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Wang T, Cao Y, Zhang H, Wang Z, Man CH, Yang Y, Chen L, Xu S, Yan X, Zheng Q, Wang YP. COVID-19 metabolism: Mechanisms and therapeutic targets. MedComm (Beijing) 2022; 3:e157. [PMID: 35958432 PMCID: PMC9363584 DOI: 10.1002/mco2.157] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 01/18/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) dysregulates antiviral signaling, immune response, and cell metabolism in human body. Viral genome and proteins hijack host metabolic network to support viral biogenesis and propagation. However, the regulatory mechanism of SARS‐CoV‐2‐induced metabolic dysfunction has not been elucidated until recently. Multiomic studies of coronavirus disease 2019 (COVID‐19) revealed an intensive interaction between host metabolic regulators and viral proteins. SARS‐CoV‐2 deregulated cellular metabolism in blood, intestine, liver, pancreas, fat, and immune cells. Host metabolism supported almost every stage of viral lifecycle. Strikingly, viral proteins were found to interact with metabolic enzymes in different cellular compartments. Biochemical and genetic assays also identified key regulatory nodes and metabolic dependencies of viral replication. Of note, cholesterol metabolism, lipid metabolism, and glucose metabolism are broadly involved in viral lifecycle. Here, we summarized the current understanding of the hallmarks of COVID‐19 metabolism. SARS‐CoV‐2 infection remodels host cell metabolism, which in turn modulates viral biogenesis and replication. Remodeling of host metabolism creates metabolic vulnerability of SARS‐CoV‐2 replication, which could be explored to uncover new therapeutic targets. The efficacy of metabolic inhibitors against COVID‐19 is under investigation in several clinical trials. Ultimately, the knowledge of SARS‐CoV‐2‐induced metabolic reprogramming would accelerate drug repurposing or screening to combat the COVID‐19 pandemic.
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Affiliation(s)
- Tianshi Wang
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation Department of Biochemistry and Molecular Cell Biology Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Ying Cao
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Haiyan Zhang
- Bai Jia Obstetrics and Gynecology Hospital Shanghai China
| | - Zihao Wang
- Fudan University Shanghai Cancer Center Key Laboratory of Breast Cancer in Shanghai Shanghai Key Laboratory of Radiation Oncology Cancer Institute and The Shanghai Key Laboratory of Medical Epigenetics Institutes of Biomedical Sciences Shanghai Medical College Fudan University Shanghai China.,Department of Oncology Shanghai Medical College Fudan University Shanghai China.,The International Co-laboratory of Medical Epigenetics and Metabolism Ministry of Science and Technology Shanghai China
| | - Cheuk Him Man
- Division of Hematology Department of Medicine University of Hong Kong Pokfulam Hong Kong, China
| | - Yunfan Yang
- Department of Cell Biology School of Basic Medical Sciences Cheeloo College of Medicine Shandong University Jinan China
| | - Lingchao Chen
- Department of Neurosurgery Huashan Hospital Shanghai Medical College Fudan University National Center for Neurological Disorders Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration Neurosurgical Institute of Fudan University Shanghai Clinical Medical Center of Neurosurgery Shanghai China
| | - Shuangnian Xu
- Department of Hematology Southwest Hospital Army Medical University Chongqing China
| | - Xiaojing Yan
- Department of Hematology The First Affiliated Hospital of China Medical University Shenyang China
| | - Quan Zheng
- Center for Single-Cell Omics School of Public Health Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Yi-Ping Wang
- Fudan University Shanghai Cancer Center Key Laboratory of Breast Cancer in Shanghai Shanghai Key Laboratory of Radiation Oncology Cancer Institute and The Shanghai Key Laboratory of Medical Epigenetics Institutes of Biomedical Sciences Shanghai Medical College Fudan University Shanghai China.,Department of Oncology Shanghai Medical College Fudan University Shanghai China.,The International Co-laboratory of Medical Epigenetics and Metabolism Ministry of Science and Technology Shanghai China
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52
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Aliper ET, Krylov NA, Nolde DE, Polyansky AA, Efremov RG. A Uniquely Stable Trimeric Model of SARS-CoV-2 Spike Transmembrane Domain. Int J Mol Sci 2022; 23:ijms23169221. [PMID: 36012488 PMCID: PMC9409440 DOI: 10.3390/ijms23169221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Understanding fusion mechanisms employed by SARS-CoV-2 spike protein entails realistic transmembrane domain (TMD) models, while no reliable approaches towards predicting the 3D structure of transmembrane (TM) trimers exist. Here, we propose a comprehensive computational framework to model the spike TMD only based on its primary structure. We performed amino acid sequence pattern matching and compared the molecular hydrophobicity potential (MHP) distribution on the helix surface against TM homotrimers with known 3D structures and selected an appropriate template for homology modeling. We then iteratively built a model of spike TMD, adjusting “dynamic MHP portraits” and residue variability motifs. The stability of this model, with and without palmitoyl modifications downstream of the TMD, and several alternative configurations (including a recent NMR structure), was tested in all-atom molecular dynamics simulations in a POPC bilayer mimicking the viral envelope. Our model demonstrated unique stability under the conditions applied and conforms to known basic principles of TM helix packing. The original computational framework looks promising and could potentially be employed in the construction of 3D models of TM trimers for a wide range of membrane proteins.
