1
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Rosochowicz MA, Kulcenty K, Suchorska WM. Exploring the Role of HtrA Family Genes in Cancer: A Systematic Review. Mol Diagn Ther 2024; 28:347-377. [PMID: 38717523 PMCID: PMC11211202 DOI: 10.1007/s40291-024-00712-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/26/2023] [Indexed: 06/28/2024]
Abstract
PURPOSE HtrA1, HtrA2, HtrA3 and HtrA4 appear to be involved in the development of pathologies such as cancer. This systematic review reports the results of a literature search performed to compare the expression of HtrA family genes and proteins in cancer versus non-cancer tissues and cell lines, assess relationships between HtrA expression and cancer clinical features in cancer, and analyse the molecular mechanism, by which HtrA family affects cancer. METHODS The literature search was conducted according to the PRISMA statement among four databases (PubMed, Web of Science, Embase and Scopus). RESULTS A total of 38 articles met the inclusion criteria and involved the expression of HtrA family members and concerned the effect of HtrA expression on cancer and metastasis development or on the factor that influences it. Additionally, 31 reports were retrieved manually. Most articles highlighted that HtrA1 and HtrA3 exhibited tumour suppressor activity, while HtrA2 was associated with tumour growth and metastasis. There were too few studies to clearly define the role of the HtrA4 protease in tumours. CONCLUSION Although the expression of serine proteases of the HtrA family was dependent on tumour type, stage and the presence of metastases, most articles indicated that HtrA1 and HtrA3 expression in tumours was downregulated compared with healthy tissue or cell lines. The expression of HtrA2 was completely study dependent. The limited number of studies on HtrA4 expression made it impossible to draw conclusions about differences in expression between healthy and tumour tissue. The conclusions drawn from the study suggest that HtrA1 and HtrA3 act as tumour suppressors.
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Affiliation(s)
- Monika Anna Rosochowicz
- Doctoral School, Poznan University of Medical Sciences, Poznan, Poland.
- Radiobiology Laboratory, Greater Poland Cancer Centre, Poznan, Poland.
- Department of Orthopaedics and Traumatology, Poznan University of Medical Sciences, Poznan, Poland.
| | | | - Wiktoria Maria Suchorska
- Radiobiology Laboratory, Greater Poland Cancer Centre, Poznan, Poland
- Department of Electroradiology, Poznan University of Medical Sciences, Poznan, Poland
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2
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Hobohm L, Koudelka T, Bahr FH, Truberg J, Kapell S, Schacht SS, Meisinger D, Mengel M, Jochimsen A, Hofmann A, Heintz L, Tholey A, Voss M. N-terminome analyses underscore the prevalence of SPPL3-mediated intramembrane proteolysis among Golgi-resident enzymes and its role in Golgi enzyme secretion. Cell Mol Life Sci 2022; 79:185. [PMID: 35279766 PMCID: PMC8918473 DOI: 10.1007/s00018-022-04163-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/07/2022] [Accepted: 01/22/2022] [Indexed: 12/17/2022]
Abstract
Golgi membrane proteins such as glycosyltransferases and other glycan-modifying enzymes are key to glycosylation of proteins and lipids. Secretion of soluble Golgi enzymes that are released from their membrane anchor by endoprotease activity is a wide-spread yet largely unexplored phenomenon. The intramembrane protease SPPL3 can specifically cleave select Golgi enzymes, enabling their secretion and concomitantly altering global cellular glycosylation, yet the entire range of Golgi enzymes cleaved by SPPL3 under physiological conditions remains to be defined. Here, we established isogenic SPPL3-deficient HEK293 and HeLa cell lines and applied N-terminomics to identify substrates cleaved by SPPL3 and released into cell culture supernatants. With high confidence, our study identifies more than 20 substrates of SPPL3, including entirely novel substrates. Notably, our N-terminome analyses provide a comprehensive list of SPPL3 cleavage sites demonstrating that SPPL3-mediated shedding of Golgi enzymes occurs through intramembrane proteolysis. Through the use of chimeric glycosyltransferase constructs we show that transmembrane domains can determine cleavage by SPPL3. Using our cleavage site data, we surveyed public proteome data and found that SPPL3 cleavage products are present in human blood. We also generated HEK293 knock-in cells expressing the active site mutant D271A from the endogenous SPPL3 locus. Immunoblot analyses revealed that secretion of select novel substrates such as the key mucin-type O-glycosylation enzyme GALNT2 is dependent on endogenous SPPL3 protease activity. In sum, our study expands the spectrum of known physiological substrates of SPPL3 corroborating its significant role in Golgi enzyme turnover and secretion as well as in the regulation of global glycosylation pathways.
