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Horikawa M, Fukuyama M, Antebi A, Mizunuma M. Regulatory mechanism of cold-inducible diapause in Caenorhabditis elegans. Nat Commun 2024; 15:5793. [PMID: 38987256 PMCID: PMC11237089 DOI: 10.1038/s41467-024-50111-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Temperature is a critical environmental cue that controls the development and lifespan of many animal species; however, mechanisms underlying low-temperature adaptation are poorly understood. Here, we describe cold-inducible diapause (CID), another type of diapause induced by low temperatures in Caenorhabditis elegans. A premature stop codon in heat shock factor 1 (hsf-1) triggers entry into CID at 9 °C, whereas wild-type animals enter CID at 4 °C. Furthermore, both wild-type and hsf-1(sy441) mutant animals undergoing CID can survive for weeks, and resume growth at 20 °C. Using epistasis analysis, we demonstrate that neural signalling pathways, namely tyraminergic and neuromedin U signalling, regulate entry into CID of the hsf-1 mutant. Overexpression of anti-ageing genes, such as hsf-1, XBP1/xbp-1, FOXO/daf-16, Nrf2/skn-1, and TFEB/hlh-30, also inhibits CID entry of the hsf-1 mutant. Based on these findings, we hypothesise that regulators of the hsf-1 mutant CID may impact longevity, and successfully isolate 16 long-lived mutants among 49 non-CID mutants via genetic screening. Furthermore, we demonstrate that the nonsense mutation of MED23/sur-2 prevents CID entry of the hsf-1(sy441) mutant and extends lifespan. Thus, CID is a powerful model to investigate neural networks involving cold acclimation and to explore new ageing mechanisms.
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Affiliation(s)
- Makoto Horikawa
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
| | - Masamitsu Fukuyama
- Laboratory of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Masaki Mizunuma
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Higashi-Hiroshima, Japan.
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2
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Ma Z, Sharma R, Rogers AN. Physiological Consequences of Nonsense-Mediated Decay and Its Role in Adaptive Responses. Biomedicines 2024; 12:1110. [PMID: 38791071 PMCID: PMC11117581 DOI: 10.3390/biomedicines12051110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
The evolutionarily conserved nonsense-mediated mRNA decay (NMD) pathway is a quality control mechanism that degrades aberrant mRNA containing one or more premature termination codons (PTCs). Recent discoveries indicate that NMD also differentially regulates mRNA from wild-type protein-coding genes despite lacking PTCs. Together with studies showing that NMD is involved in development and adaptive responses that influence health and longevity, these findings point to an expanded role of NMD that adds a new layer of complexity in the post-transcriptional regulation of gene expression. However, the extent of its control, whether different types of NMD play different roles, and the resulting physiological outcomes remain unclear and need further elucidation. Here, we review different branches of NMD and what is known of the physiological outcomes associated with this type of regulation. We identify significant gaps in the understanding of this process and the utility of genetic tools in accelerating progress in this area.
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Affiliation(s)
- Zhengxin Ma
- MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Ratna Sharma
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA;
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3
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Fiore APZP, Maity S, Jeffery L, An D, Rendleman J, Iannitelli D, Choi H, Mazzoni E, Vogel C. Identification of molecular signatures defines the differential proteostasis response in induced spinal and cranial motor neurons. Cell Rep 2024; 43:113885. [PMID: 38457337 PMCID: PMC11018139 DOI: 10.1016/j.celrep.2024.113885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 12/12/2023] [Accepted: 02/13/2024] [Indexed: 03/10/2024] Open
Abstract
Amyotrophic lateral sclerosis damages proteostasis, affecting spinal and upper motor neurons earlier than a subset of cranial motor neurons. To aid disease understanding, we exposed induced cranial and spinal motor neurons (iCrMNs and iSpMNs) to proteotoxic stress, under which iCrMNs showed superior survival, quantifying the transcriptome and proteome for >8,200 genes at 0, 12, and 36 h. Two-thirds of the proteome showed cell-type differences. iSpMN-enriched proteins related to DNA/RNA metabolism, and iCrMN-enriched proteins acted in the endoplasmic reticulum (ER)/ER chaperone complex, tRNA aminoacylation, mitochondria, and the plasma/synaptic membrane, suggesting that iCrMNs expressed higher levels of proteins supporting proteostasis and neuronal function. When investigating the increased proteasome levels in iCrMNs, we showed that the activity of the 26S proteasome, but not of the 20S proteasome, was higher in iCrMNs than in iSpMNs, even after a stress-induced decrease. We identified Ublcp1 as an iCrMN-specific regulator of the nuclear 26S activity.
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Affiliation(s)
| | - Shuvadeep Maity
- New York University, Department of Biology, New York, NY 10003, USA; Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, India
| | - Lauren Jeffery
- New York University, Department of Biology, New York, NY 10003, USA
| | - Disi An
- New York University, Department of Biology, New York, NY 10003, USA
| | - Justin Rendleman
- New York University, Department of Biology, New York, NY 10003, USA
| | - Dylan Iannitelli
- New York University, Department of Biology, New York, NY 10003, USA
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Esteban Mazzoni
- New York University, Department of Biology, New York, NY 10003, USA; Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Christine Vogel
- New York University, Department of Biology, New York, NY 10003, USA.
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4
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Ashraf A, Majeed Y, Gul I, Banday M, Ramzan K, Fazili KM. Elucidating the EXOSC3-IRE1α interaction: a convergent study incorporating computational, in vitro and in vivo studies. J Biomol Struct Dyn 2024:1-11. [PMID: 38407190 DOI: 10.1080/07391102.2024.2320252] [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: 11/10/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024]
Abstract
The Unfolded protein response (UPR) is an adaptive signalling pathway which is triggered by accumulation of unfolded/misfolded protein in ER lumen. The UPR consist of three transmembrane proteins-IRE1α, PERK and ATF6 that sense ER stress which leads to activation and downstream signaling from ER lumen to cytosol to restore homeostasis. IRE1α is an evolutionary conserved arm of UPR and acts as an interaction platform for many potential proteins that become activated under ER stress conditions. We investigated potential partners of IRE1 α through MS studies and found EXOSC3 as one of the binding partner of IRE1α. Exosomal complex proteins have 3'5' exonuclease properties (EXOSC3) that play an important role in mRNA surveillance. This property of exosomal proteins coincides with IRE1α ribonuclease activities and its mechanism of action is similar to that of IRE1α-RIDD pathway which degrades any unstable mRNA that disrupts cellular homeostasis. At the same time, studies have shown that knockdown of EXOSC3 causes ER stress in human cells, so we speculated that there might be a functional crosstalk between IRE1α and EXOSC3 under ER stress conditions. Therefore, we employed computational tools to predict and explore the stability and dynamics of the IRE1α-EXOSC3 complex. The analysis indicates that IRE1α and EXOSC3 exhibit potential interaction with the involvement of ScanNet, predicting binding pockets between the two proteins. Further, the interaction was validated via co-immunoprecipitation and yeast two-hybrid assays, thus suggesting EXOSC3 as a component of the UPRosome complex. Hence, this functional crosstalk might influence the dynamic functional output of IRE1α.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ariha Ashraf
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Younis Majeed
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Irfan Gul
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Mariam Banday
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Khalida Ramzan
- Department of Biotechnology, University of Kashmir, Srinagar, India
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5
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Yang Y, Lu D, Wang M, Liu G, Feng Y, Ren Y, Sun X, Chen Z, Wang Z. Endoplasmic reticulum stress and the unfolded protein response: emerging regulators in progression of traumatic brain injury. Cell Death Dis 2024; 15:156. [PMID: 38378666 PMCID: PMC10879178 DOI: 10.1038/s41419-024-06515-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024]
Abstract
Traumatic brain injury (TBI) is a common trauma with high mortality and disability rates worldwide. However, the current management of this disease is still unsatisfactory. Therefore, it is necessary to investigate the pathophysiological mechanisms of TBI in depth to improve the treatment options. In recent decades, abundant evidence has highlighted the significance of endoplasmic reticulum stress (ERS) in advancing central nervous system (CNS) disorders, including TBI. ERS following TBI leads to the accumulation of unfolded proteins, initiating the unfolded protein response (UPR). Protein kinase RNA-like ER kinase (PERK), inositol-requiring protein 1 (IRE1), and activating transcription factor 6 (ATF6) are the three major pathways of UPR initiation that determine whether a cell survives or dies. This review focuses on the dual effects of ERS on TBI and discusses the underlying mechanisms. It is suggested that ERS may crosstalk with a series of molecular cascade responses, such as mitochondrial dysfunction, oxidative stress, neuroinflammation, autophagy, and cell death, and is thus involved in the progression of secondary injury after TBI. Hence, ERS is a promising candidate for the management of TBI.
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Affiliation(s)
- Yayi Yang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188Shizi Street, Suzhou, 215006, Jiangsu Province, China
- Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Dengfeng Lu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188Shizi Street, Suzhou, 215006, Jiangsu Province, China
| | - Menghan Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188Shizi Street, Suzhou, 215006, Jiangsu Province, China
- Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Guangjie Liu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188Shizi Street, Suzhou, 215006, Jiangsu Province, China
| | - Yun Feng
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188Shizi Street, Suzhou, 215006, Jiangsu Province, China
- Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Yubo Ren
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188Shizi Street, Suzhou, 215006, Jiangsu Province, China
| | - Xiaoou Sun
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188Shizi Street, Suzhou, 215006, Jiangsu Province, China.
| | - Zhouqing Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188Shizi Street, Suzhou, 215006, Jiangsu Province, China.
| | - Zhong Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188Shizi Street, Suzhou, 215006, Jiangsu Province, China.
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6
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Ottens F, Efstathiou S, Hoppe T. Cutting through the stress: RNA decay pathways at the endoplasmic reticulum. Trends Cell Biol 2023:S0962-8924(23)00236-2. [PMID: 38008608 DOI: 10.1016/j.tcb.2023.11.003] [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: 09/28/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/28/2023]
Abstract
The endoplasmic reticulum (ER) is central to the processing of luminal, transmembrane, and secretory proteins, and maintaining a functional ER is essential for organismal physiology and health. Increased protein-folding load on the ER causes ER stress, which activates quality control mechanisms to restore ER function and protein homeostasis. Beyond protein quality control, mRNA decay pathways have emerged as potent ER fidelity regulators, but their mechanistic roles in ER quality control and their interrelationships remain incompletely understood. Herein, we review ER-associated RNA decay pathways - including regulated inositol-requiring enzyme 1α (IRE1α)-dependent mRNA decay (RIDD), nonsense-mediated mRNA decay (NMD), and Argonaute-dependent RNA silencing - in ER homeostasis, and highlight the intricate coordination of ER-targeted RNA and protein decay mechanisms and their association with antiviral defense.