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Affiliation(s)
- Elena T. Aliper
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
| | - Nikolay A. Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Dmitry E. Nolde
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Anton A. Polyansky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna BioCenter 5, A-1030 Vienna, Austria
| | - Roman G. Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 101000 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- Correspondence:
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53
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The Acid Ceramidase Is a SARS-CoV-2 Host Factor. Cells 2022; 11:cells11162532. [PMID: 36010608 PMCID: PMC9406565 DOI: 10.3390/cells11162532] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2 variants such as the delta or omicron variants, with higher transmission rates, accelerated the global COVID-19 pandemic. Thus, novel therapeutic strategies need to be deployed. The inhibition of acid sphingomyelinase (ASM), interfering with viral entry by fluoxetine was reported. Here, we described the acid ceramidase as an additional target of fluoxetine. To discover these effects, we synthesized an ASM-independent fluoxetine derivative, AKS466. High-resolution SARS-CoV-2–RNA FISH and RTqPCR analyses demonstrate that AKS466 down-regulates viral gene expression. It is shown that SARS-CoV-2 deacidifies the lysosomal pH using the ORF3 protein. However, treatment with AKS488 or fluoxetine lowers the lysosomal pH. Our biochemical results show that AKS466 localizes to the endo-lysosomal replication compartments of infected cells, and demonstrate the enrichment of the viral genomic, minus-stranded RNA and mRNAs there. Both fluoxetine and AKS466 inhibit the acid ceramidase activity, cause endo-lysosomal ceramide elevation, and interfere with viral replication. Furthermore, Ceranib-2, a specific acid ceramidase inhibitor, reduces SARS-CoV-2 replication and, most importantly, the exogenous supplementation of C6-ceramide interferes with viral replication. These results support the hypotheses that the acid ceramidase is a SARS-CoV-2 host factor.
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54
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Odendall C, Sa Pessoa J, Mesquita FS. Meeting report - Cell dynamics: host-pathogen interface. J Cell Sci 2022; 135:276364. [PMID: 35979931 DOI: 10.1242/jcs.260456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two years into the most significant infectious disease event of our generation, infections have populated every conversation and in-depth understanding of host-pathogen interactions has, perhaps, never been more important. In a successful return to in-person conferences, the host-pathogen interface was the focus of the third Cell Dynamics meeting, which took place at the glorious Wotton House in Surrey, UK. The meeting organised by Michaela Gack, Maximiliano Gutierrez, Dominique Soldati-Favre and Michael Way gathered an international group of scientists who shared their recent discoveries and views on numerous aspects, including cell-autonomous defence mechanisms, pathogen interactions with host cytoskeletal or membrane dynamics, and cellular immune regulation. More than 30 years into the beginning of cellular microbiology as a field, the meeting exhibited the unique aspect of the host-pathogen interface in uncovering the fundamentals of both pathogens and their hosts.
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Affiliation(s)
- Charlotte Odendall
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, SE1 9RT London, UK
| | - Joana Sa Pessoa
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL Belfast, UK
| | - Francisco S Mesquita
- Global Health Institute, School of Life Sciences, EPFL, CH-1015 Lausanne, Switzerland
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55
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Transcriptome Analysis Revealed Inhibition of Lipid Metabolism in 2-D Porcine Enteroids by Infection with Porcine Epidemic Diarrhea Virus. Vet Microbiol 2022; 273:109525. [DOI: 10.1016/j.vetmic.2022.109525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 07/20/2022] [Accepted: 07/31/2022] [Indexed: 11/16/2022]
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56
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Brucato N, André M, Hudjashov G, Mondal M, Cox MP, Leavesley M, Ricaut FX. Chronology of natural selection in Oceanian genomes. iScience 2022; 25:104583. [PMID: 35880026 PMCID: PMC9308150 DOI: 10.1016/j.isci.2022.104583] [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: 03/15/2022] [Revised: 05/11/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
As human populations left Asia to first settle in Oceania around 50,000 years ago, they entered a territory ecologically separated from the Old World for millions of years. We analyzed genomic data of 239 modern Oceanian individuals to detect and date signals of selection specific to this region. Combining both relative and absolute dating approaches, we identified a strong selection pattern between 52,000 and 54,000 years ago in the genomes of descendants of the first settlers of Sahul. This strikingly corresponds to the dates of initial settlement as inferred from archaeological evidence. Loci under selection during this period, some showing enrichment in Denisovan ancestry, overlap genes involved in the immune response and diet, especially based on plants. Pathogens and natural resources, especially from endemic plants, therefore appear to have acted as strong selective pressures on the genomes of the first settlers of Sahul. 239 human genomes from both sides of the Wallacean ecogeographical barriers Signals of selection are dated between -54,000 to -52,000 in modern Oceanian genomes Genes related to immunity and diet were under strong selection Denisovan introgressions participated to the genetic adaptations present in Oceanians
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Affiliation(s)
- Nicolas Brucato
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France
| | - Mathilde André
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France.,Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Georgi Hudjashov
- Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Mayukh Mondal
- Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, National Capital District 134, Papua New Guinea.,College of Arts, Society and Education, James Cook University, P.O. Box 6811, Cairns, QLD 4870, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW 2522, Australia
| | - François-Xavier Ricaut
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France
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57
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Tien CF, Tsai WT, Chen CH, Chou HJ, Zhang MM, Lin JJ, Lin EJ, Dai SS, Ping YH, Yu CY, Kuo YP, Tsai WH, Chen HW, Yu GY. Glycosylation and S-palmitoylation regulate SARS-CoV-2 spike protein intracellular trafficking. iScience 2022; 25:104709. [PMID: 35813875 PMCID: PMC9250814 DOI: 10.1016/j.isci.2022.104709] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/19/2022] [Accepted: 06/28/2022] [Indexed: 11/03/2022] Open
