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Moghadam RK, Daraei A, Haddadi M, Mardi A, Karamali N, Rezaiemanesh A. Casting Light on the Janus-Faced HMG-CoA Reductase Degradation Protein 1: A Comprehensive Review of Its Dualistic Impact on Apoptosis in Various Diseases. Mol Neurobiol 2024:10.1007/s12035-024-03994-z. [PMID: 38356096 DOI: 10.1007/s12035-024-03994-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024]
Abstract
Nowadays, it is well recognized that apoptosis, as a highly regulated cellular process, plays a crucial role in various biological processes, such as cell differentiation. Dysregulation of apoptosis is strongly implicated in the pathophysiology of numerous disorders, making it essential to comprehend its underlying mechanisms. One key factor that has garnered significant attention in the regulation of apoptotic pathways is HMG-CoA reductase degradation protein 1, also known as HRD1. HRD1 is an E3 ubiquitin ligase located in the endoplasmic reticulum (ER) membrane. Its primary role involves maintaining the quality control of ER proteins by facilitating the ER-associated degradation (ERAD) pathway. During ER stress, HRD1 aids in the elimination of misfolded proteins that accumulate within the ER. Therefore, HRD1 plays a pivotal role in the regulation of apoptotic pathways and maintenance of ER protein quality control. By targeting specific protein substrates and affecting apoptosis-related pathways, HRD1 could be an exclusive therapeutic target in different disorders. Dysregulation of HRD1-mediated processes contributes significantly to the pathophysiology of various diseases. The purpose of this review is to assess the effect of HRD1 on the pathways related to apoptosis in various diseases from a therapeutic perspective.
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Affiliation(s)
- Reihaneh Khaleghi Moghadam
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Daneshgah Street, Shahid Shiroudi Boulevard, PO-Box: 6714869914, Kermanshah, Iran
| | - Arshia Daraei
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Daneshgah Street, Shahid Shiroudi Boulevard, PO-Box: 6714869914, Kermanshah, Iran
| | - Maryam Haddadi
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Daneshgah Street, Shahid Shiroudi Boulevard, PO-Box: 6714869914, Kermanshah, Iran
| | - Amirhossein Mardi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Negin Karamali
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Alireza Rezaiemanesh
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Daneshgah Street, Shahid Shiroudi Boulevard, PO-Box: 6714869914, Kermanshah, Iran.
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Autophagy/Mitophagy Regulated by Ubiquitination: A Promising Pathway in Cancer Therapeutics. Cancers (Basel) 2023; 15:cancers15041112. [PMID: 36831455 PMCID: PMC9954143 DOI: 10.3390/cancers15041112] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Autophagy is essential for organismal development, maintenance of energy homeostasis, and quality control of organelles and proteins. As a selective form of autophagy, mitophagy is necessary for effectively eliminating dysfunctional mitochondria. Both autophagy and mitophagy are linked with tumor progression and inhibition. The regulation of mitophagy and autophagy depend upon tumor type and stage. In tumors, mitophagy has dual roles: it removes damaged mitochondria to maintain healthy mitochondria and energy production, which are necessary for tumor growth. In contrast, mitophagy has been shown to inhibit tumor growth by mitigating excessive ROS production, thus preventing mutation and chromosomal instability. Ubiquitination and deubiquitination are important modifications that regulate autophagy. Multiple E3 ubiquitin ligases and DUBs modulate the activity of the autophagy and mitophagy machinery, thereby influencing cancer progression. In this review, we summarize the mechanistic association between cancer development and autophagy/mitophagy activities regulated by the ubiquitin modification of autophagic proteins. In addition, we discuss the function of multiple proteins involved in autophagy/mitophagy in tumors that may represent potential therapeutic targets.