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Affiliation(s)
- Franziska Ottens
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sotirios Efstathiou
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, Cologne, Germany.
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7
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Leeksma AC, Derks IAM, Garrick B, Jongejan A, Colombo M, Bloedjes T, Trowe T, Leisten JC, Howarth M, Malek M, Mortensen DS, Blease K, Groza MC, Narla RK, Loos R, Kersten M, Moerland PD, Guikema JEJ, Kater AP, Eldering E, Filvaroff EH. SMG1, a nonsense-mediated mRNA decay (NMD) regulator, as a candidate therapeutic target in multiple myeloma. Mol Oncol 2022; 17:284-297. [PMID: 36400430 PMCID: PMC9892823 DOI: 10.1002/1878-0261.13343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/16/2022] [Accepted: 11/17/2022] [Indexed: 11/20/2022] Open
Abstract
Early data suggested that CC-115, a clinical molecule, already known to inhibit the mammalian target of rapamycin kinase (TORK) and DNA-dependent protein kinase (DNA-PK) may have additional targets beyond TORK and DNA-PK. Therefore, we aimed to identify such target(s) and investigate a potential therapeutic applicability. Functional profiling of 141 cancer cell lines revealed inhibition of kinase suppressor of morphogenesis in genitalia 1 (SMG1), a key regulator of the RNA degradation mechanism nonsense-mediated mRNA decay (NMD), as an additional target of CC-115. CC-115 treatment showed a dose-dependent increase of SMG1-mediated NMD transcripts. A subset of cell lines, including multiple myeloma (MM) cell lines sensitive to the endoplasmic reticulum stress-inducing compound thapsigargin, were highly susceptible to SMG1 inhibition. CC-115 caused the induction of UPR transcripts and cell death by mitochondrial apoptosis, requiring the presence of BAX/BAK and caspase activity. Superior antitumor activity of CC-115 over TORK inhibitors in primary human MM cells and three xenograft mouse models appeared to be via inhibition of SMG1. Our data support further development of SMG1 inhibitors as possible therapeutics in MM.
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Affiliation(s)
- Alexander C. Leeksma
- Department of Hematology, Amsterdam University Medical CentersUniversity of AmsterdamThe Netherlands,Department of Experimental ImmunologyAmsterdam University Medical CentersUniversity of AmsterdamThe Netherlands,Lymphoma and myeloma center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII)The Netherlands
| | - Ingrid A. M. Derks
- Department of Experimental ImmunologyAmsterdam University Medical CentersUniversity of AmsterdamThe Netherlands,Lymphoma and myeloma center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII)The Netherlands
| | - Brett Garrick
- Translational Research, Bristol Myers SquibbSan FranciscoCAUSA
| | - Aldo Jongejan
- Department of Clinical Epidemiology, Biostatistics and BioinformaticsAmsterdam University Medical Centers, University of AmsterdamThe Netherlands
| | - Martino Colombo
- Bristol Myers Squibb's Center for Innovation and Translational Research Europe (CITRE)SevilleSpain
| | - Timon Bloedjes
- Department of Pathology, Amsterdam University Medical Centers, Lymphoma and Myeloma Center Amsterdam (LYMMCARE)University of AmsterdamThe Netherlands
| | - Torsten Trowe
- Translational Research, Bristol Myers SquibbSan FranciscoCAUSA
| | | | | | - Mehnaz Malek
- Translational Research, Bristol Myers SquibbSan FranciscoCAUSA
| | | | - Kate Blease
- Discovery, Bristol Myers SquibbSan DiegoCAUSA
| | | | | | - Remco Loos
- Bristol Myers Squibb's Center for Innovation and Translational Research Europe (CITRE)SevilleSpain
| | - Marie‐José Kersten
- Department of Hematology, Amsterdam University Medical CentersUniversity of AmsterdamThe Netherlands
| | - Perry D. Moerland
- Department of Clinical Epidemiology, Biostatistics and BioinformaticsAmsterdam University Medical Centers, University of AmsterdamThe Netherlands
| | - Jeroen E. J. Guikema
- Department of Pathology, Amsterdam University Medical Centers, Lymphoma and Myeloma Center Amsterdam (LYMMCARE)University of AmsterdamThe Netherlands
| | - Arnon P. Kater
- Department of Hematology, Amsterdam University Medical CentersUniversity of AmsterdamThe Netherlands,Lymphoma and myeloma center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII)The Netherlands
| | - Eric Eldering
- Department of Experimental ImmunologyAmsterdam University Medical CentersUniversity of AmsterdamThe Netherlands,Lymphoma and myeloma center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII)The Netherlands
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8
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Chen L, Bi M, Zhang Z, Du X, Chen X, Jiao Q, Jiang H. The functions of IRE1α in neurodegenerative diseases: Beyond ER stress. Ageing Res Rev 2022; 82:101774. [PMID: 36332756 DOI: 10.1016/j.arr.2022.101774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/19/2022] [Accepted: 10/29/2022] [Indexed: 11/05/2022]
Abstract
Inositol-requiring enzyme 1 α (IRE1α) is a type I transmembrane protein that resides in the endoplasmic reticulum (ER). IRE1α, which is the primary sensor of ER stress, has been proven to maintain intracellular protein homeostasis by activating X-box binding protein 1 (XBP1). Further studies have revealed novel physiological functions of the IRE1α, such as its roles in mRNA and protein degradation, inflammation, immunity, cell proliferation and cell death. Therefore, the function of IRE1α is not limited to its role in ER stress; IRE1α is also important for regulating other processes related to cellular physiology. Furthermore, IRE1α plays a key role in neurodegenerative diseases that are caused by the phosphorylation of Tau protein, the accumulation of α-synuclein (α-syn) and the toxic effects of mutant Huntingtin (mHtt). Therefore, targeting IRE1α is a valuable approach for treating neurodegenerative diseases and regulating cell functions. This review discusses the role of IRE1α in different cellular processes, and emphasizes the importance of IRE1α in neurodegenerative diseases.
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Affiliation(s)
- Ling Chen
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Mingxia Bi
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Zhen Zhang
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xixun Du
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xi Chen
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Qian Jiao
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Qingdao University, Qingdao, China.
| | - Hong Jiang
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Qingdao University, Qingdao, China; University of Health and Rehabilitation Sciences, Qingdao, China.
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9
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Lee BY, Kim J, Lee J. Intraspecific de novo gene birth revealed by presence-absence variant genes in Caenorhabditis elegans. NAR Genom Bioinform 2022; 4:lqac031. [PMID: 35464238 PMCID: PMC9022459 DOI: 10.1093/nargab/lqac031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/30/2022] [Accepted: 04/13/2022] [Indexed: 12/24/2022] Open
Abstract
Genes embed their evolutionary history in the form of various alleles. Presence-absence variants (PAVs) are extreme cases of such alleles, where a gene present in one haplotype does not exist in another. Because PAVs may result from either birth or death of a gene, PAV genes and their alternative alleles, if available, can represent a basis for rapid intraspecific gene evolution. Using long-read sequencing technologies, this study traced the possible evolution of PAV genes in the PD1074 and CB4856 C. elegans strains as well as their alternative alleles in 14 other wild strains. We updated the CB4856 genome by filling 18 gaps and identified 46 genes and 7,460 isoforms from both strains not annotated previously. We verified 328 PAV genes, out of which 46 were C. elegans-specific. Among these possible newly born genes, 12 had alternative alleles in other wild strains; in particular, the alternative alleles of three genes showed signatures of active transposons. Alternative alleles of three other genes showed another type of signature reflected in accumulation of small insertions or deletions. Research on gene evolution using both species-specific PAV genes and their alternative alleles may provide new insights into the process of gene evolution.
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Affiliation(s)
- Bo Yun Lee
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea
| | - Jun Kim
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea
| | - Junho Lee
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea
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10
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Mailliot J, Vivoli-Vega M, Schaffitzel C. No-nonsense: insights into the functional interplay of nonsense-mediated mRNA decay factors. Biochem J 2022; 479:973-993. [PMID: 35551602 PMCID: PMC9162471 DOI: 10.1042/bcj20210556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 11/22/2022]
Abstract
Nonsense-mediated messenger RNA decay (NMD) represents one of the main surveillance pathways used by eukaryotic cells to control the quality and abundance of mRNAs and to degrade viral RNA. NMD recognises mRNAs with a premature termination codon (PTC) and targets them to decay. Markers for a mRNA with a PTC, and thus NMD, are a long a 3'-untranslated region and the presence of an exon-junction complex (EJC) downstream of the stop codon. Here, we review our structural understanding of mammalian NMD factors and their functional interplay leading to a branched network of different interconnected but specialised mRNA decay pathways. We discuss recent insights into the potential impact of EJC composition on NMD pathway choice. We highlight the coexistence and function of different isoforms of up-frameshift protein 1 (UPF1) with an emphasis of their role at the endoplasmic reticulum and during stress, and the role of the paralogs UPF3B and UPF3A, underscoring that gene regulation by mammalian NMD is tightly controlled and context-dependent being conditional on developmental stage, tissue and cell types.
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Affiliation(s)
- Justine Mailliot
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - Mirella Vivoli-Vega
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
- Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave, Bristol BS8 1TQ, U.K
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11
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Transcriptome Analysis of the Nematodes Caenorhabditis elegans and Litoditis marina in Different Food Environments. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10050580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Diets regulate animal development, reproduction, and lifespan. However, the underlying molecular mechanisms remain elusive. We previously showed that a chemically defined CeMM diet attenuates the development and promotes the longevity of C. elegans, but whether it impacts other nematodes is unknown. Here, we studied the effects of the CeMM diet on the development and longevity of the marine nematode Litoditis marina, which belongs to the same family as C. elegans. We further investigated genome-wide transcriptional responses to the CeMM and OP50 diets for both nematodes, respectively. We observed that the CeMM diet attenuated L. marina development but did not extend its lifespan. Through KEEG enrichment analysis, we found that many of the FOXO DAF-16 signaling and lysosome and xenobiotic metabolism related genes were significantly increased in C. elegans on the CeMM diet, which might contribute to the lifespan extension of C. elegans. Notably, we found that the expression of lysosome and xenobiotic metabolism pathway genes was significantly down-regulated in L. marina on CeMM, which might explain why the CeMM diet could not promote the lifespan of L. marina compared to bacterial feeding. Additionally, the down-regulation of several RNA transcription and protein generation and related processes genes in C. elegans on CeMM might not only be involved in extending longevity, but also contribute to attenuating the development of C. elegans on the CeMM diet, while the down-regulation of unsaturated fatty acids synthesis genes in L. marina might contribute to slow down its growth while on CeMM. This study provided important insights into how different diets regulate development and lifespan, and further genetic analysis of the candidate gene(s) of development and longevity will facilitate exploring the molecular mechanisms underlying how diets regulate animal physiology and health in the context of variable nutritional environments.