Abstract
Post-translational modifications (PTMs), such as glycosylation and palmitoylation, are critical to protein folding, stability, intracellular trafficking, and function. Understanding regulation of PTMs of SARS-CoV-2 spike (S) protein could help the therapeutic drug design. Herein, the VSV vector was used to produce SARS-CoV-2 S pseudoviruses to examine the roles of the 611LYQD614 and cysteine-rich motifs in S protein maturation and virus infectivity. Our results show that 611LY612 mutation alters S protein intracellular trafficking and reduces cell surface expression level. It also changes S protein glycosylation pattern and decreases pseudovirus infectivity. The S protein contains four cysteine-rich clusters with clusters I and II as the main palmitoylation sites. Mutations of clusters I and II disrupt S protein trafficking from ER-to-Golgi, suppress pseudovirus production, and reduce spike-mediated membrane fusion activity. Taken together, glycosylation and palmitoylation orchestrate the S protein maturation processing and are critical for S protein-mediated membrane fusion and infection. 611LY612 mutation alters the glycosylation pattern of the SARS-CoV-2 S protein 611LY612 mutation reduces S protein surface expression level Palmitoylation targets mature S protein to the Golgi and plasma membrane Palmitoylation is required for pseudovirus and SARS-CoV-2 production
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58
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Mekhail K, Lee M, Sugiyama M, Astori A, St-Germain J, Latreille E, Khosraviani N, Wei K, Li Z, Rini J, Lee WL, Antonescu C, Raught B, Fairn GD. Fatty Acid Synthase inhibitor TVB-3166 prevents S-acylation of the Spike protein of human coronaviruses. J Lipid Res 2022; 63:100256. [PMID: 35921881 PMCID: PMC9339154 DOI: 10.1016/j.jlr.2022.100256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/24/2022] Open
Abstract
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other coronaviruses mediates host cell entry and is S-acylated on multiple phylogenetically conserved cysteine residues. Multiple protein acyltransferase enzymes have been reported to post-translationally modify spike proteins; however, strategies to exploit this modification are lacking. Using resin-assisted capture MS, we demonstrate that the spike protein is S-acylated in SARS-CoV-2-infected human and monkey epithelial cells. We further show that increased abundance of the acyltransferase ZDHHC5 associates with increased S-acylation of the spike protein, whereas ZDHHC5 knockout cells had a 40% reduction in the incorporation of an alkynyl-palmitate using click chemistry detection. We also found that the S-acylation of the spike protein is not limited to palmitate, as clickable versions of myristate and stearate were also labelled the protein. Yet, we observed that ZDHHC5 was only modified when incubated with alkyne-palmitate, suggesting it has specificity for this acyl-CoA, and that other ZDHHC enzymes may use additional fatty acids to modify the spike protein. Since multiple ZDHHC isoforms may modify the spike protein, we also examined the ability of the FASN inhibitor TVB-3166 to prevent S-acylation of the spike proteins of SARS-CoV-2 and human CoV-229E. We show that treating cells with TVB-3166 inhibited S-acylation of expressed spike proteins and attenuated the ability of SARS-CoV-2 and human CoV-229E to spread in vitro. Our findings further substantiate the necessity of CoV spike protein S-acylation and demonstrate that de novo fatty acid synthesis is critical for the proper S-acylation of the spike protein.
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Affiliation(s)
- Katrina Mekhail
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Minhyoung Lee
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Michael Sugiyama
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Audrey Astori
- Princess Margaret Cancer Centre, University Health Network, Ontario, Canada
| | | | - Elyse Latreille
- Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Negar Khosraviani
- Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Kuiru Wei
- Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Zhijie Li
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - James Rini
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Warren L Lee
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Costin Antonescu
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Gregory D Fairn
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Department of Surgery, University of Toronto, Toronto, Ontario, Canada; Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada.
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59
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Zou X, Lin F, Yang Y, Chen J, Zhang H, Li L, Ouyang H, Pang D, Tang X. Cholesterol Biosynthesis Modulates CSFV Replication. Viruses 2022; 14:v14071450. [PMID: 35891429 PMCID: PMC9316236 DOI: 10.3390/v14071450] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 12/13/2022] Open
Abstract
Classical swine fever (CSF) caused by the classical swine fever virus (CSFV) has resulted in severe losses to the pig industry worldwide. It has been proposed that lipid synthesis is essential for viral replication, and lipids are involved in viral protein maturation and envelope production. However, the specific crosstalk between CSFV and host cell lipid metabolism is still unknown. In this study, we found that CSFV infection increased intracellular cholesterol levels in PK-15 cells. Further analysis demonstrated that CSFV infection upregulated PCSK9 expression to block the uptake of exogenous cholesterol by LDLR and enhanced the cholesterol biosynthesis pathway, which disrupted the type I IFN response in PK-15 cells. Our findings provide new insight into the mechanisms underpinning the pathogenesis of CSFV and hint at methods for controlling the disease.
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Affiliation(s)
- Xiaodong Zou
- College of Animal Sciences, Jilin University, Changchun 130062, China; (X.Z.); (F.L.); (Y.Y.); (J.C.); (H.Z.); (L.L.); (H.O.); (D.P.)
| | - Feng Lin
- College of Animal Sciences, Jilin University, Changchun 130062, China; (X.Z.); (F.L.); (Y.Y.); (J.C.); (H.Z.); (L.L.); (H.O.); (D.P.)
| | - Yang Yang
- College of Animal Sciences, Jilin University, Changchun 130062, China; (X.Z.); (F.L.); (Y.Y.); (J.C.); (H.Z.); (L.L.); (H.O.); (D.P.)
| | - Jiahuan Chen
- College of Animal Sciences, Jilin University, Changchun 130062, China; (X.Z.); (F.L.); (Y.Y.); (J.C.); (H.Z.); (L.L.); (H.O.); (D.P.)
| | - Huanyu Zhang
- College of Animal Sciences, Jilin University, Changchun 130062, China; (X.Z.); (F.L.); (Y.Y.); (J.C.); (H.Z.); (L.L.); (H.O.); (D.P.)
| | - Linquan Li
- College of Animal Sciences, Jilin University, Changchun 130062, China; (X.Z.); (F.L.); (Y.Y.); (J.C.); (H.Z.); (L.L.); (H.O.); (D.P.)
| | - Hongsheng Ouyang
- College of Animal Sciences, Jilin University, Changchun 130062, China; (X.Z.); (F.L.); (Y.Y.); (J.C.); (H.Z.); (L.L.); (H.O.); (D.P.)