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Zou HX, Qiu BQ, Zhang ZY, Hu T, Wan L, Liu JC, Huang H, Lai SQ. Dysregulated autophagy-related genes in septic cardiomyopathy: Comprehensive bioinformatics analysis based on the human transcriptomes and experimental validation. Front Cardiovasc Med 2022; 9:923066. [PMID: 35983185 PMCID: PMC9378994 DOI: 10.3389/fcvm.2022.923066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Septic cardiomyopathy (SCM) is severe organ dysfunction caused by sepsis that is associated with poor prognosis, and its pathobiological mechanisms remain unclear. Autophagy is a biological process that has recently been focused on SCM, yet the current understanding of the role of dysregulated autophagy in the pathogenesis of SCM remains limited and uncertain. Exploring the molecular mechanisms of disease based on the transcriptomes of human pathological samples may bring the closest insights. In this study, we analyzed the differential expression of autophagy-related genes in SCM based on the transcriptomes of human septic hearts, and further explored their potential crosstalk and functional pathways. Key functional module and hub genes were identified by constructing a protein–protein interaction network. Eight key genes (CCL2, MYC, TP53, SOD2, HIF1A, CTNNB1, CAT, and ADIPOQ) that regulate autophagy in SCM were identified after validation in a lipopolysaccharide (LPS)-induced H9c2 cardiomyoblast injury model, as well as the autophagic characteristic features. Furthermore, we found that key genes were associated with abnormal immune infiltration in septic hearts and have the potential to serve as biomarkers. Finally, we predicted drugs that may play a protective role in SCM by regulating autophagy based on our results. Our study provides evidence and new insights into the role of autophagy in SCM based on human septic heart transcriptomes, which would be of great benefit to reveal the molecular pathological mechanisms and explore the diagnostic and therapeutic targets for SCM.
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Affiliation(s)
- Hua-Xi Zou
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Institute of Cardiovascular Diseases, Jiangxi Academy of Clinical Medical Sciences, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Department of Cardiovascular Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Bai-Quan Qiu
- Institute of Cardiovascular Diseases, Jiangxi Academy of Clinical Medical Sciences, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Department of Cardiovascular Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ze-Yu Zhang
- Institute of Nanchang University Trauma Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tie Hu
- Institute of Cardiovascular Diseases, Jiangxi Academy of Clinical Medical Sciences, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Department of Cardiovascular Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Li Wan
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Institute of Cardiovascular Diseases, Jiangxi Academy of Clinical Medical Sciences, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ji-Chun Liu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Institute of Cardiovascular Diseases, Jiangxi Academy of Clinical Medical Sciences, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Department of Cardiovascular Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Huang Huang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Institute of Cardiovascular Diseases, Jiangxi Academy of Clinical Medical Sciences, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Huang Huang,
| | - Song-Qing Lai
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Institute of Cardiovascular Diseases, Jiangxi Academy of Clinical Medical Sciences, The First Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Song-Qing Lai,
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Peng J, Li W, Wang B, Zhang S, Xiao Y, Han F, Wang Z. UBE2G1 Is a Critical Component of Immune Response to the Infection of Pseudomonas Plecoglossicida in Large Yellow Croaker (Larimichthys crocea). Int J Mol Sci 2022; 23:ijms23158298. [PMID: 35955424 PMCID: PMC9368838 DOI: 10.3390/ijms23158298] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 12/07/2022] Open
Abstract
The large yellow croaker (Larimichthys crocea) is one of the most economically valuable mariculture fish in China. Infection of Pseudomonas plecoglossicida can cause an outbreak of “internal organ white-spot disease”, which seriously affects the aquaculture of the large yellow croaker. Ubiquitylation is closely related to the post-translation modification of proteins and plays a vital role in many hosts’ immune defense pathways, while the E2-binding enzyme is a key factor in ubiquitination. Our previous genome-wide association study found that the ubiquitin-binding enzyme E2G1 (designed LcUbe2g1) was one of the candidate genes related to disease resistance in large yellow croaker. In this study, we analyzed the molecular characteristics, function, and immune mechanism of the LcUbe2g1. The full-length cDNA is 812 bp, with an open reading frame of 513 bp, encoding 170 amino acid residues. The results of the RT-qPCR and immunohistochemistry analysis revealed that its transcription and translation were significantly activated by the infection of P. plecoglossicida in large yellow croaker. Immunocytochemistry experiments verified the co-localization of LcUBE2G1 and the ubiquitin proteins in the head kidney cells of large yellow croaker. Through GST pull-down, we found that LcUBE2G1 interacted with NEDD8 to co-regulate the ubiquitination process. The above results indicate that LcUBE2G1 is essential in the regulation of ubiquitination against P. plecoglossicida infection in large yellow croaker, which lays a foundation for further study on the resistance mechanism of internal organ white-spot disease.
