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Gummadi S, Kang T, Fonseka P, Chitti SV, Ang CS, Mathivanan S. Pep2Graph: A standalone tool to analyse proteolytic cleavages by proteases from gel-based mass spectrometry data. Proteomics 2022; 22:e2200147. [PMID: 35924633 DOI: 10.1002/pmic.202200147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/14/2022] [Accepted: 07/28/2022] [Indexed: 12/29/2022]
Abstract
Proteases are enzymes that regulate substrates via proteolytic activation and coordinate essential cellular functions including DNA replication, DNA transcription, cell proliferation, differentiation, migration and apoptosis. However, techniques to identify proteolytic events in a high-throughput manner is limited. PROtein TOpography and Migration Analysis Platform (PROTOMAP) is a technique that relies on mass spectrometry-based proteomics to globally identify the shifts in the in-gel migration of proteins and their corresponding fragments that are obtained by proteolysis. However, user-friendly software tool to analyse the proteomic data to identify proteolytic events is needed. Here, we report Pep2Graph, a user-friendly standalone tool that integrates peptide sequence information from in-gel proteomics and presents the data as two-dimensional peptographs with in-gel migration, sequence coverage and MS/MS spectra counts. Pep2Graph (http://www.mathivananlab.org/Pep2Graph) allows users to utilize in-gel proteomics data to study proteolytic events that may play a significant role in normal physiology and pathology.
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Affiliation(s)
- Sriram Gummadi
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Taeyoung Kang
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Pamali Fonseka
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Sai V Chitti
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Ching-Seng Ang
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
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Román-Meléndez GD, Venkataraman T, Monaco DR, Larman HB. Protease Activity Profiling via Programmable Phage Display of Comprehensive Proteome-Scale Peptide Libraries. Cell Syst 2020; 11:375-381.e4. [PMID: 33099407 DOI: 10.1016/j.cels.2020.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/10/2020] [Accepted: 08/18/2020] [Indexed: 12/28/2022]
Abstract
Endopeptidases catalyze the internal cleavage of proteins, playing pivotal roles in protein turnover, substrate maturation, and the activation of signaling cascades. A broad range of biological functions in health and disease are controlled by proteases, yet assays to characterize their activities at a proteomic scale do not exist. To address this unmet need, we developed Sensing EndoPeptidase Activity via Release and recapture using flAnking Tag Epitopes (SEPARATE), which uses a monovalent phage display of the human proteome at a 90-aa peptide resolution. We demonstrate that SEPARATE is compatible with several human proteases from distinct catalytic classes, including caspase-1, ADAM17, and thrombin. Both well-characterized and newly identified substrates of these enzymes were detected in the assay. SEPARATE was used to discover a non-canonical caspase-1 substrate, the E3 ubiquitin ligase HUWE1, a key mediator of apoptotic cell death. SEPARATE enables efficient, unbiased assessment of endopeptidase activity by using a phage-displayed proteome. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.
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Affiliation(s)
- Gabriel D Román-Meléndez
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA 21205
| | - Thiagarajan Venkataraman
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA 21205
| | - Daniel R Monaco
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA 21205
| | - H Benjamin Larman
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA 21205.
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3
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Satz-Jacobowitz B, Hubmacher D. The quest for substrates and binding partners: A critical barrier for understanding the role of ADAMTS proteases in musculoskeletal development and disease. Dev Dyn 2020; 250:8-26. [PMID: 32875613 DOI: 10.1002/dvdy.248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 12/16/2022] Open
Abstract
Secreted ADAMTS metalloproteases are involved in the sculpting, remodeling, and erosion of connective tissues throughout the body, including in the musculoskeletal system. ADAMTS proteases contribute to musculoskeletal development, pathological tissue destruction, and are mutated in congenital musculoskeletal disorders. Examples include versican cleavage by ADAMTS9 which is required for interdigital web regression during limb development, ADAMTS5-mediated aggrecan degradation in osteoarthritis resulting in joint erosion, and mutations in ADAMTS10 or ADAMTS17 that cause Weill-Marchesani syndrome, a short stature syndrome with bone, joint, muscle, cardiac, and eye involvement. Since the function of ADAMTS proteases and proteases in general is primarily defined by the molecular consequences of proteolysis of their respective substrates, it is paramount to identify all physiological substrates for each individual ADAMTS protease. Here, we review the current knowledge of ADAMTS proteases and their involvement in musculoskeletal development and disease, focusing on some of their known physiological substrates and the consequences of substrate cleavage. We further emphasize the critical need for the identification and validation of novel ADAMTS substrates and binding partners by describing the principles of mass spectrometry-based approaches and by emphasizing strategies that need to be considered for validating the physiological relevance for ADAMTS-mediated proteolysis of novel putative substrates.
