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Xie J, Zhang Z. Recent Advances and Therapeutic Implications of 2-Oxoglutarate-Dependent Dioxygenases in Ischemic Stroke. Mol Neurobiol 2024; 61:3949-3975. [PMID: 38041714 DOI: 10.1007/s12035-023-03790-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/08/2023] [Indexed: 12/03/2023]
Abstract
Ischemic stroke is a common disease with a high disability rate and mortality, which brings heavy pressure on families and medical insurance. Nowadays, the golden treatments for ischemic stroke in the acute phase mainly include endovascular therapy and intravenous thrombolysis. Some drugs are used to alleviate brain injury in patients with ischemic stroke, such as edaravone and 3-n-butylphthalide. However, no effective neuroprotective drug for ischemic stroke has been acknowledged. 2-Oxoglutarate-dependent dioxygenases (2OGDDs) are conserved and common dioxygenases whose activities depend on O2, Fe2+, and 2OG. Most 2OGDDs are expressed in the brain and are essential for the development and functions of the brain. Therefore, 2OGDDs likely play essential roles in ischemic brain injury. In this review, we briefly elucidate the functions of most 2OGDDs, particularly the effects of regulations of 2OGDDs on various cells in different phases after ischemic stroke. It would also provide promising potential therapeutic targets and directions of drug development for protecting the brain against ischemic injury and improving outcomes of ischemic stroke.
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Affiliation(s)
- Jian Xie
- Department of Neurology, Affiliated Zhongda Hospital, Research Institution of Neuropsychiatry, School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China
| | - Zhijun Zhang
- Department of Neurology, Affiliated Zhongda Hospital, Research Institution of Neuropsychiatry, School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China.
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Department of Mental Health and Public Health, Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China.
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2
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Rodriguez R, Harris M, Kennedy LM. Deleting the ribosomal prolyl hydroxylase OGFOD1 protects mice against diet-induced obesity and insulin resistance. PLoS One 2024; 19:e0304761. [PMID: 38843265 PMCID: PMC11156292 DOI: 10.1371/journal.pone.0304761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/19/2024] [Indexed: 06/09/2024] Open
Abstract
Type 2 diabetes predisposes patients to heart disease, which is the primary cause of death across the globe. Type 2 diabetes often accompanies obesity and is defined by insulin resistance and abnormal glucose handling. Insulin resistance impairs glucose uptake and results in hyperglycemia, which damages tissues such as kidneys, liver, and heart. 2-oxoglutarate (2-OG)- and iron-dependent oxygenases (2-OGDOs), a family of enzymes regulating various aspects of cellular physiology, have been studied for their role in obesity and diet-induced insulin resistance. However, nothing is known of the 2-OGDO family member 2-oxoglutarate and iron-dependent prolyl hydroxylase domain containing protein 1 (OGFOD1) in this setting. OGFOD1 deletion leads to protection in cardiac ischemia-reperfusion injury and cardiac hypertrophy, which are two cardiac events that can lead to heart failure. Considering the remarkable correlation between heart disease and diabetes, the cardioprotection observed in OGFOD1-knockout mice led us to challenge these knockouts with high-fat diet. Wildtype mice fed a high-fat diet developed diet-induced obesity, insulin resistance, and glucose intolerance, but OGFOD1 knockout mice fed this same diet were resistant to diet-induced obesity and insulin resistance. These results support OGFOD1 down-regulation as a strategy for preventing obesity and insulin handling defects.
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Affiliation(s)
- Rebeca Rodriguez
- National Heart Lung Blood Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Michael Harris
- National Heart Lung Blood Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Leslie M. Kennedy
- National Heart Lung Blood Institute, National Institutes of Health, Bethesda, MD, United States of America
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, United States of America
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3
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Perugino F, Pedroni L, Galaverna G, Dall'Asta C, Dellafiora L. Virtual display of targets: A new level to rise the current understanding of ochratoxin A toxicity from a molecular standpoint. Toxicology 2024; 503:153765. [PMID: 38432407 DOI: 10.1016/j.tox.2024.153765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Ochratoxin A (OTA) is a mycotoxin spread worldwide contaminating several food and feed commodities and rising concerns for humans and animals. OTA toxicity has been thoroughly assessed over the last 60 years revealing a variety of adverse effects, including nephrotoxicity, hepatotoxicity and possible carcinogenicity. However, the underpinning mechanisms of action have yet to be completely displayed and understood. In this framework, we applied a virtual pipeline based on molecular docking, dynamics and umbrella simulations to display new OTA potential targets. The results collected consistently identified OGFOD1, a key player in protein translation, as possibly inhibited by OTA and its 2'R diastereomer. This is consistent with the current knowledge of OTA's molecular toxicology and may fill some gaps from a mechanistic standpoint. This could pave the way for further dedicated analysis focusing their attention on the OTA-OGFOD1 interaction, expanding the current understanding of OTA toxicity at a molecular level.
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Affiliation(s)
- Florinda Perugino
- Department of Food and Drug, University of Parma, Parma, Italy; Department of Biology, University of Naples Federico II, Naples, Italy
| | - Lorenzo Pedroni
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | | | - Luca Dellafiora
- Department of Food and Drug, University of Parma, Parma, Italy.
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4
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Smailys J, Jiang F, Prioleau T, Kelley K, Mitchell O, Nour S, Ali L, Buchser W, Zavada L, Hinton SD. The DUSP domain of pseudophosphatase MK-STYX interacts with G3BP1 to decrease stress granules. Arch Biochem Biophys 2023; 744:109702. [PMID: 37516290 PMCID: PMC10500436 DOI: 10.1016/j.abb.2023.109702] [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: 07/08/2023] [Revised: 07/16/2023] [Accepted: 07/25/2023] [Indexed: 07/31/2023]
Abstract
Mitogen activated protein kinase phosphoserine/threonine/tyrosine-binding protein (MK-STYX) is a dual specificity (DUSP) member of the protein tyrosine phosphatase family. It is a pseudophosphatase, which lacks the essential amino acids histidine and cysteine in the catalytic active signature motif (HCX5R). We previously reported that MK-STYX interacts with G3BP1 [Ras-GAP (GTPase-activating protein) SH3 (Src homology 3) domain-binding-1] and reduces stress granules, stalled mRNA. To determine how MK-STYX reduces stress granules, truncated domains, CH2 (cell division cycle 25 phosphatase homology 2) and DUSP, of MK-STYX were used. Wild-type MK-STYX and the DUSP domain significantly decreased stressed granules that were induced by sodium arsenite, in which G3BP1 (a stress granule nucleator) was used as the marker. In addition, HEK/293 and HeLa cells co-expressing G3BP1-GFP and mCherry-MK-STYX, mCherry-MK-STYX-CH2, mCherry-MK-STYX-DUSP or mCherry showed that stress granules were significantly decreased in the presence of wild-type MK-STYX and the DUSP domain of MK-STYX. Further characterization of these dynamics in HeLa cells showed that the CH2 domain increased the number of stress granules within a cell, relative to wild-type and DUSP domain of MK-STYX. To further analyze the interaction of G3BP1 and the domains of MK-STYX, coimmunoprecipitation experiments were performed. Cells co-expressing G3BP1-GFP and mCherry, mCherry-MK-STYX, mCherry-MK-STYX-CH2, or mCherry-MK-STYX-DUSP demonstrated that the DUSP domain of MK-STYX interacts with both G3BP1-GFP and endogenous G3BP1, whereas the CH2 domain of MK-STYX did not coimmunoprecipitate with G3BP1. In addition, G3BP1 tyrosine phosphorylation, which is required for stress granule formation, was decreased in the presence of wild-type MK-STYX or the DUSP domain but increased in the presence of CH2. These data highlight a model for how MK-STYX decreases G3BP1-induced stress granules. The DUSP domain of MK-STYX interacts with G3BP1 and negatively alters its tyrosine phosphorylation- decreasing stress granule formation.
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Affiliation(s)
- Jonathan Smailys
- Department of Biology, Integrated Science Center, William and Mary, Williamsburg, VA, 23185, USA
| | - Fei Jiang
- Department of Biology, Integrated Science Center, William and Mary, Williamsburg, VA, 23185, USA
| | - Tatiana Prioleau
- Department of Biology, Integrated Science Center, William and Mary, Williamsburg, VA, 23185, USA
| | - Kylan Kelley
- Department of Biology, Integrated Science Center, William and Mary, Williamsburg, VA, 23185, USA; Department of Genetics, Washington University, St. Louis, MO, 63110, USA
| | - Olivia Mitchell
- Department of Biology, Hampton University, Hampton, VA, 23666, USA
| | - Samah Nour
- Department of Genetics, Washington University, St. Louis, MO, 63110, USA
| | - Lina Ali
- Department of Genetics, Washington University, St. Louis, MO, 63110, USA
| | - William Buchser
- Department of Genetics, Washington University, St. Louis, MO, 63110, USA
| | - Lynn Zavada
- Department of Biology, Integrated Science Center, William and Mary, Williamsburg, VA, 23185, USA
| | - Shantá D Hinton
- Department of Biology, Integrated Science Center, William and Mary, Williamsburg, VA, 23185, USA.
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5
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Rodriguez R, Harris M, Murphy E, Kennedy LM. OGFOD1 modulates the transcriptional and proteomic landscapes to alter isoproterenol-induced hypertrophy susceptibility. J Mol Cell Cardiol 2023; 179:42-46. [PMID: 37084634 PMCID: PMC10862384 DOI: 10.1016/j.yjmcc.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/16/2023] [Accepted: 04/07/2023] [Indexed: 04/23/2023]
Abstract
Cardiac hypertrophy is associated with increased translation. However, little is known of the mechanisms that regulate translation in hypertrophy. Members of the 2-oxoglutarate-dependent dioxygenase family regulate several aspects of gene expression, including translation. An important member of this family is OGFOD1. Here, we show OGFOD1 accumulates in failing human hearts. Upon OGFOD1 deletion, murine hearts showed transcriptomic and proteomic changes, with only 21 proteins and mRNAs (0.6%) changing in the same direction. Additionally, OGFOD1-KO mice were protected from induced hypertrophy, supporting a role for OGFOD1 in the cardiac response to chronic stress.
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Affiliation(s)
- Rebeca Rodriguez
- Cardiovascular Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Michael Harris
- Cardiovascular Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Elizabeth Murphy
- Cardiovascular Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Leslie M Kennedy
- Cardiovascular Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States of America.
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6
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Fujisaki T, Saito K, Kikuchi T, Kondo E. The prolyl hydroxylase OGFOD1 promotes cancer cell proliferation by regulating the expression of cell cycle regulators. FEBS Lett 2022; 597:1073-1085. [PMID: 36464654 DOI: 10.1002/1873-3468.14547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 12/12/2022]
Abstract
OGFOD1, a prolyl-hydroxylase, has been reported to translocate from the nucleus to the cytoplasm in response to cellular stress. Here, we demonstrate that OGFOD1 regulates the transcription and post-transcriptional stabilization of cell cycle-related genes. OGFOD1 knockdown in lung cancer cells induced cell cycle arrest through the specific depletion of cyclin-dependent kinase (CDK) 1, CDK2 and cyclin B1 (CCNB1) mRNAs and the nuclear accumulation of p21Cip1 . Analysis of the mRNA dynamics in these cells revealed that CDK1 decreased in a time-dependent manner, reflecting post-transcriptional regulation by OGFOD1 and the RNA-binding protein HuR. In contrast, the depletion of CDK2 and CCNB1 resulted from decreased transcription mediated by OGFOD1. These results indicate that OGFOD1 is required to maintain the function of specific cell cycle regulators during cancer cell proliferation.
