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Cigalotto L, Martinvalet D. Granzymes in health and diseases: the good, the bad and the ugly. Front Immunol 2024; 15:1371743. [PMID: 38646541 PMCID: PMC11026543 DOI: 10.3389/fimmu.2024.1371743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Granzymes are a family of serine proteases, composed of five human members: GA, B, H, M and K. They were first discovered in the 1980s within cytotoxic granules released during NK cell- and T cell-mediated killing. Through their various proteolytic activities, granzymes can trigger different pathways within cells, all of which ultimately lead to the same result, cell death. Over the years, the initial consideration of granzymes as mere cytotoxic mediators has changed due to surprising findings demonstrating their expression in cells other than immune effectors as well as new intracellular and extracellular activities. Additional roles have been identified in the extracellular milieu, following granzyme escape from the immunological synapse or their release by specific cell types. Outside the cell, granzyme activities mediate extracellular matrix alteration via the degradation of matrix proteins or surface receptors. In certain contexts, these processes are essential for tissue homeostasis; in others, excessive matrix degradation and extensive cell death contribute to the onset of chronic diseases, inflammation, and autoimmunity. Here, we provide an overview of both the physiological and pathological roles of granzymes, highlighting their utility while also recognizing how their unregulated presence can trigger the development and/or worsening of diseases.
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Affiliation(s)
- Lavinia Cigalotto
- Laboratory of Reactive Oxygen Species and Cytotoxic Immunity, Department Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute Of Molecular Medicine (VIMM), Padova, Italy
| | - Denis Martinvalet
- Laboratory of Reactive Oxygen Species and Cytotoxic Immunity, Department Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute Of Molecular Medicine (VIMM), Padova, Italy
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2
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Aybay E, Ryu J, Fu Z, Akula S, Enriquez EM, Hallgren J, Wernersson S, Olsson AK, Hellman L. Extended cleavage specificities of human granzymes A and K, two closely related enzymes with conserved but still poorly defined functions in T and NK cell-mediated immunity. Front Immunol 2023; 14:1211295. [PMID: 37497217 PMCID: PMC10366535 DOI: 10.3389/fimmu.2023.1211295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/23/2023] [Indexed: 07/28/2023] Open
Abstract
Granzymes A and K are two highly homologous serine proteases expressed by mammalian cytotoxic T cells (CTL) and natural killer cells (NK). Granzyme A is the most abundant of the different granzymes (gzms) expressed by these two cell types. Gzms A and K are found in all jawed vertebrates and are the most well conserved of all hematopoietic serine proteases. Their potential functions have been studied extensively for many years, however, without clear conclusions. Gzm A was for many years thought to serve as a key component in the defense against viral infection by the induction of apoptosis in virus-infected cells, similar to gzm B. However, later studies have questioned this role and instead indicated that gzm A may act as a potent inducer of inflammatory cytokines and chemokines. Gzms A and K form clearly separate branches in a phylogenetic tree indicating separate functions. Transcriptional analyses presented here demonstrate the presence of gzm A and K transcripts in both CD4+ and CD8+ T cells. To enable screening for their primary biological targets we have made a detailed analysis of their extended cleavage specificities. Phage display analysis of the cleavage specificity of the recombinant enzymes showed that both gzms A and K are strict tryptases with high selectivity for Arg over Lys in the P1 position. The major differences in the specificities of these two enzymes are located N-terminally of the cleavage site, where gzm A prefers small amino acids such as Gly in the P3 position and shows a relatively relaxed selectivity in the P2 position. In contrast, gzm K prefers large amino acids such as Phe, Tyr, and Trp in both the P2 and P3 positions and does not tolerate negatively charged residues in the P2 position. This major distinction in extended specificities is likely reflected also in preferred in vivo targets of these two enzymes. This information can now be utilized for high-precision screening of primary targets for gzms A and K in search of their highly conserved but still poorly defined functions in vertebrate immunity.