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12
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Child JR, Chen Q, Reid DW, Jagannathan S, Nicchitta CV. Recruitment of endoplasmic reticulum-targeted and cytosolic mRNAs into membrane-associated stress granules. RNA (NEW YORK, N.Y.) 2021; 27:1241-1256. [PMID: 34244458 PMCID: PMC8456999 DOI: 10.1261/rna.078858.121] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
Stress granules (SGs) are membraneless organelles composed of mRNAs and RNA binding proteins which undergo assembly in response to stress-induced inactivation of translation initiation. In general, SG recruitment is limited to a subpopulation of a given mRNA species and RNA-seq analyses of purified SGs revealed that signal sequence-encoding (i.e., endoplasmic reticulum [ER]-targeted) transcripts are significantly underrepresented, consistent with prior reports that ER localization can protect mRNAs from SG recruitment. Using translational profiling, cell fractionation, and single molecule mRNA imaging, we examined SG biogenesis following activation of the unfolded protein response (UPR) by 1,4-dithiothreitol (DTT) and report that gene-specific subsets of cytosolic and ER-targeted mRNAs can be recruited into SGs. Furthermore, we demonstrate that SGs form in close proximity to or directly associated with the ER membrane. ER-associated SG assembly was also observed during arsenite stress, suggesting broad roles for the ER in SG biogenesis. Recruitment of a given mRNA into SGs required stress-induced translational repression, though translational inhibition was not solely predictive of an mRNA's propensity for SG recruitment. SG formation was prevented by the transcriptional inhibitors actinomycin D or triptolide, suggesting a functional link between gene transcriptional state and SG biogenesis. Collectively these data demonstrate that ER-targeted and cytosolic mRNAs can be recruited into ER-associated SGs and this recruitment is sensitive to transcriptional inhibition. We propose that newly transcribed mRNAs exported under conditions of suppressed translation initiation are primary SG substrates, with the ER serving as the central subcellular site of SG formation.
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Affiliation(s)
- Jessica R Child
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Qiang Chen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - David W Reid
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Denver, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado, Anschutz Medical Campus, Denver, Colorado 80045, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
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13
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Dalal JS, Winden KD, Salussolia CL, Sundberg M, Singh A, Pham TT, Zhou P, Pu WT, Miller MT, Sahin M. Loss of Tsc1 in cerebellar Purkinje cells induces transcriptional and translation changes in FMRP target transcripts. eLife 2021; 10:e67399. [PMID: 34259631 PMCID: PMC8279760 DOI: 10.7554/elife.67399] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/29/2021] [Indexed: 12/19/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is a genetic disorder that is associated with multiple neurological manifestations. Previously, we demonstrated that Tsc1 loss in cerebellar Purkinje cells (PCs) can cause altered social behavior in mice. Here, we performed detailed transcriptional and translational analyses of Tsc1-deficient PCs to understand the molecular alterations in these cells. We found that target transcripts of the Fragile X Mental Retardation Protein (FMRP) are reduced in mutant PCs with evidence of increased degradation. Surprisingly, we observed unchanged ribosomal binding for many of these genes using translating ribosome affinity purification. Finally, we found that multiple FMRP targets, including SHANK2, were reduced, suggesting that compensatory increases in ribosomal binding efficiency may be unable to overcome reduced transcript levels. These data further implicate dysfunction of FMRP and its targets in TSC and suggest that treatments aimed at restoring the function of these pathways may be beneficial.
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Affiliation(s)
- Jasbir Singh Dalal
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Kellen Diamond Winden
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Catherine Lourdes Salussolia
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Maria Sundberg
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Achint Singh
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Truc Thanh Pham
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Pingzhu Zhou
- Department of Cardiology, Boston Children’s HospitalBostonUnited States
| | - William T Pu
- Department of Cardiology, Boston Children’s HospitalBostonUnited States
- Harvard Medical SchoolBostonUnited States
| | - Meghan T Miller
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center BaselBaselSwitzerland
| | - Mustafa Sahin
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
- Harvard Medical SchoolBostonUnited States
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14
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Traumatic Brain Injury: Ultrastructural Features in Neuronal Ferroptosis, Glial Cell Activation and Polarization, and Blood-Brain Barrier Breakdown. Cells 2021; 10:cells10051009. [PMID: 33923370 PMCID: PMC8146242 DOI: 10.3390/cells10051009] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 12/21/2022] Open
Abstract
The secondary injury process after traumatic brain injury (TBI) results in motor dysfunction, cognitive and emotional impairment, and poor outcomes. These injury cascades include excitotoxic injury, mitochondrial dysfunction, oxidative stress, ion imbalance, inflammation, and increased vascular permeability. Electron microscopy is an irreplaceable tool to understand the complex pathogenesis of TBI as the secondary injury is usually accompanied by a series of pathologic changes at the ultra-micro level of the brain cells. These changes include the ultrastructural changes in different parts of the neurons (cell body, axon, and synapses), glial cells, and blood–brain barrier, etc. In view of the current difficulties in the treatment of TBI, identifying the changes in subcellular structures can help us better understand the complex pathologic cascade reactions after TBI and improve clinical diagnosis and treatment. The purpose of this review is to summarize and discuss the ultrastructural changes related to neurons (e.g., condensed mitochondrial membrane in ferroptosis), glial cells, and blood–brain barrier in the existing reports of TBI, to deepen the in-depth study of TBI pathomechanism, hoping to provide a future research direction of pathogenesis and treatment, with the ultimate aim of improving the prognosis of patients with TBI.
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15
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Xiong S, Chng WJ, Zhou J. Crosstalk between endoplasmic reticulum stress and oxidative stress: a dynamic duo in multiple myeloma. Cell Mol Life Sci 2021; 78:3883-3906. [PMID: 33599798 PMCID: PMC8106603 DOI: 10.1007/s00018-021-03756-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/19/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023]
Abstract
Under physiological and pathological conditions, cells activate the unfolded protein response (UPR) to deal with the accumulation of unfolded or misfolded proteins in the endoplasmic reticulum. Multiple myeloma (MM) is a hematological malignancy arising from immunoglobulin-secreting plasma cells. MM cells are subject to continual ER stress and highly dependent on the UPR signaling activation due to overproduction of paraproteins. Mounting evidence suggests the close linkage between ER stress and oxidative stress, demonstrated by overlapping signaling pathways and inter-organelle communication pivotal to cell fate decision. Imbalance of intracellular homeostasis can lead to deranged control of cellular functions and engage apoptosis due to mutual activation between ER stress and reactive oxygen species generation through a self-perpetuating cycle. Here, we present accumulating evidence showing the interactive roles of redox homeostasis and proteostasis in MM pathogenesis and drug resistance, which would be helpful in elucidating the still underdefined molecular pathways linking ER stress and oxidative stress in MM. Lastly, we highlight future research directions in the development of anti-myeloma therapy, focusing particularly on targeting redox signaling and ER stress responses.
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Affiliation(s)
- Sinan Xiong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore
| | - Wee-Joo Chng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore.
- Centre for Translational Medicine, Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore.
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Republic of Singapore.
| | - Jianbiao Zhou
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore.
- Centre for Translational Medicine, Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore.
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16
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Lee SK. Endoplasmic Reticulum Homeostasis and Stress Responses in Caenorhabditis elegans. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 59:279-303. [PMID: 34050871 DOI: 10.1007/978-3-030-67696-4_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The unfolded protein response (UPR) is an evolutionarily conserved adaptive regulatory pathway that alleviates protein-folding defects in the endoplasmic reticulum (ER). Physiological demands, environmental perturbations and pathological conditions can cause accumulation of unfolded proteins in the ER and the stress signal is transmitted to the nucleus to turn on a series of genes to respond the challenge. In metazoan, the UPR pathways consisted of IRE1/XBP1, PEK-1 and ATF6, which function in parallel and downstream transcriptional activation triggers the proteostasis networks consisting of molecular chaperones, protein degradation machinery and other stress response pathways ((Labbadia J, Morimoto RI, F1000Prime Rep 6:7, 2014); (Shen X, Ellis RE, Lee K, Annu Rev Biochem 28:893-903, 2014)). The integrated responses act on to resolve the ER stress by increasing protein folding capacity, attenuating ER-loading translation, activating ER-associated proteasomal degradation (ERAD), and regulating IRE1-dependent decay of mRNA (RIDD). Therefore, the effective UPR to internal and external causes is linked to the multiple pathophysiological conditions such as aging, immunity, and neurodegenerative diseases. Recent development in the research of the UPR includes cell-nonautonomous features of the UPR, interplay between the UPR and other stress response pathways, unconventional UPR inducers, and noncanonical UPR independent of the three major branches, originated from multiple cellular and molecular machineries in addition to ER. Caenorhabditis elegans model system has critically contributed to these unprecedented aspects of the ER UPR and broadens the possible therapeutic targets to treat the ER-stress associated human disorders and time-dependent physiological deterioration of aging.
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Affiliation(s)
- Sun-Kyung Lee
- Department of Life Science, Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, Republic of Korea.
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17
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Bashir S, Banday M, Qadri O, Bashir A, Hilal N, Nida-I-Fatima, Rader S, Fazili KM. The molecular mechanism and functional diversity of UPR signaling sensor IRE1. Life Sci 2020; 265:118740. [PMID: 33188833 DOI: 10.1016/j.lfs.2020.118740] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/03/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023]
Abstract
The endoplasmic reticulum is primarily responsible for protein folding and maturation. However, the organelle is subject to varied stress conditions from time to time, which lead to the activation of a signaling program known as the Unfolded Protein Response (UPR) pathway. This pathway, upon sensing any disturbance in the protein-folding milieu sends signals to the nucleus and cytoplasm in order to restore homeostasis. One of the prime UPR signaling sensors is Inositol-requiring enzyme 1 (IRE1); an ER membrane embedded protein with dual enzyme activities, kinase and endoribonuclease. The ribonuclease activity of IRE1 results in Xbp1 splicing in mammals or Hac1 splicing in yeast. However, IRE1 can switch its substrate specificity to the mRNAs that are co-transnationally transported to the ER, a phenomenon known as Regulated IRE1 Dependent Decay (RIDD). IRE1 is also reported to act as a principal molecule that coordinates with other proteins and signaling pathways, which in turn might be responsible for its regulation. The current review highlights studies on IRE1 explaining the structural features and molecular mechanism behind its ribonuclease outputs. The emphasis is also laid on the molecular effectors, which directly or indirectly interact with IRE1 to either modulate its function or connect it to other pathways. This is important in understanding the functional pleiotropy of IRE1, by which it can switch its activity from pro-survival to pro-apoptotic, thus determining the fate of cells.
