability to promote the translation of mRNAs such as reticulon 3 (RTN3).8 METHODS: Hypoxia ischemia or control procedure was conducted in Sprague Dawley rat pups on postnatal day 10 (PND10). Pups were immediately assigned to normothermia or hypothermia at the end of the hypoxia. In adulthood, cerebellum-dependent learning was tested using the conditioned eyeblink reflex. The volume of the cerebellum and the magnitude of cerebral injury were measured. A second study quantified RBM3 and RTN3 protein levels in the cerebellum and hippocampus collected during hypothermia. RESULTS Hypothermia reduced cerebral tissue loss and protected cerebellar volume. Hypothermia also improved learning of the conditioned eyeblink response. RBM3 and RTN3 protein expression were increased in the cerebellum and hippocampus of rat pups subjected to hypothermia on PND10. CONCLUSIONS Hypothermia was neuroprotective in male and female pups and reversed subtle changes in the cerebellum after hypoxic ischemic. IMPACT Hypoxic ischemic produced tissue loss and a learning deficit in the cerebellum. Hypothermia reversed both the tissue loss and learning deficit. Hypothermia increased cold-responsive protein expression in the cerebellum and hippocampus. Our results confirm cerebellar volume loss contralateral to the carotid artery ligation and injured cerebral hemisphere, suggesting crossed-cerebellar diaschisis in this model. Understanding the endogenous response to hypothermia might improve adjuvant interventions and expand the clinical utility of this intervention.
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Affiliation(s)
| | - Ayodele Jaiyesimi
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Keti Bardhi
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jaylyn Waddell
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Aditi Banerjee
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
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5
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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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6
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Knight TJ, Povey JF, Vito D, Mohindra A, Jaques CM, Smales CM. Manipulation of mRNA translation elongation influences the fragmentation of a biotherapeutic Fc-fusion protein produced in CHO cells. Biotechnol Bioeng 2022; 119:3408-3420. [PMID: 36082414 PMCID: PMC9826484 DOI: 10.1002/bit.28230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/05/2022] [Accepted: 09/01/2022] [Indexed: 01/11/2023]
Abstract
Mammalian cells, particularly Chinese hamster ovary cells, are the dominant system for the production of protein-based biotherapeutics, however, product degradation, particularly of Fc-fusion proteins, is sometimes observed that impacts the quality of the protein generated. Here, we identify the site of fragmentation of a model immunoglobulin G1 Fc-fusion protein, show that the observed clipping and aggregation are decreased by reduced temperature culturing, that the fragmentation/clipping is intracellular, and that reduced clipping at a lower temperature (<37°C) relates to mesenger RNA (mRNA) translation elongation. We subsequently show that reduced fragmentation can be achieved at 37°C by addition of chemical reagents that slow translation elongation. We then modified mRNA translation elongation speeds by designing different transcript sequences for the Fc-fusion protein based on alternative codon usage and improved the product yield at 37°C, and the ratio of intact to a fragmented product. Our data suggest that rapid elongation results in misfolding that decreases product fidelity, generating a region susceptible to degradation/proteolysis, whilst the slowing of mRNA translation improves the folding, reducing susceptibility to fragmentation. Manipulation of mRNA translation and/or the target Fc-fusion transcript is, therefore, an approach that can be applied to potentially reduce fragmentation of clipping-prone Fc-fusion proteins.
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Affiliation(s)
- Tanya J. Knight
- School of Biosciences, Industrial Biotechnology CentreUniversity of KentCanterbury, KentUK
| | - Jane F. Povey
- School of Biosciences, Industrial Biotechnology CentreUniversity of KentCanterbury, KentUK
| | - Davide Vito
- School of Biosciences, Industrial Biotechnology CentreUniversity of KentCanterbury, KentUK
| | | | | | - C. Mark Smales
- School of Biosciences, Industrial Biotechnology CentreUniversity of KentCanterbury, KentUK,National Institute for Bioprocessing Research and TrainingBlackrock Co.DublinIreland
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7
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Li Y, Liu Y, Jin L, Peng R. Crosstalk between Ca 2+ and Other Regulators Assists Plants in Responding to Abiotic Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11101351. [PMID: 35631776 PMCID: PMC9148064 DOI: 10.3390/plants11101351] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 05/08/2023]
Abstract
Plants have evolved many strategies for adaptation to extreme environments. Ca2+, acting as an important secondary messenger in plant cells, is a signaling molecule involved in plants' response and adaptation to external stress. In plant cells, almost all kinds of abiotic stresses are able to raise cytosolic Ca2+ levels, and the spatiotemporal distribution of this molecule in distant cells suggests that Ca2+ may be a universal signal regulating different kinds of abiotic stress. Ca2+ is used to sense and transduce various stress signals through its downstream calcium-binding proteins, thereby inducing a series of biochemical reactions to adapt to or resist various stresses. This review summarizes the roles and molecular mechanisms of cytosolic Ca2+ in response to abiotic stresses such as drought, high salinity, ultraviolet light, heavy metals, waterlogging, extreme temperature and wounding. Furthermore, we focused on the crosstalk between Ca2+ and other signaling molecules in plants suffering from extreme environmental stress.
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8
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Stoneley M, Harvey RF, Mulroney TE, Mordue R, Jukes-Jones R, Cain K, Lilley KS, Sawarkar R, Willis AE. Unresolved stalled ribosome complexes restrict cell-cycle progression after genotoxic stress. Mol Cell 2022; 82:1557-1572.e7. [PMID: 35180429 PMCID: PMC9098122 DOI: 10.1016/j.molcel.2022.01.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 01/01/2023]
Abstract
During the translation surveillance mechanism known as ribosome-associated quality control, the ASC-1 complex (ASCC) disassembles ribosomes stalled on the mRNA. Here, we show that there are two distinct classes of stalled ribosome. Ribosomes stalled by translation elongation inhibitors or methylated mRNA are short lived in human cells because they are split by the ASCC. In contrast, although ultraviolet light and 4-nitroquinoline 1-oxide induce ribosome stalling by damaging mRNA, and the ASCC is recruited to these stalled ribosomes, we found that they are refractory to the ASCC. Consequently, unresolved UV- and 4NQO-stalled ribosomes persist in human cells. We show that ribosome stalling activates cell-cycle arrest, partly through ZAK-p38MAPK signaling, and that this cell-cycle delay is prolonged when the ASCC cannot resolve stalled ribosomes. Thus, we propose that the sensitivity of stalled ribosomes to the ASCC influences the kinetics of stall resolution, which in turn controls the adaptive stress response.
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Affiliation(s)
- Mark Stoneley
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
| | - Robert F Harvey
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Thomas E Mulroney
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Ryan Mordue
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Rebekah Jukes-Jones
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Kelvin Cain
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, UK
| | - Ritwick Sawarkar
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
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9
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Ku YS, Cheung MY, Cheng SS, Nadeem MA, Chung G, Lam HM. Using the Knowledge of Post-transcriptional Regulations to Guide Gene Selections for Molecular Breeding in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:867731. [PMID: 35432392 PMCID: PMC9009170 DOI: 10.3389/fpls.2022.867731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The omics approaches allow the scientific community to successfully identify genomic regions associated with traits of interest for marker-assisted breeding. Agronomic traits such as seed color, yield, growth habit, and stress tolerance have been the targets for soybean molecular breeding. Genes governing these traits often undergo post-transcriptional modifications, which should be taken into consideration when choosing elite genes for molecular breeding. Post-transcriptional regulations of genes include transcript regulations, protein modifications, and even the regulation of the translational machinery. Transcript regulations involve elements such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) for the maintenance of transcript stability or regulation of translation efficiency. Protein modifications involve molecular modifications of target proteins and the alterations of their interacting partners. Regulations of the translational machinery include those on translation factors and the ribosomal protein complex. Post-transcriptional regulations usually involve a set of genes instead of a single gene. Such a property may facilitate molecular breeding. In this review, we will discuss the post-transcriptional modifications of genes related to favorable agronomic traits such as stress tolerance, growth, and nutrient uptake, using examples from soybean as well as other crops. The examples from other crops may guide the selection of genes for marker-assisted breeding in soybean.
