1
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Keramidas P, Pitou M, Papachristou E, Choli-Papadopoulou T. Insights into the Activation of Unfolded Protein Response Mechanism during Coronavirus Infection. Curr Issues Mol Biol 2024; 46:4286-4308. [PMID: 38785529 PMCID: PMC11120126 DOI: 10.3390/cimb46050261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Coronaviruses represent a significant class of viruses that affect both animals and humans. Their replication cycle is strongly associated with the endoplasmic reticulum (ER), which, upon virus invasion, triggers ER stress responses. The activation of the unfolded protein response (UPR) within infected cells is performed from three transmembrane receptors, IRE1, PERK, and ATF6, and results in a reduction in protein production, a boost in the ER's ability to fold proteins properly, and the initiation of ER-associated degradation (ERAD) to remove misfolded or unfolded proteins. However, in cases of prolonged and severe ER stress, the UPR can also instigate apoptotic cell death and inflammation. Herein, we discuss the ER-triggered host responses after coronavirus infection, as well as the pharmaceutical targeting of the UPR as a potential antiviral strategy.
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Affiliation(s)
| | | | | | - Theodora Choli-Papadopoulou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.K.); (M.P.); (E.P.)
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2
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Zhu D, Liang H, Du Z, Liu Q, Li G, Zhang W, Wu D, Zhou X, Song Y, Yang C. Altered Metabolism and Inflammation Driven by Post-translational Modifications in Intervertebral Disc Degeneration. RESEARCH (WASHINGTON, D.C.) 2024; 7:0350. [PMID: 38585329 PMCID: PMC10997488 DOI: 10.34133/research.0350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024]
Abstract
Intervertebral disc degeneration (IVDD) is a prevalent cause of low back pain and a leading contributor to disability. IVDD progression involves pathological shifts marked by low-grade inflammation, extracellular matrix remodeling, and metabolic disruptions characterized by heightened glycolytic pathways, mitochondrial dysfunction, and cellular senescence. Extensive posttranslational modifications of proteins within nucleus pulposus cells and chondrocytes play crucial roles in reshaping the intervertebral disc phenotype and orchestrating metabolism and inflammation in diverse contexts. This review focuses on the pivotal roles of phosphorylation, ubiquitination, acetylation, glycosylation, methylation, and lactylation in IVDD pathogenesis. It integrates the latest insights into various posttranslational modification-mediated metabolic and inflammatory signaling networks, laying the groundwork for targeted proteomics and metabolomics for IVDD treatment. The discussion also highlights unexplored territories, emphasizing the need for future research, particularly in understanding the role of lactylation in intervertebral disc health, an area currently shrouded in mystery.
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Affiliation(s)
- Dingchao Zhu
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Huaizhen Liang
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Zhi Du
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Qian Liu
- College of Life Sciences,
Wuhan University, Wuhan 430072, Hubei Province, China
| | - Gaocai Li
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Weifeng Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Di Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Xingyu Zhou
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Yu Song
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Cao Yang
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
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3
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Zhang J, Cruz-Cosme R, Zhang C, Liu D, Tang Q, Zhao RY. Endoplasmic reticulum-associated SARS-CoV-2 ORF3a elicits heightened cytopathic effects despite robust ER-associated degradation. mBio 2024; 15:e0303023. [PMID: 38078754 PMCID: PMC10790703 DOI: 10.1128/mbio.03030-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has tragically claimed millions of lives through coronavirus disease 2019 (COVID-19), and there remains a critical gap in our understanding of the precise molecular mechanisms responsible for the associated fatality. One key viral factor of interest is the SARS-CoV-2 ORF3a protein, which has been identified as a potent inducer of host cellular proinflammatory responses capable of triggering the catastrophic cytokine storm, a primary contributor to COVID-19-related deaths. Moreover, ORF3a, much like the spike protein, exhibits a propensity for frequent mutations, with certain variants linked to the severity of COVID-19. Our previous research unveiled two distinct types of ORF3a mutant proteins, categorized by their subcellular localizations, setting the stage for a comparative investigation into the functional and mechanistic disparities between these two types of ORF3a variants. Given the clinical significance and functional implications of the natural ORF3a mutations, the findings of this study promise to provide invaluable insights into the potential roles undertaken by these mutant ORF3a proteins in the pathogenesis of COVID-19.
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Affiliation(s)
- Jiantao Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ruth Cruz-Cosme
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - Chenyu Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Dongxiao Liu
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - Richard Y. Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute of Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research & Development Service, VA Maryland Health Care System, Baltimore, Maryland, USA
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4
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Sun X, Yang Y, Meng X, Li J, Liu X, Liu H. PANoptosis: Mechanisms, biology, and role in disease. Immunol Rev 2024; 321:246-262. [PMID: 37823450 DOI: 10.1111/imr.13279] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
Cell death can be executed through distinct subroutines. PANoptosis is a unique inflammatory cell death modality involving the interactions between pyroptosis, apoptosis, and necroptosis, which can be mediated by multifaceted PANoptosome complexes assembled via integrating components from other cell death modalities. There is growing interest in the process and function of PANoptosis. Accumulating evidence suggests that PANoptosis occurs under diverse stimuli, for example, viral or bacterial infection, cytokine storm, and cancer. Given the impact of PANoptosis across the disease spectrum, this review briefly describes the relationships between pyroptosis, apoptosis, and necroptosis, highlights the key molecules in PANoptosome formation and PANoptosis activation, and outlines the multifaceted roles of PANoptosis in diseases together with a potential for therapeutic targeting. We also discuss important concepts and pressing issues for future PANoptosis research. Improved understanding of PANoptosis and its mechanisms is crucial for identifying novel therapeutic targets and strategies.