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Affiliation(s)
- Brandon Satz-Jacobowitz
- Orthopedic Research Laboratories, Leni & Peter W. May Department of Orthopedics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dirk Hubmacher
- Orthopedic Research Laboratories, Leni & Peter W. May Department of Orthopedics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Radchenko T, Brink A, Siegrist Y, Kochansky C, Bateman A, Fontaine F, Morettoni L, Zamora I. Software-aided approach to investigate peptide structure and metabolic susceptibility of amide bonds in peptide drugs based on high resolution mass spectrometry. PLoS One 2017; 12:e0186461. [PMID: 29091918 PMCID: PMC5665424 DOI: 10.1371/journal.pone.0186461] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/02/2017] [Indexed: 01/08/2023] Open
Abstract
Interest in using peptide molecules as therapeutic agents due to high selectivity and efficacy is increasing within the pharmaceutical industry. However, most peptide-derived drugs cannot be administered orally because of low bioavailability and instability in the gastrointestinal tract due to protease activity. Therefore, structural modifications peptides are required to improve their stability. For this purpose, several in-silico software tools have been developed such as PeptideCutter or PoPS, which aim to predict peptide cleavage sites for different proteases. Moreover, several databases exist where this information is collected and stored from public sources such as MEROPS and ExPASy ENZYME databases. These tools can help design a peptide drug with increased stability against proteolysis, though they are limited to natural amino acids or cannot process cyclic peptides, for example. We worked to develop a new methodology to analyze peptide structure and amide bond metabolic stability based on the peptide structure (linear/cyclic, natural/unnatural amino acids). This approach used liquid chromatography / high resolution, mass spectrometry to obtain the analytical data from in vitro incubations. We collected experimental data for a set (linear/cyclic, natural/unnatural amino acids) of fourteen peptide drugs and four substrate peptides incubated with different proteolytic media: trypsin, chymotrypsin, pepsin, pancreatic elastase, dipeptidyl peptidase-4 and neprilysin. Mass spectrometry data was analyzed to find metabolites and determine their structures, then all the results were stored in a chemically aware manner, which allows us to compute the peptide bond susceptibility by using a frequency analysis of the metabolic-liable bonds. In total 132 metabolites were found from the various in vitro conditions tested resulting in 77 distinct cleavage sites. The most frequent observed cleavage sites agreed with those reported in the literature. The main advantages of the developed approach are the abilities to elucidate metabolite structure of cyclic peptides and those containing unnatural amino acids, store processed information in a searchable format within a database leading to frequency analysis of the labile sites for the analyzed peptides. The presented algorithm may be useful to optimize peptide drug properties with regards to cleavage sites, stability, metabolism and degradation products in drug discovery.
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Affiliation(s)
- Tatiana Radchenko
- Pompeu Fabra University, Barcelona, Spain
- Lead Molecular Design, S.L, Sant Cugat del Vallés, Spain
- * E-mail: (TR); (IZ)
| | - Andreas Brink
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Yves Siegrist
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Christopher Kochansky
- Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., West Point, Pennsylvania, United States of America
| | - Alison Bateman
- Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., West Point, Pennsylvania, United States of America
| | | | | | - Ismael Zamora
- Pompeu Fabra University, Barcelona, Spain
- Lead Molecular Design, S.L, Sant Cugat del Vallés, Spain
- * E-mail: (TR); (IZ)
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Coradin M, Karch KR, Garcia BA. Monitoring proteolytic processing events by quantitative mass spectrometry. Expert Rev Proteomics 2017; 14:409-418. [PMID: 28395554 DOI: 10.1080/14789450.2017.1316977] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Protease activity plays a key role in a wide variety of biological processes including gene expression, protein turnover and development. misregulation of these proteins has been associated with many cancer types such as prostate, breast, and skin cancer. thus, the identification of protease substrates will provide key information to understand proteolysis-related pathologies. Areas covered: Proteomics-based methods to investigate proteolysis activity, focusing on substrate identification, protease specificity and their applications in systems biology are reviewed. Their quantification strategies, challenges and pitfalls are underlined and the biological implications of protease malfunction are highlighted. Expert commentary: Dysregulated protease activity is a hallmark for some disease pathologies such as cancer. Current biochemical approaches are low throughput and some are limited by the amount of sample required to obtain reliable results. Mass spectrometry based proteomics provides a suitable platform to investigate protease activity, providing information about substrate specificity and mapping cleavage sites.