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Affiliation(s)
- Toshiya Fujisaki
- Division of Molecular and Cellular Pathology, Niigata University Graduate School of Medical and Dental Sciences, Japan.,Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Japan
| | - Ken Saito
- Department of Clinical Engineering and Medical Technology, Niigata University of Health and Welfare, Japan
| | - Toshiaki Kikuchi
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Japan
| | - Eisaku Kondo
- Division of Molecular and Cellular Pathology, Niigata University Graduate School of Medical and Dental Sciences, Japan.,Division of Tumor Pathology, Near Infrared Photo-Immunotherapy Research Institute, Kansai Medical University, Osaka, Japan
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7
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Metz JB, Hornstein NJ, Sharma SD, Worley J, Gonzalez C, Sims PA. High-throughput translational profiling with riboPLATE-seq. Sci Rep 2022; 12:5718. [PMID: 35383235 PMCID: PMC8983706 DOI: 10.1038/s41598-022-09638-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/18/2022] [Indexed: 11/11/2022] Open
Abstract
Protein synthesis is dysregulated in many diseases, but we lack a systems-level picture of how signaling molecules and RNA binding proteins interact with the translational machinery, largely due to technological limitations. Here we present riboPLATE-seq, a scalable method for generating paired libraries of ribosome-associated and total mRNA. As an extension of the PLATE-seq protocol, riboPLATE-seq utilizes barcoded primers for pooled library preparation, but additionally leverages anti-rRNA ribosome immunoprecipitation on whole polysomes to measure ribosome association (RA). We compare RA to its analogue in ribosome profiling and RNA sequencing, translation efficiency, and demonstrate both the performance of riboPLATE-seq and its utility in detecting translational alterations induced by specific inhibitors of protein kinases.
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Affiliation(s)
- Jordan B Metz
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Nicholas J Hornstein
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, 10032, USA
- MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sohani Das Sharma
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jeremy Worley
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Christian Gonzalez
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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8
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YB1 associates with oncogenetic roles and poor prognosis in nasopharyngeal carcinoma. Sci Rep 2022; 12:3699. [PMID: 35260638 PMCID: PMC8904596 DOI: 10.1038/s41598-022-07636-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 02/22/2022] [Indexed: 12/16/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is the malignant tumor arising from the nasopharynx epithelium with ethnic and geographical distribution preference. Y-box binding protein-1 (YB1) is the highly expressed DNA/RNA-binding protein with cold shock domain, and enhanced YB1 expression was proved to be associated with many kinds of malignant tumors. There is no systematic study about the regulation of YB1 and cell proliferation, migration, invasion and stress granules (SGs) in NPC, and the relationship between YB1 expression and clinical characteristics and prognosis of NPC patients. We analyzed the mRNA expression of YBX1 in head and neck squamous carcinoma (HNSC) and NPC in databases, investigated the functions of YB1 in cell proliferation, migration and invasion and SGs formation of NPC cells, and detected expression of YB1 protein in a large scale of NPC samples and analyzed their association with clinicopathological features and prognostic significance of NPC patients. YBX1 mRNA was significantly high expression in HNSC and NPC by bioinformatic analysis, and higher expression of YBX1 mRNA indicated poorer prognosis of HNSC patients. Clinically, the expression of YB1 in NPC tissues was significantly higher than these in the control nasopharyngeal epithelial tissues. We further found that the expression of YB1 had an evidently positive relation with advanced clinical stages of patients with NPC. The overall survival rates (OS) were significantly lower for NPC patients with positive expression of YB1. Multivariate analysis confirmed that positive expression of YB1 was the independent poorer prognostic factor for patients with NPC. Moreover, compared with the immortalized nasopharyngeal epithelial cell line (NP69), the basal level of YB1 in NPC cell lines was significantly higher. Knocking down YB1 may inhibit Akt/mTOR pathway in NPC cells. Knocking down YB1 by small interfering RNAs can reduce the ability of proliferation, migration, invasion and SGs formation of NPC cells. The expression of YB1 in NPC cell lines or patients with NPC was significantly higher. The high expression of YB1 protein may act as one valuable independent biomarker to predict poor prognosis for patients with NPC. Knocking down YB1 may release the malignant phenotype of NPC cells.
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Harris M, Sun J, Keeran K, Aponte A, Singh K, Springer D, Gucek M, Pirooznia M, Cockman ME, Murphy E, Kennedy LM. Ogfod1 deletion increases cardiac beta-alanine levels and protects mice against ischemia-reperfusion injury. Cardiovasc Res 2021; 118:2847-2858. [PMID: 34668514 DOI: 10.1093/cvr/cvab323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 08/09/2021] [Indexed: 11/14/2022] Open
Abstract
AIMS Prolyl hydroxylation is a post-translational modification that regulates protein stability, turnover, and activity. The proteins that catalyze prolyl hydroxylation belong to the 2-oxoglutarate- and iron-dependent oxygenase family of proteins. 2-oxoglutarate- and iron-dependent oxygenase domain-containing protein 1 (Ogfod1), which hydroxylates a proline in ribosomal protein s23 is a newly-described member of this family. The aims of this study were to investigate roles for Ogfod1 in the heart, and in the heart's response to stress. METHODS AND RESULTS We isolated hearts from wild type (WT) and Ogfod1 knockout (KO) mice and performed quantitative proteomics using Tandem Mass Tag labelling coupled to Liquid Chromatography and tandem Mass Spectrometry (LC-MS/MS) to identify protein changes. Ingenuity Pathway Analysis identified "Urate Biosynthesis/Inosine 5'-phosphate Degradation" and "Purine Nucleotides Degradation II (Aerobic)" as the most significantly-enriched pathways. We performed metabolomics analysis and found that both purine and pyrimidine pathways were altered with the purine nucleotide inosine 5'-monophosphate (IMP) showing a 3.5-fold enrichment in KO hearts (P = 0.011) and the pyrimidine catabolism product beta-alanine showing a 1.7-fold enrichment in KO hearts (P = 0.014). As changes in these pathways have been shown to contribute to cardioprotection, we subjected isolated perfused hearts to ischemia and reperfusion (I/R). KO hearts showed a 41.4% decrease in infarct size and a 34% improvement in cardiac function compared to WT hearts. This protection was also evident in an in vivo I/R model. Additionally, our data show that treating isolated perfused WT hearts with carnosine, a metabolite of beta-alanine, improved protection in the context of I/R injury, whereas treating KO hearts with carnosine had no impact on recovery of function or infarct size. CONCLUSIONS Taken together, these data show that Ogfod1 deletion alters the myocardial proteome and metabolome to confer protection against I/R injury. TRANSLATIONAL PERSPECTIVE Heart disease is the leading cause of death in the US. In characterizing the cardiovascular effects of deleting the prolyl hydroxylase Ogfod1 and investigating its role in disease pathology, we found that deleting Ogfod1 protected hearts against ex vivo and in vivo I/R injury. Ogfod1-KO hearts showed significant metabolomic and proteomic changes that supported altered purine and pyrimidine nucleotide synthesis and turnover. Beta-alanine, a precursor of the anti-oxidant carnosine and a product of pyrimidine degradation, accumulated in KO hearts to help confer cardioprotection. Altogether, these data suggest a role for Ogfod1 downregulation as a therapeutic strategy for heart disease.
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Affiliation(s)
- Michael Harris
- Cardiovascular Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Junhui Sun
- Cardiovascular Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Karen Keeran
- Animal Surgery and Resources Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Angel Aponte
- Proteomics Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Komudi Singh
- Bioinformatics and Computational Biology Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Danielle Springer
- Murine Phenotyping Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Marjan Gucek
- Proteomics Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD
| | | | - Elizabeth Murphy
- Cardiovascular Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Leslie M Kennedy
- Cardiovascular Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD
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10
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Lee HT, Lee IH, Kim JH, Lee S, Kwak S, Suh MY, Hwang IY, Kang BG, Cha SS, Lee BI, Lee SE, Choi J, Roe JS, Cho EJ, Youn HD. Phosphorylation of OGFOD1 by Cell Cycle-Dependent Kinase 7/9 Enhances the Transcriptional Activity of RNA Polymerase II in Breast Cancer Cells. Cancers (Basel) 2021; 13:cancers13143418. [PMID: 34298635 PMCID: PMC8304009 DOI: 10.3390/cancers13143418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Among the causes of accelerating cancer properties, dysregulated transcription is considerably prominent in many cancers. However, it is difficult to target transcriptional machineries due to their fundamental importance. Compared to breast cancer cell lines, we found that OGFOD1 aggravates cancers by enhancing RNA polymerase II transcriptional activity and it is improved by cell cycle-dependent kinases. Overall, we uncovered the novel mechanism for how OGFOD1 maliciously functions in breast cancers, suggesting it as a rational cancer treatment target protein. Abstract 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1 (OGFOD1) expression is upregulated in a variety of cancers and has been related to poor prognosis. However, despite this significance to cancer progression, the precise oncogenic mechanism of OGFOD1 is not understood. We demonstrated that OGFOD1 plays a role in enhancing the transcriptional activity of RNA polymerase II in breast cancer cells. OGFOD1 directly binds to the C-terminal domain of RNA polymerase II to alter phosphorylation status. The elimination of OGFOD1 resulted in decreased tumor development. Additionally, cell cycle-dependent kinase 7 and cell cycle-dependent kinase 9, critical enzymes for activating RNA polymerase II, phosphorylated serine 256 of OGFOD1, whereas a non-phosphorylated mutant OGFOD1 failed to enhance transcriptional activation and tumor growth. Consequently, OGFOD1 helps promote tumor growth by enhancing RNA polymerase II, whereas simultaneous phosphorylation of OGFOD1 by CDK enzymes is essential in stimulating RNA polymerase II-mediated transcription both in vitro and in vivo, and expression of target genes.
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Affiliation(s)
- Han-Teo Lee
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (H.-T.L.); (I.-H.L.); (J.-H.K.); (S.L.); (S.K.); (M.-Y.S.); (I.-Y.H.); (J.C.)
- Department of Molecular Medicine & Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Korea
| | - Il-Hwan Lee
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (H.-T.L.); (I.-H.L.); (J.-H.K.); (S.L.); (S.K.); (M.-Y.S.); (I.-Y.H.); (J.C.)
| | - Jae-Hwan Kim
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (H.-T.L.); (I.-H.L.); (J.-H.K.); (S.L.); (S.K.); (M.-Y.S.); (I.-Y.H.); (J.C.)
| | - Sangho Lee
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (H.-T.L.); (I.-H.L.); (J.-H.K.); (S.L.); (S.K.); (M.-Y.S.); (I.-Y.H.); (J.C.)
- Department of Molecular Medicine & Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Korea
| | - Sojung Kwak
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (H.-T.L.); (I.-H.L.); (J.-H.K.); (S.L.); (S.K.); (M.-Y.S.); (I.-Y.H.); (J.C.)
| | - Min-Young Suh
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (H.-T.L.); (I.-H.L.); (J.-H.K.); (S.L.); (S.K.); (M.-Y.S.); (I.-Y.H.); (J.C.)
| | - In-Young Hwang
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (H.-T.L.); (I.-H.L.); (J.-H.K.); (S.L.); (S.K.); (M.-Y.S.); (I.-Y.H.); (J.C.)
| | - Bu-Gyeong Kang
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Korea; (B.-G.K.); (S.-S.C.)
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Korea; (B.-G.K.); (S.-S.C.)
| | - Byung-Il Lee
- Research Institute, National Cancer Center, Goyang-si 10408, Korea;
| | - Sang-Eun Lee
- Cardiology Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
| | - Jinmi Choi
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (H.-T.L.); (I.-H.L.); (J.-H.K.); (S.L.); (S.K.); (M.-Y.S.); (I.-Y.H.); (J.C.)
- College of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea;
| | - Jae-Seok Roe
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea;
| | - Eun-Jung Cho
- College of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea;
| | - Hong-Duk Youn
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (H.-T.L.); (I.-H.L.); (J.-H.K.); (S.L.); (S.K.); (M.-Y.S.); (I.-Y.H.); (J.C.)