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Affiliation(s)
- Xu Sun
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yanpeng Yang
- Cardiac Care Unit, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Xiaona Meng
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Jia Li
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Xiaoli Liu
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Huaimin Liu
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
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5
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Knupp J, Pletan ML, Arvan P, Tsai B. Autophagy of the ER: the secretome finds the lysosome. FEBS J 2023; 290:5656-5673. [PMID: 37920925 PMCID: PMC11044768 DOI: 10.1111/febs.16986] [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: 08/03/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
Lysosomal degradation of the endoplasmic reticulum (ER) and its components through the autophagy pathway has emerged as a major regulator of ER proteostasis. Commonly referred to as ER-phagy and ER-to-lysosome-associated degradation (ERLAD), how the ER is targeted to the lysosome has been recently clarified by a growing number of studies. Here, we summarize the discoveries of the molecular components required for lysosomal degradation of the ER and their proposed mechanisms of action. Additionally, we discuss how cells employ these machineries to create the different routes of ER-lysosome-associated degradation. Further, we review the role of ER-phagy in viral infection pathways, as well as the implication of ER-phagy in human disease. In sum, we provide a comprehensive overview of the current field of ER-phagy.
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Affiliation(s)
- Jeffrey Knupp
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Madison L Pletan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter Arvan
- Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
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6
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Sandeep, Subba R, Mondal AC. Does COVID-19 Trigger the Risk for the Development of Parkinson's Disease? Therapeutic Potential of Vitamin C. Mol Neurobiol 2023:10.1007/s12035-023-03756-3. [PMID: 37957424 DOI: 10.1007/s12035-023-03756-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), which was proclaimed a pandemic by the World Health Organization (WHO) in March 2020. There is mounting evidence that older patients with multimorbidity are more susceptible to COVID-19 complications than are younger, healthy people. Having neuroinvasive potential, SARS-CoV-2 infection may increase susceptibility toward the development of Parkinson's disease (PD), a progressive neurodegenerative disorder with extensive motor deficits. PD is characterized by the aggregation of α-synuclein in the form of Lewy bodies and the loss of dopaminergic neurons in the dorsal striatum and substantia nigra pars compacta (SNpc) of the nigrostriatal pathway in the brain. Increasing reports suggest that SARS-CoV-2 infection is linked with the worsening of motor and non-motor symptoms with high rates of hospitalization and mortality in PD patients. Common pathological changes in both diseases involve oxidative stress, mitochondrial dysfunction, neuroinflammation, and neurodegeneration. COVID-19 exacerbates the damage ensuing from the dysregulation of those processes, furthering neurological complications, and increasing the severity of PD symptomatology. Phytochemicals have antioxidant, anti-inflammatory, and anti-apoptotic properties. Vitamin C supplementation is found to ameliorate the common pathological changes in both diseases to some extent. This review aims to present the available evidence on the association between COVID-19 and PD, and discusses the therapeutic potential of vitamin C for its better management.
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Affiliation(s)
- Sandeep
- Laboratory of Cellular & Molecular Neurobiology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rhea Subba
- Laboratory of Cellular & Molecular Neurobiology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Amal Chandra Mondal
- Laboratory of Cellular & Molecular Neurobiology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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7
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Li S, Li X, Liang H, Yu K, Zhai J, Xue M, Luo Z, Zheng C, Zhang H. SARS-CoV-2 ORF7a blocked autophagy flux by intervening in the fusion between autophagosome and lysosome to promote viral infection and pathogenesis. J Med Virol 2023; 95:e29200. [PMID: 37916857 DOI: 10.1002/jmv.29200] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
The coronavirus disease 2019 (COVID-19) continues to pose a major threat to public health worldwide. Although many studies have clarified the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection process, the underlying mechanisms of viral invasion and immune evasion were still unclear. This study focused on SARS-CoV-2 ORF7a (open reading frame-7a), one of the essential open reading frames (ORFs) in infection and pathogenesis. First, by analyzing its physical and chemical characteristics, SARS-CoV-2 ORF7a is an unstable hydrophobic transmembrane protein. Then, the ORF7a transmembrane domain three-dimensional crystal structure model was predicted and verified. SARS-CoV-2 ORF7a localized in the endoplasmic reticulum and participated in the autophagy-lysosome pathway via interacting with p62. In addition, we elucidated the underlying molecular mechanisms by which ORF7a intercepted autophagic flux, promoted double membrane vesicle formation, and evaded host autophagy-lysosome degradation and antiviral innate immunity. This study demonstrated that ORF7a could be a therapeutic target, and Glecaprevir may be a potential drug against SARS-CoV-2 by targeting ORF7a. A comprehensive understanding of ORF7a's functions may contribute to developing novel therapies and clinical drugs against COVID-19.