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Affiliation(s)
- Mariel Coradin
- a Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Kelly R Karch
- a Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Benjamin A Garcia
- a Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
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Te Boekhorst V, Friedl P. Plasticity of Cancer Cell Invasion-Mechanisms and Implications for Therapy. Adv Cancer Res 2016; 132:209-64. [PMID: 27613134 DOI: 10.1016/bs.acr.2016.07.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer cell migration is a plastic and adaptive process integrating cytoskeletal dynamics, cell-extracellular matrix and cell-cell adhesion, as well as tissue remodeling. In response to molecular and physical microenvironmental cues during metastatic dissemination, cancer cells exploit a versatile repertoire of invasion and dissemination strategies, including collective and single-cell migration programs. This diversity generates molecular and physical heterogeneity of migration mechanisms and metastatic routes, and provides a basis for adaptation in response to microenvironmental and therapeutic challenge. We here summarize how cytoskeletal dynamics, protease systems, cell-matrix and cell-cell adhesion pathways control cancer cell invasion programs, and how reciprocal interaction of tumor cells with the microenvironment contributes to plasticity of invasion and dissemination strategies. We discuss the potential and future implications of predicted "antimigration" therapies that target cytoskeletal dynamics, adhesion, and protease systems to interfere with metastatic dissemination, and the options for integrating antimigration therapy into the spectrum of targeted molecular therapies.
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Affiliation(s)
- V Te Boekhorst
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - P Friedl
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX, United States; Radboud University Medical Centre, Nijmegen, The Netherlands; Cancer Genomics Center (CGC.nl), Utrecht, The Netherlands.
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Arguello Casteleiro M, Klein J, Stevens R. The Proteasix Ontology. J Biomed Semantics 2016; 7:33. [PMID: 27259807 PMCID: PMC4893253 DOI: 10.1186/s13326-016-0078-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/19/2016] [Indexed: 11/10/2022] Open
Abstract
Background The Proteasix Ontology (PxO) is an ontology that supports the Proteasix tool; an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases involved in the generation of proteolytic cleavage fragments (peptides) Methods The PxO re-uses parts of the Protein Ontology, the three Gene Ontology sub-ontologies, the Chemical Entities of Biological Interest Ontology, the Sequence Ontology and bespoke extensions to the PxO in support of a series of roles: 1. To describe the known proteases and their target cleaveage sites. 2. To enable the description of proteolytic cleaveage fragments as the outputs of observed and predicted proteolysis. 3. To use knowledge about the function, species and cellular location of a protease and protein substrate to support the prioritisation of proteases in observed and predicted proteolysis. Results The PxO is designed to describe the biological underpinnings of the generation of peptides. The peptide-centric PxO seeks to support the Proteasix tool by separating domain knowledge from the operational knowledge used in protease prediction by Proteasix and to support the confirmation of its analyses and results. Availability The Proteasix Ontology may be found at: http://bioportal.bioontology.org/ontologies/PXO. This ontology is free and open for use by everyone. Electronic supplementary material The online version of this article (doi:10.1186/s13326-016-0078-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Julie Klein
- Institut National de la Sante et de la Recherche Medicale (INSERM), U1048, Toulouse, 24105, France
| | - Robert Stevens
- School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
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8
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Carvalho LAR, Ruivo EFP, Lucas SD, Moreira R. Activity-based probes as molecular tools for biomarker discovery. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00417e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Activity-based protein profiling has emerged as an exceptional tool for biomarker discovery and validation.
