1
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Grin PM, Baid K, de Jesus HCR, Kozarac N, Bell PA, Jiang SZ, Kappelhoff R, Butler GS, Leborgne NGF, Pan C, Pablos I, Machado Y, Vederas JC, Kim H, Benarafa C, Banerjee A, Overall CM. SARS-CoV-2 3CL pro (main protease) regulates caspase activation of gasdermin-D/E pores leading to secretion and extracellular activity of 3CL pro. Cell Rep 2024; 43:115080. [PMID: 39673710 DOI: 10.1016/j.celrep.2024.115080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 10/27/2024] [Accepted: 11/26/2024] [Indexed: 12/16/2024] Open
Abstract
SARS-CoV-2 3C-like protease (3CLpro or Mpro) cleaves the SARS-CoV-2 polyprotein and >300 intracellular host proteins to enhance viral replication. By lytic cell death following gasdermin (GSDM) pore formation in cell membranes, antiviral pyroptosis decreases 3CLpro expression and viral replication. Unexpectedly, 3CLpro and nucleocapsid proteins undergo unconventional secretion from infected cells via caspase-activated GSDMD/E pores in the absence of cell lysis. Bronchoalveolar lavage fluid of wild-type SARS-CoV-2-infected mice contains 3CLpro, which decreases in Gsdmd-/-Gsdme-/- mice. We identify new 3CLpro cut-sites in GSDMD at LQ29↓30SS, which blocks pore formation by 3CLpro cleavage at LH270↓N lying adjacent to the caspase activation site (NFLTD275↓G). Cleavage inactivation of GSDMD prevents excessive pore formation, thus countering antiviral pyroptosis and increasing 3CLpro secretion. Extracellular 3CLpro retains activity in serum, dampens platelet activation and aggregation, and inactivates antiviral interferon-λ1. Thus, in countering gasdermin pore formation and pyroptosis in SARS-CoV-2 infection, 3CLpro is secreted with extracellular pathological sequelae.
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Affiliation(s)
- Peter M Grin
- Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Kaushal Baid
- Vaccine and Infectious Diseases Organization, Department of Veterinary Microbiology, University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK S7N 5E3, Canada
| | - Hugo C R de Jesus
- Centre for Blood Research, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Nedim Kozarac
- Institute for Virology and Immunology IVI, Sensemattstrasse 293, 3147 Mittelhäusern, Switzerland; Department of Infectious Diseases and Pathology, Vetsuisse Faculty, University of Bern, Sensemattstrasse 293, 3147 Mittelhäusern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstrasse 43, 3012 Bern, Switzerland
| | - Peter A Bell
- Centre for Blood Research, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Steven Z Jiang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Georgina S Butler
- Centre for Blood Research, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Nathan G F Leborgne
- Institute for Virology and Immunology IVI, Sensemattstrasse 293, 3147 Mittelhäusern, Switzerland; Department of Infectious Diseases and Pathology, Vetsuisse Faculty, University of Bern, Sensemattstrasse 293, 3147 Mittelhäusern, Switzerland
| | - Christina Pan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Isabel Pablos
- Centre for Blood Research, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Yoan Machado
- Centre for Blood Research, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr. NW, Edmonton, AB T6G 2N4, Canada
| | - Hugh Kim
- Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Charaf Benarafa
- Department of Infectious Diseases and Pathology, Vetsuisse Faculty, University of Bern, Sensemattstrasse 293, 3147 Mittelhäusern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstrasse 43, 3012 Bern, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Sensemattstrasse 293, 3147 Mittelhäusern, Switzerland.
| | - Arinjay Banerjee
- Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Vaccine and Infectious Diseases Organization, Department of Veterinary Microbiology, University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK S7N 5E3, Canada; Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Simcoe Hall, 1 King's College Cir., Toronto, ON M5S 1A8, Canada.
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Yonsei Frontier Lab, Yonsei University, 50 Yonsei-ro, Sudaemoon-ku, Seoul 03722, Republic of Korea.