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Affiliation(s)
- Shun Li
- Department of Spine Surgery, People's Hospital of Longhua, Affiliated Hospital of Southern Medical University, Shenzhen, China
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China
| | - Xiaobo Li
- Department of Respiratory, Chengdu Seventh People's Hospital (Affiliated Cancer Hospital of Chengdu Medical College), Chengdu, Sichuan, China
| | - Haowei Liang
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
| | - Kuike Yu
- Department of Spine Surgery, People's Hospital of Longhua, Affiliated Hospital of Southern Medical University, Shenzhen, China
| | - Jingbo Zhai
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Medical College, Inner Mongolia Minzu University, Tongliao, China
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhuojing Luo
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology & Infection Diseases, University of Calgary, Calgary, Canada
| | - Hao Zhang
- Department of Spine Surgery, People's Hospital of Longhua, Affiliated Hospital of Southern Medical University, Shenzhen, China
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8
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Yuan C, Ma Z, Xie J, Li W, Su L, Zhang G, Xu J, Wu Y, Zhang M, Liu W. The role of cell death in SARS-CoV-2 infection. Signal Transduct Target Ther 2023; 8:357. [PMID: 37726282 PMCID: PMC10509267 DOI: 10.1038/s41392-023-01580-8] [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: 01/20/2023] [Revised: 06/09/2023] [Accepted: 07/31/2023] [Indexed: 09/21/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), showing high infectiousness, resulted in an ongoing pandemic termed coronavirus disease 2019 (COVID-19). COVID-19 cases often experience acute respiratory distress syndrome, which has caused millions of deaths. Apart from triggering inflammatory and immune responses, many viral infections can cause programmed cell death in infected cells. Cell death mechanisms have a vital role in maintaining a suitable environment to achieve normal cell functionality. Nonetheless, these processes are dysregulated, potentially contributing to disease pathogenesis. Over the past decades, multiple cell death pathways are becoming better understood. Growing evidence suggests that the induction of cell death by the coronavirus may significantly contributes to viral infection and pathogenicity. However, the interaction of SARS-CoV-2 with cell death, together with its associated mechanisms, is yet to be elucidated. In this review, we summarize the existing evidence concerning the molecular modulation of cell death in SARS-CoV-2 infection as well as viral-host interactions, which may shed new light on antiviral therapy against SARS-CoV-2.
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Affiliation(s)
- Cui Yuan
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhenling Ma
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jiufeng Xie
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wenqing Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Lijuan Su
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Guozhi Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jun Xu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yaru Wu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Min Zhang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Wei Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China.
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9
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Jiao S, Miranda P, Li Y, Maric D, Holmgren M. Some aspects of the life of SARS-CoV-2 ORF3a protein in mammalian cells. Heliyon 2023; 9:e18754. [PMID: 37609425 PMCID: PMC10440475 DOI: 10.1016/j.heliyon.2023.e18754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/24/2023] Open
Abstract
The accessory protein ORF3a, from SARS-CoV-2, plays a critical role in viral infection and pathogenesis. Here, we characterized ORF3a assembly, ion channel activity, subcellular localization, and interactome. At the plasma membrane, ORF3a exists mostly as monomers and dimers, which do not alter the native cell membrane conductance, suggesting that ORF3a does not function as a viroporin at the cell surface. As a membrane protein, ORF3a is synthesized at the ER and sorted via a canonical route. ORF3a overexpression induced an approximately 25% increase in cell death. By developing an APEX2-based proximity labeling assay, we uncovered proteins proximal to ORF3a, suggesting that ORF3a recruits some host proteins to weaken the cell. In addition, it exposed a set of mitochondria related proteins that triggered mitochondrial fission. Overall, this work can be an important instrument in understanding the role of ORF3a in the virus pathogenicity and searching for potential therapeutic treatments for COVID-19.
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Affiliation(s)
- Song Jiao
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Pablo Miranda
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Miguel Holmgren
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
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10
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Qu Y, Wang W, Xiao MZX, Zheng Y, Liang Q. The interplay between lipid droplets and virus infection. J Med Virol 2023; 95:e28967. [PMID: 37496184 DOI: 10.1002/jmv.28967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023]
Abstract
As an intracellular parasite, the virus usurps cellular machinery and modulates cellular metabolism pathways to replicate itself in cells. Lipid droplets (LDs) are universally conserved energy storage organelles that not only play vital roles in maintaining lipid homeostasis but are also involved in viral replication. Increasing evidence has demonstrated that viruses take advantage of cellular lipid metabolism by targeting the biogenesis, hydrolysis, and lipophagy of LD during viral infection. In this review, we summarize the current knowledge about the modulation of cellular LD by different viruses, with a special emphasis on the Hepatitis C virus, Dengue virus, and SARS-CoV-2.