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Affiliation(s)
- L. A. R. Carvalho
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa. Av. Prof. Gama Pinto
- 1649-003 Lisboa
- Portugal
| | - E. F. P. Ruivo
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa. Av. Prof. Gama Pinto
- 1649-003 Lisboa
- Portugal
| | - S. D. Lucas
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa. Av. Prof. Gama Pinto
- 1649-003 Lisboa
- Portugal
| | - R. Moreira
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa. Av. Prof. Gama Pinto
- 1649-003 Lisboa
- Portugal
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van Wijk KJ. Protein maturation and proteolysis in plant plastids, mitochondria, and peroxisomes. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:75-111. [PMID: 25580835 DOI: 10.1146/annurev-arplant-043014-115547] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plastids, mitochondria, and peroxisomes are key organelles with dynamic proteomes in photosynthetic eukaryotes. Their biogenesis and activity must be coordinated and require intraorganellar protein maturation, degradation, and recycling. The three organelles together are predicted to contain ∼200 presequence peptidases, proteases, aminopeptidases, and specific protease chaperones/adaptors, but the substrates and substrate selection mechanisms are poorly understood. Similarly, lifetime determinants of organellar proteins, such as N-end degrons and tagging systems, have not been identified, but the substrate recognition mechanisms likely share similarities between organelles. Novel degradomics tools for systematic analysis of protein lifetime and proteolysis could define such protease-substrate relationships, degrons, and protein lifetime. Intraorganellar proteolysis is complemented by autophagy of whole organelles or selected organellar content, as well as by cytosolic protein ubiquitination and degradation by the proteasome. This review summarizes (putative) plant organellar protease functions and substrate-protease relationships. Examples illustrate key proteolytic events.
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Affiliation(s)
- Klaas J van Wijk
- Department of Plant Biology, Cornell University, Ithaca, New York 14853;
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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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Reumer A, Maes E, Mertens I, Cho WCS, Landuyt B, Valkenborg D, Schoofs L, Baggerman G. Colorectal cancer biomarker discovery and validation using LC-MS/MS-based proteomics in blood: truth or dare? Expert Rev Proteomics 2014; 11:449-463. [PMID: 24702250 DOI: 10.1586/14789450.2014.905743] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Globally, colorectal cancer (CRC) is the third most common malignant neoplasm. However, highly sensitive, specific, noninvasive tests that allow CRC diagnosis at an early stage are still needed. As circulatory blood reflects the physiological status of an individual and/or the disease status for several disorders, efforts have been undertaken to identify candidate diagnostic CRC markers in plasma and serum. In this review, the challenges, bottlenecks and promising properties of mass spectrometry (MS)-based proteomics in blood are discussed. More specifically, important aspects in clinical design, sample retrieval, sample preparation, and MS analysis are presented. The recent developments in targeted MS approaches in plasma or serum are highlighted as well.
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Affiliation(s)
- Ank Reumer
- KU Leuven, Animal Physiology and Neurobiology Section, Naamsestraat 59, BE-3000 Leuven, Belgium
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Filip S, Pontillo C, Peter Schanstra J, Vlahou A, Mischak H, Klein J. Urinary proteomics and molecular determinants of chronic kidney disease: possible link to proteases. Expert Rev Proteomics 2014; 11:535-48. [DOI: 10.1586/14789450.2014.926224] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Stingl C, Söderquist M, Karlsson O, Borén M, Luider TM. Uncovering Effects of Ex Vivo Protease Activity during Proteomics and Peptidomics Sample Extraction in Rat Brain Tissue by Oxygen-18 Labeling. J Proteome Res 2014; 13:2807-17. [DOI: 10.1021/pr401232e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Christoph Stingl
- Department
of Neurology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | | | - Oskar Karlsson
- Department
of Pharmaceutical Biosciences, Uppsala University, 751 05 Uppsala, Sweden
| | | | - Theo M. Luider
- Department
of Neurology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
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Shahinian H, Tholen S, Schilling O. Proteomic identification of protease cleavage sites: cell-biological and biomedical applications. Expert Rev Proteomics 2014; 10:421-33. [DOI: 10.1586/14789450.2013.841547] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Abstract
Proteolysis is a critical modification leading to alteration of protein function with important outcomes in many biological processes. However, for the majority of proteases, we have an incomplete understanding of both cellular substrates and downstream effects. Here, we describe detailed protocols and applications for using the rationally engineered peptide ligase, subtiligase, to specifically label and capture protein N-termini generated by proteases either induced or added to complex biological samples. This method allows identification of the protein targets as well as their precise cleavage locations. This approach has revealed >8000 proteolytic sites in healthy and apoptotic cells including >1700 caspase cleavages. One can further determine substrate preferences through rate analysis with quantitative mass spectrometry, physiological substrate specificities, and even infer the identity of proteases operating in the cell. In this chapter, we also describe how this experimental method can be generalized to investigate proteolysis in any biological sample.