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Affiliation(s)
- Erdem Aybay
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, The Biomedical Center, Uppsala, Sweden
| | - Jinhye Ryu
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, The Biomedical Center, Uppsala, Sweden
| | - Zhirong Fu
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, The Biomedical Center, Uppsala, Sweden
| | - Srinivas Akula
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, The Biomedical Center, Uppsala, Sweden
- Department of Anatomy, Physiology, and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erika Mendez Enriquez
- Department of Medical Biochemistry and Microbiology, The Biomedical Center, Uppsala, Sweden
| | - Jenny Hallgren
- Department of Medical Biochemistry and Microbiology, The Biomedical Center, Uppsala, Sweden
| | - Sara Wernersson
- Department of Anatomy, Physiology, and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna-Karin Olsson
- Department of Medical Biochemistry and Microbiology, The Biomedical Center, Uppsala, Sweden
| | - Lars Hellman
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, The Biomedical Center, Uppsala, Sweden
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3
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Lavergne M, Hernández-Castañeda MA, Mantel PY, Martinvalet D, Walch M. Oxidative and Non-Oxidative Antimicrobial Activities of the Granzymes. Front Immunol 2021; 12:750512. [PMID: 34707614 PMCID: PMC8542974 DOI: 10.3389/fimmu.2021.750512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/23/2021] [Indexed: 01/11/2023] Open
Abstract
Cell-mediated cytotoxicity is an essential immune defense mechanism to fight against viral, bacterial or parasitic infections. Upon recognition of an infected target cell, killer lymphocytes form an immunological synapse to release the content of their cytotoxic granules. Cytotoxic granules of humans contain two membrane-disrupting proteins, perforin and granulysin, as well as a homologous family of five death-inducing serine proteases, the granzymes. The granzymes, after delivery into infected host cells by the membrane disrupting proteins, may contribute to the clearance of microbial pathogens through different mechanisms. The granzymes can induce host cell apoptosis, which deprives intracellular pathogens of their protective niche, therefore limiting their replication. However, many obligate intracellular pathogens have evolved mechanisms to inhibit programed cells death. To overcome these limitations, the granzymes can exert non-cytolytic antimicrobial activities by directly degrading microbial substrates or hijacked host proteins crucial for the replication or survival of the pathogens. The granzymes may also attack factors that mediate microbial virulence, therefore directly affecting their pathogenicity. Many mechanisms applied by the granzymes to eliminate infected cells and microbial pathogens rely on the induction of reactive oxygen species. These reactive oxygen species may be directly cytotoxic or enhance death programs triggered by the granzymes. Here, in the light of the latest advances, we review the antimicrobial activities of the granzymes in regards to their cytolytic and non-cytolytic activities to inhibit pathogen replication and invasion. We also discuss how reactive oxygen species contribute to the various antimicrobial mechanisms exerted by the granzymes.
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Affiliation(s)
- Marilyne Lavergne
- Department of Oncology, Microbiology and Immunology, Anatomy Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Maria Andrea Hernández-Castañeda
- Division Infectious Disease and International Medicine, Department of Medicine, Center for Immunology, Minneapolis, MN, United States
| | - Pierre-Yves Mantel
- Department of Oncology, Microbiology and Immunology, Anatomy Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Denis Martinvalet
- Department of Biomedical Sciences, Venetian Institute of Molecular Medicine, Padova, Italy.,Department of Biomedical Sciences, University of Padua, Padova, Italy
| | - Michael Walch
- Department of Oncology, Microbiology and Immunology, Anatomy Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
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4
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Abou-El-Hassan H, Sukhon F, Assaf EJ, Bahmad H, Abou-Abbass H, Jourdi H, Kobeissy FH. Degradomics in Neurotrauma: Profiling Traumatic Brain Injury. Methods Mol Biol 2017; 1598:65-99. [PMID: 28508358 DOI: 10.1007/978-1-4939-6952-4_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Degradomics has recently emerged as a subdiscipline in the omics era with a focus on characterizing signature breakdown products implicated in various disease processes. Driven by promising experimental findings in cancer, neuroscience, and metabolomic disorders, degradomics has significantly promoted the notion of disease-specific "degradome." A degradome arises from the activation of several proteases that target specific substrates and generate signature protein fragments. Several proteases such as calpains, caspases, cathepsins, and matrix metalloproteinases (MMPs) are involved in the pathogenesis of numerous diseases that disturb the physiologic balance between protein synthesis and protein degradation. While regulated proteolytic activities are needed for development, growth, and regeneration, uncontrolled proteolysis initiated under pathological conditions ultimately culminates into apoptotic and necrotic processes. In this chapter, we aim to review the protease-substrate repertoires in neural injury concentrating on traumatic brain injury. A striking diversity of protease substrates, essential for neuronal and brain structural and functional integrity, namely, encryptic biomarker neoproteins, have been characterized in brain injury. These include cytoskeletal proteins, transcription factors, cell cycle regulatory proteins, synaptic proteins, and cell junction proteins. As these substrates are subject to proteolytic fragmentation, they are ceaselessly exposed to activated proteases. Characterization of these molecules allows for a surge of "possible" therapeutic approaches of intervention at various levels of the proteolytic cascade.