- Chongqing Research Institute, Jilin University, Chongqing 401120, China
| | - Daxin Pang
- College of Animal Sciences, Jilin University, Changchun 130062, China; (X.Z.); (F.L.); (Y.Y.); (J.C.); (H.Z.); (L.L.); (H.O.); (D.P.)
- Chongqing Research Institute, Jilin University, Chongqing 401120, China
| | - Xiaochun Tang
- College of Animal Sciences, Jilin University, Changchun 130062, China; (X.Z.); (F.L.); (Y.Y.); (J.C.); (H.Z.); (L.L.); (H.O.); (D.P.)
- Chongqing Research Institute, Jilin University, Chongqing 401120, China
- Correspondence:
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60
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Miao G, Peng H, Tang H, Liu Y, Zheng X, Liu B, Jiang L, Tang W, He Y, Liu Y, Ren H, Zhao P, Qi Z, Ding C. Antiviral efficacy of selective estrogen receptor modulators against SARS-CoV-2 infection in vitro and in vivo reveals bazedoxifene acetate as an entry inhibitor. J Med Virol 2022; 94:4809-4819. [PMID: 35733297 PMCID: PMC9350378 DOI: 10.1002/jmv.27951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/08/2022] [Accepted: 06/11/2022] [Indexed: 11/05/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the seventh member of the coronavirus family that can infect humans. Recently, more contagious and pathogenic variants of SARS-CoV-2 have been continuously emerging. Clinical candidates with high efficacy and ready availability are still in urgent need. To identify potent anti-SARS-CoV-2 repurposing drugs, we evaluated the antiviral efficacy of 18 selective estrogen receptor modulators (SERMs) against SARS-CoV-2 infection. Six SERMs exhibited excellent anti-SARS-CoV-2 effects in Vero E6 cells and three human cell lines. Clomifene citrate, tamoxifen, toremifene citrate, and bazedoxifene acetate reduced the weight loss of hamsters challenged with SARS-CoV-2, and reduced hamster pulmonary viral load and IL-6 expression when assayed at 4 days post-infection. In particular, bazedoxifene acetate was identified to act on the penetration stage of the post-attachment step via altering cholesterol distribution and endosome acidification. And, bazedoxifene acetate inhibited pseudoviruses infection of original SARS-CoV-2, Delta variant, Omicron variant and SARS-CoV. These results offer critical information supporting bazedoxifene acetate as a promising agent against coronaviruses. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gen Miao
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Haoran Peng
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Hailin Tang
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Yangang Liu
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Xu Zheng
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Bin Liu
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Liangliang Jiang
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Wanda Tang
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Yanhua He
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Yan Liu
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Hao Ren
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Ping Zhao
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Zhongtian Qi
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Cuiling Ding
- Department of Microbiology, Naval Medical University, Shanghai Key, Laboratory of Medical Biodefense, Shanghai, 200433, China
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61
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Režen T, Martins A, Mraz M, Zimic N, Rozman D, Moškon M. Integration of omics data to generate and analyse COVID-19 specific genome-scale metabolic models. Comput Biol Med 2022; 145:105428. [PMID: 35339845 PMCID: PMC8940269 DOI: 10.1016/j.compbiomed.2022.105428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 12/16/2022]
Abstract
COVID-19 presents a complex disease that needs to be addressed using systems medicine approaches that include genome-scale metabolic models (GEMs). Previous studies have used a single model extraction method (MEM) and/or a single transcriptomic dataset to reconstruct context-specific models, which proved to be insufficient for the broader biological contexts. We have applied four MEMs in combination with five COVID-19 datasets. Models produced by GIMME were separated by infection, while tINIT preserved the biological variability in the data and enabled the best prediction of the enrichment of metabolic subsystems. Vitamin D3 metabolism was predicted to be down-regulated in one dataset by GIMME, and in all by tINIT. Models generated by tINIT and GIMME predicted downregulation of retinol metabolism in different datasets, while downregulated cholesterol metabolism was predicted only by tINIT-generated models. Predictions are in line with the observations in COVID-19 patients. Our data indicated that GIMME and tINIT models provided the most biologically relevant results and should have a larger emphasis in further analyses. Particularly tINIT models identified the metabolic pathways that are a part of the host response and are potential antiviral targets. The code and the results of the analyses are available to download from https://github.com/CompBioLj/COVID_GEMs_and_MEMs.
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Affiliation(s)
- Tadeja Režen
- Centre for Functional Genomics and Bio-Chips, Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | - Miha Mraz
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Nikolaj Zimic
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Miha Moškon
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.
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Evidence for the role of Rab11-positive recycling endosomes as intermediates in coronavirus egress from epithelial cells. Histochem Cell Biol 2022; 158:241-251. [PMID: 35604431 PMCID: PMC9124743 DOI: 10.1007/s00418-022-02115-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2022] [Indexed: 12/19/2022]
Abstract
AbstractAfter their assembly by budding into the lumen of the intermediate compartment (IC) at the endoplasmic reticulum (ER)–Golgi interface, coronaviruses (CoVs) are released from their host cells following a pathway that remains poorly understood. The traditional view that CoV exit occurs via the constitutive secretory route has recently been questioned by studies suggesting that this process involves unconventional secretion. Here, using the avian infectious bronchitis virus (IBV) as a well-established model virus, we have applied confocal microscopy to investigate the pathway of CoV egress from epithelial Vero cells. We report a novel effect of IBV infection on cellular endomembranes, namely, the compaction of the pericentrosomal endocytic recycling compartment (ERC) defined by the GTPase Rab11, which coincides with the previously described Golgi fragmentation, as well as virus release. Despite Golgi disassembly, the IC elements containing the major IBV membrane protein (M)—which mostly associates with newly formed virus particles—maintain their close spatial connection with the Rab11-positive endocytic recycling system. Moreover, partial colocalization of the M protein with Rab11 was observed, whereas M displayed negligible overlap with LAMP-1, indicating that IBV egress does not occur via late endosomes or lysosomes. Synchronization of virus release using temperature-shift protocols was accompanied by increased colocalization of M and Rab11 in vesicular and vacuolar structures in the pericentrosomal region and at the cell periphery, most likely representing IBV-containing transport carriers. In conclusion, these results add CoVs to the growing list of viruses exploiting the endocytic recycling apparatus defined by Rab11 for their assembly and/or release.