- Correspondence: ; Tel.: +82-2-740-8250; Fax: +82-2-3668-7622
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Porcine Epidemic Diarrhea Virus Infection Induces Caspase-8-Mediated G3BP1 Cleavage and Subverts Stress Granules To Promote Viral Replication. J Virol 2021; 95:JVI.02344-20. [PMID: 33568512 DOI: 10.1128/jvi.02344-20] [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: 12/08/2020] [Accepted: 02/03/2021] [Indexed: 12/19/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is an α-coronavirus causing severe diarrhea and high mortality rates in suckling piglets and posing significant economic impact. PEDV replication is completed and results in a large amount of RNA in the cytoplasm. Stress granules (SGs) are dynamic cytosolic RNA granules formed under various stress conditions, including viral infections. Several previous studies suggested that SGs were involved in the antiviral activity of host cells to limit viral propagation. However, the underlying mechanisms are poorly understood. This study aimed to delineate the molecular mechanisms regulating the SG response to PEDV infection. SG formation is induced early during PEDV infection, but as infection proceeds, this ability is lost and SGs disappear at late stages of infection (>18 h postinfection). PEDV infection resulted in the cleavage of Ras-GTPase-activating protein-binding protein 1 (G3BP1) mediated by caspase-8. Using mutational analysis, the PEDV-induced cleavage site within G3BP1 was identified, which differed from the 3C protease cleavage site previously identified. Furthermore, G3BP1 cleavage by caspase-8 at D168 and D169 was confirmed in vitro as well as in vivo The overexpression of cleavage-resistant G3BP1 conferred persistent SG formation and suppression of viral replication. Additionally, the knockdown of endogenous G3BP1 abolished SG formation and potentiated viral replication. Taken together, these data provide new insights into novel strategies in which PEDV limits the host stress response and antiviral responses and indicate that caspase-8-mediated G3BP1 cleavage is important in the failure of host defense against PEDV infection.IMPORTANCE Coronaviruses (CoVs) are drawing extensive attention again since the outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019. CoVs are prone to variation and own the transmission capability by crossing the species barrier resulting in reemergence. How CoVs manipulate the antiviral responses of their hosts needs to be explored. Overall, the study provides new insight into how porcine epidemic diarrhea virus (PEDV) impaired SG assembly by targeting G3BP1 via the host proteinase caspase-8. These findings enhanced the understanding of PEDV infection and might help identify new antiviral targets that could inhibit viral replication and limit the pathogenesis of PEDV.
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12
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Kundu S. Fe(2)OG: an integrated HMM profile-based web server to predict and analyze putative non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenase function in protein sequences. BMC Res Notes 2021; 14:80. [PMID: 33648553 PMCID: PMC7923460 DOI: 10.1186/s13104-021-05477-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 02/03/2021] [Indexed: 12/16/2022] Open
Abstract
Objective Non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenases (i2OGdd), are a taxonomically and functionally diverse group of enzymes. The active site comprises ferrous iron in a hexa-coordinated distorted octahedron with the apoenzyme, 2-oxoglutarate and a displaceable water molecule. Current information on novel i2OGdd members is sparse and relies on computationally-derived annotation schema. The dissimilar amino acid composition and variable active site geometry thereof, results in differing reaction chemistries amongst i2OGdd members. An additional need of researchers is a curated list of sequences with putative i2OGdd function which can be probed further for empirical data. Results This work reports the implementation of \documentclass[12pt]{minimal}
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\begin{document}$$Fe\left(2\right)OG$$\end{document}Fe2OG, a web server with dual functionality and an extension of previous work on i2OGdd enzymes \documentclass[12pt]{minimal}
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\begin{document}$$\left(Fe\left(2\right)OG\equiv \{H2OGpred,DB2OG\}\right)$$\end{document}Fe2OG≡{H2OGpred,DB2OG}. \documentclass[12pt]{minimal}
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\begin{document}$$Fe\left(2\right)OG$$\end{document}Fe2OG, in this form is completely revised, updated (URL, scripts, repository) and will strengthen the knowledge base of investigators on i2OGdd biochemistry and function. \documentclass[12pt]{minimal}
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\begin{document}$$Fe\left(2\right)OG$$\end{document}Fe2OG, utilizes the superior predictive propensity of HMM-profiles of laboratory validated i2OGdd members to predict probable active site geometries in user-defined protein sequences. \documentclass[12pt]{minimal}
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\begin{document}$$Fe\left(2\right)OG$$\end{document}Fe2OG, also provides researchers with a pre-compiled list of analyzed and searchable i2OGdd-like sequences, many of which may be clinically relevant. \documentclass[12pt]{minimal}
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\begin{document}$$Fe(2)OG$$\end{document}Fe(2)OG, is freely available (http://204.152.217.16/Fe2OG.html) and supersedes all previous versions, i.e., H2OGpred, DB2OG.
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
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13
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Fletcher SC, Coleman ML. Human 2-oxoglutarate-dependent oxygenases: nutrient sensors, stress responders, and disease mediators. Biochem Soc Trans 2020; 48:1843-1858. [PMID: 32985654 PMCID: PMC7609023 DOI: 10.1042/bst20190333] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/30/2020] [Accepted: 09/07/2020] [Indexed: 12/12/2022]
Abstract
Fe(II)/2-oxoglutarate (2OG)-dependent oxygenases are a conserved enzyme class that catalyse diverse oxidative reactions across nature. In humans, these enzymes hydroxylate a broad range of biological substrates including DNA, RNA, proteins and some metabolic intermediates. Correspondingly, members of the 2OG-dependent oxygenase superfamily have been linked to fundamental biological processes, and found dysregulated in numerous human diseases. Such findings have stimulated efforts to understand both the biochemical activities and cellular functions of these enzymes, as many have been poorly studied. In this review, we focus on human 2OG-dependent oxygenases catalysing the hydroxylation of protein and polynucleotide substrates. We discuss their modulation by changes in the cellular microenvironment, particularly with respect to oxygen, iron, 2OG and the effects of oncometabolites. We also describe emerging evidence that these enzymes are responsive to cellular stresses including hypoxia and DNA damage. Moreover, we examine how dysregulation of 2OG-dependent oxygenases is associated with human disease, and the apparent paradoxical role for some of these enzymes during cancer development. Finally, we discuss some of the challenges associated with assigning biochemical activities and cellular functions to 2OG-dependent oxygenases.
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Affiliation(s)
- Sally C. Fletcher
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Mathew L. Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, U.K
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14
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Frydrýšková K, Mašek T, Pospíšek M. Changing faces of stress: Impact of heat and arsenite treatment on the composition of stress granules. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1596. [PMID: 32362075 DOI: 10.1002/wrna.1596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 03/19/2020] [Accepted: 03/23/2020] [Indexed: 11/07/2022]
Abstract
Stress granules (SGs), hallmarks of the cellular adaptation to stress, promote survival, conserve cellular energy, and are fully dissolved upon the cessation of stress treatment. Different stresses can initiate the assembly of SGs, but arsenite and heat are the best studied of these stresses. The composition of SGs and posttranslational modifications of SG proteins differ depending on the type and severity of the stress insult, methodology used, cell line, and presence of overexpressed and tagged proteins. A group of 18 proteins showing differential localization to SGs in heat- and arsenite-stressed mammalian cell lines is described. Upon severe and prolonged stress, physiological SGs transform into more solid protein aggregates that are no longer reversible and do not contain mRNA. Similar pathological inclusions are hallmarks of neurodegenerative diseases. SGs induced by heat stress are less dynamic than SGs induced by arsenite and contain a set of unique proteins and linkage-specific polyubiquitinated proteins. The same types of ubiquitin linkages have been found to contribute to the development of neurodegenerative disorders such as Parkinson disease, Alzheimer disease, and amyotrophic lateral sclerosis (ALS). We propose heat stress-induced SGs as a possible model of an intermediate stage along the transition from dynamic, fully reversible arsenite stress-induced SGs toward aberrant SGs, the hallmark of neurodegenerative diseases. Stress- and methodology-specific differences in the compositions of SGs and the transition of SGs to aberrant protein aggregates are discussed. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Export and Localization > RNA Localization.
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Affiliation(s)
| | | | - Martin Pospíšek
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czechia
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15
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OGFOD1 negatively regulated by miR-1224-5p promotes proliferation in human papillomavirus-infected laryngeal papillomas. Mol Genet Genomics 2020; 295:675-684. [PMID: 32002629 DOI: 10.1007/s00438-020-01649-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/18/2020] [Indexed: 02/01/2023]
Abstract
Laryngeal papillomas (LP) is a difficult disease to manage due to its frequent recurrence, airway compromise, and risk of cancer. Recently, growing evidence indicates the aberrant expression of OGFPD1, a stress granule protein, links closely to the development of tumorigenesis; however, little is known about its role in LP progression. Here, we investigated the tumor promoting action of OGFOD1 in LP. The transcriptional and translational levels of OGFOD1 were significantly up-regulated in LP tissues and cells. Moreover, OGFOD1 promoted viability and proliferation, and inhibited LP cells apoptosis. We further revealed that OGFOD1 was directly targeted by miR-1224-5p, which was significantly down-regulated in LP. Overexpression of the miR-1224-5p suppressed OGFOD1-induced cell proliferation and viability, and promoted apoptosis of LP. In accordance, knockdown of miR-1224-5p inversed the inhibitory effects. In confederation of the central involvement of OGFOD1 in LP progression, targeting the miR-1224-5p/OGFOD1 pathway might provide a novel strategy for LP treatment.
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16
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Stoehr A, Kennedy L, Yang Y, Patel S, Lin Y, Linask KL, Fergusson M, Zhu J, Gucek M, Zou J, Murphy E. The ribosomal prolyl-hydroxylase OGFOD1 decreases during cardiac differentiation and modulates translation and splicing. JCI Insight 2019; 5:128496. [PMID: 31112528 DOI: 10.1172/jci.insight.128496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The mechanisms regulating translation and splicing are not well understood. We provide insight into a new regulator of translation, OGFOD1 (2-oxoglutarate and iron dependent oxygenase domain-containing protein 1), which is a prolyl-hydroxylase that catalyzes the posttranslational hydroxylation of Pro-62 in the small ribosomal protein S23. We show that deletion of OGFOD1 in an in vitro model of human cardiomyocytes decreases translation of specific proteins (e.g., RNA-binding proteins) and alters splicing. RNA sequencing showed poor correlation between changes in mRNA and protein synthesis, suggesting that posttranscriptional regulation was the primary cause for the observed differences. We found that loss of OGFOD1 and the resultant alterations in protein translation modulates the cardiac proteome, shifting it towards higher protein amounts of sarcomeric proteins such as cardiac troponins, titin and cardiac myosin binding protein C. Furthermore, we found a decrease of OGFOD1 during cardiomyocyte differentiation. These results suggest that loss of OGFOD1 modulates protein translation and splicing, thereby leading to alterations in the cardiac proteome and highlight the role of altered translation and splicing in regulating the proteome..