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Affiliation(s)
- Hadi Abou-El-Hassan
- Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon.
| | - Fares Sukhon
- Faculty of Medicine, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Edwyn Jeremy Assaf
- Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hisham Bahmad
- Faculty of Medical, Neuroscience Research Center, Beirut Arab University, Beirut, Lebanon
- Faculty of Medicine, Department of Anatomy, Cell Biology and Physiological Sciences, American University of Beirut, Beirut, Lebanon
| | - Hussein Abou-Abbass
- Faculty of Medical Sciences, Neuroscience Research Center, Lebanese University, Beirut, Lebanon
- Faculty of Medicine, Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Hussam Jourdi
- Faculty of Science¸ Department of Biology, University of Balamand, Souk-el-Gharb Campus, Aley, Lebanon
| | - Firas H Kobeissy
- Faculty of Medicine, Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon.
- Department of Psychiatry, Center for Neuroproteomics and Biomarkers Research, University of Florida, Gainesville, FL, USA.
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5
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Udukala DN, Wang H, Wendel SO, Malalasekera AP, Samarakoon TN, Yapa AS, Abayaweera G, Basel MT, Maynez P, Ortega R, Toledo Y, Bossmann L, Robinson C, Janik KE, Koper OB, Li P, Motamedi M, Higgins DA, Gadbury G, Zhu G, Troyer DL, Bossmann SH. Early breast cancer screening using iron/iron oxide-based nanoplatforms with sub-femtomolar limits of detection. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:364-373. [PMID: 27335730 PMCID: PMC4901534 DOI: 10.3762/bjnano.7.33] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/17/2016] [Indexed: 06/06/2023]
Abstract
Proteases, including matrix metalloproteinases (MMPs), tissue serine proteases, and cathepsins (CTS) exhibit numerous functions in tumor biology. Solid tumors are characterized by changes in protease expression levels by tumor and surrounding tissue. Therefore, monitoring protease levels in tissue samples and liquid biopsies is a vital strategy for early cancer detection. Water-dispersable Fe/Fe3O4-core/shell based nanoplatforms for protease detection are capable of detecting protease activity down to sub-femtomolar limits of detection. They feature one dye (tetrakis(carboxyphenyl)porphyrin (TCPP)) that is tethered to the central nanoparticle by means of a protease-cleavable consensus sequence and a second dye (Cy 5.5) that is directly linked. Based on the protease activities of urokinase plasminogen activator (uPA), MMPs 1, 2, 3, 7, 9, and 13, as well as CTS B and L, human breast cancer can be detected at stage I by means of a simple serum test. By monitoring CTS B and L stage 0 detection may be achieved. This initial study, comprised of 46 breast cancer patients and 20 apparently healthy human subjects, demonstrates the feasibility of protease-activity-based liquid biopsies for early cancer diagnosis.