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2
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Cui W, Duan Y, Gao Y, Wang W, Yang H. Structural review of SARS-CoV-2 antiviral targets. Structure 2024; 32:1301-1321. [PMID: 39241763 DOI: 10.1016/j.str.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/25/2024] [Accepted: 08/06/2024] [Indexed: 09/09/2024]
Abstract
The coronavirus disease 2019 (COVID-19), the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents the most disastrous infectious disease pandemic of the past century. As a member of the Betacoronavirus genus, the SARS-CoV-2 genome encodes a total of 29 proteins. The spike protein, RNA-dependent RNA polymerase, and proteases play crucial roles in the virus replication process and are promising targets for drug development. In recent years, structural studies of these viral proteins and of their complexes with antibodies and inhibitors have provided valuable insights into their functions and laid a solid foundation for drug development. In this review, we summarize the structural features of these proteins and discuss recent progress in research regarding therapeutic development, highlighting mechanistically representative molecules and those that have already been approved or are under clinical investigation.
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Affiliation(s)
- Wen Cui
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201203, China
| | - Wei Wang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201203, China.
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3
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Taefehshokr N, Lac A, Vrieze AM, Dickson BH, Guo PN, Jung C, Blythe EN, Fink C, Aktar A, Dikeakos JD, Dekaban GA, Heit B. SARS-CoV-2 NSP5 antagonizes MHC II expression by subverting histone deacetylase 2. J Cell Sci 2024; 137:jcs262172. [PMID: 38682259 PMCID: PMC11166459 DOI: 10.1242/jcs.262172] [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: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024] Open
Abstract
SARS-CoV-2 interferes with antigen presentation by downregulating major histocompatibility complex (MHC) II on antigen-presenting cells, but the mechanism mediating this process is unelucidated. Herein, analysis of protein and gene expression in human antigen-presenting cells reveals that MHC II is downregulated by the SARS-CoV-2 main protease, NSP5. This suppression of MHC II expression occurs via decreased expression of the MHC II regulatory protein CIITA. CIITA downregulation is independent of the proteolytic activity of NSP5, and rather, NSP5 delivers HDAC2 to the transcription factor IRF3 at an IRF-binding site within the CIITA promoter. Here, HDAC2 deacetylates and inactivates the CIITA promoter. This loss of CIITA expression prevents further expression of MHC II, with this suppression alleviated by ectopic expression of CIITA or knockdown of HDAC2. These results identify a mechanism by which SARS-CoV-2 limits MHC II expression, thereby delaying or weakening the subsequent adaptive immune response.
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Affiliation(s)
- Nima Taefehshokr
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Alex Lac
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Angela M. Vrieze
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Brandon H. Dickson
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Peter N. Guo
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Catherine Jung
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Eoin N. Blythe
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Corby Fink
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Amena Aktar
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Jimmy D. Dikeakos
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Gregory A. Dekaban
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Bryan Heit
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
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4
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Zhou J, Sun P, Wang Y, Qiu R, Yang Z, Guo J, Li Z, Xiao S, Fang L. Deep profiling of potential substrate atlas of porcine epidemic diarrhea virus 3C-like protease. J Virol 2024; 98:e0025324. [PMID: 38591878 PMCID: PMC11092332 DOI: 10.1128/jvi.00253-24] [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: 02/05/2024] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