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Affiliation(s)
| | | | | | | | - Yongshun Lin
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Kaari L Linask
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | | | - Jun Zhu
- DNA Sequencing and Genomics Core
| | | | - Jizhong Zou
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
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17
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Mimura J, Inose-Maruyama A, Taniuchi S, Kosaka K, Yoshida H, Yamazaki H, Kasai S, Harada N, Kaufman RJ, Oyadomari S, Itoh K. Concomitant Nrf2- and ATF4-activation by Carnosic Acid Cooperatively Induces Expression of Cytoprotective Genes. Int J Mol Sci 2019; 20:E1706. [PMID: 30959808 PMCID: PMC6480217 DOI: 10.3390/ijms20071706] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 03/29/2019] [Accepted: 03/30/2019] [Indexed: 12/12/2022] Open
Abstract
: Carnosic acid (CA) is a phytochemical found in some dietary herbs, such as Rosmarinus officinalis L., and possesses antioxidative and anti-microbial properties. We previously demonstrated that CA functions as an activator of nuclear factor, erythroid 2 (NF-E2)-related factor 2 (Nrf2), an oxidative stress-responsive transcription factor in human and rodent cells. CA enhances the expression of nerve growth factor (NGF) and antioxidant genes, such as HO-1 in an Nrf2-dependent manner in U373MG human astrocytoma cells. However, CA also induces NGF gene expression in an Nrf2-independent manner, since 50 μM of CA administration showed striking NGF gene induction compared with the classical Nrf2 inducer tert-butylhydroquinone (tBHQ) in U373MG cells. By comparative transcriptome analysis, we found that CA activates activating transcription factor 4 (ATF4) in addition to Nrf2 at high doses. CA activated ATF4 in phospho-eIF2α- and heme-regulated inhibitor kinase (HRI)-dependent manners, indicating that CA activates ATF4 through the integrated stress response (ISR) pathway. Furthermore, CA activated Nrf2 and ATF4 cooperatively enhanced the expression of NGF and many antioxidant genes while acting independently to certain client genes. Taken together, these results represent a novel mechanism of CA-mediated gene regulation evoked by Nrf2 and ATF4 cooperation.
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Affiliation(s)
- Junsei Mimura
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
| | - Atsushi Inose-Maruyama
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
- Department of Microbiology, Tohoku Medical and Pharmaceutical University, Sendai 981-8558, Japan.
| | - Shusuke Taniuchi
- Division of Molecular Biology, Institute of Advanced Medical Sciences, The University of Tokushima, Tokushima 770-8503, Japan.
| | - Kunio Kosaka
- Research and Development Center, Nagase & Co. Ltd., Kobe 651-2241, Japan.
| | - Hidemi Yoshida
- Department of Vascular Biology, Institute of Brain Science, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
| | - Hiromi Yamazaki
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
| | - Shuya Kasai
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
| | - Nobuhiko Harada
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
- Institute for Animal Experimentation, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.
| | - Randal J Kaufman
- Degenerative Diseases Research Program, Sanford Burnham Prebys Medical Discovery Research Institute, La Jolla, CA 92037, USA.
| | - Seiichi Oyadomari
- Division of Molecular Biology, Institute of Advanced Medical Sciences, The University of Tokushima, Tokushima 770-8503, Japan.
| | - Ken Itoh
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
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18
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Biegel JM, Henderson E, Cox EM, Bonenfant G, Netzband R, Kahn S, Eager R, Pager CT. Cellular DEAD-box RNA helicase DDX6 modulates interaction of miR-122 with the 5' untranslated region of hepatitis C virus RNA. Virology 2017; 507:231-241. [PMID: 28456022 DOI: 10.1016/j.virol.2017.04.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/13/2017] [Accepted: 04/14/2017] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) subverts the cellular DEAD-box RNA helicase DDX6 to promote virus infection. Using polysome gradient analysis and the subgenomic HCV Renilla reporter replicon genome, we determined that DDX6 does not affect HCV translation. Rather expression of the subgenomic HCV Renilla luciferase reporter at late times, as well as labeling of newly synthesized viral RNA with 4-thiouridine showed that DDX6 modulates replication. Because DDX6 is an effector protein of the microRNA pathway, we also investigated its role in miR-122-directed HCV gene expression. Similar to sequestering miR-122, depletion of DDX6 modulated HCV RNA stability. Interestingly, miR-122-HCV RNA interaction assays with mutant HCV genomes sites and compensatory exogenous miR-122 showed that DDX6 affects the function of miR-122 at one particular binding site. We propose that DDX6 facilitates the miR-122 interaction with HCV 5' UTR, which is necessary for stabilizing the viral genome and the switch between translation and replication.
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Affiliation(s)
- Jason M Biegel
- Department of Biological Sciences, The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Eric Henderson
- Department of Biological Sciences, The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Erica M Cox
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gaston Bonenfant
- Department of Biological Sciences, The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Rachel Netzband
- Department of Biological Sciences, The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Samantha Kahn
- Department of Biological Sciences, The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Rachel Eager
- Department of Biological Sciences, The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Cara T Pager
- Department of Biological Sciences, The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA.
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19
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Fung SK, Zou T, Cao B, Lee PY, Fung YME, Hu D, Lok CN, Che CM. Cyclometalated Gold(III) Complexes Containing N-Heterocyclic Carbene Ligands Engage Multiple Anti-Cancer Molecular Targets. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612583] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sin Ki Fung
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Taotao Zou
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Bei Cao
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Pui-Yan Lee
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Yi Man Eva Fung
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Di Hu
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Chun-Nam Lok
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Chi-Ming Che
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
- HKU Shenzhen Institute of Research and Innovation; Shenzhen 518053 China
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20
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Fung SK, Zou T, Cao B, Lee PY, Fung YME, Hu D, Lok CN, Che CM. Cyclometalated Gold(III) Complexes Containing N-Heterocyclic Carbene Ligands Engage Multiple Anti-Cancer Molecular Targets. Angew Chem Int Ed Engl 2017; 56:3892-3896. [PMID: 28247451 DOI: 10.1002/anie.201612583] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 01/03/2023]
Abstract
Metal N-heterocyclic carbene (NHC) complexes are a promising class of anti-cancer agents displaying potent in vitro and in vivo activities. Taking a multi-faceted approach employing two clickable photoaffinity probes, herein we report the identification of multiple molecular targets for anti-cancer active pincer gold(III) NHC complexes. These complexes display potent and selective cytotoxicity against cultured cancer cells and in vivo anti-tumor activities in mice bearing xenografts of human cervical and lung cancers. Our experiments revealed the specific engagement of the gold(III) complexes with multiple cellular targets, including HSP60, vimentin, nucleophosmin, and YB-1, accompanied by expected downstream mechanisms of action. Additionally, PtII and PdII analogues can also bind the cellular proteins targeted by the gold(III) complexes, uncovering a distinct pincer cyclometalated metal-NHC scaffold in the design of anti-cancer metal medicines with multiple molecular targets.
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Affiliation(s)
- Sin Ki Fung
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Taotao Zou
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Bei Cao
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Pui-Yan Lee
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yi Man Eva Fung
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Di Hu
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chun-Nam Lok
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chi-Ming Che
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,HKU Shenzhen Institute of Research and Innovation, Shenzhen, 518053, China
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21
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Pozhitkov AE, Neme R, Domazet-Lošo T, Leroux BG, Soni S, Tautz D, Noble PA. Tracing the dynamics of gene transcripts after organismal death. Open Biol 2017; 7:160267. [PMID: 28123054 PMCID: PMC5303275 DOI: 10.1098/rsob.160267] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 12/12/2016] [Indexed: 12/13/2022] Open
Abstract
In life, genetic and epigenetic networks precisely coordinate the expression of genes-but in death, it is not known if gene expression diminishes gradually or abruptly stops or if specific genes and pathways are involved. We studied this by identifying mRNA transcripts that apparently increase in relative abundance after death, assessing their functions, and comparing their abundance profiles through postmortem time in two species, mouse and zebrafish. We found mRNA transcript profiles of 1063 genes became significantly more abundant after death of healthy adult animals in a time series spanning up to 96 h postmortem. Ordination plots revealed non-random patterns in the profiles by time. While most of these transcript levels increased within 0.5 h postmortem, some increased only at 24 and 48 h postmortem. Functional characterization of the most abundant transcripts revealed the following categories: stress, immunity, inflammation, apoptosis, transport, development, epigenetic regulation and cancer. The data suggest a step-wise shutdown occurs in organismal death that is manifested by the apparent increase of certain transcripts with various abundance maxima and durations.
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Affiliation(s)
- Alex E Pozhitkov
- Department of Oral Health Sciences, University of Washington, PO Box 357444, Seattle, WA 98195, USA
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen, Germany
| | - Rafik Neme
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen, Germany
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, 10002 Zagreb, Croatia
- Catholic University of Croatia, Ilica 242, Zagreb, Croatia
| | - Brian G Leroux
- Department of Oral Health Sciences, University of Washington, PO Box 357444, Seattle, WA 98195, USA
| | - Shivani Soni
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36101-0271, USA
| | - Diethard Tautz
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen, Germany
| | - Peter A Noble
- Department of Periodontics, University of Washington, PO Box 357444, Seattle, WA 98195, USA
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36101-0271, USA
- PhD Program in Microbiology, Alabama State University, Montgomery, AL 36101-0271, USA
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22
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Kedersha N, Panas MD, Achorn CA, Lyons S, Tisdale S, Hickman T, Thomas M, Lieberman J, McInerney GM, Ivanov P, Anderson P. G3BP-Caprin1-USP10 complexes mediate stress granule condensation and associate with 40S subunits. J Cell Biol 2016; 212:845-60. [PMID: 27022092 PMCID: PMC4810302 DOI: 10.1083/jcb.201508028] [Citation(s) in RCA: 425] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 02/17/2016] [Indexed: 12/11/2022] Open
Abstract
Stress granule condensation (SGC) of translationally arrested mRNAs requires G3BP, and G3BP-mediated SGC is inhibited by serine 149 phosphorylation, regulated by mutually exclusive binding of Caprin1 and USP10, and requires its RGG region for SGC and for interactions with 40S ribosomal subunits. Mammalian stress granules (SGs) contain stalled translation preinitiation complexes that are assembled into discrete granules by specific RNA-binding proteins such as G3BP. We now show that cells lacking both G3BP1 and G3BP2 cannot form SGs in response to eukaryotic initiation factor 2α phosphorylation or eIF4A inhibition, but are still SG-competent when challenged with severe heat or osmotic stress. Rescue experiments using G3BP1 mutants show that phosphomimetic G3BP1-S149E fails to rescue SG formation, whereas G3BP1-F33W, a mutant unable to bind G3BP partner proteins Caprin1 or USP10, rescues SG formation. Caprin1/USP10 binding to G3BP is mutually exclusive: Caprin binding promotes, but USP10 binding inhibits, SG formation. G3BP interacts with 40S ribosomal subunits through its RGG motif, which is also required for G3BP-mediated SG formation. We propose that G3BP mediates the condensation of SGs by shifting between two different states that are controlled by the phosphorylation of S149 and by binding to Caprin1 or USP10.
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Affiliation(s)
- Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Marc D Panas
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Christopher A Achorn
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Shawn Lyons
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Sarah Tisdale
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Tyler Hickman
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Marshall Thomas
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115 The Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Paul Anderson
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
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23
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Poblete-Durán N, Prades-Pérez Y, Vera-Otarola J, Soto-Rifo R, Valiente-Echeverría F. Who Regulates Whom? An Overview of RNA Granules and Viral Infections. Viruses 2016; 8:v8070180. [PMID: 27367717 PMCID: PMC4974515 DOI: 10.3390/v8070180] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/10/2016] [Accepted: 06/21/2016] [Indexed: 12/22/2022] Open
Abstract
After viral infection, host cells respond by mounting an anti-viral stress response in order to create a hostile atmosphere for viral replication, leading to the shut-off of mRNA translation (protein synthesis) and the assembly of RNA granules. Two of these RNA granules have been well characterized in yeast and mammalian cells, stress granules (SGs), which are translationally silent sites of RNA triage and processing bodies (PBs), which are involved in mRNA degradation. This review discusses the role of these RNA granules in the evasion of anti-viral stress responses through virus-induced remodeling of cellular ribonucleoproteins (RNPs).