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Tran A, Kervin TA, Overduin M. Multifaceted membrane binding head of the SARS-CoV-2 spike protein. Curr Res Struct Biol 2022; 4:146-157. [PMID: 35602928 PMCID: PMC9109970 DOI: 10.1016/j.crstbi.2022.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 04/04/2022] [Accepted: 05/05/2022] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 spike protein presents a surface with enormous membrane binding potential to host tissues and organelles of infected cells. Its exposed trimeric head binds not only the angiotensin-converting enzyme 2 (ACE2), but also host phospholipids which are missing from all existing structures. Hence, the membrane interaction surfaces that mediate viral fusion, entry, assembly and egress remain unclear. Here the spike:membrane docking sites are identified based on membrane optimal docking area (MODA) analysis of 3D structures of spike proteins in closed and open conformations at endocytic and neutral pH levels as well as ligand complexes. This reveals multiple membrane binding sites in the closed spike head that together prefer convex membranes and are modulated by pH, fatty acids and post-translational modifications including glycosylation. The exposure of the various membrane interaction sites adjusts upon domain repositioning within the trimer, allowing formation of intermediate bilayer complexes that lead to the prefusion state while also enabling ACE2 receptor recognition. In contrast, all antibodies that target the spike head would block the membrane docking process that precedes ACE2 recognition. Together this illuminates the engagements of the spike protein with plasma, endocytic, ER or exocytic vesicle membranes that help to drive the cycle of viral infection, and offers novel sites for intervention.
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Affiliation(s)
- Anh Tran
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Troy A. Kervin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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Molecular Dynamics of DHHC20 Acyltransferase Suggests Principles of Lipid and Protein Substrate Selectivity. Int J Mol Sci 2022; 23:ijms23095091. [PMID: 35563480 PMCID: PMC9105814 DOI: 10.3390/ijms23095091] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 12/17/2022] Open
Abstract
Lipid modification of viral proteins with fatty acids of different lengths (S-acylation) is crucial for virus pathogenesis. The reaction is catalyzed by members of the DHHC family and proceeds in two steps: the autoacylation is followed by the acyl chain transfer onto protein substrates. The crystal structure of human DHHC20 (hDHHC20), an enzyme involved in the acylation of S-protein of SARS-CoV-2, revealed that the acyl chain may be inserted into a hydrophobic cavity formed by four transmembrane (TM) α-helices. To test this model, we used molecular dynamics of membrane-embedded hDHHC20 and its mutants either in the absence or presence of various acyl-CoAs. We found that among a range of acyl chain lengths probed only C16 adopts a conformation suitable for hDHHC20 autoacylation. This specificity is altered if the small or bulky residues at the cavity's ceiling are exchanged, e.g., the V185G mutant obtains strong preferences for binding C18. Surprisingly, an unusual hydrophilic ridge was found in TM helix 4 of hDHHC20, and the responsive hydrophilic patch supposedly involved in association was found in the 3D model of the S-protein TM-domain trimer. Finally, the exchange of critical Thr and Ser residues in the spike led to a significant decrease in its S-acylation. Our data allow further development of peptide/lipid-based inhibitors of hDHHC20 that might impede replication of Corona- and other enveloped viruses.
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Prydz K, Saraste J. The life cycle and enigmatic egress of coronaviruses. Mol Microbiol 2022; 117:1308-1316. [PMID: 35434857 PMCID: PMC9321882 DOI: 10.1111/mmi.14907] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Abstract
There has been considerable recent interest in the life cycle of Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2), the causative agent of the Covid‐19 pandemic. Practically every step in CoV replication—from cell attachment and uptake via genome replication and expression to virion assembly has been considered as a specific event that potentially could be targeted by existing or novel drugs. Interference with cellular egress of progeny viruses could also be adopted as a possible therapeutic strategy; however, the situation is complicated by the fact that there is no broad consensus on how CoVs find their way out of their host cells. The viral nucleocapsid, consisting of the genomic RNA complexed with nucleocapsid proteins obtains a membrane envelope during virus budding into the lumen of the intermediate compartment (IC) at the endoplasmic reticulum (ER)–Golgi interface. From here, several alternative routes for CoV extracellular release have been proposed. Strikingly, recent studies have shown that CoV infection leads to the disassembly of the Golgi ribbon and the mobilization of host cell compartments and protein machineries that are known to promote Golgi‐independent trafficking to the cell surface. Here, we discuss the life cycle of CoVs with a special focus on different possible pathways for virus egress.