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Affiliation(s)
- Yee-Shan Ku
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Sau-Shan Cheng
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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10
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Woodward K, Shirokikh NE. Translational control in cell ageing: an update. Biochem Soc Trans 2021; 49:2853-2869. [PMID: 34913471 PMCID: PMC8786278 DOI: 10.1042/bst20210844] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 12/28/2022]
Abstract
Cellular ageing is one of the main drivers of organismal ageing and holds keys towards improving the longevity and quality of the extended life. Elucidating mechanisms underlying the emergence of the aged cells as well as their altered responses to the environment will help understanding the evolutionarily defined longevity preferences across species with different strategies of survival. Much is understood about the role of alterations in the DNA, including many epigenetic modifications such as methylation, in relation to the aged cell phenotype. While transcriptomes of the aged cells are beginning to be better-characterised, their translational responses remain under active investigation. Many of the translationally controlled homeostatic pathways are centred around mitigation of DNA damage, cell stress response and regulation of the proliferative potential of the cells, and thus are critical for the aged cell function. Translation profiling-type studies have boosted the opportunities in discovering the function of protein biosynthesis control and are starting to be applied to the aged cells. Here, we provide a summary of the current knowledge about translational mechanisms considered to be commonly altered in the aged cells, including the integrated stress response-, mechanistic target of Rapamycin- and elongation factor 2 kinase-mediated pathways. We enlist and discuss findings of the recent works that use broad profiling-type approaches to investigate the age-related translational pathways. We outline the limitations of the methods and the remaining unknowns in the established ageing-associated translation mechanisms, and flag translational mechanisms with high prospective importance in ageing, for future studies.
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Affiliation(s)
- Katrina Woodward
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra, ACT 2601, Australia
| | - Nikolay E. Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra, ACT 2601, Australia
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11
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Knight JRP, Vlahov N, Gay DM, Ridgway RA, Faller WJ, Proud C, Mallucci GR, von der Haar T, Smales CM, Willis AE, Sansom OJ. Rpl24Bst mutation suppresses colorectal cancer by promoting eEF2 phosphorylation via eEF2K. eLife 2021; 10:e69729. [PMID: 34895463 PMCID: PMC8668188 DOI: 10.7554/elife.69729] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 11/26/2021] [Indexed: 12/15/2022] Open
Abstract
Increased protein synthesis supports the rapid cell proliferation associated with cancer. The Rpl24Bst mutant mouse reduces the expression of the ribosomal protein RPL24 and has been used to suppress translation and limit tumorigenesis in multiple mouse models of cancer. Here, we show that Rpl24Bst also suppresses tumorigenesis and proliferation in a model of colorectal cancer (CRC) with two common patient mutations, Apc and Kras. In contrast to previous reports, Rpl24Bst mutation has no effect on ribosomal subunit abundance but suppresses translation elongation through phosphorylation of eEF2, reducing protein synthesis by 40% in tumour cells. Ablating eEF2 phosphorylation in Rpl24Bst mutant mice by inactivating its kinase, eEF2K, completely restores the rates of elongation and protein synthesis. Furthermore, eEF2K activity is required for the Rpl24Bst mutant to suppress tumorigenesis. This work demonstrates that elevation of eEF2 phosphorylation is an effective means to suppress colorectal tumorigenesis with two driver mutations. This positions translation elongation as a therapeutic target in CRC, as well as in other cancers where the Rpl24Bst mutation has a tumour suppressive effect in mouse models.
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Affiliation(s)
- John RP Knight
- CRUK Beatson Institute, Garscube EstateGlasgowUnited Kingdom
| | - Nikola Vlahov
- CRUK Beatson Institute, Garscube EstateGlasgowUnited Kingdom
| | - David M Gay
- CRUK Beatson Institute, Garscube EstateGlasgowUnited Kingdom
- Institute of Cancer Sciences, University of GlasgowGlasgowUnited Kingdom
| | | | | | - Christopher Proud
- Department of Biological Sciences, University of AdelaideAdelaideAustralia
- Lifelong Health, South Australian Health and Medical Research InstituteAdelaideAustralia
| | - Giovanna R Mallucci
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of CambridgeCambridgeUnited Kingdom
| | - Tobias von der Haar
- School of Biosciences, Division of Natural Sciences, University of KentKentUnited Kingdom
| | | | - Anne E Willis
- MRC Toxicology Unit, University of CambridgeCambridgeUnited Kingdom
| | - Owen J Sansom
- CRUK Beatson Institute, Garscube EstateGlasgowUnited Kingdom
- Institute of Cancer Sciences, University of GlasgowGlasgowUnited Kingdom
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12
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Peretti D, Smith HL, Verity N, Humoud I, de Weerd L, Swinden DP, Hayes J, Mallucci GR. TrkB signaling regulates the cold-shock protein RBM3-mediated neuroprotection. Life Sci Alliance 2021; 4:4/4/e202000884. [PMID: 33563652 PMCID: PMC7893816 DOI: 10.26508/lsa.202000884] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 02/02/2023] Open
Abstract
Increasing levels of the cold-shock protein, RNA-binding motif 3 (RBM3), either through cooling or by ectopic over-expression, prevents synapse and neuronal loss in mouse models of neurodegeneration. To exploit this process therapeutically requires an understanding of mechanisms controlling cold-induced RBM3 expression. Here, we show that cooling increases RBM3 through activation of TrkB via PLCγ1 and pCREB signaling. RBM3, in turn, has a hitherto unrecognized negative feedback on TrkB-induced ERK activation through induction of its specific phosphatase, DUSP6. Thus, RBM3 mediates structural plasticity through a distinct, non-canonical activation of TrkB signaling, which is abolished in RBM3-null neurons. Both genetic reduction and pharmacological antagonism of TrkB and its downstream mediators abrogate cooling-induced RBM3 induction and prevent structural plasticity, whereas TrkB inhibition similarly prevents RBM3 induction and the neuroprotective effects of cooling in prion-diseased mice. Conversely, TrkB agonism induces RBM3 without cooling, preventing synapse loss and neurodegeneration. TrkB signaling is, therefore, necessary for the induction of RBM3 and related neuroprotective effects and provides a target by which RBM3-mediated synapse-regenerative therapies in neurodegenerative disorders can be used therapeutically without the need for inducing hypothermia.