Coronavirus (CoV) 3C-like protease (3CLpro) is essential for viral replication and is involved in immune escape by proteolyzing host proteins. Deep profiling the 3CLpro substrates in the host proteome extends our understanding of viral pathogenesis and facilitates antiviral drug discovery. Here, 3CLpro from porcine epidemic diarrhea virus (PEDV), an enteropathogenic CoV, was used as a model which to identify the potential 3CLpro cleavage motifs in all porcine proteins. We characterized the selectivity of PEDV 3CLpro at sites P5-P4'. We then compiled the 3CLpro substrate preferences into a position-specific scoring matrix and developed a 3CLpro profiling strategy to delineate the protein substrate landscape of CoV 3CLpro. We identified 1,398 potential targets in the porcine proteome containing at least one putative cleavage site and experimentally validated the reliability of the substrate degradome. The PEDV 3CLpro-targeted pathways are involved in mRNA processing, translation, and key effectors of autophagy and the immune system. We also demonstrated that PEDV 3CLpro suppresses the type 1 interferon (IFN-I) cascade via the proteolysis of multiple signaling adaptors in the retinoic acid-inducible gene I (RIG-I) signaling pathway. Our composite method is reproducible and accurate, with an unprecedented depth of coverage for substrate motifs. The 3CLpro substrate degradome establishes a comprehensive substrate atlas that will accelerate the investigation of CoV pathogenicity and the development of anti-CoV drugs.IMPORTANCECoronaviruses (CoVs) are major pathogens that infect humans and animals. The 3C-like protease (3CLpro) encoded by CoV not only cleaves the CoV polyproteins but also degrades host proteins and is considered an attractive target for the development of anti-CoV drugs. However, the comprehensive characterization of an atlas of CoV 3CLpro substrates is a long-standing challenge. Using porcine epidemic diarrhea virus (PEDV) 3CLpro as a model, we developed a method that accurately predicts the substrates of 3CLpro and comprehensively maps the substrate degradome of PEDV 3CLpro. Interestingly, we found that 3CLpro may simultaneously degrade multiple molecules responsible for a specific function. For instance, it cleaves at least four adaptors in the RIG-I signaling pathway to suppress type 1 interferon production. These findings highlight the complexity of the 3CLpro substrate degradome and provide new insights to facilitate the development of anti-CoV drugs.
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Affiliation(s)
- Junwei Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Peng Sun
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Yuanqing Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Runhui Qiu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Zhixiang Yang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jiahui Guo
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Zhuang Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liurong Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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5
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Hartley B, Bassiouni W, Roczkowsky A, Fahlman R, Schulz R, Julien O. Data-Independent Acquisition Proteomics and N-Terminomics Methods Reveal Alterations in Mitochondrial Function and Metabolism in Ischemic-Reperfused Hearts. J Proteome Res 2024; 23:844-856. [PMID: 38264990 PMCID: PMC10846531 DOI: 10.1021/acs.jproteome.3c00754] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/25/2024]
Abstract
Myocardial ischemia-reperfusion (IR) (stunning) injury triggers changes in the proteome and degradome of the heart. Here, we utilize quantitative proteomics and comprehensive degradomics to investigate the molecular mechanisms of IR injury in isolated rat hearts. The control group underwent aerobic perfusion, while the IR injury group underwent 20 min of ischemia and 30 min of reperfusion to induce a stunning injury. As MMP-2 activation has been shown to contribute to myocardial injury, hearts also underwent IR injury with ARP-100, an MMP-2-preferring inhibitor, to dissect the contribution of MMP-2 to IR injury. Using data-independent acquisition (DIA) and mass spectroscopy, we quantified 4468 proteins in ventricular extracts, whereby 447 proteins showed significant alterations among the three groups. We then used subtiligase-mediated N-terminomic labeling to identify more than a hundred specific cleavage sites. Among these protease substrates, 15 were identified following IR injury. We identified alterations in numerous proteins involved in mitochondrial function and metabolism following IR injury. Our findings provide valuable insights into the biochemical mechanisms of myocardial IR injury, suggesting alterations in reactive oxygen/nitrogen species handling and generation, fatty acid metabolism, mitochondrial function and metabolism, and cardiomyocyte contraction.