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Affiliation(s)
- Samirul Bashir
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Mariam Banday
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Ozaira Qadri
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Arif Bashir
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Nazia Hilal
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Nida-I-Fatima
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Stephen Rader
- Department of Chemistry, University of Northern British Columbia, Prince George, BC, Canada
| | - Khalid Majid Fazili
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India.
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18
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Caenorhabditis elegans algn-2 Is Critical for Longevity Conferred by Enhanced Nonsense-Mediated mRNA Decay. iScience 2020; 23:101713. [PMID: 33225240 PMCID: PMC7662852 DOI: 10.1016/j.isci.2020.101713] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/10/2020] [Accepted: 10/16/2020] [Indexed: 11/23/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a biological surveillance mechanism that eliminates mRNA transcripts with premature termination codons. In Caenorhabditis elegans, NMD contributes to longevity by enhancing RNA quality. Here, we aimed at identifying NMD-modulating factors that are crucial for longevity in C. elegans by performing genetic screens. We showed that knocking down each of algn-2/asparagine-linked glycosylation protein, zip-1/bZIP transcription factor, and C44B11.1/FAS apoptotic inhibitory molecule increased the transcript levels of NMD targets. Among these, algn-2 exhibited an age-dependent decrease in its expression and was required for maintaining normal lifespan and for longevity caused by various genetic interventions. We further demonstrated that upregulation of ALGN-2 by inhibition of daf-2/insulin/IGF-1 receptor contributed to longevity in an NMD-dependent manner. Thus, algn-2, a positive regulator of NMD, plays a crucial role in longevity in C. elegans, likely by enhancing RNA surveillance. Our study will help understand how NMD-mediated mRNA quality control extends animal lifespan. C. elegans algn-2 is a positive regulator of nonsense-mediated mRNA decay (NMD) algn-2 is downregulated during aging and contributes to maintaining normal lifespan algn-2 is required for longevity caused by various genetic interventions Upregulation of ALGN-2 by inhibition of daf-2 promotes longevity via increasing NMD
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19
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The Branched Nature of the Nonsense-Mediated mRNA Decay Pathway. Trends Genet 2020; 37:143-159. [PMID: 33008628 DOI: 10.1016/j.tig.2020.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/11/2020] [Accepted: 08/18/2020] [Indexed: 12/16/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a conserved translation-coupled quality control mechanism in all eukaryotes that regulates the expression of a significant fraction of both the aberrant and normal transcriptomes. In vertebrates, NMD has become an essential process owing to expansion of the diversity of NMD-regulated transcripts, particularly during various developmental processes. Surprisingly, however, some core NMD factors that are essential for NMD in simpler organisms appear to be dispensable for vertebrate NMD. At the same time, numerous NMD enhancers and suppressors have been identified in multicellular organisms including vertebrates. Collectively, the available data suggest that vertebrate NMD is a complex, branched pathway wherein individual branches regulate specific mRNA subsets to fulfill distinct physiological functions.
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20
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Longman D, Jackson-Jones KA, Maslon MM, Murphy LC, Young RS, Stoddart JJ, Hug N, Taylor MS, Papadopoulos DK, Cáceres JF. Identification of a localized nonsense-mediated decay pathway at the endoplasmic reticulum. Genes Dev 2020; 34:1075-1088. [PMID: 32616520 PMCID: PMC7397857 DOI: 10.1101/gad.338061.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/05/2020] [Indexed: 12/25/2022]
Abstract
Nonsense-mediated decay (NMD) is a translation-dependent RNA quality control mechanism that occurs in the cytoplasm. However, it is unknown how NMD regulates the stability of RNAs translated at the endoplasmic reticulum (ER). Here, we identify a localized NMD pathway dedicated to ER-translated mRNAs. We previously identified NBAS, a component of the Syntaxin 18 complex involved in Golgi-to-ER trafficking, as a novel NMD factor. Furthermore, we show that NBAS fulfills an independent function in NMD. This ER-NMD pathway requires the interaction of NBAS with the core NMD factor UPF1, which is partially localized at the ER in the proximity of the translocon. NBAS and UPF1 coregulate the stability of ER-associated transcripts, in particular those associated with the cellular stress response. We propose a model where NBAS recruits UPF1 to the membrane of the ER and activates an ER-dedicated NMD pathway, thus providing an ER-protective function by ensuring quality control of ER-translated mRNAs.
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Affiliation(s)
- Dasa Longman
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Kathryn A Jackson-Jones
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Magdalena M Maslon
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Robert S Young
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Jack J Stoddart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Nele Hug
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Martin S Taylor
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Dimitrios K Papadopoulos
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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21
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Bartoszewski R, Gebert M, Janaszak-Jasiecka A, Cabaj A, Króliczewski J, Bartoszewska S, Sobolewska A, Crossman DK, Ochocka R, Kamysz W, Kalinowski L, Dąbrowski M, Collawn JF. Genome-wide mRNA profiling identifies RCAN1 and GADD45A as regulators of the transitional switch from survival to apoptosis during ER stress. FEBS J 2020; 287:2923-2947. [PMID: 31880863 DOI: 10.1111/febs.15195] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/26/2019] [Accepted: 12/23/2019] [Indexed: 12/17/2022]
Abstract
Endoplasmic reticulum (ER) stress conditions promote a cellular adaptive mechanism called the unfolded protein response (UPR) that utilizes three stress sensors, inositol-requiring protein 1, protein kinase RNA-like ER kinase, and activating transcription factor 6. These sensors activate a number of pathways to reduce the stress and facilitate cell survival. While much is known about the mechanisms involved that modulate apoptosis during chronic stress, less is known about the transition between the prosurvival and proapoptotic factors that determine cell fate. Here, we employed a genetic screen that utilized three different pharmacological stressors to induce ER stress in a human-immortalized airway epithelial cell line, immortalized human bronchial epithelial cells. We followed the stress responses over an 18-h time course and utilized real-time monitoring of cell survival, next-generation sequencing, and quantitative real-time PCR to identify and validate genes that were upregulated with all three commonly employed ER stressors, inhibitor of calpain 1, tunicamycin, and thapsigargin. growth arrest and DNA damage-inducible alpha (GADD45A), a proapoptotic factor, and regulator of calcineurin 1 (RCAN1) mRNAs were identified and verified by showing that small interfering RNA (siRNA) knockdown of GADD45A decreased CCAAT-enhancer-binding protein homologous protein (a.k.a DDIT3), BCL2-binding component 3 (a.k.a. BBC3), and phorbol-12-myristate-13-acetate-induced protein 1 expression, 3 proapoptotic factors, and increased cell viability during ER stress conditions, whereas siRNA knockdown of RCAN1 dramatically decreased cell viability. These results suggest that the relative levels of these two genes regulate cell fate decisions during ER stress independent of the type of ER stressor.
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Affiliation(s)
- Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Poland
| | - Magdalena Gebert
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Poland
| | | | - Aleksandra Cabaj
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Króliczewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Poland
| | | | - Aleksandra Sobolewska
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Poland
| | - David K Crossman
- Department of Genetics, Heflin Center for Genomic Science, University of Alabama at Birmingham, AL, USA
| | - Renata Ochocka
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Poland
| | - Wojciech Kamysz
- Department of Inorganic Chemistry, Medical University of Gdansk, Poland
| | - Leszek Kalinowski
- Department of Medical Laboratory Diagnostics and Central Bank of Frozen Tissues & Genetic Specimens, Medical University of Gdansk, Poland
| | - Michał Dąbrowski
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - James F Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, AL, USA
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22
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Dyle MC, Kolakada D, Cortazar MA, Jagannathan S. How to get away with nonsense: Mechanisms and consequences of escape from nonsense-mediated RNA decay. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1560. [PMID: 31359616 PMCID: PMC10685860 DOI: 10.1002/wrna.1560] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/25/2019] [Accepted: 07/04/2019] [Indexed: 11/04/2023]
Abstract
Nonsense-mediated RNA decay (NMD) is an evolutionarily conserved RNA quality control process that serves both as a mechanism to eliminate aberrant transcripts carrying premature stop codons, and to regulate expression of some normal transcripts. For a quality control process, NMD exhibits surprising variability in its efficiency across transcripts, cells, tissues, and individuals in both physiological and pathological contexts. Whether an aberrant RNA is spared or degraded, and by what mechanism, could determine the phenotypic outcome of a disease-causing mutation. Hence, understanding the variability in NMD is not only important for clinical interpretation of genetic variants but also may provide clues to identify novel therapeutic approaches to counter genetic disorders caused by nonsense mutations. Here, we discuss the current knowledge of NMD variability and the mechanisms that allow certain transcripts to escape NMD despite the presence of NMD-inducing features. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA in Disease and Development > RNA in Disease RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Michael C. Dyle
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Divya Kolakada
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael A. Cortazar
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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23
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Ashkavand Z, Sarasija S, Ryan KC, Laboy JT, Norman KR. Corrupted ER-mitochondrial calcium homeostasis promotes the collapse of proteostasis. Aging Cell 2020; 19:e13065. [PMID: 31714672 PMCID: PMC6974732 DOI: 10.1111/acel.13065] [Citation(s) in RCA: 13] [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: 05/31/2019] [Revised: 09/30/2019] [Accepted: 10/17/2019] [Indexed: 11/28/2022] Open
Abstract
Aging and age-related diseases are associated with a decline of protein homeostasis (proteostasis), but the mechanisms underlying this decline are not clear. In particular, decreased proteostasis is a widespread molecular feature of neurodegenerative diseases, such as Alzheimer's disease (AD). Familial AD is largely caused by mutations in the presenilin encoding genes; however, their role in AD is not understood. In this study, we investigate the role of presenilins in proteostasis using the model system Caenorhabditis elegans. Previously, we found that mutations in C. elegans presenilin cause elevated ER to mitochondria calcium signaling, which leads to an increase in mitochondrial generated oxidative stress. This, in turn, promotes neurodegeneration. To understand the cellular mechanisms driving neurodegeneration, using several molecular readouts of protein stability in C. elegans, we find that presenilin mutants have widespread defects in proteostasis. Markedly, we demonstrate that these defects are independent of the protease activity of presenilin and that reduction in ER to mitochondrial calcium signaling can significantly prevent the proteostasis defects observed in presenilin mutants. Furthermore, we show that supplementing presenilin mutants with antioxidants suppresses the proteostasis defects. Our findings indicate that defective ER to mitochondria calcium signaling promotes proteostatic collapse in presenilin mutants by increasing oxidative stress.