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Affiliation(s)
- Natalia Poblete-Durán
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Yara Prades-Pérez
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Jorge Vera-Otarola
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago 8330024, Chile.
| | - Ricardo Soto-Rifo
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Fernando Valiente-Echeverría
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
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24
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Stoehr A, Yang Y, Patel S, Evangelista AM, Aponte A, Wang G, Liu P, Boylston J, Kloner PH, Lin Y, Gucek M, Zhu J, Murphy E. Prolyl hydroxylation regulates protein degradation, synthesis, and splicing in human induced pluripotent stem cell-derived cardiomyocytes. Cardiovasc Res 2016; 110:346-58. [PMID: 27095734 DOI: 10.1093/cvr/cvw081] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/12/2016] [Indexed: 12/12/2022] Open
Abstract
AIMS Protein hydroxylases are oxygen- and α-ketoglutarate-dependent enzymes that catalyse hydroxylation of amino acids such as proline, thus linking oxygen and metabolism to enzymatic activity. Prolyl hydroxylation is a dynamic post-translational modification that regulates protein stability and protein-protein interactions; however, the extent of this modification is largely uncharacterized. The goals of this study are to investigate the biological consequences of prolyl hydroxylation and to identify new targets that undergo prolyl hydroxylation in human cardiomyocytes. METHODS AND RESULTS We used human induced pluripotent stem cell-derived cardiomyocytes in combination with pulse-chase amino acid labelling and proteomics to analyse the effects of prolyl hydroxylation on protein degradation and synthesis. We identified 167 proteins that exhibit differences in degradation with inhibition of prolyl hydroxylation by dimethyloxalylglycine (DMOG); 164 were stabilized. Proteins involved in RNA splicing such as serine/arginine-rich splicing factor 2 (SRSF2) and splicing factor and proline- and glutamine-rich (SFPQ) were stabilized with DMOG. DMOG also decreased protein translation of cytoskeletal and sarcomeric proteins such as α-cardiac actin. We searched the mass spectrometry data for proline hydroxylation and identified 134 high confidence peptides mapping to 78 unique proteins. We identified SRSF2, SFPQ, α-cardiac actin, and cardiac titin as prolyl hydroxylated. We identified 29 prolyl hydroxylated proteins that showed a significant difference in either protein degradation or synthesis. Additionally, we performed next-generation RNA sequencing and showed that the observed decrease in protein synthesis was not due to changes in mRNA levels. Because RNA splicing factors were prolyl hydroxylated, we investigated splicing ± inhibition of prolyl hydroxylation and detected 369 alternative splicing events, with a preponderance of exon skipping. CONCLUSIONS This study provides the first extensive characterization of the cardiac prolyl hydroxylome and demonstrates that inhibition of α-ketoglutarate hydroxylases alters protein stability, translation, and splicing.
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Affiliation(s)
- Andrea Stoehr
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yanqin Yang
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sajni Patel
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alicia M Evangelista
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Angel Aponte
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Guanghui Wang
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Poching Liu
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Boylston
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Philip H Kloner
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yongshun Lin
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marjan Gucek
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jun Zhu
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth Murphy
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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25
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Salminen A, Kauppinen A, Kaarniranta K. 2-Oxoglutarate-dependent dioxygenases are sensors of energy metabolism, oxygen availability, and iron homeostasis: potential role in the regulation of aging process. Cell Mol Life Sci 2015; 72:3897-914. [PMID: 26118662 PMCID: PMC11114064 DOI: 10.1007/s00018-015-1978-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/10/2015] [Accepted: 06/22/2015] [Indexed: 02/06/2023]
Abstract
Recent studies have revealed that the members of an ancient family of nonheme Fe(2+)/2-oxoglutarate-dependent dioxygenases (2-OGDO) are involved in the functions associated with the aging process. 2-Oxoglutarate and O2 are the obligatory substrates and Fe(2+) a cofactor in the activation of 2-OGDO enzymes, which can induce the hydroxylation of distinct proteins and the demethylation of DNA and histones. For instance, ten-eleven translocation 1-3 (TET1-3) are the demethylases of DNA, whereas Jumonji C domain-containing histone lysine demethylases (KDM2-7) are the major epigenetic regulators of chromatin landscape, known to be altered with aging. The functions of hypoxia-inducible factor (HIF) prolyl hydroxylases (PHD1-3) as well as those of collagen hydroxylases are associated with age-related degeneration. Moreover, the ribosomal hydroxylase OGFOD1 controls mRNA translation, which is known to decline with aging. 2-OGDO enzymes are the sensors of energy metabolism, since the Krebs cycle intermediate 2-oxoglutarate is an activator whereas succinate and fumarate are the potent inhibitors of 2-OGDO enzymes. In addition, O2 availability and iron redox homeostasis control the activities of 2-OGDO enzymes in tissues. We will briefly elucidate the catalytic mechanisms of 2-OGDO enzymes and then review the potential functions of the above-mentioned 2-OGDO enzymes in the control of the aging process.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
| | - Anu Kauppinen
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
- Department of Ophthalmology, Kuopio University Hospital, P.O.B. 100, 70029, Kuopio, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
- Department of Ophthalmology, Kuopio University Hospital, P.O.B. 100, 70029, Kuopio, Finland.
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26
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Townley-Tilson WHD, Pi X, Xie L. The Role of Oxygen Sensors, Hydroxylases, and HIF in Cardiac Function and Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2015:676893. [PMID: 26491535 PMCID: PMC4600863 DOI: 10.1155/2015/676893] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 03/26/2015] [Accepted: 04/10/2015] [Indexed: 12/14/2022]
Abstract
Ischemic heart disease is the leading cause of death worldwide. Oxygen-sensing proteins are critical components of the physiological response to hypoxia and reperfusion injury, but the role of oxygen and oxygen-mediated effects is complex in that they can be cardioprotective or deleterious to the cardiac tissue. Over 200 oxygen-sensing proteins mediate the effects of oxygen tension and use oxygen as a substrate for posttranslational modification of other proteins. Hydroxylases are an essential component of these oxygen-sensing proteins. While a major role of hydroxylases is regulating the transcription factor HIF, we investigate the increasing scope of hydroxylase substrates. This review discusses the importance of oxygen-mediated effects in the heart as well as how the field of oxygen-sensing proteins is expanding, providing a more complete picture into how these enzymes play a multifaceted role in cardiac function and disease. We also review how oxygen-sensing proteins and hydroxylase function could prove to be invaluable in drug design and therapeutic targets for heart disease.
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Affiliation(s)
- W. H. Davin Townley-Tilson
- Department of Medicine, Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xinchun Pi
- Department of Medicine, Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liang Xie
- Department of Medicine, Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
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27
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Kim JH, Lee SM, Lee JH, Chun S, Kang BH, Kwak S, Roe JS, Kim TW, Kim H, Kim WH, Cho EJ, Youn HD. OGFOD1 is required for breast cancer cell proliferation and is associated with poor prognosis in breast cancer. Oncotarget 2015; 6:19528-41. [PMID: 25909288 PMCID: PMC4637303 DOI: 10.18632/oncotarget.3683] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/1969] [Accepted: 03/11/2015] [Indexed: 12/31/2022] Open
Abstract
2-oxogluatrate and Fe(II)-dependent oxygenase domain-containing protein 1 (OGFOD1) was recently revealed to be a proline hydroxylase of RPS23 for translational termination. However, OGFOD1 is nuclear, whereas translational termination occurs in the cytoplasm, raising the possibility of another function of OGFOD1 in the nucleus. In this study, we demonstrate that OGFOD1 is involved in cell cycle regulation. OGFOD1 knockdown in MDA-MB-231 breast cancer cells significantly impeded cell proliferation and resulted in the accumulation of G1 and G2/M cells by decreasing the mRNA levels of G1/S transition- and G2/M-related transcription factors and their target genes. We also confirmed that OGFOD1 is highly expressed in breast cancer tissues by bioinformatic analysis and immunohistochemistry. Thus, we propose that OGFOD1 is required for breast cancer cell proliferation and is associated with poor prognosis in breast cancer.
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Affiliation(s)
- Jae-Hwan Kim
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soon-Min Lee
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jong-Hyuk Lee
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sohyun Chun
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science, Seoul National University, Seoul, Republic of Korea
| | - Byung-Hee Kang
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sojung Kwak
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jae-Seok Roe
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Tae Wan Kim
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyunsoo Kim
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eun-Jung Cho
- College of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hong-Duk Youn
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science, Seoul National University, Seoul, Republic of Korea
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28
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Kundu S. Co-operative intermolecular kinetics of 2-oxoglutarate dependent dioxygenases may be essential for system-level regulation of plant cell physiology. FRONTIERS IN PLANT SCIENCE 2015; 6:489. [PMID: 26236316 PMCID: PMC4502536 DOI: 10.3389/fpls.2015.00489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 06/19/2015] [Indexed: 05/24/2023]
Abstract
Can the stimulus-driven synergistic association of 2-oxoglutarate dependent dioxygenases be influenced by the kinetic parameters of binding and catalysis?In this manuscript, I posit that these indices are necessary and specific for a particular stimulus, and are key determinants of a dynamic clustering that may function to mitigate the effects of this trigger. The protein(s)/sequence(s) that comprise this group are representative of all major kingdoms of life, and catalyze a generic hydroxylation, which is, in most cases accompanied by a specialized conversion of the substrate molecule. Iron is an essential co-factor for this transformation and the response to waning levels is systemic, and mandates the simultaneous participation of molecular sensors, transporters, and signal transducers. Here, I present a proof-of-concept model, that an evolving molecular network of 2OG-dependent enzymes can maintain iron homeostasis in the cytosol of root hair cells of members of the family Gramineae by actuating a non-reductive compensatory chelation by the phytosiderophores. Regression models of empirically available kinetic data (iron and alpha-ketoglutarate) were formulated, analyzed, and compared. The results, when viewed in context of the superfamily responding as a unit, suggest that members can indeed, work together to accomplish system-level function. This is achieved by the establishment of transient metabolic conduits, wherein the flux is dictated by kinetic compatibility of the participating enzymes. The approach adopted, i.e., predictive mathematical modeling, is integral to the hypothesis-driven acquisition of experimental data points and, in association with suitable visualization aids may be utilized for exploring complex plant biochemical systems.
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Affiliation(s)
- Siddhartha Kundu
- *Correspondence: Siddhartha Kundu, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India ;
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29
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Sedano CD, Sarnow P. Hepatitis C virus subverts liver-specific miR-122 to protect the viral genome from exoribonuclease Xrn2. Cell Host Microbe 2015; 16:257-264. [PMID: 25121753 DOI: 10.1016/j.chom.2014.07.006] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 04/23/2014] [Accepted: 07/03/2014] [Indexed: 12/11/2022]
Abstract
The abundant, liver-specific microRNA miR-122 forms extensive base-pairing interactions with the 5' noncoding region of the hepatitis C virus (HCV) RNA genome, protecting the viral RNA from degradation. We discovered that the 5'-3' exoribonuclease Xrn2, which plays a crucial role in the transcription termination of RNA polymerase II, modulates HCV RNA abundance in the cytoplasm, but is counteracted by miR-122-mediated protection. Specifically, Xrn2 depletion results in increased accumulation of viral RNA, while Xrn2 overexpression diminishes viral RNA abundance. Depletion of Xrn2 did not alter translation or replication rates of HCV RNA, but affected viral RNA stability. Importantly, during sequestration of miR-122, Xrn2 depletion restored HCV RNA abundance, arguing that Xrn2 depletion eliminates the miR-122 requirement for viral RNA stability. Thus, Xrn2 has a cytoplasmic, antiviral function against HCV that is counteracted by HCV's subversion of miR-122 to form a protective oligomeric complex at the 5' end of the viral genome.