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Affiliation(s)
- Jia Peng
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Fisheries College, Jimei University, Xiamen 361021, China; (J.P.); (W.L.); (B.W.); (S.Z.); (Y.X.)
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Fisheries College, Jimei University, Xiamen 361021, China; (J.P.); (W.L.); (B.W.); (S.Z.); (Y.X.)
| | - Bi Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Fisheries College, Jimei University, Xiamen 361021, China; (J.P.); (W.L.); (B.W.); (S.Z.); (Y.X.)
| | - Sen Zhang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Fisheries College, Jimei University, Xiamen 361021, China; (J.P.); (W.L.); (B.W.); (S.Z.); (Y.X.)
| | - Yao Xiao
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Fisheries College, Jimei University, Xiamen 361021, China; (J.P.); (W.L.); (B.W.); (S.Z.); (Y.X.)
| | - Fang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Fisheries College, Jimei University, Xiamen 361021, China; (J.P.); (W.L.); (B.W.); (S.Z.); (Y.X.)
- Correspondence: (F.H.); (Z.W.); Tel.: +86-592-618-3816 (F.H.); +86-1-89-5012-4893 (Z.W.)
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Fisheries College, Jimei University, Xiamen 361021, China; (J.P.); (W.L.); (B.W.); (S.Z.); (Y.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence: (F.H.); (Z.W.); Tel.: +86-592-618-3816 (F.H.); +86-1-89-5012-4893 (Z.W.)
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5
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Ubiquitination-Proteasome System (UPS) and Autophagy Two Main Protein Degradation Machineries in Response to Cell Stress. Cells 2022; 11:cells11050851. [PMID: 35269473 PMCID: PMC8909305 DOI: 10.3390/cells11050851] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 02/07/2023] Open
Abstract
In response to environmental stimuli, cells make a series of adaptive changes to combat the injury, repair the damage, and increase the tolerance to the stress. However, once the damage is too serious to repair, the cells will undergo apoptosis to protect the overall cells through suicidal behavior. Upon external stimulation, some intracellular proteins turn into unfolded or misfolded protein, exposing their hydrophobic regions to form protein aggregation, which may ultimately produce serious damage to the cells. Ubiquitin plays an important role in the degradation of these unnatural proteins by tagging with ubiquitin chains in the ubiquitin-proteasome or autophagy system. If the two processes fail to eliminate the abnormal protein aggregates, the cells will move to apoptosis and death. Dysregulation of ubiquitin-proteasome system (UPS) and autophagy may result in the development of numerous diseases. This review focuses on the molecular mechanisms of UPS and autophagy in clearance of intracellular protein aggregates, and the relationship between dysregulation of ubiquitin network and diseases.