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Affiliation(s)
- Zahra Ashkavand
- Department of Regenerative and Cancer Cell BiologyAlbany Medical CollegeAlbanyNYUSA
| | - Shaarika Sarasija
- Department of Regenerative and Cancer Cell BiologyAlbany Medical CollegeAlbanyNYUSA
| | - Kerry C. Ryan
- Department of Regenerative and Cancer Cell BiologyAlbany Medical CollegeAlbanyNYUSA
| | - Jocelyn T. Laboy
- Department of Regenerative and Cancer Cell BiologyAlbany Medical CollegeAlbanyNYUSA
| | - Kenneth R. Norman
- Department of Regenerative and Cancer Cell BiologyAlbany Medical CollegeAlbanyNYUSA
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Gao P, Chai Y, Song J, Liu T, Chen P, Zhou L, Ge X, Guo X, Han J, Yang H. Reprogramming the unfolded protein response for replication by porcine reproductive and respiratory syndrome virus. PLoS Pathog 2019; 15:e1008169. [PMID: 31738790 PMCID: PMC6932825 DOI: 10.1371/journal.ppat.1008169] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 12/26/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022] Open
Abstract
The unfolded protein response (UPR) in the endoplasmic reticulum (ER) constitutes a critical component of host innate immunity against microbial infections. In this report, we show that porcine reproductive and respiratory syndrome virus (PRRSV) utilizes the UPR machinery for its own benefit. We provide evidence that the virus targets the UPR central regulator GRP78 for proteasomal degradation via a mechanism that requires viral glycoprotein GP2a, while both IRE1-XBP1s and PERK-eIF2α-ATF4 signaling branches of the UPR are turned on at early stage of infection. The activated effector XBP1s was found to enter the nucleus, but ATF4 was unexpectedly diverted to cytoplasmic viral replication complexes by means of nonstructural proteins nsp2/3 to promote viral RNA synthesis. RNAi knockdown of either ATF4 or XBP1s dramatically attenuated virus titers, while overexpression caused increases. These observations reveal attractive host targets (e.g., ATF4 and XBP1s) for antiviral drugs and have implications in vaccine development. Porcine reproductive and respiratory syndrome virus (PRRSV) poses a major threat to the worldwide swine industry, but no effective vaccines or antiviral drugs are available. A better understanding of the pathogen-host interactions that support PRRSV replication is essential for understanding viral pathogenesis and the development of preventive measures. Here we report that PRRSV utilizes unconventional strategies to reprogram the unfolded protein response (UPR) of the host to its own advantage. The virus targets GRP78 for partial degradation to create a favorable environment for UPR induction and hijacks ATF4 into cytoplasmic replication complexes to promote viral RNA synthesis. The data also reveal potential targets (e.g., ATF4 and XBP1s) for antiviral drugs and have implications in vaccine development.
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Affiliation(s)
- Peng Gao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, China Agricultural University College of Veterinary Medicine, Beijing, People’s Republic of China
| | - Yue Chai
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, China Agricultural University College of Veterinary Medicine, Beijing, People’s Republic of China
| | - Jiangwei Song
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, China Agricultural University College of Veterinary Medicine, Beijing, People’s Republic of China
| | - Teng Liu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, China Agricultural University College of Veterinary Medicine, Beijing, People’s Republic of China
| | - Peng Chen
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, China Agricultural University College of Veterinary Medicine, Beijing, People’s Republic of China
| | - Lei Zhou
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, China Agricultural University College of Veterinary Medicine, Beijing, People’s Republic of China
| | - Xinna Ge
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, China Agricultural University College of Veterinary Medicine, Beijing, People’s Republic of China
| | - Xin Guo
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, China Agricultural University College of Veterinary Medicine, Beijing, People’s Republic of China
| | - Jun Han
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, China Agricultural University College of Veterinary Medicine, Beijing, People’s Republic of China
- * E-mail:
| | - Hanchun Yang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, China Agricultural University College of Veterinary Medicine, Beijing, People’s Republic of China
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Wood KA, Rowlands CF, Qureshi WMS, Thomas HB, Buczek WA, Briggs TA, Hubbard SJ, Hentges KE, Newman WG, O’Keefe RT. Disease modeling of core pre-mRNA splicing factor haploinsufficiency. Hum Mol Genet 2019; 28:3704-3723. [PMID: 31304552 PMCID: PMC6935387 DOI: 10.1093/hmg/ddz169] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/04/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022] Open
Abstract
The craniofacial disorder mandibulofacial dysostosis Guion-Almeida type is caused by haploinsufficiency of the U5 snRNP gene EFTUD2/SNU114. However, it is unclear how reduced expression of this core pre-mRNA splicing factor leads to craniofacial defects. Here we use a CRISPR-Cas9 nickase strategy to generate a human EFTUD2-knockdown cell line and show that reduced expression of EFTUD2 leads to diminished proliferative ability of these cells, increased sensitivity to endoplasmic reticulum (ER) stress and the mis-expression of several genes involved in the ER stress response. RNA-Seq analysis of the EFTUD2-knockdown cell line revealed transcriptome-wide changes in gene expression, with an enrichment for genes associated with processes involved in craniofacial development. Additionally, our RNA-Seq data identified widespread mis-splicing in EFTUD2-knockdown cells. Analysis of the functional and physical characteristics of mis-spliced pre-mRNAs highlighted conserved properties, including length and splice site strengths, of retained introns and skipped exons in our disease model. We also identified enriched processes associated with the affected genes, including cell death, cell and organ morphology and embryonic development. Together, these data support a model in which EFTUD2 haploinsufficiency leads to the mis-splicing of a distinct subset of pre-mRNAs with a widespread effect on gene expression, including altering the expression of ER stress response genes and genes involved in the development of the craniofacial region. The increased burden of unfolded proteins in the ER resulting from mis-splicing would exceed the capacity of the defective ER stress response, inducing apoptosis in cranial neural crest cells that would result in craniofacial abnormalities during development.
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Affiliation(s)
- Katherine A Wood
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
- Center for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, St. Mary’s Hospital, The University of Manchester, Manchester Academic Health Science Centre Manchester, M13 9PT, UK
| | - Charlie F Rowlands
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
- Center for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, St. Mary’s Hospital, The University of Manchester, Manchester Academic Health Science Centre Manchester, M13 9PT, UK
| | - Wasay Mohiuddin Shaikh Qureshi
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - Huw B Thomas
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - Weronika A Buczek
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - Tracy A Briggs
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
- Center for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, St. Mary’s Hospital, The University of Manchester, Manchester Academic Health Science Centre Manchester, M13 9PT, UK
| | - Simon J Hubbard
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - Kathryn E Hentges
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
- Center for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, St. Mary’s Hospital, The University of Manchester, Manchester Academic Health Science Centre Manchester, M13 9PT, UK
| | - Raymond T O’Keefe
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
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26
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Lloyd JPB, Lang D, Zimmer AD, Causier B, Reski R, Davies B. The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens. Nucleic Acids Res 2019; 46:5822-5836. [PMID: 29596649 PMCID: PMC6009662 DOI: 10.1093/nar/gky225] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/16/2018] [Indexed: 12/16/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is important for RNA quality control and gene regulation in eukaryotes. NMD targets aberrant transcripts for decay and also directly influences the abundance of non-aberrant transcripts. In animals, the SMG1 kinase plays an essential role in NMD by phosphorylating the core NMD factor UPF1. Despite SMG1 being ubiquitous throughout the plant kingdom, little is known about its function, probably because SMG1 is atypically absent from the genome of the model plant, Arabidopsis thaliana. By combining our previously established SMG1 knockout in moss with transcriptome-wide analysis, we reveal the range of processes involving SMG1 in plants. Machine learning assisted analysis suggests that 32% of multi-isoform genes produce NMD-targeted transcripts and that splice junctions downstream of a stop codon act as the major determinant of NMD targeting. Furthermore, we suggest that SMG1 is involved in other quality control pathways, affecting DNA repair and the unfolded protein response, in addition to its role in mRNA quality control. Consistent with this, smg1 plants have increased susceptibility to DNA damage, but increased tolerance to unfolded protein inducing agents. The potential involvement of SMG1 in RNA, DNA and protein quality control has major implications for the study of these processes in plants.
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Affiliation(s)
- James P B Lloyd
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, UK
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Barry Causier
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, UK
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,BIOSS - Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Brendan Davies
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, UK
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27
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Han X, Wei Y, Wang H, Wang F, Ju Z, Li T. Nonsense-mediated mRNA decay: a 'nonsense' pathway makes sense in stem cell biology. Nucleic Acids Res 2019; 46:1038-1051. [PMID: 29272451 PMCID: PMC5814811 DOI: 10.1093/nar/gkx1272] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/09/2017] [Indexed: 01/04/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a highly conserved post-transcriptional regulatory mechanism of gene expression in eukaryotes. Originally, NMD was identified as an RNA surveillance machinery in degrading 'aberrant' mRNA species with premature termination codons. Recent studies indicate that NMD regulates the stability of natural gene transcripts that play significant roles in cell functions. Although components and action modes of the NMD machinery in degrading its RNA targets have been extensively studied with biochemical and structural approaches, the biological roles of NMD remain to be defined. Stem cells are rare cell populations, which play essential roles in tissue homeostasis and hold great promises in regenerative medicine. Stem cells self-renew to maintain the cellular identity and differentiate into somatic lineages with specialized functions to sustain tissue integrity. Transcriptional regulations and epigenetic modulations have been extensively implicated in stem cell biology. However, post-transcriptional regulatory mechanisms, such as NMD, in stem cell regulation are largely unknown. In this paper, we summarize the recent findings on biological roles of NMD factors in embryonic and tissue-specific stem cells. Furthermore, we discuss the possible mechanisms of NMD in regulating stem cell fates.
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Affiliation(s)
- Xin Han
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Yanling Wei
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Hua Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Feilong Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Zhenyu Ju
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Tangliang Li
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
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28
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Xiaoliang Hou, Sun J, Wang Y, Jiang X. Identification of Specific Genes and Pathways by a Comparative Transcriptomic Study of Hypodermal and Body Muscle Development. Russ J Dev Biol 2019. [DOI: 10.1134/s106236041903007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Fernandes R, Nogueira G, da Costa PJ, Pinto F, Romão L. Nonsense-Mediated mRNA Decay in Development, Stress and Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:41-83. [DOI: 10.1007/978-3-030-19966-1_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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30
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Role of the Death Receptor and Endoplasmic Reticulum Stress Signaling Pathways in Polyphyllin I-Regulated Apoptosis of Human Hepatocellular Carcinoma HepG2 Cells. BIOMED RESEARCH INTERNATIONAL 2018; 2018:5241941. [PMID: 30671458 PMCID: PMC6323420 DOI: 10.1155/2018/5241941] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 12/17/2022]
Abstract
Polyphyllin has been reported to exhibit anticancer effects against various types of cancer via the proapoptotic signaling pathway. The aim of the present study was to investigate the role of the endoplasmic reticulum stress and death receptor signaling pathways in PPI-induced apoptosis of human hepatocellular carcinoma HepG2 cells. Analysis demonstrated that PPI could significantly inhibit the proliferation and induce apoptosis of HepG2 cells in a dose- and time-dependent manner. Investigation into the molecular mechanism of PPI indicated that PPI notably mediated ER stress activation via IRE-1 overexpression and activation of the caspase-12 to protect HepG2 cells against apoptosis. In addition, PPI markedly induced the expression of death receptors signaling pathways-associated factors, including tumor necrosis factor (TNF) receptor 1/TNF-α and FAS/FASL. Additionally, suppression of the death receptor signaling pathways with a caspase-8 inhibitor, Z-IETD-FMK, revealed an increase in the death rate and apoptotic rate of HepG2 cells. Collectively, the findings of the present study suggested that the ER stress and death receptor signaling pathways were associated with PPI-induced HepG2 cell apoptosis; however, endoplasmic reticulum stress may serve a protective role in this process. The combination of PPI and Z-IETD-FMK may activate necroptosis, which enhances apoptosis. Therefore, the results of the present study may improve understanding regarding the roles of signaling pathways in PPI regulated apoptosis and contribute to the development of novel therapies for the treatment of HCC.