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Affiliation(s)
- Laura Hobohm
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Tomas Koudelka
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany
| | - Fenja H Bahr
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Jule Truberg
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Sebastian Kapell
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Sarah-Sophie Schacht
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
- Institute of Immunology, University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Daniel Meisinger
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Marion Mengel
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Alexander Jochimsen
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Anna Hofmann
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Lukas Heintz
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
- Institute for Cellular and Integrative Physiology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany
| | - Matthias Voss
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany.
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3
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Uzozie AC, Smith TG, Chen S, Lange PF. Sensitive Identification of Known and Unknown Protease Activities by Unsupervised Linear Motif Deconvolution. Anal Chem 2022; 94:2244-2254. [PMID: 35029975 DOI: 10.1021/acs.analchem.1c04937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The cleavage-site specificities for many proteases are not well understood, restricting the utility of supervised classification methods. We present an algorithm and web interface to overcome this limitation through the unsupervised detection of overrepresented patterns in protein sequence data, providing insight into the mixture of protease activities contributing to a complex system. Here, we apply the RObust LInear Motif Deconvolution (RoLiM) algorithm to confidently detect substrate cleavage patterns for SARS-CoV-2 MPro protease in the N-terminome data of an infected human cell line. Using mass spectrometry-based peptide data from a case-control comparison of 341 primary urothelial bladder cancer cases and 110 controls, we identified distinct sequence motifs indicative of increased matrix metallopeptidase activity in urine from cancer patients. The evaluation of N-terminal peptides from patient plasma post-chemotherapy detected novel granzyme B/corin activity. RoLiM will enhance the unbiased investigation of peptide sequences to establish the composition of known and uncharacterized protease activities in biological systems. RoLiM is available at http://langelab.org/rolim/.
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Affiliation(s)
- Anuli C Uzozie
- Department of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Theodore G Smith
- Department of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Siyuan Chen
- Department of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Philipp F Lange
- Department of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada.,Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
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4
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Al-Essa MK, Alzayadneh E, Al-Hadidi K. Assessment of Proteolysis by Pyrylium and Other Fluorogenic Reagents. Protein Pept Lett 2021; 28:809-816. [PMID: 33390107 PMCID: PMC9175085 DOI: 10.2174/0929866528999201231214954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 11/22/2022]
Abstract
Aims We aim to evaluate the potential application of amine reactive fluorogenic reagents for estimating enzymatic proteolysis. Background Proteolytic enzymes play important roles in regulating many physiological processes in living organisms. Objectives
Assessment of protein degradation by using reagents for protein assay techniques. Methods We have assayed samples at the start and after 30-60 minutes incubation with trypsin by Chromeo P503 (Py 1 pyrylium compound) and CBQCA (3-(4-carboxybenzoyl) quinoline-2-carboxaldehyde) as amine reactive reagents and NanoOrange as non-amine reactive dye. Results All BSA prepared samples with trypsin have shown significantly higher fluorescence intensity (FI) versus controls (which reflects proteolysis) when assayed by Chromeo P503 (Py 1 pyrylium compound) and CBQCA (3-(4-carboxybenzoyl) quinoline-2-carboxaldehyde) as amine reactive reagents. However, same samples assayed with NanoOrange as non-amine reactive reagent did not show any significant variation between samples containing trypsin and controls. Conclusion These results are confirming reliability of highly sensitive protein assays utilizing amine reactive fluorogenic reagents for general estimation of proteolysis.