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Affiliation(s)
- Cecilia D Sedano
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter Sarnow
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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30
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Horita S, Scotti JS, Thinnes C, Mottaghi-Taromsari YS, Thalhammer A, Ge W, Aik W, Loenarz C, Schofield CJ, McDonough MA. Structure of the ribosomal oxygenase OGFOD1 provides insights into the regio- and stereoselectivity of prolyl hydroxylases. Structure 2015; 23:639-52. [PMID: 25728928 PMCID: PMC4396695 DOI: 10.1016/j.str.2015.01.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/13/2015] [Accepted: 01/21/2015] [Indexed: 01/24/2023]
Abstract
Post-translational ribosomal protein hydroxylation is catalyzed by 2-oxoglutarate (2OG) and ferrous iron dependent oxygenases, and occurs in prokaryotes and eukaryotes. OGFOD1 catalyzes trans-3 prolyl hydroxylation at Pro62 of the small ribosomal subunit protein uS12 (RPS23) and is conserved from yeasts to humans. We describe crystal structures of the human uS12 prolyl 3-hydroxylase (OGFOD1) and its homolog from Saccharomyces cerevisiae (Tpa1p): OGFOD1 in complex with the broad-spectrum 2OG oxygenase inhibitors; N-oxalylglycine (NOG) and pyridine-2,4-dicarboxylate (2,4-PDCA) to 2.1 and 2.6 Å resolution, respectively; and Tpa1p in complex with NOG, 2,4-PDCA, and 1-chloro-4-hydroxyisoquinoline-3-carbonylglycine (a more selective prolyl hydroxylase inhibitor) to 2.8, 1.9, and 1.9 Å resolution, respectively. Comparison of uS12 hydroxylase structures with those of other prolyl hydroxylases, including the human hypoxia-inducible factor (HIF) prolyl hydroxylases (PHDs), reveals differences between the prolyl 3- and prolyl 4-hydroxylase active sites, which can be exploited for developing selective inhibitors of the different subfamilies.
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Affiliation(s)
- Shoichiro Horita
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK; Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
| | - John S Scotti
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Cyrille Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Yousef S Mottaghi-Taromsari
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Armin Thalhammer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Wei Ge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - WeiShen Aik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Christoph Loenarz
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
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31
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Panas MD, Schulte T, Thaa B, Sandalova T, Kedersha N, Achour A, McInerney GM. Viral and cellular proteins containing FGDF motifs bind G3BP to block stress granule formation. PLoS Pathog 2015; 11:e1004659. [PMID: 25658430 PMCID: PMC4450067 DOI: 10.1371/journal.ppat.1004659] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 01/06/2015] [Indexed: 02/08/2023] Open
Abstract
The Ras-GAP SH3 domain-binding proteins (G3BP) are essential regulators of the formation of stress granules (SG), cytosolic aggregates of proteins and RNA that are induced upon cellular stress, such as virus infection. Many viruses, including Semliki Forest virus (SFV), block SG induction by targeting G3BP. In this work, we demonstrate that the G3BP-binding motif of SFV nsP3 consists of two FGDF motifs, in which both phenylalanine and the glycine residue are essential for binding. In addition, we show that binding of the cellular G3BP-binding partner USP10 is also mediated by an FGDF motif. Overexpression of wt USP10, but not a mutant lacking the FGDF-motif, blocks SG assembly. Further, we identified FGDF-mediated G3BP binding site in herpes simplex virus (HSV) protein ICP8, and show that ICP8 binding to G3BP also inhibits SG formation, which is a novel function of HSV ICP8. We present a model of the three-dimensional structure of G3BP bound to an FGDF-containing peptide, likely representing a binding mode shared by many proteins to target G3BP.
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Affiliation(s)
- Marc D. Panas
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tim Schulte
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Bastian Thaa
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tatiana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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32
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SAMD9 is an innate antiviral host factor with stress response properties that can be antagonized by poxviruses. J Virol 2014; 89:1925-31. [PMID: 25428864 DOI: 10.1128/jvi.02262-14] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We show that SAMD9 is an innate host antiviral stress response element that participates in the formation of antiviral granules. Poxviruses, myxoma virus and vaccinia virus specifically, utilize a virus-encoded host range factor(s), such as a member of the C7L superfamily, to antagonize SAMD9 to prevent granule formation in a eukaryotic initiation factor 2α (eIF2α)-independent manner. When SAMD9 is stimulated due to failure of the viral antagonism during infection, the resulting antiviral granules exhibit properties different from those of the canonical stress granules.
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Quadri M, Yang X, Cossu G, Olgiati S, Saddi VM, Breedveld GJ, Ouyang L, Hu J, Xu N, Graafland J, Ricchi V, Murgia D, Guedes LC, Mariani C, Marti MJ, Tarantino P, Asselta R, Valldeoriola F, Gagliardi M, Pezzoli G, Ezquerra M, Quattrone A, Ferreira J, Annesi G, Goldwurm S, Tolosa E, Oostra BA, Melis M, Wang J, Bonifati V. An exome study of Parkinson's disease in Sardinia, a Mediterranean genetic isolate. Neurogenetics 2014; 16:55-64. [PMID: 25294124 DOI: 10.1007/s10048-014-0425-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/15/2014] [Indexed: 12/21/2022]
Abstract
Parkinson's disease (PD) is a common neurodegenerative disorder of complex aetiology. Rare, highly penetrant PD-causing mutations and common risk factors of small effect size have been identified in several genes/loci. However, these mutations and risk factors only explain a fraction of the disease burden, suggesting that additional, substantial genetic determinants remain to be found. Genetically isolated populations offer advantages for dissecting the genetic architecture of complex disorders, such as PD. We performed exome sequencing in 100 unrelated PD patients from Sardinia, a genetic isolate. SNPs absent from dbSNP129 and 1000 Genomes, shared by at least five patients, and of functional effects were genotyped in an independent Sardinian case-control sample (n = 500). Variants associated with PD with nominal p value <0.05 and those with odds ratio (OR) ≥3 were validated by Sanger sequencing and typed in a replication sample of 2965 patients and 2678 controls from Italy, Spain, and Portugal. We identified novel moderately rare variants in several genes, including SCAPER, HYDIN, UBE2H, EZR, MMRN2 and OGFOD1 that were specifically present in PD patients or enriched among them, nominating these as novel candidate risk genes for PD, although no variants achieved genome-wide significance after Bonferroni correction. Our results suggest that the genetic bases of PD are highly heterogeneous, with implications for the design of future large-scale exome or whole-genome analyses of this disease.
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Affiliation(s)
- Marialuisa Quadri
- Department of Clinical Genetics, Erasmus MC, PO Box 2040, 3000, CA, Rotterdam, The Netherlands
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Onomoto K, Yoneyama M, Fung G, Kato H, Fujita T. Antiviral innate immunity and stress granule responses. Trends Immunol 2014; 35:420-8. [PMID: 25153707 PMCID: PMC7185371 DOI: 10.1016/j.it.2014.07.006] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 07/16/2014] [Accepted: 07/16/2014] [Indexed: 12/13/2022]
Abstract
Viral infection triggers the activation of antiviral innate immune responses in mammalian cells. Viral RNA in the cytoplasm activates signaling pathways that result in the production of interferons (IFNs) and IFN-stimulated genes. Some viral infections have been shown to induce cytoplasmic granular aggregates similar to the dynamic ribonucleoprotein aggregates termed stress granules (SGs), suggesting that these viruses may utilize this stress response for their own benefit. By contrast, some viruses actively inhibit SG formation, suggesting an antiviral function for these structures. We review here the relationship between different viral infections and SG formation. We examine the evidence for antiviral functions for SGs and highlight important areas of inquiry towards understanding cellular stress responses to viral infection.
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Affiliation(s)
- Koji Onomoto
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
| | - Mitsutoshi Yoneyama
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
| | - Gabriel Fung
- University of British Columbia (UBC) James Hogg Research Center, Providence Heart and Lung Institute, St. Paul's Hospital and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Hiroki Kato
- Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan; Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
| | - Takashi Fujita
- Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan; Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan.
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Abstract
Human enamel development of the permanent teeth takes place during childhood and stresses encountered during this period can have lasting effects on the appearance and structural integrity of the enamel. One of the most common examples of this is the development of dental fluorosis after childhood exposure to excess fluoride, an elemental agent used to increase enamel hardness and prevent dental caries. Currently the molecular mechanism responsible for dental fluorosis remains unknown; however, recent work suggests dental fluorosis may be the result of activated stress response pathways in ameloblasts during the development of permanent teeth. Using fluorosis as an example, the role of stress response pathways during enamel maturation is discussed.
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Singleton RS, Liu-Yi P, Formenti F, Ge W, Sekirnik R, Fischer R, Adam J, Pollard PJ, Wolf A, Thalhammer A, Loenarz C, Flashman E, Yamamoto A, Coleman ML, Kessler BM, Wappner P, Schofield CJ, Ratcliffe PJ, Cockman ME. OGFOD1 catalyzes prolyl hydroxylation of RPS23 and is involved in translation control and stress granule formation. Proc Natl Acad Sci U S A 2014; 111:4031-6. [PMID: 24550447 PMCID: PMC3964040 DOI: 10.1073/pnas.1314482111] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
2-Oxoglutarate (2OG) and Fe(II)-dependent oxygenase domain-containing protein 1 (OGFOD1) is predicted to be a conserved 2OG oxygenase, the catalytic domain of which is related to hypoxia-inducible factor prolyl hydroxylases. OGFOD1 homologs in yeast are implicated in diverse cellular functions ranging from oxygen-dependent regulation of sterol response genes (Ofd1, Schizosaccharomyces pombe) to translation termination/mRNA polyadenylation (Tpa1p, Saccharomyces cerevisiae). However, neither the biochemical activity of OGFOD1 nor the identity of its substrate has been defined. Here we show that OGFOD1 is a prolyl hydroxylase that catalyzes the posttranslational hydroxylation of a highly conserved residue (Pro-62) in the small ribosomal protein S23 (RPS23). Unusually OGFOD1 retained a high affinity for, and forms a stable complex with, the hydroxylated RPS23 substrate. Knockdown or inactivation of OGFOD1 caused a cell type-dependent induction of stress granules, translational arrest, and growth impairment in a manner complemented by wild-type but not inactive OGFOD1. The work identifies a human prolyl hydroxylase with a role in translational regulation.
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Affiliation(s)
- Rachelle S. Singleton
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Phebee Liu-Yi
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
- Institute of Analytical Chemistry, Peking University, Beijing 100871, China
| | - Fabio Formenti
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Wei Ge
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Rok Sekirnik
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, United Kingdom; and
| | - Julie Adam
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Patrick J. Pollard
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Alexander Wolf
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Armin Thalhammer
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Christoph Loenarz
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Emily Flashman
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Atsushi Yamamoto
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Mathew L. Coleman
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Benedikt M. Kessler
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, United Kingdom; and
| | - Pablo Wappner
- Fundación Instituto Leloir, C1405BWE Buenos Aires, Argentina
| | - Christopher J. Schofield
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Peter J. Ratcliffe
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Matthew E. Cockman
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
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Kustatscher G, Hégarat N, Wills KLH, Furlan C, Bukowski-Wills JC, Hochegger H, Rappsilber J. Proteomics of a fuzzy organelle: interphase chromatin. EMBO J 2014; 33:648-64. [PMID: 24534090 PMCID: PMC3983682 DOI: 10.1002/embj.201387614] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/12/2014] [Accepted: 01/14/2014] [Indexed: 12/30/2022] Open
Abstract
Chromatin proteins mediate replication, regulate expression, and ensure integrity of the genome. So far, a comprehensive inventory of interphase chromatin has not been determined. This is largely due to its heterogeneous and dynamic composition, which makes conclusive biochemical purification difficult, if not impossible. As a fuzzy organelle, it defies classical organellar proteomics and cannot be described by a single and ultimate list of protein components. Instead, we propose a new approach that provides a quantitative assessment of a protein's probability to function in chromatin. We integrate chromatin composition over a range of different biochemical and biological conditions. This resulted in interphase chromatin probabilities for 7635 human proteins, including 1840 previously uncharacterized proteins. We demonstrate the power of our large-scale data-driven annotation during the analysis of cyclin-dependent kinase (CDK) regulation in chromatin. Quantitative protein ontologies may provide a general alternative to list-based investigations of organelles and complement Gene Ontology.