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31
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Roy D, Kahler DJ, Yun C, Hubbard EJA. Functional Interactions Between rsks-1/S6K, glp-1/Notch, and Regulators of Caenorhabditis elegans Fertility and Germline Stem Cell Maintenance. G3 (BETHESDA, MD.) 2018; 8:3293-3309. [PMID: 30126834 PMCID: PMC6169383 DOI: 10.1534/g3.118.200511] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/06/2018] [Indexed: 12/17/2022]
Abstract
The proper accumulation and maintenance of stem cells is critical for organ development and homeostasis. The Notch signaling pathway maintains stem cells in diverse organisms and organ systems. In Caenorhabditis elegans, GLP-1/Notch activity prevents germline stem cell (GSC) differentiation. Other signaling mechanisms also influence the maintenance of GSCs, including the highly-conserved TOR substrate ribosomal protein S6 kinase (S6K). Although C. elegans bearing either a null mutation in rsks-1/S6K or a reduction-of-function (rf) mutation in glp-1/Notch produce half the normal number of adult germline progenitors, virtually all these single mutant animals are fertile. However, glp-1(rf) rsks-1(null) double mutant animals are all sterile, and in about half of their gonads, all GSCs differentiate, a distinctive phenotype associated with a significant reduction or loss of GLP-1 signaling. How rsks-1/S6K promotes GSC fate is unknown. Here, we determine that rsks-1/S6K acts germline-autonomously to maintain GSCs, and that it does not act through Cyclin-E or MAP kinase in this role. We found that interfering with translation also enhances glp-1(rf), but that regulation through rsks-1 cannot fully account for this effect. In a genome-scale RNAi screen for genes that act similarly to rsks-1/S6K, we identified 56 RNAi enhancers of glp-1(rf) sterility, many of which were previously not known to interact functionally with Notch. Further investigation revealed at least six candidates that, by genetic criteria, act linearly with rsks-1/S6K. These include genes encoding translation-related proteins, cacn-1/Cactin, an RNA exosome component, and a Hedgehog-related ligand. We found that additional Hedgehog-related ligands may share functional relationships with glp-1/Notch and rsks-1/S6K in maintaining germline progenitors.
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Affiliation(s)
- Debasmita Roy
- Skirball Institute of Biomolecular Medicine, Departments of Cell Biology and Pathology, New York University School of Medicine, New York, NY 10016
| | - David J Kahler
- NYU High Throughput Biology Laboratory, NYU Langone Health, New York, NY 10016
| | - Chi Yun
- NYU High Throughput Biology Laboratory, NYU Langone Health, New York, NY 10016
| | - E Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Departments of Cell Biology and Pathology, New York University School of Medicine, New York, NY 10016
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32
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Hsu JCC, Reid DW, Hoffman AM, Sarkar D, Nicchitta CV. Oncoprotein AEG-1 is an endoplasmic reticulum RNA-binding protein whose interactome is enriched in organelle resident protein-encoding mRNAs. RNA (NEW YORK, N.Y.) 2018; 24:688-703. [PMID: 29438049 PMCID: PMC5900566 DOI: 10.1261/rna.063313.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 01/30/2018] [Indexed: 05/04/2023]
Abstract
Astrocyte elevated gene-1 (AEG-1), an oncogene whose overexpression promotes tumor cell proliferation, angiogenesis, invasion, and enhanced chemoresistance, is thought to function primarily as a scaffolding protein, regulating PI3K/Akt and Wnt/β-catenin signaling pathways. Here we report that AEG-1 is an endoplasmic reticulum (ER) resident integral membrane RNA-binding protein (RBP). Examination of the AEG-1 RNA interactome by HITS-CLIP and PAR-CLIP methodologies revealed a high enrichment for endomembrane organelle-encoding transcripts, most prominently those encoding ER resident proteins, and within this cohort, for integral membrane protein-encoding RNAs. Cluster mapping of the AEG-1/RNA interaction sites demonstrated a normalized rank order interaction of coding sequence >5' untranslated region, with 3' untranslated region interactions only weakly represented. Intriguingly, AEG-1/membrane protein mRNA interaction sites clustered downstream from encoded transmembrane domains, suggestive of a role in membrane protein biogenesis. Secretory and cytosolic protein-encoding mRNAs were also represented in the AEG-1 RNA interactome, with the latter category notably enriched in genes functioning in mRNA localization, translational regulation, and RNA quality control. Bioinformatic analyses of RNA-binding motifs and predicted secondary structure characteristics indicate that AEG-1 lacks established RNA-binding sites though shares the property of high intrinsic disorder commonly seen in RBPs. These data implicate AEG-1 in the localization and regulation of secretory and membrane protein-encoding mRNAs and provide a framework for understanding AEG-1 function in health and disease.
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Affiliation(s)
- Jack C-C Hsu
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - David W Reid
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Alyson M Hoffman
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University Massey Cancer Center, Virginia Commonwealth University Institute of Molecular Medicine, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298, USA
| | - Christopher V Nicchitta
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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Targeting the spliceosome for cutaneous squamous cell carcinoma therapy: a role for c-MYC and wild-type p53 in determining the degree of tumour selectivity. Oncotarget 2018; 9:23029-23046. [PMID: 29796170 PMCID: PMC5955416 DOI: 10.18632/oncotarget.25196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/04/2018] [Indexed: 12/25/2022] Open
Abstract
We show that suppression of the spliceosome has potential for the treatment of cutaneous squamous cell carcinoma (cSCC). The small-molecule inhibitors of the spliceosome at the most advanced stage of development target the splicing factor SF3B1/SF3b155. The majority of cSCC cell lines are more sensitive than normal skin cells to death induced by the SF3B1 inhibitor pladienolide B. Knockdown of SF3B1 and a range of other splicing factors with diverse roles in the spliceosome can also selectively kill cSCC cells. We demonstrate that endogenous c-MYC participates in conferring sensitivity to spliceosome inhibition. c-MYC expression is elevated in cSCC lines and its knockdown reduces alterations in mRNA splicing and attenuates cell death caused by interference with the spliceosome. In addition, this study provides further support for a key role of the p53 pathway in the response to spliceosome disruption. SF3B1 inhibition causes wild-type p53 upregulation associated with altered mRNA splicing and reduced protein expression of both principal p53 negative regulators MDMX/MDM4 and MDM2. We observed that wild-type p53 can promote pladienolide B-induced death in tumour cells. However, p53 is commonly inactivated by mutation in cSCCs and p53 participates in killing normal skin cells at high concentrations of pladienolide B. This may limit the therapeutic window of SF3B1 inhibitors for cSCC. We provide evidence that, while suppression of SF3B1 has promise for treating cSCCs with mutant p53, inhibitors which target the spliceosome through SF3B1-independent mechanisms could have greater cSCC selectivity as a consequence of reduced p53 upregulation in normal cells.
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34
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Ni H, Rui Q, Li D, Gao R, Chen G. The Role of IRE1 Signaling in the Central Nervous System Diseases. Curr Neuropharmacol 2018; 16:1340-1347. [PMID: 29663887 PMCID: PMC6251047 DOI: 10.2174/1570159x16666180416094646] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 08/07/2017] [Accepted: 02/28/2018] [Indexed: 01/14/2023] Open
Abstract
The accumulation of misfolded or unfolded proteins in endoplasmic reticulum (ER) lumen results in the activation of an adaptive stress process called the unfolded protein response (UPR). As the most conserved signaling branch of the UPR, Inositol-requiring enzyme 1 (IRE1) possesses both Ser/Thr kinase and RNase activities operating as major stress sensors, mediating both adaptive and pro-apoptotic pathways under ER stress. Over the last three decades, a mounting body of evidence has shown that IRE1 signaling dysfunction is involved in the pathology of various neurological disorders. Targeting this pathway has emerged as a promising therapeutic strategy against these diseases. In this review, we provide a general overview about the expression and physiological function of IRE1 signaling and its pathophysiological roles in the central nervous system diseases.
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Affiliation(s)
| | | | - Di Li
- Address correspondence to this author at the Department of Translational Medicine Center, The First People’s Hospital of Zhangjiagang City, Suzhou, Jiangsu, P.R. China; Tel: +86-18921962599; E-mail:
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35
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Benzethonium chloride activates ER stress and reduces proliferation in HNSCC. Oral Oncol 2017; 76:27-33. [PMID: 29290283 DOI: 10.1016/j.oraloncology.2017.11.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/03/2017] [Accepted: 11/18/2017] [Indexed: 12/29/2022]
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36
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Goetz AE, Wilkinson M. Stress and the nonsense-mediated RNA decay pathway. Cell Mol Life Sci 2017; 74:3509-3531. [PMID: 28503708 PMCID: PMC5683946 DOI: 10.1007/s00018-017-2537-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 01/09/2023]
Abstract
Cells respond to internal and external cellular stressors by activating stress-response pathways that re-establish homeostasis. If homeostasis is not achieved in a timely manner, stress pathways trigger programmed cell death (apoptosis) to preserve organism integrity. A highly conserved stress pathway is the unfolded protein response (UPR), which senses excessive amounts of unfolded proteins in the ER. While a physiologically beneficial pathway, the UPR requires tight regulation to provide a beneficial outcome and avoid deleterious consequences. Recent work has demonstrated that a conserved and highly selective RNA degradation pathway-nonsense-mediated RNA decay (NMD)-serves as a major regulator of the UPR pathway. NMD degrades mRNAs encoding UPR components to prevent UPR activation in response to innocuous ER stress. In response to strong ER stress, NMD is inhibited by the UPR to allow for a full-magnitude UPR response. Recent studies have indicated that NMD also has other stress-related functions, including promoting the timely termination of the UPR to avoid apoptosis; NMD also regulates responses to non-ER stressors, including hypoxia, amino-acid deprivation, and pathogen infection. NMD regulates stress responses in species across the phylogenetic scale, suggesting that it has conserved roles in shaping stress responses. Stress pathways are frequently constitutively activated or dysregulated in human disease, raising the possibility that "NMD therapy" may provide clinical benefit by downmodulating stress responses.