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Affiliation(s)
- Yafei Qu
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weili Wang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Maggie Z X Xiao
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yuejuan Zheng
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai University of Traditional Medicine, Shanghai, China
- Center for Traditional Chinese Medicine and Immunology Research, School of Basic Medical Sciences, Shanghai University of Traditional Medicine, Shanghai, China
| | - Qiming Liang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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11
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Shariq M, Malik AA, Sheikh JA, Hasnain SE, Ehtesham NZ. Regulation of autophagy by SARS-CoV-2: The multifunctional contributions of ORF3a. J Med Virol 2023; 95:e28959. [PMID: 37485696 DOI: 10.1002/jmv.28959] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/01/2023] [Accepted: 07/04/2023] [Indexed: 07/25/2023]
Abstract
Severe acute respiratory syndrome-coronavirus-1 (SARS-CoV-2) regulates autophagic flux by blocking the fusion of autophagosomes with lysosomes, causing the accumulation of membranous vesicles for replication. Multiple SARS-CoV-2 proteins regulate autophagy with significant roles attributed to ORF3a. Mechanistically, open reading frame 3a (ORF3a) forms a complex with UV radiation resistance associated, regulating the functions of the PIK3C3-1 and PIK3C3-2 lipid kinase complexes, thereby modulating autophagosome biogenesis. ORF3a sequesters VPS39 onto the late endosome/lysosome, inhibiting assembly of the soluble NSF attachement protein REceptor (SNARE) complex and preventing autolysosome formation. ORF3a promotes the interaction between BECN1 and HMGB1, inducing the assembly of PIK3CA kinases into the ER (endoplasmic reticulum) and activating reticulophagy, proinflammatory responses, and ER stress. ORF3a recruits BORCS6 and ARL8B to lysosomes, initiating the anterograde transport of the virus to the plasma membrane. ORF3a also activates the SNARE complex (STX4-SNAP23-VAMP7), inducing fusion of lysosomes with the plasma membrane for viral egress. These mechanistic details can provide multiple targets for inhibiting SARS-CoV-2 by developing host- or host-pathogen interface-based therapeutics.
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Affiliation(s)
- Mohd Shariq
- Inflammation Biology and Cell Signalling Laboratory, ICMR-National Institute of Pathology, New Delhi, India
| | - Asrar A Malik
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Javaid A Sheikh
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi, India
| | - Seyed E Hasnain
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Nasreen Z Ehtesham
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
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12
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Kanamori A, Hinaga S, Hirata Y, Amaya F, Oh-Hashi K. Molecular characterization of wild-type and HSAN2B-linked FAM134B. Mol Biol Rep 2023:10.1007/s11033-023-08517-y. [PMID: 37273064 DOI: 10.1007/s11033-023-08517-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/11/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Family with sequence similarity 134, member B (FAM134B), also known as Reticulophagy regulator 1 (RETREG1), is an ER-phagy receptor involved in ER homeostasis. Congenital mutations in the FAM134B gene have been reported to be associated with hereditary sensory and autonomic neuropathy type 2B (HSAN2B); however, the molecular differences between wild-type and HSAN2B-linked FAM134B are not fully understood. METHODS AND RESULTS We prepared several human FAM134B constructs, such as the HSAN2B-linked mutant, and compared their features with those of wild-type FAM134B by transfecting these constructs into FAM134B-deficient Neuro2a cells. Although intrinsic FAM134B protein expression in wild-type Neuro2a cells was affected by the supply of amino acids in the culture medium, the expression of each HSAN2B-linked mutant FAM134B protein was hardly affected by serum and amino acid deprivation. On the other hand, the intracellular localization of GFP-tagged HSAN2B-linked mutants, except for P7Gfs133X, overlapped well with ER-localized SP-RFPKDEL and did not differ from that of GFP-tagged wild-type FAM134B. However, analysis of protein‒protein interactions using the NanoBiT reporter assay revealed the difference between wild-type and C-terminal truncated mutant FAM134B. Furthermore, this NanoBiT assay demonstrated that both wild-type and G216R FAM134B interacted with LC3/GABARAPL1 to the same extent, but the FAM134B construct with mutations near the LC3-interacting region (LIR) did not. Similar to the NanoBiT assay, the C-terminal-truncated FAM134B showed lower ER-phagy activities, as assessed by the cotransfection of GFP-tagged reporters. CONCLUSIONS We showed that wild-type and HSAN2B-linked FAM134B have different molecular characteristics by transfecting cells with various types of constructs. Thus, this study provides new insights into the molecular mechanisms underlying HSAN2B as well as the regulation of ER-phagy.