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Affiliation(s)
- Mohamed K Al-Essa
- Department of Physiology and Biochemistry, School of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Ebaa Alzayadneh
- Department of Physiology and Biochemistry, School of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Kamal Al-Hadidi
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
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5
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Martiáñez-Vendrell X, Kikkert M. Proteomics approaches for the identification of protease substrates during virus infection. Adv Virus Res 2021; 109:135-161. [PMID: 33934826 DOI: 10.1016/bs.aivir.2021.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Proteases precisely and irreversibly catalyze the hydrolysis of peptide bonds, regulating the fate, localization, and activity of many proteins. Consequently, proteolytic activity plays an important role in fundamental cellular processes such as differentiation and migration, immunological and inflammatory reactions, apoptosis and survival. During virus infection, host proteases are involved in several processes, from cell entry to initiation, progression and resolution of inflammation. On the other hand, many viruses encode their own highly specific proteases, responsible for the proteolytic processing of viral proteins, but, at the same time, to cleave host proteins to corrupt antiviral host responses and adjust protein activity to favor viral replication. Traditionally, protease substrate identification has been addressed by means of hypothesis-driven approaches, but recent advances in proteomics have made a toolkit available to uncover the extensive repertoire of host proteins cleaved during infection, either by viral or host proteases. Here, we review the currently available proteomics-based methods that can and have contributed to the systematic and unbiased identification of new protease substrates in the context of virus-host interactions. The role of specific proteases during the course of virus infections will also be highlighted.
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Affiliation(s)
- Xavier Martiáñez-Vendrell
- Molecular Virology Laboratory, Department of Medical Microbiology, LUMC Center for Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Kikkert
- Molecular Virology Laboratory, Department of Medical Microbiology, LUMC Center for Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands.
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6
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Discovery of a caspase cleavage motif antibody reveals insights into noncanonical inflammasome function. Proc Natl Acad Sci U S A 2021; 118:2018024118. [PMID: 33723046 DOI: 10.1073/pnas.2018024118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Inflammasomes sense a number of pathogen and host damage signals to initiate a signaling cascade that triggers inflammatory cell death, termed pyroptosis. The inflammatory caspases (1/4/5/11) are the key effectors of this process through cleavage and activation of the pore-forming protein gasdermin D. Caspase-1 also activates proinflammatory interleukins, IL-1β and IL-18, via proteolysis. However, compared to the well-studied apoptotic caspases, the identity of substrates and therefore biological functions of the inflammatory caspases remain limited. Here, we construct, validate, and apply an antibody toolset for direct detection of neo-C termini generated by inflammatory caspase proteolysis. By combining rabbit immune phage display with a set of degenerate and defined target peptides, we discovered two monoclonal antibodies that bind peptides with a similar degenerate recognition motif as the inflammatory caspases without recognizing the canonical apoptotic caspase recognition motif. Crystal structure analyses revealed the molecular basis of this strong yet paradoxical degenerate mode of peptide recognition. One antibody selectively immunoprecipitated cleaved forms of known and unknown inflammatory caspase substrates, allowing the identification of over 300 putative substrates of the caspase-4 noncanonical inflammasome, including caspase-7. This dataset will provide a path toward developing blood-based biomarkers of inflammasome activation. Overall, our study establishes tools to discover and detect inflammatory caspase substrates and functions, provides a workflow for designing antibody reagents to study cell signaling, and extends the growing evidence of biological cross talk between the apoptotic and inflammatory caspases.
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7
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New strategies to identify protease substrates. Curr Opin Chem Biol 2020; 60:89-96. [PMID: 33220627 DOI: 10.1016/j.cbpa.2020.09.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 12/31/2022]
Abstract
Proteome dynamics is governed by transcription, translation, and post-translational modifications. Limited proteolysis is an irreversible post-translational modification that generates multiple but unique proteoforms from almost every native protein. Elucidating these proteoforms and understanding their dynamics at a system-wide level is of utmost importance because uncontrolled proteolytic cleavages correlate with many pathologies. Mass spectrometry-based degradomics has revolutionized protease research and invented workflows for global identification of protease substrates with resolution down to precise cleavage sites. In this review, we provide an overview of current strategies in protease substrate degradomics and introduce the concept of workflow, mass spectrometry-based and in silico enrichment of protein termini with the perspective of full deconvolution of digital proteome maps for precision medicine, and degradomics biomarker diagnostics.