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Affiliation(s)
- Kristian Prydz
- Department of Biosciences, University of Oslo, Norway and Department of Biomedicine and Molecular Imaging Center University of Bergen Norway
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Elliot Murphy R, Banerjee A. In vitro reconstitution of substrate S-acylation by the zDHHC family of protein acyltransferases. Open Biol 2022; 12:210390. [PMID: 35414257 PMCID: PMC9006032 DOI: 10.1098/rsob.210390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/21/2022] [Indexed: 01/09/2023] Open
Abstract
Protein S-acylation, more commonly known as protein palmitoylation, is a biological process defined by the covalent attachment of long chain fatty acids onto cysteine residues of a protein, effectively altering the local hydrophobicity and influencing its stability, localization and overall function. Observed ubiquitously in all eukaryotes, this post translational modification is mediated by the 23-member family of zDHHC protein acyltransferases in mammals. There are thousands of proteins that are S-acylated and multiple zDHHC enzymes can potentially act on a single substrate. Since its discovery, numerous methods have been developed for the identification of zDHHC substrates and the individual members of the family that catalyse their acylation. Despite these recent advances in assay development, there is a persistent gap in knowledge relating to zDHHC substrate specificity and recognition, that can only be thoroughly addressed through in vitro reconstitution. Herein, we will review the various methods currently available for reconstitution of protein S-acylation for the purposes of identifying enzyme-substrate pairs with a particular emphasis on the advantages and disadvantages of each approach.
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Affiliation(s)
- R. Elliot Murphy
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Anirban Banerjee
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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Ramadan AA, Mayilsamy K, McGill AR, Ghosh A, Giulianotti MA, Donow HM, Mohapatra SS, Mohapatra S, Chandran B, Deschenes RJ, Roy A. Identification of SARS-CoV-2 Spike Palmitoylation Inhibitors That Results in Release of Attenuated Virus with Reduced Infectivity. Viruses 2022; 14:v14030531. [PMID: 35336938 PMCID: PMC8950683 DOI: 10.3390/v14030531] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 02/02/2023] Open
Abstract
The spike proteins of enveloped viruses are transmembrane glycoproteins that typically undergo post-translational attachment of palmitate on cysteine residues on the cytoplasmic facing tail of the protein. The role of spike protein palmitoylation in virus biogenesis and infectivity is being actively studied as a potential target of novel antivirals. Here, we report that palmitoylation of the first five cysteine residues of the C-terminal cysteine-rich domain of the SARS-CoV-2 S protein are indispensable for infection, and palmitoylation-deficient spike mutants are defective in membrane fusion. The DHHC9 palmitoyltransferase interacts with and palmitoylates the spike protein in the ER and Golgi and knockdown of DHHC9 results in reduced fusion and infection of SARS-CoV-2. Two bis-piperazine backbone-based DHHC9 inhibitors inhibit SARS-CoV-2 S protein palmitoylation and the resulting progeny virion particles released are defective in fusion and infection. This establishes these palmitoyltransferase inhibitors as potential new intervention strategies against SARS-CoV-2.
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Affiliation(s)
- Ahmed A. Ramadan
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
| | - Karthick Mayilsamy
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
- Department of Veterans Affairs, James A Haley Veterans Hospital, Tampa, FL 33612, USA
| | - Andrew R. McGill
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
- Department of Veterans Affairs, James A Haley Veterans Hospital, Tampa, FL 33612, USA
- Department of Internal Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Anandita Ghosh
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
| | - Marc A. Giulianotti
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA; (M.A.G.); (H.M.D.)
| | - Haley M. Donow
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA; (M.A.G.); (H.M.D.)
| | - Shyam S. Mohapatra
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
- Department of Veterans Affairs, James A Haley Veterans Hospital, Tampa, FL 33612, USA
- Department of Internal Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Subhra Mohapatra
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
- Department of Veterans Affairs, James A Haley Veterans Hospital, Tampa, FL 33612, USA
| | - Bala Chandran
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
| | - Robert J. Deschenes
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
- Correspondence: (R.J.D.); (A.R.); Tel.: +1-(813)-974-6393 (R.J.D.); +1-(813)-974-5540 (A.R.)
| | - Arunava Roy
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
- Correspondence: (R.J.D.); (A.R.); Tel.: +1-(813)-974-6393 (R.J.D.); +1-(813)-974-5540 (A.R.)
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Bivalent recognition of fatty acyl-CoA by a human integral membrane palmitoyltransferase. Proc Natl Acad Sci U S A 2022; 119:2022050119. [PMID: 35140179 PMCID: PMC8851515 DOI: 10.1073/pnas.2022050119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
Protein palmitoylation is one of the most highly abundant protein modifications, through which long-chain fatty acids get attached to cysteines by a thioester linkage. It plays critically important roles in growth signaling, the organization of synaptic receptors, and the regulation of ion channel function. Yet the molecular mechanism of the DHHC family of integral membrane enzymes that catalyze this modification remains poorly understood. Here, we present the structure of a precatalytic complex of human DHHC20 with palmitoyl CoA. Together with the accompanying functional data, the structure shows how a bivalent recognition of palmitoyl CoA by the DHHC enzyme, simultaneously at both the fatty acyl group and the CoA headgroup, is essential for catalytic chemistry to proceed. S-acylation, also known as palmitoylation, is the most abundant form of protein lipidation in humans. This reversible posttranslational modification, which targets thousands of proteins, is catalyzed by 23 members of the DHHC family of integral membrane enzymes. DHHC enzymes use fatty acyl-CoA as the ubiquitous fatty acyl donor and become autoacylated at a catalytic cysteine; this intermediate subsequently transfers the fatty acyl group to a cysteine in the target protein. Protein S-acylation intersects with almost all areas of human physiology, and several DHHC enzymes are considered as possible therapeutic targets against diseases such as cancer. These efforts would greatly benefit from a detailed understanding of the molecular basis for this crucial enzymatic reaction. Here, we combine X-ray crystallography with all-atom molecular dynamics simulations to elucidate the structure of the precatalytic complex of human DHHC20 in complex with palmitoyl CoA. The resulting structure reveals that the fatty acyl chain inserts into a hydrophobic pocket within the transmembrane spanning region of the protein, whereas the CoA headgroup is recognized by the cytosolic domain through polar and ionic interactions. Biochemical experiments corroborate the predictions from our structural model. We show, using both computational and experimental analyses, that palmitoyl CoA acts as a bivalent ligand where the interaction of the DHHC enzyme with both the fatty acyl chain and the CoA headgroup is important for catalytic chemistry to proceed. This bivalency explains how, in the presence of high concentrations of free CoA under physiological conditions, DHHC enzymes can efficiently use palmitoyl CoA as a substrate for autoacylation.