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Affiliation(s)
- Bridgette Hartley
- Department
of Biochemistry, University of Alberta, Edmonton T6G 2H7, Canada
| | - Wesam Bassiouni
- Department
of Pharmacology, University of Alberta, Edmonton T6G 2S2, Canada
| | - Andrej Roczkowsky
- Department
of Pharmacology, University of Alberta, Edmonton T6G 2S2, Canada
| | - Richard Fahlman
- Department
of Biochemistry, University of Alberta, Edmonton T6G 2H7, Canada
| | - Richard Schulz
- Department
of Pharmacology, University of Alberta, Edmonton T6G 2S2, Canada
- Department
of Pediatrics, University of Alberta, Edmonton T6G 2S2, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton T6G 2H7, Canada
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6
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Gomez-Cardona E, Eskandari-Sedighi G, Fahlman R, Westaway D, Julien O. Application of N-Terminal Labeling Methods Provide Novel Insights into Endoproteolysis of the Prion Protein in Vivo. ACS Chem Neurosci 2024; 15:134-146. [PMID: 38095594 PMCID: PMC10768724 DOI: 10.1021/acschemneuro.3c00533] [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: 08/12/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/04/2024] Open
Abstract
Alternative α- and β-cleavage events in the cellular prion protein (PrPC) central region generate fragments with distinct biochemical features that affect prion disease pathogenesis, but the assignment of precise cleavage positions has proven challenging. Exploiting mouse transgenic models expressing wild-type (WT) PrPC and an octarepeat region mutant allele (S3) with increased β-fragmentation, cleavage sites were defined using LC-MS/MS in conjunction with N-terminal enzymatic labeling and chemical in-gel acetylation. Our studies profile the net proteolytic repertoire of the adult brain, as deduced from defining hundreds of proteolytic events in other proteins, and position individual cleavage events in PrPC α- and β-target areas imputed from earlier, lower resolution methods; these latter analyses established site heterogeneity, with six cleavage sites positioned in the β-cleavage region of WT PrPC and nine positions for S3 PrPC. Regarding α-cleavage, aside from reported N-termini at His110 and Val111, we identified a total of five shorter fragments in the brain of both mice lines. We infer that aminopeptidase activity in the brain could contribute to the ragged N-termini observed around PrPC's α- and β-cleavage sites, with this work providing a point of departure for further in vivo studies of brain proteases.
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Affiliation(s)
- Erik Gomez-Cardona
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Ghazaleh Eskandari-Sedighi
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Center
for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G 2M8, Canada
| | - Richard Fahlman
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - David Westaway
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Center
for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G 2M8, Canada
- Department
of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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7
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Bell PA, Overall CM. No Substrate Left behind-Mining of Shotgun Proteomics Datasets Rescues Evidence of Proteolysis by SARS-CoV-2 3CL pro Main Protease. Int J Mol Sci 2023; 24:ijms24108723. [PMID: 37240067 DOI: 10.3390/ijms24108723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Proteolytic processing is the most ubiquitous post-translational modification and regulator of protein function. To identify protease substrates, and hence the function of proteases, terminomics workflows have been developed to enrich and detect proteolytically generated protein termini from mass spectrometry data. The mining of shotgun proteomics datasets for such 'neo'-termini, to increase the understanding of proteolytic processing, is an underutilized opportunity. However, to date, this approach has been hindered by the lack of software with sufficient speed to make searching for the relatively low numbers of protease-generated semi-tryptic peptides present in non-enriched samples viable. We reanalyzed published shotgun proteomics datasets for evidence of proteolytic processing in COVID-19 using the recently upgraded MSFragger/FragPipe software, which searches data with a speed that is an order of magnitude greater than many equivalent tools. The number of protein termini identified was higher than expected and constituted around half the number of termini detected by two different N-terminomics methods. We identified neo-N- and C-termini generated during SARS-CoV-2 infection that were indicative of proteolysis and were mediated by both viral and host proteases-a number of which had been recently validated by in vitro assays. Thus, re-analyzing existing shotgun proteomics data is a valuable adjunct for terminomics research that can be readily tapped (for example, in the next pandemic where data would be scarce) to increase the understanding of protease function and virus-host interactions, or other diverse biological processes.
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Affiliation(s)
- Peter A Bell
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Christopher M Overall
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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