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Cheng F, De Luca A, Hogan AL, Rayner SL, Davidson JM, Watchon M, Stevens CH, Muñoz SS, Ooi L, Yerbury JJ, Don EK, Fifita JA, Villalva MD, Suddull H, Chapman TR, Hedl TJ, Walker AK, Yang S, Morsch M, Shi B, Blair IP, Laird AS, Chung RS, Lee A. Unbiased Label-Free Quantitative Proteomics of Cells Expressing Amyotrophic Lateral Sclerosis (ALS) Mutations in CCNF Reveals Activation of the Apoptosis Pathway: A Workflow to Screen Pathogenic Gene Mutations. Front Mol Neurosci 2021; 14:627740. [PMID: 33986643 PMCID: PMC8111008 DOI: 10.3389/fnmol.2021.627740] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
The past decade has seen a rapid acceleration in the discovery of new genetic causes of ALS, with more than 20 putative ALS-causing genes now cited. These genes encode proteins that cover a diverse range of molecular functions, including free radical scavenging (e.g., SOD1), regulation of RNA homeostasis (e.g., TDP-43 and FUS), and protein degradation through the ubiquitin-proteasome system (e.g., ubiquilin-2 and cyclin F) and autophagy (TBK1 and sequestosome-1/p62). It is likely that the various initial triggers of disease (either genetic, environmental and/or gene-environment interaction) must converge upon a common set of molecular pathways that underlie ALS pathogenesis. Given the complexity, it is not surprising that a catalog of molecular pathways and proteostasis dysfunctions have been linked to ALS. One of the challenges in ALS research is determining, at the early stage of discovery, whether a new gene mutation is indeed disease-specific, and if it is linked to signaling pathways that trigger neuronal cell death. We have established a proof-of-concept proteogenomic workflow to assess new gene mutations, using CCNF (cyclin F) as an example, in cell culture models to screen whether potential gene candidates fit the criteria of activating apoptosis. This can provide an informative and time-efficient output that can be extended further for validation in a variety of in vitro and in vivo models and/or for mechanistic studies. As a proof-of-concept, we expressed cyclin F mutations (K97R, S195R, S509P, R574Q, S621G) in HEK293 cells for label-free quantitative proteomics that bioinformatically predicted activation of the neuronal cell death pathways, which was validated by immunoblot analysis. Proteomic analysis of induced pluripotent stem cells (iPSCs) derived from patient fibroblasts bearing the S621G mutation showed the same activation of these pathways providing compelling evidence for these candidate gene mutations to be strong candidates for further validation and mechanistic studies (such as E3 enzymatic activity assays, protein-protein and protein-substrate studies, and neuronal apoptosis and aberrant branching measurements in zebrafish). Our proteogenomics approach has great utility and provides a relatively high-throughput screening platform to explore candidate gene mutations for their propensity to cause neuronal cell death, which will guide a researcher for further experimental studies.
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Affiliation(s)
- Flora Cheng
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Alana De Luca
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Alison L Hogan
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Stephanie L Rayner
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Jennilee M Davidson
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Maxinne Watchon
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Claire H Stevens
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW, Australia.,School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Sonia Sanz Muñoz
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW, Australia.,School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW, Australia.,School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW, Australia.,School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Emily K Don
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Jennifer A Fifita
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Maria D Villalva
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Hannah Suddull
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Tyler R Chapman
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Thomas J Hedl
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
| | - Adam K Walker
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia.,Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
| | - Shu Yang
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Marco Morsch
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Bingyang Shi
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Angela S Laird
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Roger S Chung
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Albert Lee
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
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7
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Cheuk A, Ouellet F, Houde M. The barley stripe mosaic virus expression system reveals the wheat C2H2 zinc finger protein TaZFP1B as a key regulator of drought tolerance. BMC PLANT BIOLOGY 2020; 20:144. [PMID: 32264833 PMCID: PMC7140352 DOI: 10.1186/s12870-020-02355-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/23/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Drought stress is one of the major factors limiting wheat production globally. Improving drought tolerance is important for agriculture sustainability. Although various morphological, physiological and biochemical responses associated with drought tolerance have been documented, the molecular mechanisms and regulatory genes that are needed to improve drought tolerance in crops require further investigation. We have used a novel 4-component version (for overexpression) and a 3-component version (for underexpression) of a barley stripe mosaic virus-based (BSMV) system for functional characterization of the C2H2-type zinc finger protein TaZFP1B in wheat. These expression systems avoid the need to produce transgenic plant lines and greatly speed up functional gene characterization. RESULTS We show that overexpression of TaZFP1B stimulates plant growth and up-regulates different oxidative stress-responsive genes under well-watered conditions. Plants that overexpress TaZFP1B are more drought tolerant at critical periods of the plant's life cycle. Furthermore, RNA-Seq analysis revealed that plants overexpressing TaZFP1B reprogram their transcriptome, resulting in physiological and physical modifications that help wheat to grow and survive under drought stress. In contrast, plants transformed to underexpress TaZFP1B are significantly less tolerant to drought and growth is negatively affected. CONCLUSIONS This study clearly shows that the two versions of the BSMV system can be used for fast and efficient functional characterization of genes in crops. The extent of transcriptome reprogramming in plants that overexpress TaZFP1B indicates that the encoded transcription factor is a key regulator of drought tolerance in wheat.