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69
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Li X, Shen L, Xu Z, Liu W, Li A, Xu J. Protein Palmitoylation Modification During Viral Infection and Detection Methods of Palmitoylated Proteins. Front Cell Infect Microbiol 2022; 12:821596. [PMID: 35155279 PMCID: PMC8829041 DOI: 10.3389/fcimb.2022.821596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/12/2022] [Indexed: 01/31/2023] Open
Abstract
Protein palmitoylation—a lipid modification in which one or more cysteine thiols on a substrate protein are modified to form a thioester with a palmitoyl group—is a significant post-translational biological process. This process regulates the trafficking, subcellular localization, and stability of different proteins in cells. Since palmitoylation participates in various biological processes, it is related to the occurrence and development of multiple diseases. It has been well evidenced that the proteins whose functions are palmitoylation-dependent or directly involved in key proteins’ palmitoylation/depalmitoylation cycle may be a potential source of novel therapeutic drugs for the related diseases. Many researchers have reported palmitoylation of proteins, which are crucial for host-virus interactions during viral infection. Quite a few explorations have focused on figuring out whether targeting the acylation of viral or host proteins might be a strategy to combat viral diseases. All these remarkable achievements in protein palmitoylation have been made to technological advances. This paper gives an overview of protein palmitoylation modification during viral infection and the methods for palmitoylated protein detection. Future challenges and potential developments are proposed.
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Affiliation(s)
- Xiaoling Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Lingyi Shen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhao Xu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wei Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Aihua Li
- Clinical Lab, Henan Provincial Chest Hospital, Zhengzhou, China
| | - Jun Xu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Jun Xu, ;
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70
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Pike DP, McGuffee RM, Geerling E, Albert CJ, Hoft DF, Shashaty MGS, Meyer NJ, Pinto AK, Ford DA. Plasmalogen Loss in Sepsis and SARS-CoV-2 Infection. Front Cell Dev Biol 2022; 10:912880. [PMID: 35784479 PMCID: PMC9242022 DOI: 10.3389/fcell.2022.912880] [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: 04/05/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Plasmalogens are plasma-borne antioxidant phospholipid species that provide protection as cellular lipid components during cellular oxidative stress. In this study we investigated plasma plasmalogen levels in human sepsis as well as in rodent models of infection. In humans, levels of multiple plasmenylethanolamine molecular species were decreased in septic patient plasma compared to control subject plasma as well as an age-aligned control subject cohort. Additionally, lysoplasmenylcholine levels were significantly decreased in septic patients compared to the control cohorts. In contrast, plasma diacyl phosphatidylethanolamine and phosphatidylcholine levels were elevated in septic patients. Lipid changes were also determined in rats subjected to cecal slurry sepsis. Plasma plasmenylcholine, plasmenylethanolamine, and lysoplasmenylcholine levels were decreased while diacyl phosphatidylethanolamine levels were increased in septic rats compared to control treated rats. Kidney levels of lysoplasmenylcholine as well as plasmenylethanolamine molecular species were decreased in septic rats. Interestingly, liver plasmenylcholine and plasmenylethanolamine levels were increased in septic rats. Since COVID-19 is associated with sepsis-like acute respiratory distress syndrome and oxidative stress, plasmalogen levels were also determined in a mouse model of COVID-19 (intranasal inoculation of K18 mice with SARS-CoV-2). 3 days following infection, lung infection was confirmed as well as cytokine expression in the lung. Multiple molecular species of lung plasmenylcholine and plasmenylethanolamine were decreased in infected mice. In contrast, the predominant lung phospholipid, dipalmitoyl phosphatidylcholine, was not decreased following SARS-CoV-2 infection. Additionally total plasmenylcholine levels were decreased in the plasma of SARS-CoV-2 infected mice. Collectively, these data demonstrate the loss of plasmalogens during both sepsis and SARS-CoV-2 infection. This study also indicates plasma plasmalogens should be considered in future studies as biomarkers of infection and as prognostic indicators for sepsis and COVID-19 outcomes.
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Affiliation(s)
- Daniel P Pike
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, United States.,Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Reagan M McGuffee
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, United States.,Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Elizabeth Geerling
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Carolyn J Albert
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, United States.,Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Daniel F Hoft
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, United States.,Department of Internal Medicine, Division of Infectious Diseases, Allergy and Immunology, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Michael G S Shashaty
- Pulmonary, Allergy, and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States.,Center for Translational Lung Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Nuala J Meyer
- Pulmonary, Allergy, and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States.,Center for Translational Lung Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Amelia K Pinto
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - David A Ford
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, United States.,Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO, United States
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Sardar A, Dewangan N, Panda B, Bhowmick D, Tarafdar PK. Lipid and Lipidation in Membrane Fusion. J Membr Biol 2022; 255:691-703. [PMID: 36102950 PMCID: PMC9472184 DOI: 10.1007/s00232-022-00267-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022]
Abstract
Membrane fusion plays a lead role in the transport of vesicles, neurotransmission, mitochondrial dynamics, and viral infection. There are fusion proteins that catalyze and regulate the fusion. Interestingly, various types of fusion proteins are present in nature and they possess diverse mechanisms of action. We have highlighted the importance of the functional domains of intracellular heterotypic fusion, homotypic endoplasmic reticulum (ER), homotypic mitochondrial, and type-I viral fusion. During intracellular heterotypic fusion, the SNAREs and four-helix bundle formation are prevalent. Type-I viral fusion is controlled by the membrane destabilizing properties of fusion peptide and six-helix bundle formation. The ER/mitochondrial homotypic fusion is controlled by GTPase activity and the membrane destabilization properties of the amphipathic helix(s). Although the mechanism of action of these fusion proteins is diverse, they have some similarities. In all cases, the lipid composition of the membrane greatly affects membrane fusion. Next, examples of lipidation of the fusion proteins were discussed. We suggest that the fatty acyl hydrophobic tail not only acts as an anchor but may also modulate the energetics of membrane fusion intermediates. Lipidation is also important to design more effective peptide-based fusion inhibitors. Together, we have shown that membrane lipid composition and lipidation are important to modulate membrane fusion.