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Affiliation(s)
- Diego Peretti
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Heather L Smith
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Nicholas Verity
- MRC Toxicology Unit at the University of Cambridge, Leicester, UK
| | - Ibrahim Humoud
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Lis de Weerd
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Dean P Swinden
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Joseph Hayes
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Giovanna R Mallucci
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
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13
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Andrä I, Ulrich H, Dürr S, Soll D, Henkel L, Angerpointner C, Ritter J, Przibilla S, Stadler H, Effenberger M, Busch DH, Schiemann M. An Evaluation of T‐Cell Functionality After Flow Cytometry Sorting Revealed p38 MAPK Activation. Cytometry A 2020; 97:171-183. [DOI: 10.1002/cyto.a.23964] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Immanuel Andrä
- Institute for Medical Microbiology, Immunology and HygieneTechnische Universität München (TUM) Munich Germany
| | - Hanna Ulrich
- Institute for Systemic Inflammation ResearchUniversität zu Lübeck Lübeck Germany
| | - Susi Dürr
- Institute for Medical Microbiology, Immunology and HygieneTechnische Universität München (TUM) Munich Germany
| | - Dominik Soll
- Institute for Medical Microbiology, Immunology and HygieneTechnische Universität München (TUM) Munich Germany
| | - Lynette Henkel
- Institute for Medical Microbiology, Immunology and HygieneTechnische Universität München (TUM) Munich Germany
| | - Corinne Angerpointner
- Institute for Medical Microbiology, Immunology and HygieneTechnische Universität München (TUM) Munich Germany
| | - Julia Ritter
- Institute for Systemic Inflammation ResearchUniversität zu Lübeck Lübeck Germany
| | | | - Herbert Stadler
- Cell.Copedia GmbH Leipzig Germany
- IBA GmbH, IBA Lifesciences Göttingen Lower Saxony Germany
| | - Manuel Effenberger
- Institute for Medical Microbiology, Immunology and HygieneTechnische Universität München (TUM) Munich Germany
| | - Dirk H. Busch
- Institute for Medical Microbiology, Immunology and HygieneTechnische Universität München (TUM) Munich Germany
- Focus Group 'Clinical Cell Processing and Purification'Institute for Advanced Study, TUM Munich Germany
- National Centre for Infection Research (DZIF) Munich Germany
| | - Matthias Schiemann
- Institute for Medical Microbiology, Immunology and HygieneTechnische Universität München (TUM) Munich Germany
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14
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Pizzinga M, Harvey RF, Garland GD, Mordue R, Dezi V, Ramakrishna M, Sfakianos A, Monti M, Mulroney TE, Poyry T, Willis AE. The cell stress response: extreme times call for post‐transcriptional measures. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1578. [DOI: 10.1002/wrna.1578] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/09/2019] [Accepted: 10/16/2019] [Indexed: 12/26/2022]
Affiliation(s)
| | | | | | - Ryan Mordue
- MRC Toxicology Unit University of Cambridge Leicester UK
| | - Veronica Dezi
- MRC Toxicology Unit University of Cambridge Leicester UK
| | | | | | - Mie Monti
- MRC Toxicology Unit University of Cambridge Leicester UK
| | | | - Tuija Poyry
- MRC Toxicology Unit University of Cambridge Leicester UK
| | - Anne E. Willis
- MRC Toxicology Unit University of Cambridge Leicester UK
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15
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Bertalan G, Boehm-Sturm P, Schreyer S, Morr AS, Steiner B, Tzschätzsch H, Braun J, Guo J, Sack I. The influence of body temperature on tissue stiffness, blood perfusion, and water diffusion in the mouse brain. Acta Biomater 2019; 96:412-420. [PMID: 31247381 DOI: 10.1016/j.actbio.2019.06.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/28/2019] [Accepted: 06/20/2019] [Indexed: 12/11/2022]
Abstract
While hypothermia of the brain is used to reduce neuronal damage in patients with conditions such as traumatic brain injury or stroke, little is known about how temperature affects the biophysical properties of in vivo brain tissue. Therefore, we measured shear wave speed (SWS), apparent diffusion coefficient (ADC), and cerebral blood flow (CBF) in the mouse brain at different body temperatures to investigate the relationship between temperature and tissue stiffness, water diffusion, and blood perfusion in the living brain. Multifrequency magnetic resonance elastography (MRE), diffusion-weighted imaging (DWI), and arterial spin labeling (ASL) were performed in seven mice while increasing and recording body temperature from hypothermia (28-30 °C) to normothermia (36-38 °C). SWS, ADC, and CBF were analyzed in regions of whole brain, cortex, hippocampus, and diencephalon. Our results show that SWS decreases while ADC and CBF increase from hypothermia to normothermia (whole brain SWS: -6.2%, ADC: +34.0%, CBF: +80.2%; cortex SWS: -10.1%, ADC: +30.9%, CBF: +82.4%; all p > 0.05). We found a significant inverse correlation between SWS and both ADC and CBF in all analyzed regions except diencephalon (whole brain SWS-ADC: r = -0.8, p < 0.005; SWS-CBF: r = -0.84, p < 0.005; cortex SWS-ADC: r = -0.74, p < 0.05; SWS-CBF: r = -0.65, p < 0.05). These results show that in vivo brain stiffness is inversely correlated with temperature, extracellular water mobility, and microvascular blood flow. Regional differences indicate that cortical areas are more markedly affected by hypothermia than central regions such as diencephalon. Temperature should be considered as a confounder in elastographic measurements, especially in preclinical settings. STATEMENT OF SIGNIFICANCE: Hibernating mammals lower their body temperature and metabolic activity. A hypothermic state can also be induced for medical purposes to reduce the risk of neural damage in patients with neurological disease or injury. However, little is known how physical soft-tissue properties of the in-vivo brain such as water diffusion, blood perfusion or mechanical parameters correlate with each other when temperature changes. Our study demonstrates for the first time that those quantitative imaging markers are tightly linked to changes in body temperature. While water diffusion and blood perfusion are reduced during hypothermia, brain stiffness significantly increases, suggesting that multiparametric quantitative MRI should be used for the noninvasive assessment of brain metabolic activity.
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16
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Yamada S, Kamata T, Nawa H, Sekijima T, Takei N. AMPK activation, eEF2 inactivation, and reduced protein synthesis in the cerebral cortex of hibernating chipmunks. Sci Rep 2019; 9:11904. [PMID: 31417118 PMCID: PMC6695389 DOI: 10.1038/s41598-019-48172-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
During hibernation, mammalian cells are exposed to severe environmental stressors such as low temperature, lowered O2 supply, and glucose deficiency. The cellular metabolic rate is markedly reduced for adapting to these conditions. AMP-activated protein kinase (AMPK) senses the cellular energy status and regulates metabolism. Therefore, we examined AMPK signaling in several brain regions and peripheral tissues in hibernating chipmunk. Eukaryotic elongation factor 2 (eEF2) is a downstream target of AMPK. Phosphorylation of eEF2, indicating its inactivation, is enhanced in the cerebral cortex of hibernating chipmunks. The study indicated that the sequential regulation of AMPK-mammalian target of rapamycin complex 1-eEF2 signaling was altered and protein synthesis ability was reduced in the cerebral cortex of hibernating chipmunks.
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Affiliation(s)
- Shintaro Yamada
- Department of Environmental Science and Technology, Graduate School of Science and Technology, Niigata University, Niigata, 951-8585, Japan
| | - Taito Kamata
- Department of Environmental Science and Technology, Graduate School of Science and Technology, Niigata University, Niigata, 951-8585, Japan
| | - Hiroyuki Nawa
- Department of Molecular Neurobiology, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Tsuneo Sekijima
- Department of Environmental Science and Technology, Graduate School of Science and Technology, Niigata University, Niigata, 951-8585, Japan
| | - Nobuyuki Takei
- Department of Molecular Neurobiology, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan.
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17
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Shi H, He S, He X, Lu S, Guo Z. An eukaryotic elongation factor 2 from Medicago falcata (MfEF2) confers cold tolerance. BMC PLANT BIOLOGY 2019; 19:218. [PMID: 31133003 PMCID: PMC6537394 DOI: 10.1186/s12870-019-1826-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/09/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND An eukaryotic translation elongation factor-2 (eEF-2) plays an important role in protein synthesis, however, investigation on its role in abiotic stress responses is limited. A cold responsive eEF2 named as MfEF2 was isolated from yellow-flowered alfalfa [Medicago sativa subsp. falcata (L.) Arcang, thereafter M. falcata], a forage legume with great cold tolerance, and transgenic tobacco (Nicotiana tabacum L.) plants overexpressing MfEF2 were analyzed in cold tolerance and proteomic profiling was conducted under low temperature in this study. RESULTS MfEF2 transcript was induced and peaked at 24 h and remained at the high level during cold treatment up to 96 h. Overexpression of MfEF2 in trasngenic tobacco plants resulted in enhanced cold tolerance. Compared to the wild type, transgenic plants showed higher survival rate after freezing treatment, higher levels of net photosynthetic rate (A), maximum photochemical efciency of photosystem (PS) II (Fv/Fm) and nonphotochemical quenching (NPQ) and lower levels of ion leakage and reactive oxygen species (ROS) production after chilling treatment. iTRAQ-based quantitative proteomic analysis identified 336 differentially expressed proteins (DEPs) from leaves of one transgenic line versus the wild type after chilling treatment for 48 h. GO and KEGG enrichment were conducted for analysis of the major biological process, cellular component, molecular function, and pathways of the DEPs involving in. It is interesting that many down-regulated DEPs were grouped into "photosynthesis" and "photosynthesis-antenna", such as subunits of PSI and PSII as well as light harvesting chlorophyll protein complex (LHC), while many up-regulated DEPs were grouped into "spliceosome". CONCLUSIONS The results suggest that MfEF2 confers cold tolerance through regulating hundreds of proteins synthesis under low temperature conditions. The elevated cold tolerance in MfEF2 transgenic plants was associated with downregulation of the subunits of PSI and PSII as well as LHC, which leads to reduced capacity for capturing sunlight and ROS production for protection of plants, and upregulation of proteins involving in splicesome, which promotes alternative splicing of pre-mRNA under low temperature.