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Affiliation(s)
- Arnaud Cheuk
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, Québec, H3C 3P8, Canada
| | - Francois Ouellet
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, Québec, H3C 3P8, Canada
| | - Mario Houde
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, Québec, H3C 3P8, Canada.
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8
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Wade BE, Zhao J, Ma J, Hart CM, Sutliff RL. Hypoxia-induced alterations in the lung ubiquitin proteasome system during pulmonary hypertension pathogenesis. Pulm Circ 2018; 8:2045894018788267. [PMID: 29927354 PMCID: PMC6146334 DOI: 10.1177/2045894018788267] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Pulmonary hypertension (PH) is a clinical disorder characterized by sustained
increases in pulmonary vascular resistance and pressure that can lead to right
ventricular (RV) hypertrophy and ultimately RV failure and death. The molecular
pathogenesis of PH remains incompletely defined, and existing treatments are
associated with suboptimal outcomes and persistent morbidity and mortality.
Reports have suggested a role for the ubiquitin proteasome system (UPS) in PH,
but the extent of UPS-mediated non-proteolytic protein alterations during PH
pathogenesis has not been previously defined. To further examine UPS
alterations, the current study employed C57BL/6J mice exposed to normoxia or
hypoxia for 3 weeks. Lung protein ubiquitination was evaluated by mass
spectrometry to identify differentially ubiquitinated proteins relative to
normoxic controls. Hypoxia stimulated differential ubiquitination of 198
peptides within 131 proteins (p < 0.05). These proteins were
screened to identify candidates within pathways involved in PH pathogenesis.
Some 51.9% of the differentially ubiquitinated proteins were implicated in at
least one known pathway contributing to PH pathogenesis, and 13% were involved
in three or more PH pathways. Anxa2, App, Jak1, Lmna, Pdcd6ip, Prkch1, and Ywhah
were identified as mediators in PH pathways that undergo differential
ubiquitination during PH pathogenesis. To our knowledge, this is the first study
to report global changes in protein ubiquitination in the lung during PH
pathogenesis. These findings suggest signaling nodes that are dynamically
regulated by the UPS during PH pathogenesis. Further exploration of these
differentially ubiquitinated proteins and related pathways can provide new
insights into the role of the UPS in PH pathogenesis.
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Affiliation(s)
- Brandy E Wade
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
| | - Jingru Zhao
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
| | - Jing Ma
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
| | - C Michael Hart
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
| | - Roy L Sutliff
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
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9
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Lip PZY, Demasi M, Bonatto D. The role of the ubiquitin proteasome system in the memory process. Neurochem Int 2016; 102:57-65. [PMID: 27916542 DOI: 10.1016/j.neuint.2016.11.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/27/2016] [Accepted: 11/29/2016] [Indexed: 01/20/2023]
Abstract
Quite intuitive is the notion that memory formation and consolidation is orchestrated by protein synthesis because of the synaptic plasticity necessary for those processes. Nevertheless, recent advances have begun accumulating evidences of a high requirement for protein degradation on the molecular mechanisms of the memory process in the mammalian brain. Because degradation determines protein half-life, degradation has been increasingly recognized as an important intracellular regulatory mechanism. The proteasome is the main player in the degradation of intracellular proteins. Proteasomal substrates are mainly degraded after a post-translational modification by a poly-ubiquitin chain. Latter process, namely poly-ubiquitination, is highly regulated at the step of the ubiquitin molecule transferring to the protein substrate mediated by a set of proteins whose genes represent almost 2% of the human genome. Understanding the role of polyubiquitin-mediated protein degradation has challenging researchers in many fields of investigation as a new source of targets for therapeutic intervention, e.g. E3 ligases that transfer ubiquitin moieties to the substrate. The goal of present work was to uncover mechanisms underlying memory processes regarding the role of the ubiquitin-proteasome system (UPS). For that purpose, preceded of a short review on UPS and memory processes a top-down systems biology approach was applied to establish central proteins involved in memory formation and consolidation highlighting their cross-talking with the UPS. According to that approach, the pattern of expression of several elements of the UPS were found overexpressed in regions of the brain involved in processing cortical inputs.