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Affiliation(s)
- Dinusha N Udukala
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Hongwang Wang
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Sebastian O Wendel
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Aruni P Malalasekera
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Thilani N Samarakoon
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Asanka S Yapa
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Gayani Abayaweera
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Matthew T Basel
- Kansas State University, Department of Anatomy & Physiology, 228 Coles Hall, Manhattan, KS, USA
| | - Pamela Maynez
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Raquel Ortega
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Yubisela Toledo
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Leonie Bossmann
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Colette Robinson
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Katharine E Janik
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Olga B Koper
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Ping Li
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Massoud Motamedi
- The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, USA
| | - Daniel A Higgins
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
| | - Gary Gadbury
- Kansas State University, Department of Statistics, 101 Dickens Hall, Manhattan, KS, USA
| | - Gaohong Zhu
- The First Affiliated Hospital of Kunming Medical University, Department of Nuclear Medicine, 295 Xichang Road, Kunming, Yunnan, PR China
| | - Deryl L Troyer
- Kansas State University, Department of Anatomy & Physiology, 228 Coles Hall, Manhattan, KS, USA
| | - Stefan H Bossmann
- Kansas State University, Department of Chemistry, 213 CBC Building, Manhattan, KS, USA
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6
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Tanco S, Gevaert K, Van Damme P. C-terminomics: Targeted analysis of natural and posttranslationally modified protein and peptide C-termini. Proteomics 2014; 15:903-14. [PMID: 25316308 DOI: 10.1002/pmic.201400301] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/03/2014] [Accepted: 10/09/2014] [Indexed: 01/03/2023]
Abstract
The C-terminus (where C is carboxyl) of a protein can serve as a recognition signature for a variety of biological processes, including protein trafficking and protein complex formation. Hence, the identity of the in vivo protein C-termini provides valuable information about biological processes. Analysis of protein C-termini is also crucial for the study of C-terminal PTMs, particularly for monitoring proteolytic processing by endopeptidases and carboxypeptidases. Although technical difficulties have limited the study of C-termini, a range of technologies have been proposed in the last couple of years. Here, we review the current proteomics technologies for C-terminal analysis, with a focus on the biological information that can be derived from C-terminomics studies.
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Affiliation(s)
- Sebastian Tanco
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
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7
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Ferraz Franco C, Santos R, Varela Coelho A. Proteolytic events are relevant cellular responses during nervous system regeneration of the starfish Marthasterias glacialis. J Proteomics 2014; 99:1-25. [DOI: 10.1016/j.jprot.2013.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 01/12/2023]
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8
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Granzyme M: behind enemy lines. Cell Death Differ 2014; 21:359-68. [PMID: 24413154 DOI: 10.1038/cdd.2013.189] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/12/2013] [Accepted: 11/27/2013] [Indexed: 11/08/2022] Open
Abstract
The granule-exocytosis pathway is the major mechanism via which cytotoxic lymphocytes eliminate virus-infected and tumor cells. In this pathway, cytotoxic lymphocytes release granules containing the pore-forming protein perforin and a family of serine proteases known as granzymes into the immunological synapse. Pore-formation by perforin facilitates entry of granzymes into the target cell, where they can activate various (death) pathways. Humans express five different granzymes, of which granzymes A and B have been most extensively characterized. However, much less is known about granzyme M (GrM). Recently, structural analysis and advanced proteomics approaches have determined the primary and extended specificity of GrM. GrM functions have expanded over the past few years: not only can GrM efficiently induce cell death in tumor cells, it can also inhibit cytomegalovirus replication in a noncytotoxic manner. Finally, a role for GrM in lipopolysaccharide-induced inflammatory responses has been proposed. In this review, we recapitulate the current status of GrM expression, substrate specificity, functions, and inhibitors.
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Guryča V, Lamerz J, Ducret A, Cutler P. Qualitative improvement and quantitative assessment of N-terminomics. Proteomics 2012; 12:1207-16. [PMID: 22577022 DOI: 10.1002/pmic.201100430] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Proteolysis represents one of the most tightly controlled physiological processes, as proteases create events that will typically commit pathways in an irreversible manner. Despite their implication in nearly all biological systems, our understanding of the role of proteases in disease pathology is often limited. Several approaches to studying proteolytic activity as it relates to biology, pathophysiology, and drug therapy have been published, including the recently described terminal amine isotopic labeling of substrates (TAILS) strategy by Kleifeld and colleagues. Here, we investigate TAILS as a methodology based on targeted enrichment and mass spectrometric detection of endogenous N-terminal peptides from clinically relevant biological samples and its potential to provide quantitative information on proteolysis and elucidation of the protease cleavage sites. While optimizing the most current protocol, by switching to a streamlined one-tube format and simplifying the reagents' removal steps, we demonstrate the advantages over previously published methods and provide solutions to some of the technical challenges presented in the Kleifeld publication. We also identify some of the current and unresolved limitations. We use human plasma as a model system to provide data, which illustrates some of the key analytical parameters of the modified TAILS procedure, including specificity, sensitivity, quantitative precision, and accuracy.