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8
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Chen S, Yim JJ, Bogyo M. Synthetic and biological approaches to map substrate specificities of proteases. Biol Chem 2020; 401:165-182. [PMID: 31639098 DOI: 10.1515/hsz-2019-0332] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023]
Abstract
Proteases are regulators of diverse biological pathways including protein catabolism, antigen processing and inflammation, as well as various disease conditions, such as malignant metastasis, viral infection and parasite invasion. The identification of substrates of a given protease is essential to understand its function and this information can also aid in the design of specific inhibitors and active site probes. However, the diversity of putative protein and peptide substrates makes connecting a protease to its downstream substrates technically difficult and time-consuming. To address this challenge in protease research, a range of methods have been developed to identify natural protein substrates as well as map the overall substrate specificity patterns of proteases. In this review, we highlight recent examples of both synthetic and biological methods that are being used to define the substrate specificity of protease so that new protease-specific tools and therapeutic agents can be developed.
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Affiliation(s)
- Shiyu Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua J Yim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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9
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Martin DR, Witten JC, Tan CD, Rodriguez ER, Blackstone EH, Pettersson GB, Seifert DE, Willard BB, Apte SS. Proteomics identifies a convergent innate response to infective endocarditis and extensive proteolysis in vegetation components. JCI Insight 2020; 5:135317. [PMID: 32544089 DOI: 10.1172/jci.insight.135317] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 06/10/2020] [Indexed: 02/06/2023] Open
Abstract
Infective endocarditis is a life-threatening infection of heart valves and adjacent structures characterized by vegetations on valves and other endocardial surfaces, with tissue destruction and risk of embolization. We used high-resolution mass spectrometry to define the proteome of staphylococcal and non-staphylococcal vegetations and Terminal Amine Isotopic Labeling of Substrates (TAILS) to define their proteolytic landscapes. These approaches identified over 2000 human proteins in staphylococcal and non-staphylococcal vegetations. Individual vegetation proteomes demonstrated comparable profiles of quantitatively major constituents that overlapped with serum, platelet, and neutrophil proteomes. Staphylococcal vegetation proteomes resembled one another more than the proteomes of non-staphylococcal vegetations. TAILS demonstrated extensive proteolysis within vegetations, with numerous previously undescribed cleavages. Several proteases and pathogen-specific proteins, including virulence factors, were identified in most vegetations. Proteolytic peptides in fibronectin and complement C3 were identified as potential infective endocarditis biomarkers. Overlap of staphylococcal and non-staphylococcal vegetation proteomes suggests a convergent thrombotic and immune response to endocardial infection by diverse pathogens. However, the differences between staphylococcal and non-staphylococcal vegetations and internal variance within the non-staphylococcal group indicate that additional pathogen- or patient-specific effects exist. Pervasive proteolysis of vegetation components may arise from vegetation-intrinsic proteases and destabilize vegetations, contributing to embolism.