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Affiliation(s)
- Georg Kustatscher
- Wellcome Trust Centre for Cell Biology, University of EdinburghEdinburgh, UK
| | - Nadia Hégarat
- Genome Damage and Stability Centre, University of SussexBrighton, UK
| | - Karen L H Wills
- Wellcome Trust Centre for Cell Biology, University of EdinburghEdinburgh, UK
| | - Cristina Furlan
- Wellcome Trust Centre for Cell Biology, University of EdinburghEdinburgh, UK
| | | | - Helfrid Hochegger
- Genome Damage and Stability Centre, University of SussexBrighton, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of EdinburghEdinburgh, UK
- Department of Biotechnology, Technische Universität BerlinBerlin, Germany
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Droppelmann CA, Campos-Melo D, Ishtiaq M, Volkening K, Strong MJ. RNA metabolism in ALS: When normal processes become pathological. Amyotroph Lateral Scler Frontotemporal Degener 2014; 15:321-36. [DOI: 10.3109/21678421.2014.881377] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Sudestada1, a Drosophila ribosomal prolyl-hydroxylase required for mRNA translation, cell homeostasis, and organ growth. Proc Natl Acad Sci U S A 2014; 111:4025-30. [PMID: 24550463 DOI: 10.1073/pnas.1314485111] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Genome sequences predict the presence of many 2-oxoglutarate (2OG)-dependent oxygenases of unknown biochemical and biological functions in Drosophila. Ribosomal protein hydroxylation is emerging as an important 2OG oxygenase catalyzed pathway, but its biological functions are unclear. We report investigations on the function of Sudestada1 (Sud1), a Drosophila ribosomal oxygenase. As with its human and yeast homologs, OGFOD1 and Tpa1p, respectively, we identified Sud1 to catalyze prolyl-hydroxylation of the small ribosomal subunit protein RPS23. Like OGFOD1, Sud1 catalyzes a single prolyl-hydroxylation of RPS23 in contrast to yeast Tpa1p, where Pro-64 dihydroxylation is observed. RNAi-mediated Sud1 knockdown hinders normal growth in different Drosophila tissues. Growth impairment originates from both reduction of cell size and diminution of the number of cells and correlates with impaired translation efficiency and activation of the unfolded protein response in the endoplasmic reticulum. This is accompanied by phosphorylation of eIF2α and concomitant formation of stress granules, as well as promotion of autophagy and apoptosis. These observations, together with those on enzyme homologs described in the companion articles, reveal conserved biochemical and biological roles for a widely distributed ribosomal oxygenase.
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Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy. Proc Natl Acad Sci U S A 2014; 111:4019-24. [PMID: 24550462 DOI: 10.1073/pnas.1311750111] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The mechanisms by which gene expression is regulated by oxygen are of considerable interest from basic science and therapeutic perspectives. Using mass spectrometric analyses of Saccharomyces cerevisiae ribosomes, we found that the amino acid residue in closest proximity to the decoding center, Pro-64 of the 40S subunit ribosomal protein Rps23p (RPS23 Pro-62 in humans) undergoes posttranslational hydroxylation. We identify RPS23 hydroxylases as a highly conserved eukaryotic subfamily of Fe(II) and 2-oxoglutarate dependent oxygenases; their catalytic domain is closely related to transcription factor prolyl trans-4-hydroxylases that act as oxygen sensors in the hypoxic response in animals. The RPS23 hydroxylases in S. cerevisiae (Tpa1p), Schizosaccharomyces pombe and green algae catalyze an unprecedented dihydroxylation modification. This observation contrasts with higher eukaryotes, where RPS23 is monohydroxylated; the human Tpa1p homolog OGFOD1 catalyzes prolyl trans-3-hydroxylation. TPA1 deletion modulates termination efficiency up to ∼10-fold, including of pathophysiologically relevant sequences; we reveal Rps23p hydroxylation as its molecular basis. In contrast to most previously characterized accuracy modulators, including antibiotics and the prion state of the S. cerevisiae translation termination factor eRF3, Rps23p hydroxylation can either increase or decrease translational accuracy in a stop codon context-dependent manner. We identify conditions where Rps23p hydroxylation status determines viability as a consequence of nonsense codon suppression. The results reveal a direct link between oxygenase catalysis and the regulation of gene expression at the translational level. They will also aid in the development of small molecules altering translational accuracy for the treatment of genetic diseases linked to nonsense mutations.
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Sawada H, Saito T, Nickel NP, Alastalo TP, Glotzbach JP, Chan R, Haghighat L, Fuchs G, Januszyk M, Cao A, Lai YJ, Perez VDJ, Kim YM, Wang L, Chen PI, Spiekerkoetter E, Mitani Y, Gurtner GC, Sarnow P, Rabinovitch M. Reduced BMPR2 expression induces GM-CSF translation and macrophage recruitment in humans and mice to exacerbate pulmonary hypertension. ACTA ACUST UNITED AC 2014; 211:263-80. [PMID: 24446489 PMCID: PMC3920564 DOI: 10.1084/jem.20111741] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Idiopathic pulmonary arterial hypertension (PAH [IPAH]) is an insidious and potentially fatal disease linked to a mutation or reduced expression of bone morphogenetic protein receptor 2 (BMPR2). Because intravascular inflammatory cells are recruited in IPAH pathogenesis, we hypothesized that reduced BMPR2 enhances production of the potent chemokine granulocyte macrophage colony-stimulating factor (GM-CSF) in response to an inflammatory perturbation. When human pulmonary artery (PA) endothelial cells deficient in BMPR2 were stimulated with tumor necrosis factor (TNF), a twofold increase in GM-CSF was observed and related to enhanced messenger RNA (mRNA) translation. The mechanism was associated with disruption of stress granule formation. Specifically, loss of BMPR2 induced prolonged phospho-p38 mitogen-activated protein kinase (MAPK) in response to TNF, and this increased GADD34-PP1 phosphatase activity, dephosphorylating eukaryotic translation initiation factor (eIF2α), and derepressing GM-CSF mRNA translation. Lungs from IPAH patients versus unused donor controls revealed heightened PA expression of GM-CSF co-distributing with increased TNF and expanded populations of hematopoietic and endothelial GM-CSF receptor α (GM-CSFRα)-positive cells. Moreover, a 3-wk infusion of GM-CSF in mice increased hypoxia-induced PAH, in association with increased perivascular macrophages and muscularized distal arteries, whereas blockade of GM-CSF repressed these features. Thus, reduced BMPR2 can subvert a stress granule response, heighten GM-CSF mRNA translation, increase inflammatory cell recruitment, and exacerbate PAH.
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Affiliation(s)
- Hirofumi Sawada
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, 2 Department of Pediatrics, 3 Department of Surgery, 4 Department of Microbiology and Immunology, 5 Department of Medicine, and 6 Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305
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Walker AK, Soo KY, Sundaramoorthy V, Parakh S, Ma Y, Farg MA, Wallace RH, Crouch PJ, Turner BJ, Horne MK, Atkin JD. ALS-associated TDP-43 induces endoplasmic reticulum stress, which drives cytoplasmic TDP-43 accumulation and stress granule formation. PLoS One 2013; 8:e81170. [PMID: 24312274 PMCID: PMC3843686 DOI: 10.1371/journal.pone.0081170] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 10/09/2013] [Indexed: 12/12/2022] Open
Abstract
In amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration, TAR DNA binding protein 43 (TDP-43) accumulates in the cytoplasm of affected neurons and glia, where it associates with stress granules (SGs) and forms large inclusions. SGs form in response to cellular stress, including endoplasmic reticulum (ER) stress, which is induced in both familial and sporadic forms of ALS. Here we demonstrate that pharmacological induction of ER stress causes TDP-43 to accumulate in the cytoplasm, where TDP-43 also associates with SGs. Furthermore, treatment with salubrinal, an inhibitor of dephosphorylation of eukaryotic initiation factor 2-α, a key modulator of ER stress, potentiates ER stress-mediated SG formation. Inclusions of C-terminal fragment TDP-43, reminiscent of disease-pathology, form in close association with ER and Golgi compartments, further indicating the involvement of ER dysfunction in TDP-43-associated disease. Consistent with this notion, over-expression of ALS-linked mutant TDP-43, and to a lesser extent wildtype TDP-43, triggers several ER stress pathways in neuroblastoma cells. Similarly, we found an interaction between the ER chaperone protein disulphide isomerase and TDP-43 in transfected cell lysates and in the spinal cords of mutant A315T TDP-43 transgenic mice. This study provides evidence for ER stress as a pathogenic pathway in TDP-43-mediated disease.
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Affiliation(s)
- Adam K. Walker
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Kai Y. Soo
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Vinod Sundaramoorthy
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Sonam Parakh
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Yi Ma
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Manal A. Farg
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Robyn H. Wallace
- Queensland Brain Institute and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Peter J. Crouch
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Bradley J. Turner
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Malcolm K. Horne
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
- Florey Department of Neuroscience and Mental Health, Faculty of Medicine, Dentistry & Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
- Saint Vincent's Hospital, Fitzroy, Victoria, Australia
| | - Julie D. Atkin
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
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Tanaka T, Ohashi S, Kobayashi S. Roles of YB-1 under arsenite-induced stress: translational activation of HSP70 mRNA and control of the number of stress granules. Biochim Biophys Acta Gen Subj 2013; 1840:985-92. [PMID: 24231679 DOI: 10.1016/j.bbagen.2013.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/30/2013] [Accepted: 11/03/2013] [Indexed: 01/09/2023]
Abstract
BACKGROUND When cells become stressed, they form stress granules (SGs) and show an increase of the molecular chaperone HSP70. The translational regulator YB-1 is a component of SGs, but it is unclear whether it contributes to the translational induction of HSP70 mRNA. Here we examined the roles of YB-1 in SG assembly and translational regulation of HSP70 mRNA under arsenite-induced stress. METHOD Using arsenite-treated NG108-15 cells, we examined whether YB-1 was included in SGs with GluR2 mRNA, a target of YB-1, and investigated the interaction of YB-1 with HSP70 mRNA and its effect on translation of the mRNA. We also investigated the distribution of these mRNAs to SGs or polysomes, and evaluated the role of YB-1 in SG assembly. RESULTS Arsenite treatment reduced the translation level of GluR2 mRNA; concomitantly, YB-1-bound HSP70 mRNA was increased and its translation was induced. Sucrose gradient analysis revealed that the distribution of GluR2 mRNA was shifted from heavy-sedimenting to much lighter fractions, and also to SG-containing non-polysomal fractions. Conversely, HSP70 mRNA was shifted from the non-polysomal to polysome fractions. YB-1 depletion abrogated the arsenite-responsive activation of HSP70 synthesis, but SGs harboring both mRNAs were still assembled. The number of SGs was increased by YB-1 depletion and decreased by its overexpression. CONCLUSION In arsenite-treated cells, YB-1 mediates the translational activation of HSP70 mRNA and also controls the number of SGs through inhibition of their assembly. GENERAL SIGNIFICANCE Under stress conditions, YB-1 exerts simultaneous but opposing actions on the regulation of translation via SGs and polysomes.
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Affiliation(s)
- Toru Tanaka
- Department of Biochemistry, School of Pharmacy, Nihon University, 7-7-1, Narashinodai, Funabashi, Chiba 274-8555, Japan
| | - Sachiyo Ohashi
- Department of Biochemistry, School of Pharmacy, Nihon University, 7-7-1, Narashinodai, Funabashi, Chiba 274-8555, Japan
| | - Shunsuke Kobayashi
- Department of Biochemistry, School of Pharmacy, Nihon University, 7-7-1, Narashinodai, Funabashi, Chiba 274-8555, Japan.