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Affiliation(s)
- Vilém Guryča
- Translational Research Sciences, F. Hoffmann-La Roche AG, Basel, Switzerland
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van Domselaar R, Quadir R, van der Made AM, Broekhuizen R, Bovenschen N. All human granzymes target hnRNP K that is essential for tumor cell viability. J Biol Chem 2012; 287:22854-64. [PMID: 22582387 PMCID: PMC3391115 DOI: 10.1074/jbc.m112.365692] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/11/2012] [Indexed: 11/06/2022] Open
Abstract
Granule exocytosis by cytotoxic lymphocytes is the key mechanism to eliminate virus-infected cells and tumor cells. These lytic granules contain the pore-forming protein perforin and a set of five serine proteases called granzymes. All human granzymes display distinct substrate specificities and induce cell death by cleaving critical intracellular death substrates. In the present study, we show that all human granzymes directly cleaved the DNA/RNA-binding protein heterogeneous nuclear ribonucleoprotein K (hnRNP K), designating hnRNP K as the first known pan-granzyme substrate. Cleavage of hnRNP K was more efficient in the presence of RNA and occurred in two apparent proteolysis-sensitive amino acid regions, thereby dissecting the functional DNA/RNA-binding hnRNP K domains. HnRNP K was cleaved under physiological conditions when purified granzymes were delivered into living tumor cells and during lymphokine-activated killer cell-mediated attack. HnRNP K is essential for tumor cell viability, since knockdown of hnRNP K resulted in spontaneous tumor cell apoptosis with caspase activation and reactive oxygen species production. This apoptosis was more pronounced at low tumor cell density where hnRNP K knockdown also triggered a caspase-independent apoptotic pathway. This suggests that hnRNP K promotes tumor cell survival in the absence of cell-cell contact. Silencing of hnRNP K protein expression rendered tumor cells more susceptible to cellular cytotoxicity. We conclude that hnRNP K is indispensable for tumor cell viability and our data suggest that targeting of hnRNP K by granzymes contributes to or reinforces the cell death mechanisms by which cytotoxic lymphocytes eliminate tumor cells.
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Affiliation(s)
- Robert van Domselaar
- From the Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Razi Quadir
- From the Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Astrid M. van der Made
- From the Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Roel Broekhuizen
- From the Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Niels Bovenschen
- From the Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
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11
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Tsiatsiani L, Gevaert K, Van Breusegem F. Natural substrates of plant proteases: how can protease degradomics extend our knowledge? PHYSIOLOGIA PLANTARUM 2012; 145:28-40. [PMID: 22008056 DOI: 10.1111/j.1399-3054.2011.01534.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Despite the key role of proteolysis in various intensively studied biological processes, such as plant immunity, seed development and abiotic stress responses, our knowledge on the identity of natural protease substrates in plants remains scarce. In the genome of the model plant Arabidopsis thaliana, for instance, approximately 700 genes code for proteases. However, only a few natural substrates have been identified, mainly because of the previous lack of sensitive proteomics technologies enabling the identification of low abundant proteins, together with a delay in the implementation of these technologies in the field of plant research. Here, we review the current knowledge on the identity of natural plant protease substrates and describe recently established degradomics technologies that should allow proteome-wide studies of plant proteases in the near future.