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Affiliation(s)
- Haifan Shi
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Sijian He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, Guangdong Engineering Research Center for Grassland Science, South China Agricultural University, Guangzhou, 510642 China
| | - Xueying He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, Guangdong Engineering Research Center for Grassland Science, South China Agricultural University, Guangzhou, 510642 China
| | - Shaoyun Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, Guangdong Engineering Research Center for Grassland Science, South China Agricultural University, Guangzhou, 510642 China
| | - Zhenfei Guo
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095 China
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18
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Marini A, Rotblat B, Sbarrato T, Niklison-Chirou MV, Knight JRP, Dudek K, Jones C, Bushell M, Knight RA, Amelio I, Willis AE, Melino G. TAp73 contributes to the oxidative stress response by regulating protein synthesis. Proc Natl Acad Sci U S A 2018; 115:6219-6224. [PMID: 29844156 PMCID: PMC6004440 DOI: 10.1073/pnas.1718531115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TAp73 is a transcription factor that plays key roles in brain development, aging, and cancer. At the cellular level, TAp73 is a critical homeostasis-maintaining factor, particularly following oxidative stress. Although major studies focused on TAp73 transcriptional activities have indicated a contribution of TAp73 to cellular metabolism, the mechanisms underlying its role in redox homeostasis have not been completely elucidated. Here we show that TAp73 contributes to the oxidative stress response by participating in the control of protein synthesis. Regulation of mRNA translation occupies a central position in cellular homeostasis during the stress response, often by reducing global rates of protein synthesis and promoting translation of specific mRNAs. TAp73 depletion results in aberrant ribosomal RNA (rRNA) processing and impaired protein synthesis. In particular, polysomal profiles show that TAp73 promotes the integration of mRNAs that encode rRNA-processing factors in polysomes, supporting their translation. Concurrently, TAp73 depletion causes increased sensitivity to oxidative stress that correlates with reduced ATP levels, hyperactivation of AMPK, and translational defects. TAp73 is important for maintaining active translation of mitochondrial transcripts in response to oxidative stress, thus promoting mitochondrial activity. Our results indicate that TAp73 contributes to redox homeostasis by affecting the translational machinery, facilitating the translation of specific mitochondrial transcripts. This study identifies a mechanism by which TAp73 contributes to the oxidative stress response and describes a completely unexpected role for TAp73 in regulating protein synthesis.
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Affiliation(s)
- Alberto Marini
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Barak Rotblat
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Thomas Sbarrato
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Maria Victoria Niklison-Chirou
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, United Kingdom
| | - John R P Knight
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Kate Dudek
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Carolyn Jones
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Martin Bushell
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Richard A Knight
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Ivano Amelio
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Anne E Willis
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom;
| | - Gerry Melino
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom;
- Department of Experimental Medicine and Surgery, IDI-IRCCS (Istituto Dermopatico dell'Immacolata-Istituto di Ricovero e Cura a Carattere Scientifico), University of Rome Tor Vergata, 00133 Rome, Italy
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19
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Eskla KL, Porosk R, Reimets R, Visnapuu T, Vasar E, Hundahl CA, Luuk H. Hypothermia augments stress response in mammalian cells. Free Radic Biol Med 2018; 121:157-168. [PMID: 29704622 DOI: 10.1016/j.freeradbiomed.2018.04.571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 04/16/2018] [Accepted: 04/22/2018] [Indexed: 12/22/2022]
Abstract
Mild hypothermia (32 °C) is routinely used in medical practice to alleviate hypoxic ischemic damage, however, the mechanisms that underlie its protective effects remain uncertain. Using a systems approach based on genome-wide expression screens, reporter assays and biochemical studies, we find that cellular hypothermia response is associated with the augmentation of major stress-inducible transcription factors Nrf2 and HIF1Α affecting the antioxidant system and hypoxia response pathways, respectively. At the same time, NF-κB, a transcription factor involved in the control of immune and inflammatory responses, was not induced by hypothermia. Furthermore, mild hypothermia did not trigger unfolded protein response. Lower temperatures (27 °C and 22 °C) did not activate Nrf2 and HIF1A pathways as efficiently as mild hypothermia. Current findings are discussed in the context of the thermodynamic hypothesis of therapeutic hypothermia. We argue that the therapeutic effects are likely to stem both from metabolic suppression (inhibitory component) and augmentation of stress tolerance (activating component). We argue that systems coping with cellular stressors are plausible targets of therapeutic hypothermia and deserve more attention in clinical hypothermia research.
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Affiliation(s)
- Kattri-Liis Eskla
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, Tartu, Estonia.
| | - Rando Porosk
- Institute of Biomedicine and Translational Medicine, Department of Biochemistry, University of Tartu, Tartu, Estonia
| | - Riin Reimets
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, Tartu, Estonia
| | - Tanel Visnapuu
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, Tartu, Estonia
| | - Eero Vasar
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, Tartu, Estonia; Centre of Excellence for Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Christian Ansgar Hundahl
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, Tartu, Estonia
| | - Hendrik Luuk
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, Tartu, Estonia; Centre of Excellence for Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
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20
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Abstract
Interferon alpha/beta (IFN-α/β) is a critical mediator of protection against most viruses, with host survival frequently impossible in its absence. Many studies have investigated the pathways involved in the induction of IFN-α/β after virus infection and the resultant upregulation of antiviral IFN-stimulated genes (ISGs) through IFN-α/β receptor complex signaling. However, other than examining the effects of genetic deletion of induction or effector pathway components, little is known regarding the functionality of these responses in intact hosts and whether host genetic or environmental factors might influence their potency. Here, we demonstrate that the IFN-α/β response against multiple arthropod-vectored viruses, which replicate over a wide temperature range, is extremely sensitive to fluctuations in temperature, exhibiting reduced antiviral efficacy at subnormal cellular temperatures and increased efficacy at supranormal temperatures. The effect involves both IFN-α/β and ISG upregulation pathways with a major aspect of altered potency reflecting highly temperature-dependent transcription of IFN response genes that leads to altered IFN-α/β and ISG protein levels. Discordantly, signaling steps prior to transcription that were examined showed the opposite effect from gene transcription, with potentiation at low temperature and inhibition at high temperature. Finally, we demonstrate that by lowering the temperature of mice, chikungunya arbovirus replication and disease are exacerbated in an IFN-α/β-dependent manner. This finding raises the potential for use of hyperthermia as a therapeutic modality for viral infections and in other contexts such as antitumor therapy. The increased IFN-α/β efficacy at high temperatures may also reflect an innate immune-relevant aspect of the febrile response. The interferon alpha/beta (IFN-α/β) response is a first-line innate defense against arthropod-borne viruses (arboviruses). Arboviruses, such as chikungunya virus (CHIKV), can infect cells and replicate across a wide temperature range due to their replication in both mammalian/avian and arthropod hosts. Accordingly, these viruses can cause human disease in tissues regularly exposed to temperatures below the normal mammalian core temperature, 37°C. We questioned whether temperature variation could affect the efficacy of IFN-α/β responses against these viruses and help to explain some aspects of human disease manifestations. We observed that IFN-α/β efficacy was dramatically lower at subnormal temperatures and modestly enhanced at febrile temperatures, with the effects involving altered IFN-α/β response gene transcription but not IFN-α/β pathway signaling. These results provide insight into the functioning of the IFN-α/β response in vivo and suggest that temperature elevation may represent an immune-enhancing therapeutic modality for a wide variety of IFN-α/β-sensitive infections and pathologies.