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Kedersha N, Ivanov P, Anderson P. Stress granules and cell signaling: more than just a passing phase? Trends Biochem Sci 2013; 38:494-506. [PMID: 24029419 DOI: 10.1016/j.tibs.2013.07.004] [Citation(s) in RCA: 467] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/23/2013] [Accepted: 07/29/2013] [Indexed: 12/27/2022]
Abstract
Stress granules (SGs) contain translationally-stalled mRNAs, associated preinitiation factors, and specific RNA-binding proteins. In addition, many signaling proteins are recruited to SGs and/or influence their assembly, which is transient, lasting only until the cells adapt to stress or die. Beyond their role as mRNA triage centers, we posit that SGs constitute RNA-centric signaling hubs analogous to classical multiprotein signaling domains such as transmembrane receptor complexes. As signaling centers, SG formation communicates a 'state of emergency', and their transient existence alters multiple signaling pathways by intercepting and sequestering signaling components. SG assembly and downstream signaling functions may require a cytosolic phase transition facilitated by intrinsically disordered, aggregation-prone protein regions shared by RNA-binding and signaling proteins.
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Affiliation(s)
- Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Smith 652, One Jimmy Fund Way, Boston, MA 02115, USA
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Strauch AR, Hariharan S. Dynamic Interplay of Smooth Muscle α-Actin Gene-Regulatory Proteins Reflects the Biological Complexity of Myofibroblast Differentiation. BIOLOGY 2013; 2:555-86. [PMID: 24832798 PMCID: PMC3960882 DOI: 10.3390/biology2020555] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 03/01/2013] [Accepted: 03/06/2013] [Indexed: 01/06/2023]
Abstract
Myofibroblasts (MFBs) are smooth muscle-like cells that provide contractile force required for tissue repair during wound healing. The leading agonist for MFB differentiation is transforming growth factor β1 (TGFβ1) that induces transcription of genes encoding smooth muscle α-actin (SMαA) and interstitial collagen that are markers for MFB differentiation. TGFβ1 augments activation of Smad transcription factors, pro-survival Akt kinase, and p38 MAP kinase as well as Wingless/int (Wnt) developmental signaling. These actions conspire to activate β-catenin needed for expression of cyclin D, laminin, fibronectin, and metalloproteinases that aid in repairing epithelial cells and their associated basement membranes. Importantly, β-catenin also provides a feed-forward stimulus that amplifies local TGFβ1 autocrine/paracrine signaling causing transition of mesenchymal stromal cells, pericytes, and epithelial cells into contractile MFBs. Complex, mutually interactive mechanisms have evolved that permit several mammalian cell types to activate the SMαA promoter and undergo MFB differentiation. These molecular controls will be reviewed with an emphasis on the dynamic interplay between serum response factor, TGFβ1-activated Smads, Wnt-activated β-catenin, p38/calcium-activated NFAT protein, and the RNA-binding proteins, Purα, Purβ, and YB-1, in governing transcriptional and translational control of the SMαA gene in injury-activated MFBs.
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Affiliation(s)
- Arthur Roger Strauch
- Department of Physiology & Cell Biology and the Ohio State Biochemistry Program, the Dorothy M. Davis Heart & Lung Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA.
| | - Seethalakshmi Hariharan
- Department of Physiology & Cell Biology and the Ohio State Biochemistry Program, the Dorothy M. Davis Heart & Lung Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA.
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Redondo N, Sanz MA, Steinberger J, Skern T, Kusov Y, Carrasco L. Translation directed by hepatitis A virus IRES in the absence of active eIF4F complex and eIF2. PLoS One 2012; 7:e52065. [PMID: 23272212 PMCID: PMC3525551 DOI: 10.1371/journal.pone.0052065] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/08/2012] [Indexed: 12/31/2022] Open
Abstract
Translation directed by several picornavirus IRES elements can usually take place after cleavage of eIF4G by picornavirus proteases 2Apro or Lpro. The hepatitis A virus (HAV) IRES is thought to be an exception to this rule because it requires intact eIF4F complex for translation. In line with previous results we report that poliovirus (PV) 2Apro strongly blocks protein synthesis directed by HAV IRES. However, in contrast to previous findings we now demonstrate that eIF4G cleavage by foot-and-mouth disease virus (FMDV) Lpro strongly stimulates HAV IRES-driven translation. Thus, this is the first observation that 2Apro and Lpro exhibit opposite effects to what was previously thought to be the case in HAV IRES. This effect has been observed both in hamster BHK and human hepatoma Huh7 cells. In addition, this stimulation of translation is also observed in cell free systems after addition of purified Lpro. Notably, in presence of this FMDV protease, translation directed by HAV IRES takes place when eIF2α has been inactivated by phosphorylation. Our present findings clearly demonstrate that protein synthesis directed by HAV IRES can occur when eIF4G has been cleaved and after inactivation of eIF2. Therefore, translation directed by HAV IRES without intact eIF4G and active eIF2 is similar to that observed with other picornavirus IRESs.
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Affiliation(s)
- Natalia Redondo
- Centro de Biologia Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Madrid, Spain.
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Barr JE, Munyikwa MR, Frazier EA, Hinton SD. The pseudophosphatase MK-STYX inhibits stress granule assembly independently of Ser149 phosphorylation of G3BP-1. FEBS J 2012; 280:273-84. [PMID: 23163895 PMCID: PMC3586659 DOI: 10.1111/febs.12068] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 10/28/2012] [Accepted: 11/13/2012] [Indexed: 01/07/2023]
Abstract
The pseudophosphatase MK-STYX (mitogen-activated protein kinase phosphoserine/threonine/tyrosine-binding protein) has been implicated in the stress response pathway. The expression of MK-STYX inhibits the assembly of stress granules, which are cytoplasmic storage sites for mRNA that form as a protective mechanism against stressors such as heat shock, UV irradiation and hypoxia. Furthermore, MK-STYX interacts with a key component of stress granules: G3BP-1 (Ras-GTPase activating protein SH3 domain binding protein-1). Because G3BP-1 dephosphorylation at Ser149 induces stress granule assembly, we initially hypothesized that the inhibition of stress granules by MK-STYX was G3BP-1 phosphorylation-dependent. However, in the present study, using MK-STYX constructs and G3BP-1 phosphomimetic or nonphosphorylatable mutants, we show that MK-STYX inhibits stress granule formation independently of G3BP-1 phosphorylation at Ser149. The introduction of point mutations at the ‘active site’ of MK-STYX that convert serine and phenylalanine to histidine and cysteine, respectively, is sufficient to generate an active enzyme. In separate experiments, we show that this active mutant, MK-STYXactive, has opposite effects to wild-type MK-STYK. Not only does MK-STYXactive induce stress granules, but also it has the capacity to dephosphorylate G3BP-1. Taken together, these results provide evidence that the pseudophosphatase MK-STYX plays a key role in the cellular response to stress.
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Affiliation(s)
- Justinn E Barr
- Department of Biology, Integrated Science Center, College of William and Mary, Williamsburg, VA 23185, USA
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Pager CT, Schütz S, Abraham TM, Luo G, Sarnow P. Modulation of hepatitis C virus RNA abundance and virus release by dispersion of processing bodies and enrichment of stress granules. Virology 2012; 435:472-84. [PMID: 23141719 DOI: 10.1016/j.virol.2012.10.027] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/11/2012] [Accepted: 10/16/2012] [Indexed: 12/12/2022]
Abstract
Components of cytoplasmic processing bodies (P-bodies) and stress granules can be subverted during viral infections to modulate viral gene expression. Because hepatitis C virus (HCV) RNA abundance is regulated by P-body components such as microRNA miR-122, Argonaute 2 and RNA helicase RCK/p54, we examined whether HCV infection modulates P-bodies and stress granules during viral infection. It was discovered that HCV infection decreased the number of P-bodies, but induced the formation of stress granules. Immunofluorescence studies revealed that a number of P-body and stress granule proteins co-localized with viral core protein at lipid droplets, the sites for viral RNA packaging. Depletion of selected P-body proteins decreased overall HCV RNA and virion abundance. Depletion of stress granule proteins also decreased overall HCV RNA abundance, but surprisingly enhanced the accumulation of infectious, extracellular virus. These data argue that HCV subverts P-body and stress granule components to aid in viral gene expression at particular sites in the cytoplasm.
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Affiliation(s)
- Cara T Pager
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305-5124, United States
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Yip L, Creusot RJ, Pager CT, Sarnow P, Fathman CG. Reduced DEAF1 function during type 1 diabetes inhibits translation in lymph node stromal cells by suppressing Eif4g3. J Mol Cell Biol 2012; 5:99-110. [PMID: 22923498 DOI: 10.1093/jmcb/mjs052] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The transcriptional regulator deformed epidermal autoregulatory factor 1 (DEAF1) has been suggested to play a role in maintaining peripheral tolerance by controlling the transcription of peripheral tissue antigen genes in lymph node stromal cells (LNSCs). Here, we demonstrate that DEAF1 also regulates the translation of genes in LNSCs by controlling the transcription of the poorly characterized eukaryotic translation initiation factor 4 gamma 3 (Eif4g3) that encodes eIF4GII. Eif4g3 gene expression was reduced in the pancreatic lymph nodes of Deaf1-KO mice, non-obese diabetic mice, and type 1 diabetes patients, where functional Deaf1 is absent or diminished. Silencing of Deaf1 reduced Eif4g3 expression, but increased the expression of Caspase 3, a serine protease that degrades eIF4GII. Polysome profiling showed that reduced Eif4g3 expression in LNSCs resulted in the diminished translation of various genes, including Anpep, the gene for aminopeptidase N, an enzyme involved in fine-tuning antigen presentation on major histocompatibility complex (MHC) class II. Together these findings suggest that reduced DEAF1 function, and subsequent loss of Eif4g3 transcription may affect peripheral tissue antigen (PTA) expression in LNSCs and contribute to the pathology of T1D.
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Affiliation(s)
- Linda Yip
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
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Kundu S. Distribution and prediction of catalytic domains in 2-oxoglutarate dependent dioxygenases. BMC Res Notes 2012; 5:410. [PMID: 22862831 PMCID: PMC3475032 DOI: 10.1186/1756-0500-5-410] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/29/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The 2-oxoglutarate dependent superfamily is a diverse group of non-haem dioxygenases, and is present in prokaryotes, eukaryotes, and archaea. The enzymes differ in substrate preference and reaction chemistry, a factor that precludes their classification by homology studies and electronic annotation schemes alone. In this work, I propose and explore the rationale of using substrates to classify structurally similar alpha-ketoglutarate dependent enzymes. FINDINGS Differential catalysis in phylogenetic clades of 2-OG dependent enzymes, is determined by the interactions of a subset of active-site amino acids. Identifying these with existing computational methods is challenging and not feasible for all proteins. A clustering protocol based on validated mechanisms of catalysis of known molecules, in tandem with group specific hidden markov model profiles is able to differentiate and sequester these enzymes. Access to this repository is by a web server that compares user defined unknown sequences to these pre-defined profiles and outputs a list of predicted catalytic domains. The server is free and is accessible at the following URL (http://comp-biol.theacms.in/H2OGpred.html). CONCLUSIONS The proposed stratification is a novel attempt at classifying and predicting 2-oxoglutarate dependent function. In addition, the server will provide researchers with a tool to compare their data to a comprehensive list of HMM profiles of catalytic domains. This work, will aid efforts by investigators to screen and characterize putative 2-OG dependent sequences. The profile database will be updated at regular intervals.
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, Army College of Medical Sciences, Delhi Cantt., New Delhi 110010, India.
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