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Affiliation(s)
- Alexandra E Goetz
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, 9500 Gilman Dr., La Jolla, 92093, USA
| | - Miles Wilkinson
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, 9500 Gilman Dr., La Jolla, 92093, USA.
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37
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Gong J, Wang XZ, Wang T, Chen JJ, Xie XY, Hu H, Yu F, Liu HL, Jiang XY, Fan HD. Molecular signal networks and regulating mechanisms of the unfolded protein response. J Zhejiang Univ Sci B 2017; 18:1-14. [PMID: 28070992 DOI: 10.1631/jzus.b1600043] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Within the cell, several mechanisms exist to maintain homeostasis of the endoplasmic reticulum (ER). One of the primary mechanisms is the unfolded protein response (UPR). In this review, we primarily focus on the latest signal webs and regulation mechanisms of the UPR. The relationships among ER stress, apoptosis, and cancer are also discussed. Under the normal state, binding immunoglobulin protein (BiP) interacts with the three sensors (protein kinase RNA-like ER kinase (PERK), activating transcription factor 6 (ATF6), and inositol-requiring enzyme 1α (IRE1α)). Under ER stress, misfolded proteins interact with BiP, resulting in the release of BiP from the sensors. Subsequently, the three sensors dimerize and autophosphorylate to promote the signal cascades of ER stress. ER stress includes a series of positive and negative feedback signals, such as those regulating the stabilization of the sensors/BiP complex, activating and inactivating the sensors by autophosphorylation and dephosphorylation, activating specific transcription factors to enable selective transcription, and augmenting the ability to refold and export. Apart from the three basic pathways, vascular endothelial growth factor (VEGF)-VEGF receptor (VEGFR)-phospholipase C-γ (PLCγ)-mammalian target of rapamycin complex 1 (mTORC1) pathway, induced only in solid tumors, can also activate ATF6 and PERK signal cascades, and IRE1α also can be activated by activated RAC-alpha serine/threonine-protein kinase (AKT). A moderate UPR functions as a pro-survival signal to return the cell to its state of homeostasis. However, persistent ER stress will induce cells to undergo apoptosis in response to increasing reactive oxygen species (ROS), Ca2+ in the cytoplasmic matrix, and other apoptosis signal cascades, such as c-Jun N-terminal kinase (JNK), signal transducer and activator of transcription 3 (STAT3), and P38, when cellular damage exceeds the capacity of this adaptive response.
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Affiliation(s)
- Jing Gong
- Sichuan Radio and TV University, Chengdu 610073, China
| | - Xing-Zhi Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Tao Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Jiao-Jiao Chen
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Xiao-Yuan Xie
- The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Hui Hu
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Fang Yu
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Hui-Lin Liu
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Xing-Yan Jiang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Han-Dong Fan
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
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38
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Celik A, Baker R, He F, Jacobson A. High-resolution profiling of NMD targets in yeast reveals translational fidelity as a basis for substrate selection. RNA (NEW YORK, N.Y.) 2017; 23:735-748. [PMID: 28209632 PMCID: PMC5393182 DOI: 10.1261/rna.060541.116] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/09/2017] [Indexed: 05/20/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) plays an important role in eukaryotic gene expression, yet the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we reevaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. Our new RNA-seq analyses confirm previous results of microarray studies, but also uncover hundreds of new NMD-regulated transcripts that had escaped previous detection, including many intron-containing pre-mRNAs and several noncoding RNAs. The vast majority of NMD-regulated transcripts are normal-looking protein-coding mRNAs. Our bioinformatics analyses reveal that this set of NMD-regulated transcripts generally have lower translational efficiency and higher ratios of out-of-frame translation. NMD-regulated transcripts also have lower average codon optimality scores and higher transition probability to nonoptimal codons. Collectively, our results generate a comprehensive catalog of yeast NMD substrates and yield new insights into the mechanisms by which these transcripts are targeted by NMD.
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Affiliation(s)
- Alper Celik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Richard Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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Doultsinos D, Avril T, Lhomond S, Dejeans N, Guédat P, Chevet E. Control of the Unfolded Protein Response in Health and Disease. SLAS DISCOVERY 2017; 22:787-800. [PMID: 28453376 DOI: 10.1177/2472555217701685] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The unfolded protein response (UPR) is an integrated, adaptive biochemical process that is inextricably linked with cell homeostasis and paramount to maintenance of normal physiological function. Prolonged accumulation of improperly folded proteins in the endoplasmic reticulum (ER) leads to stress. This is the driving stimulus behind the UPR. As such, prolonged ER stress can push the UPR past beneficial functions such as reduced protein production and increased folding and clearance to apoptotic signaling. The UPR is thus contributory to the commencement, maintenance, and exacerbation of a multitude of disease states, making it an attractive global target to tackle conditions sorely in need of novel therapeutic intervention. The accumulation of information of screening tools, readily available therapies, and potential pathways to drug development is the cornerstone of informed clinical research and clinical trial design. Here, we review the UPR's involvement in health and disease and, beyond providing an in-depth description of the molecules found to target the three UPR arms, we compile all the tools available to screen for and develop novel therapeutic agents that modulate the UPR with the scope of future disease intervention.
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Affiliation(s)
- Dimitrios Doultsinos
- 1 Inserm U1242, Chemistry, Oncogenesis, Stress & Signaling, University of Rennes 1, Rennes, France.,2 Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | - Tony Avril
- 1 Inserm U1242, Chemistry, Oncogenesis, Stress & Signaling, University of Rennes 1, Rennes, France.,2 Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | | | | | | | - Eric Chevet
- 1 Inserm U1242, Chemistry, Oncogenesis, Stress & Signaling, University of Rennes 1, Rennes, France.,2 Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France.,3 BMYscreen, Bergonié Cancer Institute, Bordeaux, France
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40
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Harada N, Okuyama M, Yoshikatsu A, Yamamoto H, Ishiwata S, Hamada C, Hirose T, Shono M, Kuroda M, Tsutsumi R, Takeo J, Taketani Y, Nakaya Y, Sakaue H. Endoplasmic Reticulum Stress in Mice Increases Hepatic Expression of Genes Carrying a Premature Termination Codon via a Nutritional Status‐Independent GRP78‐Dependent Mechanism. J Cell Biochem 2017; 118:3810-3824. [DOI: 10.1002/jcb.26031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/04/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Nagakatsu Harada
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Maiko Okuyama
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Aya Yoshikatsu
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Hironori Yamamoto
- Faculty of Human LifeDepartment of Health and NutritionJin‐ai University3‐1‐1 Ohde‐choEchizen City915‐8586Japan
| | - Saori Ishiwata
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Chikako Hamada
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Tomoyo Hirose
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Masayuki Shono
- Support Center for Advanced Medical SciencesInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Masashi Kuroda
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Rie Tsutsumi
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Jiro Takeo
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
- Central Research LaboratoryNippon Suisan Kaisha32‐3 Nanakuni 1 ChomeHachiojiTokyo192‐0991Japan
| | - Yutaka Taketani
- Department of Clinical Nutrition and Food ManagementInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Yutaka Nakaya
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Hiroshi Sakaue
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
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Li Z, Vuong JK, Zhang M, Stork C, Zheng S. Inhibition of nonsense-mediated RNA decay by ER stress. RNA (NEW YORK, N.Y.) 2017; 23:378-394. [PMID: 27940503 PMCID: PMC5311500 DOI: 10.1261/rna.058040.116] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 12/06/2016] [Indexed: 05/26/2023]
Abstract
Nonsense-mediated RNA decay (NMD) selectively degrades mutated and aberrantly processed transcripts that contain premature termination codons (PTC). Cellular NMD activity is typically assessed using exogenous PTC-containing reporters. We overcame some inherently problematic aspects of assaying endogenous targets and developed a broadly applicable strategy to reliably and easily monitor changes in cellular NMD activity. Our new method was genetically validated for distinguishing NMD regulation from transcriptional control and alternative splicing regulation, and unexpectedly disclosed a different sensitivity of NMD targets to NMD inhibition. Applying this robust method for screening, we identified NMD-inhibiting stressors but also found that NMD inactivation was not universal to cellular stresses. The high sensitivity and broad dynamic range of our method revealed a strong correlation between NMD inhibition, endoplasmic reticulum (ER) stress, and polysome disassembly upon thapsigargin treatment in a temporal and dose-dependent manner. We found little evidence of calcium signaling mediating thapsigargin-induced NMD inhibition. Instead, we discovered that of the three unfolded protein response (UPR) pathways activated by thapsigargin, mainly protein kinase RNA-like endoplasmic reticulum kinase (PERK) was required for NMD inhibition. Finally, we showed that ER stress compounded TDP-43 depletion in the up-regulation of NMD isoforms that had been implicated in the pathogenic mechanisms of amyotrophic lateral sclerosis and frontotemporal dementia, and that the additive effect of ER stress was completely blocked by PERK deficiency.
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Affiliation(s)
- Zhelin Li
- Division of Biomedical Sciences, University of California, Riverside, California 92521, USA
| | - John K Vuong
- Division of Biomedical Sciences, University of California, Riverside, California 92521, USA
| | - Min Zhang
- Division of Biomedical Sciences, University of California, Riverside, California 92521, USA
| | - Cheryl Stork
- Division of Biomedical Sciences, University of California, Riverside, California 92521, USA
| | - Sika Zheng
- Division of Biomedical Sciences, University of California, Riverside, California 92521, USA
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42
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Brogna S, McLeod T, Petric M. The Meaning of NMD: Translate or Perish. Trends Genet 2016; 32:395-407. [PMID: 27185236 DOI: 10.1016/j.tig.2016.04.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 04/02/2016] [Accepted: 04/25/2016] [Indexed: 02/08/2023]
Abstract
Premature translation termination leads to a reduced mRNA level in all types of organisms. In eukaryotes, the phenomenon is known as nonsense-mediated mRNA decay (NMD). This is commonly regarded as the output of a specific surveillance and destruction mechanism that is activated by the presence of a premature translation termination codon (PTC) in an atypical sequence context. Despite two decades of research, it is still unclear how NMD discriminates between PTCs and normal stop codons. We suggest that cells do not possess any such mechanism and instead propose a new model in which this mRNA depletion is a consequence of the appearance of long tracts of mRNA that are unprotected by scanning ribosomes.