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Affiliation(s)
- Daniel R Martin
- Department of Biomedical Engineering, Lerner Research Institute
| | - James C Witten
- Department of Thoracic and Cardiovascular Surgery, Miller Family Heart and Vascular Institute
| | - Carmela D Tan
- Department of Pathology, Robert J. Tomsich Pathology & Laboratory Medicine Institute, and
| | - E Rene Rodriguez
- Department of Pathology, Robert J. Tomsich Pathology & Laboratory Medicine Institute, and
| | - Eugene H Blackstone
- Department of Thoracic and Cardiovascular Surgery, Miller Family Heart and Vascular Institute
| | - Gosta B Pettersson
- Department of Thoracic and Cardiovascular Surgery, Miller Family Heart and Vascular Institute
| | | | - Belinda B Willard
- Proteomics and Metabolomics Core, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Suneel S Apte
- Department of Biomedical Engineering, Lerner Research Institute
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10
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Shin S, Hong JH, Na Y, Lee M, Qian WJ, Kim VN, Kim JS. Development of Multiplexed Immuno-N-Terminomics to Reveal the Landscape of Proteolytic Processing in Early Embryogenesis of Drosophila melanogaster. Anal Chem 2020; 92:4926-4934. [DOI: 10.1021/acs.analchem.9b05035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Sanghee Shin
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Ji Hye Hong
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yongwoo Na
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Mihye Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea
| | - Wei-Jun Qian
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - V. Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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11
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Belén LH, Rangel-Yagui CDO, Beltrán Lissabet JF, Effer B, Lee-Estevez M, Pessoa A, Castillo RL, Farías JG. From Synthesis to Characterization of Site-Selective PEGylated Proteins. Front Pharmacol 2019; 10:1450. [PMID: 31920645 PMCID: PMC6930235 DOI: 10.3389/fphar.2019.01450] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/12/2019] [Indexed: 02/06/2023] Open
Abstract
Covalent attachment of therapeutic proteins to polyethylene glycol (PEG) is widely used for the improvement of its pharmacokinetic and pharmacological properties, as well as the reduction in reactogenicity and related side effects. This technique named PEGylation has been successfully employed in several approved drugs to treat various diseases, even cancer. Some methods have been developed to obtain PEGylated proteins, both in multiple protein sites or in a selected amino acid residue. This review focuses mainly on traditional and novel examples of chemical and enzymatic methods for site-selective PEGylation, emphasizing in N-terminal PEGylation, that make it possible to obtain products with a high degree of homogeneity and preserve bioactivity. In addition, the main assay methods that can be applied for the characterization of PEGylated molecules in complex biological samples are also summarized in this paper.
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Affiliation(s)
- Lisandra Herrera Belén
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
| | - Carlota de Oliveira Rangel-Yagui
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Jorge F. Beltrán Lissabet
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
| | - Brian Effer
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
| | - Manuel Lee-Estevez
- Faculty of Health Sciences, Universidad Autónoma de Chile, Temuco, Chile
| | - Adalberto Pessoa
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Rodrigo L. Castillo
- Department of Internal Medicine East, Faculty of Medicine, University of Chile, Santiago de Chile, Chile
| | - Jorge G. Farías
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
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12
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Abstract
Subtiligase-catalyzed peptide ligation is a powerful approach for site-specific protein bioconjugation, synthesis and semisynthesis of proteins and peptides, and chemoproteomic analysis of cellular N termini. Here, we provide a comprehensive review of the subtiligase technology, including its development, applications, and impacts on protein science. We highlight key advantages and limitations of the tool and compare it to other peptide ligase enzymes. Finally, we provide a perspective on future applications and challenges and how they may be addressed.
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Affiliation(s)
- Amy M Weeks
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94143, United States
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13
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Molecular stratification of idiopathic nephrotic syndrome. Nat Rev Nephrol 2019; 15:750-765. [DOI: 10.1038/s41581-019-0217-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2019] [Indexed: 01/03/2023]
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14
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Grozdanić M, Vidmar R, Vizovišek M, Fonović M. Degradomics in Biomarker Discovery. Proteomics Clin Appl 2019; 13:e1800138. [PMID: 31291060 DOI: 10.1002/prca.201800138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/01/2019] [Indexed: 12/13/2022]
Abstract
The upregulation of protease expression and proteolytic activity is implicated in numerous pathological conditions such as neurodegeneration, cancer, cardiovascular and autoimmune diseases, and bone degeneration. During disease progression, various proteases form characteristic patterns of cleaved proteins and peptides, which can affect disease severity and course of progression. It has been shown that qualitative and quantitative monitoring of cleaved protease substrates can provide relevant prognostic, diagnostic, and therapeutic information. As proteolytic fragments and peptides generated in the affected tissue are commonly translocated to blood, urine, and other proximal fluids, their possible application as biomarkers is the subject of ongoing research. The field of degradomics has been established to enable the global identification of proteolytic events on the organism level, utilizing proteomic approaches and sample preparation techniques that facilitate the detection of proteolytic processing of protease substrates in complex biological samples. In this review, some of the latest developments in degradomic methodologies used for the identification and validation of biologically relevant proteolytic events and their application in the search for clinically relevant biomarker candidates are presented. The current state of degradomics in clinics is discussed and the future perspectives of the field are outlined.