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Stoehr G, Schaab C, Graumann J, Mann M. A SILAC-based approach identifies substrates of caspase-dependent cleavage upon TRAIL-induced apoptosis. Mol Cell Proteomics 2013; 12:1436-50. [PMID: 23319142 PMCID: PMC3650350 DOI: 10.1074/mcp.m112.024679] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The extracellular ligand-induced extrinsic pathway of apoptosis is executed via caspase protease cascades that activate downstream effectors by means of site-directed proteolysis. Here we identify proteome changes upon the induction of apoptosis by the cytokine tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) in a Jurkat T cell line. We detected caspase-dependent cleavage substrates by quantifying protein intensities before and after TRAIL induction in SDS gel slices. Apoptotic protein cleavage events are identified by a characteristic stable isotope labeling with amino acids in cell culture (SILAC) ratio pattern across gel slices that results from differential migration of the cleaved and uncleaved proteins. We applied a statistical test to define apoptotic substrates in the proteome. Our approach identified more than 650 of these cleaved proteins in response to TRAIL-induced apoptosis, including many previously unknown substrates and cleavage sites. Inhibitor treatment combined with triple SILAC demonstrated that the detected cleavage events were caspase dependent. Proteins located in the lumina of organelles such as mitochondria and endoplasmic reticulum were significantly underrepresented in the substrate population. Interestingly, caspase cleavage is generally observed in not only one but several members of stable complexes, but often with lower stoichiometry. For instance, all five proteins of the condensin I complex were cleaved upon TRAIL treatment. The apoptotic substrate proteome data can be accessed and visualized in the MaxQB database and might prove useful for basic and clinical research into TRAIL-induced apoptosis. The technology described here is extensible to a wide range of other proteolytic cleavage events.
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Affiliation(s)
- Gabriele Stoehr
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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Caseiro A, Ferreira R, Quintaneiro C, Pereira A, Marinheiro R, Vitorino R, Amado F. Protease profiling of different biofluids in type 1 diabetes mellitus. Clin Biochem 2012; 45:1613-9. [PMID: 22975642 DOI: 10.1016/j.clinbiochem.2012.08.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 08/20/2012] [Accepted: 08/26/2012] [Indexed: 12/11/2022]
Abstract
OBJECTIVES We aimed to disclose the proteolytic events underlying type 1 diabetes and related complication through protease profiling in the bodily fluids serum, urine and saliva. DESIGN AND METHODS Zymography followed by LC-MS/MS was performed for protease identification and quantitative comparison of proteolytic activity between healthy, type 1 diabetic patients with no complications and with retinopathy and nephropathy. Western blotting was also accomplished for MMP-9 and MMP-2 identification and expression analysis. RESULTS Only MMP-2 and MMP-9 were observed in serum with significantly increased levels and activity observed in diabetic patients. In urine and saliva other proteases besides MMPs were identified by MS and presented disease-dependent activity variations. Among these are complex MMP-9/Neutrophil gelatinase-associated lipocalin, aminopeptidase N, azurocidin and kallikrein 1 with more activity noticed in type 1 diabetes patients with nephropathy and/or retinopathy. CONCLUSION Our data highlight the usefulness of urine and saliva for the monitoring of type-1 diabetes-related proteolytic events, where aminopeptidase N, azurocidin and kallikrein 1 appear as promising screening targets for type 1 diabetes-related complications.
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Affiliation(s)
- Armando Caseiro
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal
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