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Affiliation(s)
- Saverio Brogna
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK.
| | - Tina McLeod
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK
| | - Marija Petric
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK
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43
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Huang G, Zhang F, Ye Q, Wang H. The circadian clock regulates autophagy directly through the nuclear hormone receptor Nr1d1/Rev-erbα and indirectly via Cebpb/(C/ebpβ) in zebrafish. Autophagy 2016; 12:1292-309. [PMID: 27171500 PMCID: PMC4968235 DOI: 10.1080/15548627.2016.1183843] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Autophagy is a highly conserved intracellular degradation system, and recently was shown to display circadian rhythms in mice. The mechanisms underlying circadian regulation of autophagy, however, are still unclear. Here, we observed that numbers of autophagosomes and autolysosomes exhibit daily rhythms in the zebrafish liver, and cebpb/(c/ebpβ) and various autophagy genes are rhythmically expressed in zebrafish larvae but significantly upregulated in per1b and TALEN-generated nr1d1/rev-erbα mutant fish, indicating that both Per1b and Nr1d1 play critical roles in autophagy rhythms. Luciferase reporter and ChIP assays show that the circadian clock directly regulates autophagy genes through Nr1d1, and also regulates transcription of cebpb through Per1b. We also found that fasting leads to altered expression of both circadian clock genes and autophagy genes in zebrafish adult peripheral organs. Further, transcriptome analysis reveals multiple functions of Nr1d1 in zebrafish. Taken together, these findings provide evidence for how the circadian clock regulates autophagy, imply that nutritional signaling affects both circadian regulation and autophagy activities in peripheral organs, and shed light on how circadian gene mutations act through autophagy to contribute to common metabolic diseases such as obesity.
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Affiliation(s)
- Guodong Huang
- a Center for Circadian Clocks , Soochow University ; Suzhou , Jiangsu , China.,b School of Biology & Basic Medical Sciences , Medical College, Soochow University , Suzhou , Jiangsu , China
| | - Fanmiao Zhang
- a Center for Circadian Clocks , Soochow University ; Suzhou , Jiangsu , China.,b School of Biology & Basic Medical Sciences , Medical College, Soochow University , Suzhou , Jiangsu , China
| | - Qiang Ye
- a Center for Circadian Clocks , Soochow University ; Suzhou , Jiangsu , China.,b School of Biology & Basic Medical Sciences , Medical College, Soochow University , Suzhou , Jiangsu , China
| | - Han Wang
- a Center for Circadian Clocks , Soochow University ; Suzhou , Jiangsu , China.,b School of Biology & Basic Medical Sciences , Medical College, Soochow University , Suzhou , Jiangsu , China
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44
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Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE. Proteomic Analysis Reveals Branch-specific Regulation of the Unfolded Protein Response by Nonsense-mediated mRNA Decay. Mol Cell Proteomics 2016; 15:1584-97. [PMID: 26896796 DOI: 10.1074/mcp.m115.054056] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 12/31/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) has originally been described as a surveillance mechanism to inhibit the expression of mRNAs with truncated open reading frames (ORFs) and to contribute to the fidelity of gene expression. It is now recognized that NMD also controls the expression of physiological genes with "intact" mRNA. Stress can decrease NMD efficiency and thus increase the mRNA levels of physiological NMD targets. As stress can also inhibit translation, the net outcome for shaping the proteome is difficult to predict. We have thus analyzed de novo protein synthesis in response to NMD inhibition or the induction of mild endoplasmic reticulum (ER) stress by treatment of cells with the reducing agent dithiotreitol (DTT). For this purpose, we combined pulsed azidohomoalanine (AHA) and stable isotope labeling by amino acids in cell culture (SILAC). Labeled proteins were purified by click chemistry-based covalent coupling to agarose beads, trypsinized, fractionated, and analyzed by mass spectrometry (MS). We find that mild ER stress up-regulates the de novo synthesis of components of all three branches of the unfolded protein response (PERK, IRE1 and ATF6) without increasing eIF2α phosphorylation or impairing of protein translation. In contrast, inhibition of NMD induces de novo protein synthesis of downstream targets of the PERK and IRE1 pathways, whereas we could not detect regulation of ATF6-responsive genes. These data thus support a model that implicates a positive feedback loop of ER stress inhibiting NMD efficiency which further promotes the ER stress response in a branch-specific manner.
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Affiliation(s)
- Jana Sieber
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Christian Hauer
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany; ¶European Molecular Biology Laboratory, Heidelberg, Germany
| | - Madhuri Bhuvanagiri
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Stefan Leicht
- ¶European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Gabriele Neu-Yilik
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Matthias W Hentze
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; ¶European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas E Kulozik
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany;
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45
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Hug N, Longman D, Cáceres JF. Mechanism and regulation of the nonsense-mediated decay pathway. Nucleic Acids Res 2016; 44:1483-95. [PMID: 26773057 PMCID: PMC4770240 DOI: 10.1093/nar/gkw010] [Citation(s) in RCA: 322] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/31/2015] [Indexed: 12/11/2022] Open
Abstract
The Nonsense-mediated mRNA decay (NMD) pathway selectively degrades mRNAs harboring premature termination codons (PTCs) but also regulates the abundance of a large number of cellular RNAs. The central role of NMD in the control of gene expression requires the existence of buffering mechanisms that tightly regulate the magnitude of this pathway. Here, we will focus on the mechanism of NMD with an emphasis on the role of RNA helicases in the transition from NMD complexes that recognize a PTC to those that promote mRNA decay. We will also review recent strategies aimed at uncovering novel trans-acting factors and their functional role in the NMD pathway. Finally, we will describe recent progress in the study of the physiological role of the NMD response.
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Affiliation(s)
- Nele Hug
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Dasa Longman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Javier F Cáceres
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
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46
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47
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He F, Jacobson A. Nonsense-Mediated mRNA Decay: Degradation of Defective Transcripts Is Only Part of the Story. Annu Rev Genet 2015; 49:339-66. [PMID: 26436458 DOI: 10.1146/annurev-genet-112414-054639] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance mechanism that monitors cytoplasmic mRNA translation and targets mRNAs undergoing premature translation termination for rapid degradation. From yeasts to humans, activation of NMD requires the function of the three conserved Upf factors: Upf1, Upf2, and Upf3. Here, we summarize the progress in our understanding of the molecular mechanisms of NMD in several model systems and discuss recent experiments that address the roles of Upf1, the principal regulator of NMD, in the initial targeting and final degradation of NMD-susceptible mRNAs. We propose a unified model for NMD in which the Upf factors provide several functions during premature termination, including the stimulation of release factor activity and the dissociation and recycling of ribosomal subunits. In this model, the ultimate degradation of the mRNA is the last step in a complex premature termination process.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655; ,
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655; ,
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48
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Abstract
Stress induced by accumulation of misfolded proteins in the endoplasmic reticulum is observed in many physiological and pathological conditions. To cope with endoplasmic reticulum stress, cells activate the unfolded protein response, a dynamic signalling network that orchestrates the recovery of homeostasis or triggers apoptosis, depending on the level of damage. Here we provide an overview of recent insights into the mechanisms that cells employ to maintain proteostasis and how the unfolded protein response determines cell fate under endoplasmic reticulum stress.
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49
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Rhoads TW, Prasad A, Kwiecien NW, Merrill AE, Zawack K, Westphall MS, Schroeder FC, Kimble J, Coon JJ. NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans. Mol Cell Proteomics 2015; 14:2922-35. [PMID: 26392051 DOI: 10.1074/mcp.m115.049684] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Indexed: 01/05/2023] Open
Abstract
The nematode Caenorhabditis elegans is an important model organism for biomedical research. We previously described NeuCode stable isotope labeling by amino acids in cell culture (SILAC), a method for accurate proteome quantification with potential for multiplexing beyond the limits of traditional stable isotope labeling by amino acids in cell culture. Here we apply NeuCode SILAC to profile the proteomic and phosphoproteomic response of C. elegans to two potent members of the ascaroside family of nematode pheromones. By consuming labeled E. coli as part of their diet, C. elegans nematodes quickly and easily incorporate the NeuCode heavy lysine isotopologues by the young adult stage. Using this approach, we report, at high confidence, one of the largest proteomic and phosphoproteomic data sets to date in C. elegans: 6596 proteins at a false discovery rate ≤ 1% and 6620 phosphorylation isoforms with localization probability ≥75%. Our data reveal a post-translational signature of pheromone sensing that includes many conserved proteins implicated in longevity and response to stress.
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Affiliation(s)
| | - Aman Prasad
- ‖Biochemistry, and **Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | | | | | - Kelson Zawack
- ‡‡Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853
| | | | - Frank C Schroeder
- ‡‡Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853
| | - Judith Kimble
- ‖Biochemistry, and **Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Joshua J Coon
- From the Departments of ‡Chemistry, §Biomolecular Chemistry, ¶Genome Center,
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50
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Chevet E, Hetz C, Samali A. Endoplasmic reticulum stress-activated cell reprogramming in oncogenesis. Cancer Discov 2015; 5:586-97. [PMID: 25977222 DOI: 10.1158/2159-8290.cd-14-1490] [Citation(s) in RCA: 271] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/28/2015] [Indexed: 12/29/2022]
Abstract
UNLABELLED Stress induced by the accumulation of unfolded proteins in the endoplasmic reticulum (ER) is observed in many human diseases, including cancers. Cellular adaptation to ER stress is mediated by the unfolded protein response (UPR), which aims at restoring ER homeostasis. The UPR has emerged as a major pathway in remodeling cancer gene expression, thereby either preventing cell transformation or providing an advantage to transformed cells. UPR sensors are highly regulated by the formation of dynamic protein scaffolds, leading to integrated reprogramming of the cells. Herein, we describe the regulatory mechanisms underlying UPR signaling upon cell intrinsic or extrinsic challenges, and how they engage cell transformation programs and/or provide advantages to cancer cells, leading to enhanced aggressiveness or chemoresistance. We discuss the emerging cross-talk between the UPR and related metabolic processes to ensure maintenance of protein homeostasis and its impact on cell transformation and tumor growth. SIGNIFICANCE ER stress signaling is dysregulated in many forms of cancer and contributes to tumor growth as a survival factor, in addition to modulating other disease-associated processes, including cell migration, cell transformation, and angiogenesis. Evidence for targeting the ER stress signaling pathway as an anticancer strategy is compelling, and novel agents that selectively inhibit the UPR have demonstrated preliminary evidence of preclinical efficacy with an acceptable safety profile.
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Affiliation(s)
- Eric Chevet
- Oncogenesis, Stress, Cancer, University of Rennes, Rennes, France. Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.
| | - Claudio Hetz
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile. Institute of Biomedical Sciences, Center for Molecular Studies of the Cell, Santiago, Chile. Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts.
| | - Afshin Samali
- Apoptosis Research Centre, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
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