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21
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Acevedo JM, Hoermann B, Schlimbach T, Teleman AA. Changes in global translation elongation or initiation rates shape the proteome via the Kozak sequence. Sci Rep 2018; 8:4018. [PMID: 29507361 PMCID: PMC5838203 DOI: 10.1038/s41598-018-22330-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/21/2018] [Indexed: 11/23/2022] Open
Abstract
The sequence context surrounding the AUG start codon of an open reading frame - the ‘Kozak sequence’ - affects the probability with which a scanning ribosome will recognize the start codon and start translating there. A significant number of transcripts in animals such as Drosophila contain weak Kozak sequences. This is predicted to cause constitutively low translation of these transcripts. We study here the additional possibility that these mRNAs have weak Kozak sequences to allow for the regulation of their translation in response to stress or altered cellular signaling. We find that transcripts with weak Kozak sequences are less sensitive to drops in global elongation rates and more sensitive to drops in global initiation rates compared to transcripts with strong Kozak sequences. This provides a mechanism by which changes in these global translation parameters differentially affect different pools of mRNAs depending on their Kozak sequence, thereby shaping the proteome. Interestingly, mRNAs with weak Kozak sequences are enriched for genes involved in neurobiology, suggesting that they constitute a functional group that can be translationally co-regulated.
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Affiliation(s)
- Julieta M Acevedo
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), partner site, Heidelberg, Germany
| | - Bernhard Hoermann
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Heidelberg University, 69120, Heidelberg, Germany
| | - Tilo Schlimbach
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. .,Heidelberg University, 69120, Heidelberg, Germany. .,National Center for Tumor Diseases (NCT), partner site, Heidelberg, Germany.
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22
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El-Naggar AM, Sorensen PH. Translational control of aberrant stress responses as a hallmark of cancer. J Pathol 2018; 244:650-666. [PMID: 29293271 DOI: 10.1002/path.5030] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 12/12/2022]
Abstract
Altered mRNA translational control is emerging as a critical factor in cancer development and progression. Targeting specific elements of the translational machinery, such as mTORC1 or eIF4E, is emerging as a new strategy for innovative cancer therapy. While translation of most mRNAs takes place through cap-dependent mechanisms, a sub-population of cellular mRNA species, particularly stress-inducible mRNAs with highly structured 5'-UTR regions, are primarily translated through cap-independent mechanisms. Intriguingly, many of these mRNAs encode proteins that are involved in tumour cell adaptation to microenvironmental stress, and thus linked to aggressive behaviour including tumour invasion and metastasis. This necessitates a rigorous search for links between microenvironmental stress and aggressive tumour phenotypes. Under stress, cells block global protein synthesis to preserve energy while maintaining selective synthesis of proteins that support cell survival. One highly conserved mechanism to regulate protein synthesis under cell stress is to sequester mRNAs into cytosolic aggregates called stress granules (SGs), where their translation is silenced. SGs confer survival advantages and chemotherapeutic resistance to tumour cells under stress. Recently, it has been shown that genetically blocking SG formation dramatically reduces tumour invasive and metastatic capacity in vivo. Therefore, targeting SG formation might represent a potential treatment strategy to block cancer metastasis. Here, we present the critical link between selective mRNA translation, stress adaptation, SGs, and tumour progression. Further, we also explain how deciphering mechanisms of selective mRNA translation occurs under cell stress holds great promise for the identification of new targets in the treatment of cancer. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Amal M El-Naggar
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada.,Department of Pathology, Faculty of Medicine, Menoufia University, Egypt
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
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23
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Harvey R, Dezi V, Pizzinga M, Willis AE. Post-transcriptional control of gene expression following stress: the role of RNA-binding proteins. Biochem Soc Trans 2017; 45:1007-14. [PMID: 28710288 PMCID: PMC5655797 DOI: 10.1042/bst20160364] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/13/2017] [Accepted: 06/14/2017] [Indexed: 12/19/2022]
Abstract
The ability of mammalian cells to modulate global protein synthesis in response to cellular stress is essential for cell survival. While control of protein synthesis is mediated by the regulation of eukaryotic initiation and elongation factors, RNA-binding proteins (RBPs) provide a crucial additional layer to post-transcriptional regulation. RBPs bind specific RNA through conserved RNA-binding domains and ensure that the information contained within the genome and transcribed in the form of RNA is exported to the cytoplasm, chemically modified, and translated prior to folding into a functional protein. Thus, this group of proteins, through mediating translational reprogramming, spatial reorganisation, and chemical modification of RNA molecules, have a major influence on the robust cellular response to external stress and toxic injury.
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Affiliation(s)
- Robert Harvey
- Medical Research Council Toxicology Unit, Lancaster Rd, Leicester LE1 9HN, U.K
| | - Veronica Dezi
- Medical Research Council Toxicology Unit, Lancaster Rd, Leicester LE1 9HN, U.K
| | | | - Anne E Willis
- Medical Research Council Toxicology Unit, Lancaster Rd, Leicester LE1 9HN, U.K.
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Henry M, Power M, Kaushik P, Coleman O, Clynes M, Meleady P. Differential Phosphoproteomic Analysis of Recombinant Chinese Hamster Ovary Cells Following Temperature Shift. J Proteome Res 2017; 16:2339-2358. [DOI: 10.1021/acs.jproteome.6b00868] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michael Henry
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Power
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Prashant Kaushik
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Orla Coleman
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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Johanns M, Pyr Dit Ruys S, Houddane A, Vertommen D, Herinckx G, Hue L, Proud CG, Rider MH. Direct and indirect activation of eukaryotic elongation factor 2 kinase by AMP-activated protein kinase. Cell Signal 2017; 36:212-221. [PMID: 28502587 DOI: 10.1016/j.cellsig.2017.05.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/27/2017] [Accepted: 05/10/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Eukaryotic elongation factor 2 (eEF2) kinase (eEF2K) is a key regulator of protein synthesis in mammalian cells. It phosphorylates and inhibits eEF2, the translation factor necessary for peptide translocation during the elongation phase of protein synthesis. When cellular energy demand outweighs energy supply, AMP-activated protein kinase (AMPK) and eEF2K become activated, leading to eEF2 phosphorylation, which reduces the rate of protein synthesis, a process that consumes a large proportion of cellular energy under optimal conditions. AIM The goal of the present study was to elucidate the mechanisms by which AMPK activation leads to increased eEF2 phosphorylation to decrease protein synthesis. METHODS Using genetically modified mouse embryo fibroblasts (MEFs), effects of treatments with commonly used AMPK activators to increase eEF2 phosphorylation were compared with that of the novel compound 991. Bacterially expressed recombinant eEF2K was phosphorylated in vitro by recombinant activated AMPK for phosphorylation site-identification by mass spectrometry followed by site-directed mutagenesis of the identified sites to alanine residues to study effects on the kinetic properties of eEF2K. Wild-type eEF2K and a Ser491/Ser492 mutant were retrovirally re-introduced in eEF2K-deficient MEFs and effects of 991 treatment on eEF2 phosphorylation and protein synthesis rates were studied in these cells. RESULTS & CONCLUSIONS AMPK activation leads to increased eEF2 phosphorylation in MEFs mainly by direct activation of eEF2K and partly by inhibition of mammalian target of rapamycin complex 1 (mTORC1) signaling. Treatment of MEFs with AMPK activators can also lead to eEF2K activation independently of AMPK probably via a rise in intracellular Ca2+. AMPK activates eEF2K by multi-site phosphorylation and the newly identified Ser491/Ser492 is important for activation, leading to mTOR-independent inhibition of protein synthesis. Our study provides new insights into the control of eEF2K by AMPK, with implications for linking metabolic stress to decreased protein synthesis to conserve energy reserves, a pathway that is of major importance in cancer cell survival.