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Affiliation(s)
- Akane Kanamori
- Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Shohei Hinaga
- Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Yoko Hirata
- Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Fumimasa Amaya
- Department of Pain Management and Palliative Care Medicine, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamikyo-Ku, Kyoto, 602-0841, Japan
| | - Kentaro Oh-Hashi
- Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
- Center for One Medicine Innovative Translational Research (COMIT), Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
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13
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Bhowal C, Ghosh S, Ghatak D, De R. Pathophysiological involvement of host mitochondria in SARS-CoV-2 infection that causes COVID-19: a comprehensive evidential insight. Mol Cell Biochem 2023; 478:1325-1343. [PMID: 36308668 PMCID: PMC9617539 DOI: 10.1007/s11010-022-04593-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/13/2022] [Indexed: 10/31/2022]
Abstract
SARS-CoV-2 is a positive-strand RNA virus that infects humans through the nasopharyngeal and oral route causing COVID-19. Scientists left no stone unturned to explore a targetable key player in COVID-19 pathogenesis against which therapeutic interventions can be initiated. This article has attempted to review, coordinate and accumulate the most recent observations in support of the hypothesis predicting the altered state of mitochondria concerning mitochondrial redox homeostasis, inflammatory regulations, morphology, bioenergetics and antiviral signalling in SARS-CoV-2 infection. Mitochondria is extremely susceptible to physiological as well as pathological stimuli, including viral infections. Recent studies suggest that SARS-CoV-2 pathogeneses alter mitochondrial integrity, in turn mitochondria modulate cellular response against the infection. SARS-CoV-2 M protein inhibited mitochondrial antiviral signalling (MAVS) protein aggregation in turn hinders innate antiviral response. Viral open reading frames (ORFs) also play an instrumental role in altering mitochondrial regulation of immune response. Notably, ORF-9b and ORF-6 impair MAVS activation. In aged persons, the NLRP3 inflammasome is over-activated due to impaired mitochondrial function, increased mitochondrial reactive oxygen species (mtROS), and/or circulating free mitochondrial DNA, resulting in a hyper-response of classically activated macrophages. This article also tries to understand how mitochondrial fission-fusion dynamics is affected by the virus. This review comprehends the overall mitochondrial attribute in pathogenesis as well as prognosis in patients infected with COVID-19 taking into account pertinent in vitro, pre-clinical and clinical data encompassing subjects with a broad range of severity and morbidity. This endeavour may help in exploring novel non-canonical therapeutic strategies to COVID-19 disease and associated complications.
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Affiliation(s)
- Chandan Bhowal
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Sayak Ghosh
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Debapriya Ghatak
- Indian Association for the Cultivation of Science, Jadavpur, 700032, Kolkata, India
| | - Rudranil De
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India.
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14
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Godbold GD, Hewitt FC, Kappell AD, Scholz MB, Agar SL, Treangen TJ, Ternus KL, Sandbrink JB, Koblentz GD. Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern. Front Bioeng Biotechnol 2023; 11:1124100. [PMID: 37180048 PMCID: PMC10167326 DOI: 10.3389/fbioe.2023.1124100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
Regulation of research on microbes that cause disease in humans has historically been focused on taxonomic lists of 'bad bugs'. However, given our increased knowledge of these pathogens through inexpensive genome sequencing, 5 decades of research in microbial pathogenesis, and the burgeoning capacity of synthetic biologists, the limitations of this approach are apparent. With heightened scientific and public attention focused on biosafety and biosecurity, and an ongoing review by US authorities of dual-use research oversight, this article proposes the incorporation of sequences of concern (SoCs) into the biorisk management regime governing genetic engineering of pathogens. SoCs enable pathogenesis in all microbes infecting hosts that are 'of concern' to human civilization. Here we review the functions of SoCs (FunSoCs) and discuss how they might bring clarity to potentially problematic research outcomes involving infectious agents. We believe that annotation of SoCs with FunSoCs has the potential to improve the likelihood that dual use research of concern is recognized by both scientists and regulators before it occurs.
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Affiliation(s)
| | | | | | | | - Stacy L. Agar
- Signature Science, LLC, Charlottesville, VA, United States
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, United States
| | | | - Jonas B. Sandbrink
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gregory D. Koblentz
- Schar School of Policy and Government, George Mason University, Arlington, VA, United States
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15
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Nie Y, Mou L, Long Q, Deng D, Hu R, Cheng J, Wu J. SARS-CoV-2 ORF3a positively regulates NF-κB activity by enhancing IKKβ-NEMO interaction. Virus Res 2023; 328:199086. [PMID: 36894068 PMCID: PMC10009424 DOI: 10.1016/j.virusres.2023.199086] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a global pandemic caused by SARS-CoV-2 infection. Patients with severe COVID-19 exhibit robust induction of proinflammatory cytokines, which are closely associated with the development of acute respiratory distress syndrome. However, the underlying mechanisms of the NF-κB activation mediated by SARS-CoV-2 infection remain poorly understood. Here, we screened SARS-CoV-2 genes and found that ORF3a induces proinflammatory cytokines by activating the NF-κB pathway. Moreover, we found that ORF3a interacts with IKKβ and NEMO and enhances the interaction of IKKβ-NEMO, thereby positively regulating NF-κB activity. Together, these results suggest ORF3a may play pivotal roles in the pathogenesis of SARS-CoV-2 and provide novel insights into the interaction between host immune responses and SARS-CoV-2 infection.