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Affiliation(s)
- Liana Tsiatsiani
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium
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12
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Jakoby T, van den Berg BHJ, Tholey A. Quantitative Protease Cleavage Site Profiling using Tandem-Mass-Tag Labeling and LC–MALDI-TOF/TOF MS/MS Analysis. J Proteome Res 2012; 11:1812-20. [DOI: 10.1021/pr201051e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Thomas Jakoby
- AG Systematische Proteomforschung, Institut für
Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel, Germany
| | - Bart HJ van den Berg
- AG Systematische Proteomforschung, Institut für
Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel, Germany
| | - Andreas Tholey
- AG Systematische Proteomforschung, Institut für
Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel, Germany
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13
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Wang LS, Xia L, Shen SM, Zheng Y, Yu Y, Chen GQ. Dissecting cell death with proteomic scalpels. Proteomics 2012; 12:597-606. [DOI: 10.1002/pmic.201100353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 09/22/2011] [Accepted: 09/26/2011] [Indexed: 01/07/2023]
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14
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van den Berg BHJ, Tholey A. Mass spectrometry-based proteomics strategies for protease cleavage site identification. Proteomics 2012; 12:516-29. [PMID: 22246699 DOI: 10.1002/pmic.201100379] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 09/14/2011] [Accepted: 09/17/2011] [Indexed: 01/22/2023]
Abstract
Protease-catalyzed hydrolysis of peptide bonds is one of the most pivotal post-translational modifications fulfilling manifold functions in the regulation of cellular processes. Therefore, dysregulation of proteolytic reactions plays a central role in many pathophysiological events. For this reason, understanding the molecular mechanisms in proteolytic reactions, in particular the knowledge of proteases involved in complex processes, expression levels and activity of protease and knowledge of the targeted substrates are an indispensable prerequisite for targeted drug development. The present review focuses on mass spectrometry-based proteomic methods for the analysis of protease cleavage sites, including the identification of the hydrolyzed bonds as well as of the surrounding sequence. Peptide- and protein-centric approaches and bioinformatic tools for experimental data interpretation will be presented and the major advantages and drawbacks of the different approaches will be addressed. The recent applications of these approaches for the analysis of biological function of different protease classes and potential future directions will be discussed.
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Affiliation(s)
- Bart H J van den Berg
- AG Systematische Proteomforschung, Institut für Experimentelle Medizin, Christian-Albrechts-Universität, Kiel, Germany.
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15
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Kazanov MD, Igarashi Y, Eroshkin AM, Cieplak P, Ratnikov B, Zhang Y, Li Z, Godzik A, Osterman AL, Smith JW. Structural determinants of limited proteolysis. J Proteome Res 2011; 10:3642-51. [PMID: 21682278 DOI: 10.1021/pr200271w] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Limited or regulatory proteolysis plays a critical role in many important biological pathways like blood coagulation, cell proliferation, and apoptosis. A better understanding of mechanisms that control this process is required for discovering new proteolytic events and for developing inhibitors with potential therapeutic value. Two features that determine the susceptibility of peptide bonds to proteolysis are the sequence in the vicinity of the scissile bond and the structural context in which the bond is displayed. In this study, we assessed statistical significance and predictive power of individual structural descriptors and combination thereof for the identification of cleavage sites. The analysis was performed on a data set of >200 proteolytic events documented in CutDB for a variety of mammalian regulatory proteases and their physiological substrates with known 3D structures. The results confirmed the significance and provided a ranking within three main categories of structural features: exposure > flexibility > local interactions. Among secondary structure elements, the largest frequency of proteolytic cleavage was confirmed for loops and lower but significant frequency for helices. Limited proteolysis has lower albeit appreciable frequency of occurrence in certain types of β-strands, which is in contrast with some previous reports. Descriptors deduced directly from the amino acid sequence displayed only marginal predictive capabilities. Homology-based structural models showed a predictive performance comparable to protein substrates with experimentally established structures. Overall, this study provided a foundation for accurate automated prediction of segments of protein structure susceptible to proteolytic processing and, potentially, other post-translational modifications.
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Affiliation(s)
- Marat D Kazanov
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
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van Domselaar R, Bovenschen N. Cell death-independent functions of granzymes: hit viruses where it hurts. Rev Med Virol 2011; 21:301-14. [PMID: 21714121 DOI: 10.1002/rmv.697] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 05/03/2011] [Accepted: 05/06/2011] [Indexed: 12/24/2022]
Abstract
Granule exocytosis by cytotoxic lymphocytes is the key mechanism of our immune response to eliminate virus-infected cells. These lytic granules contain the pore-forming protein perforin and a set of five serine proteases called granzymes (GrA, GrB, GrH, GrK, GrM) that display distinct substrate specificities. Granzymes have mostly been studied for their ability to induce cell death. However, viruses have evolved many inhibitors to effectively block apoptosis. Evidence is emerging that granzymes also use noncytotoxic strategies to inhibit viral replication and potential viral reactivation from latency. Granzymes directly cleave viral or host cell proteins that are required in the viral life cycle. Furthermore, granzymes induce a pro-inflammatory cytokine response to create an antiviral environment. In this review, we summarize and discuss these novel strategies by which the immune system counteracts viral infections, and we will address the potential therapeutic applications that could emerge from this intriguing mechanism.
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Affiliation(s)
- Robert van Domselaar
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
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