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Affiliation(s)
- M Johanns
- Université catholique de Louvain (UCL), de Duve Institute, Avenue Hippocrate 75 bte 74.02, 1200-Brussels, Belgium
| | - S Pyr Dit Ruys
- Université catholique de Louvain (UCL), de Duve Institute, Avenue Hippocrate 75 bte 74.02, 1200-Brussels, Belgium
| | - A Houddane
- Université catholique de Louvain (UCL), de Duve Institute, Avenue Hippocrate 75 bte 74.02, 1200-Brussels, Belgium
| | - D Vertommen
- Université catholique de Louvain (UCL), de Duve Institute, Avenue Hippocrate 75 bte 74.02, 1200-Brussels, Belgium
| | - G Herinckx
- Université catholique de Louvain (UCL), de Duve Institute, Avenue Hippocrate 75 bte 74.02, 1200-Brussels, Belgium
| | - L Hue
- Université catholique de Louvain (UCL), de Duve Institute, Avenue Hippocrate 75 bte 74.02, 1200-Brussels, Belgium
| | - C G Proud
- South Australian Health and Medical Research Institute (SAHMRI), University of Adelaide, North Terrace, Adelaide, SA 5000, Australia
| | - M H Rider
- Université catholique de Louvain (UCL), de Duve Institute, Avenue Hippocrate 75 bte 74.02, 1200-Brussels, Belgium.
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26
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Zhu H, Song H, Chen G, Yang X, Liu J, Ge Y, Lu J, Qin Q, Zhang C, Xu L, Di X, Cai J, Ma J, Zhang S, Sun X. eEF2K promotes progression and radioresistance of esophageal squamous cell carcinoma. Radiother Oncol 2017; 124:439-447. [PMID: 28431753 DOI: 10.1016/j.radonc.2017.04.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 03/06/2017] [Accepted: 04/02/2017] [Indexed: 01/10/2023]
Abstract
OBJECTIVES To investigate the biological function of eEF2K in esophageal squamous cell carcinoma (ESCC). MATERIALS AND METHODS Tissue microarrays containing 100 pairs of ESCC tumor and adjacent normal tissues were completed. Overexpression and knockdown of eEF2K were constructed in ECA-109 and TE-13 ESCC cells. DNA damage, cell viability, migration and invasion, radioresistance, apoptosis and autophagy were determined by immunofluorescence, CCK-8, transwell assay, colony formation assay, flow cytometry and western blot, respectively. Tumor growth and radioresistance were also evaluated using xenograft models created in nude mice. RESULTS eEF2K expression was higher in ESCC tissues compared with matched non-tumor tissues (P<0.05). Proliferation was increased in eEF2K overexpressing cells compared with controls (P<0.05), while silencing eEF2K reduced cell proliferation (P<0.05). Furthermore, lower levels of eEF2K expression correlated with slower migration and invasion rates (P<0.05), while higher levels of eEF2K expression with faster migration and invasion rates (P<0.05). eEF2K overexpression resulted in radioresistance and radiation-induced autophagy, and reduced radiation-induced apoptosis compared with controls, but silencing eEF2K promoted radiosensitivity and apoptosis, and reduced autophagy. In addition, eEF2K overexpression promoted the tumor growth in vivo (P<0.01). Combined treatment of NH125 (a pharmacological inhibitor of eEF2K) and radiation was more effective at delaying xenograft tumor growth than NH125 and radiation alone (P<0.05). CONCLUSION eEF2K induced progression and radioresistance in ESCC, which may be a novel therapeutic target for ESCC to increase radiosensitivity.
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Affiliation(s)
- Hongcheng Zhu
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, China
| | - Hongmei Song
- Department of Radiation Oncology, The Second Hospital of Lianyungang, Lianyungang Hospital Affiliated to Bengbu Medical College, China
| | - Guangzong Chen
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, China
| | - Xi Yang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, China
| | - Jia Liu
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, China
| | - Yangyang Ge
- Department of Radiation Oncology, The Affiliated Tumor Hospital of Nantong University, China
| | - Jing Lu
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, China
| | - Qin Qin
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, China
| | - Chi Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, China
| | - Liping Xu
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, China
| | - Xiaoke Di
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, China
| | - Jing Cai
- Department of Radiation Oncology, The Affiliated Tumor Hospital of Nantong University, China
| | - Jianxin Ma
- Department of Radiation Oncology, The Second Hospital of Lianyungang, Lianyungang Hospital Affiliated to Bengbu Medical College, China
| | - Shu Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, China
| | - Xinchen Sun
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, China.
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RTN3 Is a Novel Cold-Induced Protein and Mediates Neuroprotective Effects of RBM3. Curr Biol 2017; 27:638-650. [PMID: 28238655 PMCID: PMC5344685 DOI: 10.1016/j.cub.2017.01.047] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/21/2016] [Accepted: 01/23/2017] [Indexed: 11/28/2022]
Abstract
Cooling and hypothermia are profoundly neuroprotective, mediated, at least in part, by the cold shock protein, RBM3. However, the neuroprotective effector proteins induced by RBM3 and the mechanisms by which mRNAs encoding cold shock proteins escape cooling-induced translational repression are unknown. Here, we show that cooling induces reprogramming of the translatome, including the upregulation of a new cold shock protein, RTN3, a reticulon protein implicated in synapse formation. We report that this has two mechanistic components. Thus, RTN3 both evades cooling-induced translational elongation repression and is also bound by RBM3, which drives the increased expression of RTN3. In mice, knockdown of RTN3 expression eliminated cooling-induced neuroprotection. However, lentivirally mediated RTN3 overexpression prevented synaptic loss and cognitive deficits in a mouse model of neurodegeneration, downstream and independently of RBM3. We conclude that RTN3 expression is a mediator of RBM3-induced neuroprotection, controlled by novel mechanisms of escape from translational inhibition on cooling. Cooling-induced reprogramming of the translatome increases synthesis of RTN3 The neuroprotective protein RBM3 binds RTN3 mRNA and drives its expression RTN3 overexpression prevents synaptic loss in mice with prion disease RTN3 expression is a mediator of RBM3-induced neuroprotection
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28
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Lee JK, Wang B, Reyes M, Armstrong JS, Kulikowicz E, Santos PT, Lee JH, Koehler RC, Martin LJ. Hypothermia and Rewarming Activate a Macroglial Unfolded Protein Response Independent of Hypoxic-Ischemic Brain Injury in Neonatal Piglets. Dev Neurosci 2016; 38:277-294. [PMID: 27622292 DOI: 10.1159/000448585] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/20/2016] [Indexed: 12/22/2022] Open
Abstract
Therapeutic hypothermia provides incomplete neuroprotection after hypoxia-ischemia (HI)-induced brain injury in neonates. We previously showed that cortical neuron and white matter apoptosis are promoted by hypothermia and early rewarming in a piglet model of HI. The unfolded protein response (UPR) may be one of the potential mediators of this cell death. Here, neonatal piglets underwent HI or sham surgery followed by 29 h of normothermia, 2 h of normothermia + 27 h of hypothermia or 18 h of hypothermia + rewarming. Piglets recovered for 29 h. Immunohistochemistry for endoplasmic reticulum to nucleus signaling-1 protein (ERN1), a marker of UPR activation, was used to determine the ratios of ERN1+ macroglia and neurons in the motor subcortical white matter and cerebral cortex. The ERN1+ macroglia were immunophenotyped as oligodendrocytes and astrocytes by immunofluorescent colabeling. Temperature (p = 0.046) and HI (p < 0.001) independently affected the ratio of ERN1+ macroglia. In sham piglets, sustained hypothermia (p = 0.011) and rewarming (p = 0.004) increased the ERN1+ macroglia ratio above that in normothermia. HI prior to hypothermia diminished the UPR. Ratios of ERN1+ macroglia correlated with white matter apoptotic profile counts in shams (r = 0.472; p = 0.026), thereby associating UPR activation with white matter apoptosis during hypothermia and rewarming. Accordingly, macroglial cell counts decreased in shams that received sustained hypothermia (p = 0.009) or rewarming (p = 0.007) compared to those in normothermic shams. HI prior to hypothermia neutralized the macroglial cell loss. Neither HI nor temperature affected ERN1+ neuron ratios. In summary, delayed hypothermia and rewarming activate the macroglial UPR, which is associated with white matter apoptosis. HI may decrease the macroglial endoplasmic reticulum stress response after hypothermia and rewarming.