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Affiliation(s)
- Ying Nie
- Department of Parasitology, Provincial Key Laboratory of Modern Pathogen Biology, College of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, China; These authors contributed equally: Ying Nie, Lumin Mou
| | - Lumin Mou
- Department of Parasitology, Provincial Key Laboratory of Modern Pathogen Biology, College of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, China; Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, China; These authors contributed equally: Ying Nie, Lumin Mou
| | - Qizhou Long
- Department of Parasitology, Provincial Key Laboratory of Modern Pathogen Biology, College of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, China
| | - Dongqing Deng
- Department of Parasitology, Provincial Key Laboratory of Modern Pathogen Biology, College of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, China
| | - Rongying Hu
- The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Jinzhi Cheng
- Department of Parasitology, Provincial Key Laboratory of Modern Pathogen Biology, College of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, China
| | - Jiahong Wu
- Department of Parasitology, Provincial Key Laboratory of Modern Pathogen Biology, College of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, China; Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, China.
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16
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Han K, Huang S, Kong J, Yang Y, Shi L, Ci Y. A novel fluorescent endoplasmic reticulum marker for super-resolution imaging in live cells. FEBS Lett 2023; 597:693-701. [PMID: 36694281 DOI: 10.1002/1873-3468.14581] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/26/2023]
Abstract
Endoplasmic reticulum (ER) is a highly complicated and dynamic organelle that actively changes its shape and communicates with other organelles. Visualization of ER in live cells is of great importance to understand cellular activities. Here, we designed a novel ER marker, RR-mNeonGreen, which comprised an N-terminal ER retention signal, a bright fluorescent protein (mNeonGreen), and a C-terminal transmembrane region. Colocalization of RR-mNeonGreen with mCherry-KDEL verified that RR-mNeonGreen perfectly labeled the ER. RR-mNeonGreen showed better continuity of ER tubules when imaged by super-resolution microscopy. Moreover, RR-mNeonGreen is competent for live-cell imaging of ER dynamics and tracing of the interaction between ER and mitochondria at high spatiotemporal resolution. In summary, RR-mNeonGreen is a novel ER marker for super-resolution live-cell imaging with multiple merits.
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Affiliation(s)
- Kai Han
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Shuhan Huang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Jie Kong
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yang Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Lei Shi
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yali Ci
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
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17
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Wang W, Qu Y, Wang X, Xiao MZX, Fu J, Chen L, Zheng Y, Liang Q. Genetic variety of ORF3a shapes SARS-CoV-2 fitness through modulation of lipid droplet. J Med Virol 2023; 95:e28630. [PMID: 36861654 DOI: 10.1002/jmv.28630] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection leads to the accumulation of lipid droplets (LD), the central hubs of the lipid metabolism, in vitro or in type II pneumocytes and monocytes from coronavirus disease 19 (COVID-19) patients and blockage of LD formation by specific inhibitors impedes SARS-CoV-2 replication. Here, we showed that ORF3a is necessary and sufficient to trigger LD accumulation during SARS-CoV-2 infection, leading to efficient virus replication. Although highly mutated during evolution, ORF3a-mediated LD modulation is conserved in most SARS-CoV-2 variants except the Beta strain and is a major difference between SARS-CoV and SARS-CoV-2 that depends on the genetic variations on the amino acid position 171, 193, and 219 of ORF3a. Importantly, T223I substitution in recent Omicron strains (BA.2-BF.8) impairs ORF3a-Vps39 association and LD accumulation, leading to less efficient replication and potentially contributing to lower pathogenesis of the Omicron strains. Our work characterized how SARS-CoV-2 modulates cellular lipid homeostasis to benefit its replication during virus evolution, making ORF3a-LD axis a promising drug target for the treatment of COVID-19.