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Affiliation(s)
- Philomena Z Y Lip
- Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo, SP, Brazil; Medical Sciences Division, University of Oxford, Oxford, UK
| | - Marilene Demasi
- Medical Sciences Division, University of Oxford, Oxford, UK.
| | - Diego Bonatto
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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Wu W, Zhang D, Pan D, Zuo G, Ren X, Chen S. Downregulation of vascular endothelial growth factor receptor-2 under oxidative stress conditions is mediated by β-transduction repeat-containing protein via glycogen synthase kinase-3β signaling. Int J Mol Med 2016; 37:911-20. [PMID: 26935904 PMCID: PMC4790698 DOI: 10.3892/ijmm.2016.2493] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/05/2016] [Indexed: 12/22/2022] Open
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR-2), which is a key determinant of the angiogenecic response, is decreased in diabetic mice under oxidative stress. β-transduction repeat-containing protein (β-TrCP) has been reported to participate in VEGFR-2 degradation in thyroid cancer cells. Additionally, glycogen synthase kinase-3β (GSK-3β) acts as a mediator in the β-TrCP-induced degradation of several proteins. However, the role played by β-TrCP and GSK-3β in the degradation of VEGFR-2 in endothelial cells where hyperglycemia had been induced was not fully understood. In the present study, we aimed to analyze the mechanisms of VEGFR-2 degradation by studying excess reactive oxygen species (ROS) induced by hyperglycemia or glucose oxidase (GO). Human umbilical vein endothelial cells (HUVECs) were treated with different concentrations of glucose (6.6, 19.8 and 33 mM), mannitol (33 mM) and GO (1 U/ml). Angiogenic function, ROS levels, the co-location of VEGFR-2 and β-TrCP were evaluated. Cells were collected for RT-qPCR and western blot analysis. We noted that angiogenesis was impaired upon increasing the glucose concentration. When HUVECs were in a hyperglycemic state, ROS production increased, comparable to exposure to GO; GO catalyzes oxidation of glucose into H2O2 and D-glucono-δ-lactone. Phosphorylated VEGFR-2 was reduced by hyperglycemia while total VEGFR-2 was almost unaltered. However, VEGFR-2 was reduced when directly exposed to ROS, with resultant co-location of β-TrCP and VEGFR-2. Through a co-immunoprecipitation assay, we noted that ubiquitinated VEGFR-2 was significantly augmented by excess ROS. Decreased VEGFR-2 caused by ROS was ameliorated by β-TrCP siRNA, proteasome inhibitor MG132 and GSK-3β activity inhibitor (lithium chloride and SB216763). We suggest that redundant ROS reduces VEGFR-2 through β-TrCP-mediated VEGFR-2 degradation, which is postulated to be regulated by GSK-3β.