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Affiliation(s)
- Jennifer K Lee
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, Md., USA
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29
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McKnight RA, Yost CC, Zinkhan EK, Fu Q, Callaway CW, Fung CM. Intrauterine growth restriction inhibits expression of eukaryotic elongation factor 2 kinase, a regulator of protein translation. Physiol Genomics 2016; 48:616-25. [PMID: 27317589 DOI: 10.1152/physiolgenomics.00045.2016] [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: 04/15/2016] [Accepted: 06/14/2016] [Indexed: 11/22/2022] Open
Abstract
Nutrient deprivation suppresses protein synthesis by blocking peptide elongation. Transcriptional upregulation and activation of eukaryotic elongation factor 2 kinase (eEF2K) blocks peptide elongation by phosphorylating eukaryotic elongation factor 2. Previous studies examining placentas from intrauterine growth restricted (IUGR) newborn infants show decreased eEF2K expression and activity despite chronic nutrient deprivation. However, the effect of IUGR on hepatic eEF2K expression in the fetus is unknown. We, therefore, examined the transcriptional regulation of hepatic eEF2K gene expression in a Sprague-Dawley rat model of IUGR. We found decreased hepatic eEF2K mRNA and protein levels in IUGR offspring at birth compared with control, consistent with previous placental observations. Furthermore, the CpG island within the eEF2K promoter demonstrated increased methylation at a critical USF 1/2 transcription factor binding site. In vitro methylation of this binding site caused near complete loss of eEF2K promoter activity, designating this promoter as methylation sensitive. The eEF2K promotor in IUGR offspring also lost the protective histone covalent modifications associated with unmethylated CGIs. In addition, the +1 nucleosome was displaced 3' and RNA polymerase loading was reduced at the IUGR eEF2K promoter. Our findings provide evidence to explain why IUGR-induced chronic nutrient deprivation does not result in the upregulation of eEF2K gene transcription.
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Affiliation(s)
- Robert A McKnight
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Christian C Yost
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Erin K Zinkhan
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Qi Fu
- Division of Neonatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Christopher W Callaway
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Camille M Fung
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
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Takatani T, Shirakawa J, Roe MW, Leech CA, Maier BF, Mirmira RG, Kulkarni RN. IRS1 deficiency protects β-cells against ER stress-induced apoptosis by modulating sXBP-1 stability and protein translation. Sci Rep 2016; 6:28177. [PMID: 27378176 PMCID: PMC4932502 DOI: 10.1038/srep28177] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/31/2016] [Indexed: 01/05/2023] Open
Abstract
Endoplasmic reticulum (ER) stress is among several pathological features that underlie β-cell failure in the development of type 1 and type 2 diabetes. Adaptor proteins in the insulin/insulin-like-growth factor-1 signaling pathways, such as insulin receptor substrate-1 (IRS1) and IRS2, differentially impact β-cell survival but the underlying mechanisms remain unclear. Here we report that β-cells deficient in IRS1 (IRS1KO) are resistant, while IRS2 deficiency (IRS2KO) makes them susceptible to ER stress-mediated apoptosis. IRS1KOs exhibited low nuclear accumulation of spliced XBP-1 due to its poor stability, in contrast to elevated accumulation in IRS2KO. The reduced nuclear accumulation in IRS1KO was due to protein instability of Xbp1 secondary to proteasomal degradation. IRS1KO also demonstrated an attenuation in their general translation status in response to ER stress revealed by polyribosomal profiling. Phosphorylation of eEF2 was dramatically increased in IRS1KO enabling the β-cells to adapt to ER stress by blocking translation. Furthermore, significantly high ER calcium (Ca2+) was detected in IRS1KO β-cells even upon induction of ER stress. These observations suggest that IRS1 could be a therapeutic target for β-cell protection against ER stress-mediated cell death by modulating XBP-1 stability, protein synthesis, and Ca2+ storage in the ER.
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Affiliation(s)
- Tomozumi Takatani
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Jun Shirakawa
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Michael W Roe
- Department of Medicine, State University of New York (SUNY), Upstate Medical University, Syracuse, NY, USA
| | - Colin A Leech
- Department of Medicine, State University of New York (SUNY), Upstate Medical University, Syracuse, NY, USA
| | - Bernhard F Maier
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Raghavendra G Mirmira
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Cellular and Integrative Physiology, Department of Biochemistry and Molecular Biology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rohit N Kulkarni
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
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31
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Ishimura R, Nagy G, Dotu I, Chuang JH, Ackerman SL. Activation of GCN2 kinase by ribosome stalling links translation elongation with translation initiation. eLife 2016; 5. [PMID: 27085088 PMCID: PMC4917338 DOI: 10.7554/elife.14295] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/14/2016] [Indexed: 12/17/2022] Open
Abstract
Ribosome stalling during translation has recently been shown to cause neurodegeneration, yet the signaling pathways triggered by stalled elongation complexes are unknown. To investigate these pathways we analyzed the brain of C57BL/6J-Gtpbp2nmf205-/- mice in which neuronal elongation complexes are stalled at AGA codons due to deficiencies in a tRNAArgUCU tRNA and GTPBP2, a mammalian ribosome rescue factor. Increased levels of phosphorylation of eIF2α (Ser51) were detected prior to neurodegeneration in these mice and transcriptome analysis demonstrated activation of ATF4, a key transcription factor in the integrated stress response (ISR) pathway. Genetic experiments showed that this pathway was activated by the eIF2α kinase, GCN2, in an apparent deacylated tRNA-independent fashion. Further we found that the ISR attenuates neurodegeneration in C57BL/6J-Gtpbp2nmf205-/- mice, underscoring the importance of cellular and stress context on the outcome of activation of this pathway. These results demonstrate the critical interplay between translation elongation and initiation in regulating neuron survival during cellular stress. DOI:http://dx.doi.org/10.7554/eLife.14295.001 Information stored in DNA is used to make proteins in a two-step process. First, the DNA is copied to make molecules of messenger ribonucleic acid (or messenger RNA for short). Next, machines called ribosomes use the messenger RNAs as templates to assemble chains of amino acids – the building blocks of proteins – in a process called translation. Another type of RNA molecule called transfer RNA carries each amino acid to the ribosomes. If a specific transfer RNA is not available for translation at the right time, the ribosome might stall as it moves along the messenger RNA. At this point, the ribosome needs to be restarted or it will fall off the mRNA without finishing the protein. In 2014, a group of researchers reported that certain types of brain cells are very sensitive to ribosome stalling, and tend to die if translation does not continue. A protein called GTPBP2 was shown to play an important role in restarting stalled ribosomes in these cells. Here, Ishimura, Nagy et al. – including some of the researchers from the earlier work – investigated the molecular pathways that ribosome stalling triggers in brain cells using mutant mice that lacked the GTPBP2 protein. The experiments show that ribosome stalling activates an enzyme known as GCN2, which was already known to sense other types of malfunctions in cellular processes. Ishimura, Nagy et al. also show that GCN2 triggers stress responses in the cells by activating a communication system called the ATF4 pathway. This pathway protects the cells from damage, and its absence results in more rapid cell deterioration and death. The next challenges are to understand the exact mechanism by which GCN2 senses stalled ribosomes, and to find out how ribosome stalling causes the death of brain cells. DOI:http://dx.doi.org/10.7554/eLife.14295.002
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Affiliation(s)
- Ryuta Ishimura
- Howard Hughes Medical Institute, The Jackson Laboratory for Mammalian Genetics, Bar Harbor, United States
| | - Gabor Nagy
- Howard Hughes Medical Institute, The Jackson Laboratory for Mammalian Genetics, Bar Harbor, United States
| | - Ivan Dotu
- Research Programme on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, United States.,Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, United States
| | - Susan L Ackerman
- Howard Hughes Medical Institute, The Jackson Laboratory for Mammalian Genetics, Bar Harbor, United States.,Department of Cell and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, United States.,Section of Neurobiology, University of California, La Jolla, United States
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Knight JRP, Bastide A, Peretti D, Roobol A, Roobol J, Mallucci GR, Smales CM, Willis AE. Cooling-induced SUMOylation of EXOSC10 down-regulates ribosome biogenesis. RNA (NEW YORK, N.Y.) 2016; 22:623-635. [PMID: 26857222 PMCID: PMC4793216 DOI: 10.1261/rna.054411.115] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
Abstract
The RNA exosome is essential for 3' processing of functional RNA species and degradation of aberrant RNAs in eukaryotic cells. Recent reports have defined the substrates of the exosome catalytic domains and solved the multimeric structure of the exosome complex. However, regulation of exosome activity remains poorly characterized, especially in response to physiological stress. Following the observation that cooling of mammalian cells results in a reduction in 40S:60S ribosomal subunit ratio, we uncover regulation of the nuclear exosome as a result of reduced temperature. Using human cells and an in vivo model system allowing whole-body cooling, we observe reduced EXOSC10 (hRrp6, Pm/Scl-100) expression in the cold. In parallel, both models of cooling increase global SUMOylation, leading to the identification of specific conjugation of SUMO1 to EXOSC10, a process that is increased by cooling. Furthermore, we define the major SUMOylation sites in EXOSC10 by mutagenesis and show that overexpression of SUMO1 alone is sufficient to suppress EXOSC10 abundance. Reducing EXOSC10 expression by RNAi in human cells correlates with the 3' preribosomal RNA processing defects seen in the cold as well as reducing the 40S:60S ratio, a previously uncharacterized consequence of EXOSC10 suppression. Together, this work illustrates that EXOSC10 can be modified by SUMOylation and identifies a physiological stress where this regulation is prevalent both in vitro and in vivo.