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Affiliation(s)
- Weili Wang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yafei Qu
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xin Wang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Maggie Z X Xiao
- Faculty of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Joyce Fu
- Department of Statistics, University of California, Riverside, Riverside, California, USA
| | - Lei Chen
- Shanghai Institute of Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuejuan Zheng
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai University of Traditional Medicine, Shanghai, China
- Center for Traditional Chinese Medicine and Immunology Research, School of Basic Medical Sciences, Shanghai University of Traditional Medicine, Shanghai, China
| | - Qiming Liang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Padilla-Blanco M, Gucciardi F, Rubio V, Lastra A, Lorenzo T, Ballester B, González-Pastor A, Veses V, Macaluso G, Sheth CC, Pascual-Ortiz M, Maiques E, Rubio-Guerri C, Purpari G, Guercio A. A SARS-CoV-2 full genome sequence of the B.1.1 lineage sheds light on viral evolution in Sicily in late 2020. Front Public Health 2023; 11:1098965. [PMID: 36778569 PMCID: PMC9909176 DOI: 10.3389/fpubh.2023.1098965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/06/2023] [Indexed: 01/27/2023] Open
Abstract
To investigate the influence of geographic constrains to mobility on SARS-CoV-2 circulation before the advent of vaccination, we recently characterized the occurrence in Sicily of viral lineages in the second pandemic wave (September to December 2020). Our data revealed wide prevalence of the then widespread through Europe B.1.177 variant, although some viral samples could not be classified with the limited Sanger sequencing tools used. A particularly interesting sample could not be fitted to a major variant then circulating in Europe and has been subjected here to full genome sequencing in an attempt to clarify its origin, lineage and relations with the seven full genome sequences deposited for that period in Sicily, hoping to provide clues on viral evolution. The obtained genome is unique (not present in databases). It hosts 20 single-base substitutions relative to the original Wuhan-Hu-1 sequence, 8 of them synonymous and the other 12 encoding 11 amino acid substitutions, all of them already reported one by one. They include four highly prevalent substitutions, NSP12:P323L, S:D614G, and N:R203K/G204R; the much less prevalent S:G181V, ORF3a:G49V and N:R209I changes; and the very rare mutations NSP3:L761I, NSP6:S106F, NSP8:S41F and NSP14:Y447H. GISAID labeled this genome as B.1.1 lineage, a lineage that appeared early on in the pandemic. Phylogenetic analysis also confirmed this lineage diagnosis. Comparison with the seven genome sequences deposited in late 2020 from Sicily revealed branching leading to B.1.177 in one branch and to Alpha in the other branch, and suggested a local origin for the S:G118V mutation.
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Affiliation(s)
- Miguel Padilla-Blanco
- Departamento de Farmacia, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU (UCH-CEU), CEU Universities, Valencia, Spain
| | - Francesca Gucciardi
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy
| | - Vicente Rubio
- Department of Genomics and Proteomics, Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas (IBV-CSIC) and Centre for Biomedical Network Research on Rare Diseases of the Instituto de Salud Carlos III (CIBERER-ISCIII), CEU Universities, Valencia, Spain
| | - Antonio Lastra
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy
| | - Teresa Lorenzo
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Beatriz Ballester
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Andrea González-Pastor
- Departamento de Medicina, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Veronica Veses
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Giusi Macaluso
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy
| | - Chirag C. Sheth
- Departamento de Medicina, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Marina Pascual-Ortiz
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Elisa Maiques
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain,*Correspondence: Elisa Maiques ✉
| | - Consuelo Rubio-Guerri
- Departamento de Farmacia, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU (UCH-CEU), CEU Universities, Valencia, Spain,Consuelo Rubio-Guerri ✉
| | - Giuseppa Purpari
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy,Giuseppa Purpari ✉
| | - Annalisa Guercio
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy
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19
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Hurtado-Tamayo J, Requena-Platek R, Enjuanes L, Bello-Perez M, Sola I. Contribution to pathogenesis of accessory proteins of deadly human coronaviruses. Front Cell Infect Microbiol 2023; 13:1166839. [PMID: 37197199 PMCID: PMC10183600 DOI: 10.3389/fcimb.2023.1166839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/11/2023] [Indexed: 05/19/2023] Open
Abstract
Coronaviruses (CoVs) are enveloped and positive-stranded RNA viruses with a large genome (∼ 30kb). CoVs include essential genes, such as the replicase and four genes coding for structural proteins (S, M, N and E), and genes encoding accessory proteins, which are variable in number, sequence and function among different CoVs. Accessory proteins are non-essential for virus replication, but are frequently involved in virus-host interactions associated with virulence. The scientific literature on CoV accessory proteins includes information analyzing the effect of deleting or mutating accessory genes in the context of viral infection, which requires the engineering of CoV genomes using reverse genetics systems. However, a considerable number of publications analyze gene function by overexpressing the protein in the absence of other viral proteins. This ectopic expression provides relevant information, although does not acknowledge the complex interplay of proteins during virus infection. A critical review of the literature may be helpful to interpret apparent discrepancies in the conclusions obtained by different experimental approaches. This review summarizes the current knowledge on human CoV accessory proteins, with an emphasis on their contribution to virus-host interactions and pathogenesis. This knowledge may help the search for antiviral drugs and vaccine development, still needed for some highly pathogenic human CoVs.
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Affiliation(s)
| | | | | | | | - Isabel Sola
- *Correspondence: Melissa Bello-Perez, ; Isabel Sola,
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20
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Pant A, Yao X, Lavedrine A, Viret C, Dockterman J, Chauhan S, Chong-Shan Shi, Manjithaya R, Cadwell K, Kufer TA, Kehrl JH, Coers J, Sibley LD, Faure M, Taylor GA, Chauhan S. Interactions of Autophagy and the Immune System in Health and Diseases. AUTOPHAGY REPORTS 2022; 1:438-515. [PMID: 37425656 PMCID: PMC10327624 DOI: 10.1080/27694127.2022.2119743] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Autophagy is a highly conserved process that utilizes lysosomes to selectively degrade a variety of intracellular cargo, thus providing quality control over cellular components and maintaining cellular regulatory functions. Autophagy is triggered by multiple stimuli ranging from nutrient starvation to microbial infection. Autophagy extensively shapes and modulates the inflammatory response, the concerted action of immune cells, and secreted mediators aimed to eradicate a microbial infection or to heal sterile tissue damage. Here, we first review how autophagy affects innate immune signaling, cell-autonomous immune defense, and adaptive immunity. Then, we discuss the role of non-canonical autophagy in microbial infections and inflammation. Finally, we review how crosstalk between autophagy and inflammation influences infectious, metabolic, and autoimmune disorders.