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Affiliation(s)
- Avijit Sardar
- grid.417960.d0000 0004 0614 7855Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur, West Bengal 741246 India
| | - Nikesh Dewangan
- grid.417960.d0000 0004 0614 7855Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur, West Bengal 741246 India
| | - Bishvanwesha Panda
- grid.417960.d0000 0004 0614 7855Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur, West Bengal 741246 India
| | - Debosmita Bhowmick
- grid.417960.d0000 0004 0614 7855Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur, West Bengal 741246 India
| | - Pradip K. Tarafdar
- grid.417960.d0000 0004 0614 7855Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur, West Bengal 741246 India
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Zeng XT, Yu XT, Cheng W. The interactions of ZDHHC5/GOLGA7 with SARS-CoV-2 spike (S) protein and their effects on S protein's subcellular localization, palmitoylation and pseudovirus entry. Virol J 2021; 18:257. [PMID: 34961524 PMCID: PMC8711289 DOI: 10.1186/s12985-021-01722-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/30/2021] [Indexed: 02/08/2023] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein determines virus entry and the palmitoylation of S protein affects virus infection. An acyltransferase complex ZDHHC5/GOGAL7 that interacts with S protein was detected by affinity purification mass spectrometry (AP-MS). However, the palmitoylated cysteine residues of S protein, the effects of ZDHHC5 or GOLGA7 knockout on S protein’s subcellular localization, palmitoylation, pseudovirus entry and the enzyme for depalmitoylation of S protein are not clear. Methods The palmitoylated cysteine residues of S protein were identified by acyl-biotin exchange (ABE) assays. The interactions between S protein and host proteins were analyzed by co-immunoprecipitation (co-IP) assays. Subcellular localizations of S protein and host proteins were analyzed by fluorescence microscopy. ZDHHC5 or GOGAL7 gene was edited by CRISPR-Cas9. The entry efficiencies of SARS-CoV-2 pseudovirus into A549 and Hela cells were analyzed by measuring the activity of Renilla luciferase. Results In this investigation, all ten cysteine residues in the endodomain of S protein were palmitoylated. The interaction of S protein with ZDHHC5 or GOLGA7 was confirmed. The interaction and colocalization of S protein with ZDHHC5 or GOLGA7 were independent of the ten cysteine residues in the endodomain of S protein. The interaction between S protein and ZDHHC5 was independent of the enzymatic activity and the PDZ-binding domain of ZDHHC5. Three cell lines HEK293T, A549 and Hela lacking ZDHHC5 or GOLGA7 were constructed. Furthermore, S proteins still interacted with one host protein in HEK293T cells lacking the other. ZDHHC5 or GOLGA7 knockout had no significant effect on S protein’s subcellular localization or palmitoylation, but significantly decreased the entry efficiencies of SARS-CoV-2 pseudovirus into A549 and Hela cells, while varying degrees of entry efficiencies may be linked to the cell types. Additionally, the S protein interacted with the depalmitoylase APT2. Conclusions ZDHHC5 and GOLGA7 played important roles in SARS-CoV-2 pseudovirus entry, but the reason why the two host proteins affected pseudovirus entry remains to be further explored. This study extends the knowledge about the interactions between SARS-CoV-2 S protein and host proteins and probably provides a reference for the corresponding antiviral methods.
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Affiliation(s)
- Xiao-Tao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Xiao-Ti Yu
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China.
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Vilmen G, Banerjee A, Freed EO. Rafting through the palms: S-acylation of SARS-CoV-2 spike protein induces lipid reorganization. Dev Cell 2021; 56:2787-2789. [PMID: 34699787 PMCID: PMC8545676 DOI: 10.1016/j.devcel.2021.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Geraldine Vilmen
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Anirban Banerjee
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences, and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
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Theken KN, Tang SY, Sengupta S, FitzGerald GA. The roles of lipids in SARS-CoV-2 viral replication and the host immune response. J Lipid Res 2021; 62:100129. [PMID: 34599996 PMCID: PMC8480132 DOI: 10.1016/j.jlr.2021.100129] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 02/06/2023] Open
Abstract
The significant morbidity and mortality associated with severe acute respiratory syndrome coronavirus 2 infection has underscored the need for novel antiviral strategies. Lipids play essential roles in the viral life cycle. The lipid composition of cell membranes can influence viral entry by mediating fusion or affecting receptor conformation. Upon infection, viruses can reprogram cellular metabolism to remodel lipid membranes and fuel the production of new virions. Furthermore, several classes of lipid mediators, including eicosanoids and sphingolipids, can regulate the host immune response to viral infection. Here, we summarize the existing literature on the mechanisms through which these lipid mediators may regulate viral burden in COVID-19. Furthermore, we define the gaps in knowledge and identify the core areas in which lipids offer therapeutic promise for severe acute respiratory syndrome coronavirus 2.
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Affiliation(s)
- Katherine N Theken
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Oral Surgery and Pharmacology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
| | - Soon Yew Tang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shaon Sengupta
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Garret A FitzGerald
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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