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Affiliation(s)
- John R P Knight
- Medical Research Council Toxicology Unit, Hodgkin Building, Leicester, LE1 9HN, United Kingdom
| | - Amandine Bastide
- Medical Research Council Toxicology Unit, Hodgkin Building, Leicester, LE1 9HN, United Kingdom
| | - Diego Peretti
- Medical Research Council Toxicology Unit, Hodgkin Building, Leicester, LE1 9HN, United Kingdom Department of Clinical Neurosciences, Clifford Allbutt Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, United Kingdom
| | - Anne Roobol
- Centre for Molecular Processing and School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, United Kingdom
| | - Jo Roobol
- Centre for Molecular Processing and School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, United Kingdom
| | - Giovanna R Mallucci
- Medical Research Council Toxicology Unit, Hodgkin Building, Leicester, LE1 9HN, United Kingdom Department of Clinical Neurosciences, Clifford Allbutt Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, United Kingdom
| | - C Mark Smales
- Centre for Molecular Processing and School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, United Kingdom
| | - Anne E Willis
- Medical Research Council Toxicology Unit, Hodgkin Building, Leicester, LE1 9HN, United Kingdom
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33
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Control of translation in the cold: implications for therapeutic hypothermia. Biochem Soc Trans 2016; 43:333-7. [PMID: 26009172 DOI: 10.1042/bst20150052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Controlled whole-body cooling has been used since the 1950s to protect the brain from injury where cerebral blood flow is reduced. Therapeutic hypothermia has been used successfully during heart surgery, following cardiac arrest and with varied success in other instances of reduced blood flow to the brain. However, why reduced temperature is beneficial is largely unknown. Here we review the use of therapeutic hypothermia with a view to understanding the underlying biology contributing to the phenomenon. Interestingly, the benefits of cooling have recently been extended to treatment of chronic neurodegenerative diseases in two mouse models. Concurrently studies have demonstrated the importance of the regulation of protein synthesis, translation, to the cooling response, which is also emerging as a targetable process in neurodegeneration. Through these studies the potential importance of the rewarming process following cooling is also beginning to emerge. Altogether, these lines of research present new opportunities to manipulate cooling pathways for therapeutic gain.
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Zhu X, Zelmer A, Kapfhammer JP, Wellmann S. Cold-inducible RBM3 inhibits PERK phosphorylation through cooperation with NF90 to protect cells from endoplasmic reticulum stress. FASEB J 2015; 30:624-34. [PMID: 26472337 DOI: 10.1096/fj.15-274639] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 09/28/2015] [Indexed: 01/01/2023]
Abstract
The cold-inducible RNA-binding motif protein 3 (RBM3) is involved in the protection of neurons in hypoxic-ischemic and neurodegenerative disorders. RBM3 belongs to a small group of proteins whose synthesis increases during hypothermia while global protein production is slowed down. To investigate the molecular mechanisms underlying RBM3 action, we subjected hippocampal organotypic slice cultures from RBM3 knockout mice to various stressors and found exuberant signaling of the endoplasmic reticulum (ER) stress pathway PRKR-like ER kinase (PERK)-eukaryotic translation initiation factor 2α (eIF2α)-CCAAT/enhancer-binding protein homologous protein (CHOP) as compared with wild-type mice. Further, blocking RBM3 expression in human embryonic kidney HEK293 cells by specific small interfering RNAs increased phosphorylation of PERK and eIF2α, whereas overexpression of RBM3 prevented PERK-eIF2α-CHOP signaling during ER stress induced by thapsigargin or tunicamycin. RBM3 did not affect expression of the ER stress sensor immunoglobulin binding protein/GRP78. However, based on affinity purification coupled with mass spectrometry, coimmunoprecipitation, and proximity ligation assay, we revealed that nuclear factor 90 (NF90) is a novel protein interactor of PERK and that this interaction is essential for RBM3-mediated regulation of PERK activity, which requires an RNA-dependent interaction. In conclusion, our data provide evidence for a central role of RBM3 in preventing cell death by inhibiting the PERK-eIF2α-CHOP ER stress pathway through cooperation with NF90.
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Affiliation(s)
- Xinzhou Zhu
- *University of Basel Children's Hospital (UKBB), Basel, Switzerland; and Anatomical Institute, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Andrea Zelmer
- *University of Basel Children's Hospital (UKBB), Basel, Switzerland; and Anatomical Institute, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Josef P Kapfhammer
- *University of Basel Children's Hospital (UKBB), Basel, Switzerland; and Anatomical Institute, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Sven Wellmann
- *University of Basel Children's Hospital (UKBB), Basel, Switzerland; and Anatomical Institute, Department of Biomedicine, University of Basel, Basel, Switzerland
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Alves V. Reactivity of vertebrate-directed phospho-eEF2 antibody against the Caenorhabditis elegans orthologue phospho-EEF-2. F1000Res 2015. [DOI: 10.12688/f1000research.7127.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eukaryotic protein translation is divided into three mains stages: initiation, elongation and termination. Regulation of this process occurs at the initiation and elongation step. eEF2 kinase phosphorylates eEF2 factor, blocking its ribosome interaction and thus translation elongation. This kinase activity can be detected by measuring eEF2 phosphorylation status. Here I show that vertebrate-specific antibody against phospho-eEF2 has excellent reactivity against C. elegans orthologue protein phospho-EEF-2.
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Aeschimann F, Xiong J, Arnold A, Dieterich C, Großhans H. Transcriptome-wide measurement of ribosomal occupancy by ribosome profiling. Methods 2015; 85:75-89. [PMID: 26102273 DOI: 10.1016/j.ymeth.2015.06.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 06/10/2015] [Accepted: 06/15/2015] [Indexed: 01/08/2023] Open
Abstract
Gene expression profiling provides a tool to analyze the internal states of cells or organisms, and their responses to perturbations. While global measurements of mRNA levels have thus been widely used for many years, it is only through the recent development of the ribosome profiling technique that an analogous examination of global mRNA translation programs has become possible. Ribosome profiling reveals which RNAs are being translated to what extent and where the translated open reading frames are located. In addition, different modes of translation regulation can be distinguished and characterized. Here, we present an optimized, step-by-step protocol for ribosome profiling. Although established in Caenorhabditis elegans, our protocol and optimization approaches should be equally usable for other model organisms or cell culture with little adaptation. Next to providing a protocol, we compare two different methods for isolation of single ribosomes and two different library preparations, and describe strategies to optimize the RNase digest and to reduce ribosomal RNA contamination in the libraries. Moreover, we discuss bioinformatic strategies to evaluate the quality of the data and explain how the data can be analyzed for different applications. In sum, this article seeks to facilitate the understanding, execution, and optimization of ribosome profiling experiments.
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Affiliation(s)
- Florian Aeschimann
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Jieyi Xiong
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Straße 9b, 50931 Cologne, Germany
| | - Andreas Arnold
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Christoph Dieterich
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Straße 9b, 50931 Cologne, Germany.
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
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