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Affiliation(s)
- Aarti Pant
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Xiaomin Yao
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, New York, United States of America
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Aude Lavedrine
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Equipe Labellisée par la Fondation pour la Recherche Médicale, FRM
| | - Christophe Viret
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Equipe Labellisée par la Fondation pour la Recherche Médicale, FRM
| | - Jake Dockterman
- Department of Immunology, Duke University, Medical Center, Durham, North Carolina, USA
| | - Swati Chauhan
- Cell biology and Infectious diseases, Institute of Life Sciences, Bhubaneswar, India
| | - Chong-Shan Shi
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Ravi Manjithaya
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, New York, United States of America
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
- Division of Gastroenterology and Hepatology, Department of Medicine, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Thomas A. Kufer
- Department of Immunology, Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - John H. Kehrl
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jörn Coers
- Department of Immunology, Duke University, Medical Center, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University, Medical Center, Durham, North Carolina, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University Sch. Med., St Louis, MO, 63110, USA
| | - Mathias Faure
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Equipe Labellisée par la Fondation pour la Recherche Médicale, FRM
| | - Gregory A Taylor
- Department of Immunology, Duke University, Medical Center, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University, Medical Center, Durham, North Carolina, USA
- Department of Molecular Microbiology, Washington University Sch. Med., St Louis, MO, 63110, USA
- Geriatric Research, Education, and Clinical Center, VA Health Care Center, Durham, North Carolina, USA
- Departments of Medicine, Division of Geriatrics, and Center for the Study of Aging and Human Development, Duke University, Medical Center, Durham, North Carolina, USA
| | - Santosh Chauhan
- Cell biology and Infectious diseases, Institute of Life Sciences, Bhubaneswar, India
- CSIR–Centre For Cellular And Molecular Biology (CCMB), Hyderabad, Telangana
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Tang L, Song Y, Xu J, Chu Y. The role of selective autophagy in pathogen infection. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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Liu J, Chen Y, Nie L, Liang X, Huang W, Li R. In silico analysis and preclinical findings uncover potential targets of anti-cervical carcinoma and COVID-19 in laminarin, a promising nutraceutical. Front Pharmacol 2022; 13:955482. [PMID: 36016559 PMCID: PMC9395986 DOI: 10.3389/fphar.2022.955482] [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: 05/30/2022] [Accepted: 07/04/2022] [Indexed: 12/03/2022] Open
Abstract
Until today, the coronavirus disease 2019 (COVID-19) pandemic has caused 6,043,094 deaths worldwide, and most of the mortality cases have been related to patients with long-term diseases, especially cancer. Autophagy is a cellular process for material degradation. Recently, studies demonstrated the association of autophagy with cancer development and immune disorder, suggesting autophagy as a possible target for cancer and immune therapy. Laminarin is a polysaccharide commonly found in brown algae and has been reported to have pharmaceutic roles in treating human diseases, including cancers. In the present report, we applied network pharmacology with systematic bioinformatic analysis, including gene ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, reactome pathway analysis, and molecular docking to determine the pharmaceutic targets of laminarin against COVID-19 and cervical cancer via the autophagic process. Our results showed that the laminarin would target ten genes: CASP8, CFTR, DNMT1, HPSE, KCNH2, PIK3CA, PIK3R1, SERPINE1, TLR4, and VEGFA. The enrichment analysis suggested their involvement in cell death, immune responses, apoptosis, and viral infection. In addition, molecular docking further demonstrated the direct binding of laminarin to its target proteins, VEGFA, TLR4, CASP8, and PIK3R1. The present findings provide evidence that laminarin could be used as a combined therapy for treating patients with COVID-19 and cervical cancer.
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Affiliation(s)
- Jiaqi Liu
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin, China
| | - Yudong Chen
- Department of Gynecology, Guigang City People’s Hospital, The Eighth Affiliated Hospital of Guangxi Medical University, Guigang, China
| | - Litao Nie
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin, China
| | - Xiao Liang
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin, China
| | - Wenjun Huang
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin, China
- *Correspondence: Wenjun Huang, ; Rong Li,
| | - Rong Li
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin, China
- Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, China
- *Correspondence: Wenjun Huang, ; Rong Li,
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23
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Li X, Kuang E. Reticulophagy Reprograms the Endoplasmic Reticulum for SARS-CoV-2 Replication. Front Cell Dev Biol 2022; 10:896618. [PMID: 35573668 PMCID: PMC9097150 DOI: 10.3389/fcell.2022.896618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Xiaojuan Li
- College of Clinic Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Ersheng Kuang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, China
- *Correspondence: Ersheng Kuang,
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