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Affiliation(s)
- Wen Wu
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Qinhuai, Nanjing 210006, P.R. China
| | - Daimin Zhang
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Qinhuai, Nanjing 210006, P.R. China
| | - Daorong Pan
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Qinhuai, Nanjing 210006, P.R. China
| | - Guangfeng Zuo
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Qinhuai, Nanjing 210006, P.R. China
| | - Xiaomin Ren
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Qinhuai, Nanjing 210006, P.R. China
| | - Shaoliang Chen
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Qinhuai, Nanjing 210006, P.R. China
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Fraisier C, Koraka P, Belghazi M, Bakli M, Granjeaud S, Pophillat M, Lim SM, Osterhaus A, Martina B, Camoin L, Almeras L. Kinetic analysis of mouse brain proteome alterations following Chikungunya virus infection before and after appearance of clinical symptoms. PLoS One 2014; 9:e91397. [PMID: 24618821 PMCID: PMC3949995 DOI: 10.1371/journal.pone.0091397] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 02/10/2014] [Indexed: 01/13/2023] Open
Abstract
Recent outbreaks of Chikungunya virus (CHIKV) infection have been characterized by an increasing number of severe cases with atypical manifestations including neurological complications. In parallel, the risk map of CHIKV outbreaks has expanded because of improved vector competence. These features make CHIKV infection a major public health concern that requires a better understanding of the underlying physiopathological processes for the development of antiviral strategies to protect individuals from severe disease. To decipher the mechanisms of CHIKV infection in the nervous system, a kinetic analysis on the host proteome modifications in the brain of CHIKV-infected mice sampled before and after the onset of clinical symptoms was performed. The combination of 2D-DIGE and iTRAQ proteomic approaches, followed by mass spectrometry protein identification revealed 177 significantly differentially expressed proteins. This kinetic analysis revealed a dramatic down-regulation of proteins before the appearance of the clinical symptoms followed by the increased expression of most of these proteins in the acute symptomatic phase. Bioinformatic analyses of the protein datasets enabled the identification of the major biological processes that were altered during the time course of CHIKV infection, such as integrin signaling and cytoskeleton dynamics, endosome machinery and receptor recycling related to virus transport and synapse function, regulation of gene expression, and the ubiquitin-proteasome pathway. These results reveal the putative mechanisms associated with severe CHIKV infection-mediated neurological disease and highlight the potential markers or targets that can be used to develop diagnostic and/or antiviral tools.
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Affiliation(s)
- Christophe Fraisier
- Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
| | - Penelope Koraka
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Maya Belghazi
- Aix-Marseille Université, CNRS, CRN2M UMR 7286, Marseille, France
| | - Mahfoud Bakli
- Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
| | - Samuel Granjeaud
- CRCM, Marseille Protéomique, Inserm, U1068, Marseille, France
- Aix-Marseille Université, UM 105, Marseille, France
| | - Matthieu Pophillat
- CRCM, Marseille Protéomique, Inserm, U1068, Marseille, France
- Aix-Marseille Université, UM 105, Marseille, France
| | - Stephanie M. Lim
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Albert Osterhaus
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Byron Martina
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Luc Camoin
- CRCM, Marseille Protéomique, Inserm, U1068, Marseille, France
- Aix-Marseille Université, UM 105, Marseille, France
| | - Lionel Almeras
- Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
- Unité de recherche en biologie et épidémiologie parasitaires (URBEP), Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France
- * E-mail:
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Tomar D, Prajapati P, Sripada L, Singh K, Singh R, Singh AK, Singh R. TRIM13 regulates caspase-8 ubiquitination, translocation to autophagosomes and activation during ER stress induced cell death. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:3134-3144. [PMID: 24021263 DOI: 10.1016/j.bbamcr.2013.08.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 08/28/2013] [Accepted: 08/30/2013] [Indexed: 01/06/2023]
Abstract
The emerging evidences suggest that endoplasmic (ER) stress is involved in onset of many pathological conditions like cancer and neurodegeneration. The persistent ER stress results in misfolded protein aggregates, which are degraded through the process of autophagy or lead to cell death through activation of caspases. The regulation of crosstalk of autophagy and cell death during ER stress is emerging. Ubiquitination plays regulatory role in crosstalk of autophagy and cell death. In the current study, we describe the role of TRIM13, RING E3 ubiquitin ligase, in regulation of ER stress induced cell death. The expression of TRIM13 sensitizes cells to ER stress induced death. TRIM13 induced autophagy is essential for ER stress induced caspase activation and cell death. TRIM13 induces K63 linked poly-ubiquitination of caspase-8, which results in its stabilization and activation during ER stress. TRIM13 regulates translocation of caspase-8 to autophagosome and its fusion with lysosome during ER stress. This study first time demonstrated the role of TRIM13 as novel regulator of caspase-8 activation and cell death during ER stress.
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Affiliation(s)
- Dhanendra Tomar
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, Gujarat, India
| | - Paresh Prajapati
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, Gujarat, India
| | - Lakshmi Sripada
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, Gujarat, India
| | - Kritarth Singh
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, Gujarat, India
| | - Rochika Singh
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, Gujarat, India
| | - Arun Kumar Singh
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, Gujarat, India
| | - Rajesh Singh
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, Gujarat, India.
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