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Affiliation(s)
- Marija Grozdanić
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, SI-1000, Ljubljana, Slovenia.,International Postgraduate School Jožef Stefan, SI-1000, Ljubljana, Slovenia
| | - Robert Vidmar
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, SI-1000, Ljubljana, Slovenia
| | - Matej Vizovišek
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, SI-1000, Ljubljana, Slovenia
| | - Marko Fonović
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, SI-1000, Ljubljana, Slovenia
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15
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Proteomics turns functional. J Proteomics 2019; 198:36-44. [DOI: 10.1016/j.jprot.2018.12.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 02/06/2023]
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16
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Mnatsakanyan R, Shema G, Basik M, Batist G, Borchers CH, Sickmann A, Zahedi RP. Detecting post-translational modification signatures as potential biomarkers in clinical mass spectrometry. Expert Rev Proteomics 2019; 15:515-535. [PMID: 29893147 DOI: 10.1080/14789450.2018.1483340] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Numerous diseases are caused by changes in post-translational modifications (PTMs). Therefore, the number of clinical proteomics studies that include the analysis of PTMs is increasing. Combining complementary information-for example changes in protein abundance, PTM levels, with the genome and transcriptome (proteogenomics)-holds great promise for discovering important drivers and markers of disease, as variations in copy number, expression levels, or mutations without spatial/functional/isoform information is often insufficient or even misleading. Areas covered: We discuss general considerations, requirements, pitfalls, and future perspectives in applying PTM-centric proteomics to clinical samples. This includes samples obtained from a human subject, for instance (i) bodily fluids such as plasma, urine, or cerebrospinal fluid, (ii) primary cells such as reproductive cells, blood cells, and (iii) tissue samples/biopsies. Expert commentary: PTM-centric discovery proteomics can substantially contribute to the understanding of disease mechanisms by identifying signatures with potential diagnostic or even therapeutic relevance but may require coordinated efforts of interdisciplinary and eventually multi-national consortia, such as initiated in the cancer moonshot program. Additionally, robust and standardized mass spectrometry (MS) assays-particularly targeted MS, MALDI imaging, and immuno-MALDI-may be transferred to the clinic to improve patient stratification for precision medicine, and guide therapies.
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Affiliation(s)
- Ruzanna Mnatsakanyan
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany
| | - Gerta Shema
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany
| | - Mark Basik
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada
| | - Gerald Batist
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada
| | - Christoph H Borchers
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,c University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria , Victoria , British Columbia V8Z 7X8 , Canada.,d Department of Biochemistry and Microbiology , University of Victoria , Victoria , British Columbia , V8P 5C2 , Canada.,e Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
| | - Albert Sickmann
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany.,f Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum , 44801 Bochum , Germany.,g Department of Chemistry , College of Physical Sciences, University of Aberdeen , Aberdeen AB24 3FX , Scotland , United Kingdom
| | - René P Zahedi
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany.,b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,e Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
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17
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Wu Y, Han M, Wang Y, Gao Y, Cui X, Xu P, Ji C, Zhong T, You L, Zeng Y. A Comparative Peptidomic Characterization of Cultured Skeletal Muscle Tissues Derived From db/db Mice. Front Endocrinol (Lausanne) 2019; 10:741. [PMID: 31736878 PMCID: PMC6828820 DOI: 10.3389/fendo.2019.00741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/14/2019] [Indexed: 12/19/2022] Open
Abstract
As an important secretory organ, skeletal muscle has drawn attention as a potential target tissue for type 2 diabetic mellitus (T2DM). Recent peptidomics approaches have been applied to identify secreted peptides with potential bioactive. However, comprehensive analysis of the secreted peptides from skeletal muscle tissues of db/db mice and elucidation of their possible roles in insulin resistance remains poorly characterized. Here, we adopted a label-free discovery using liquid chromatography tandem mass spectrometry (LC-MS/MS) technology and identified 63 peptides (42 up-regulated peptides and 21 down-regulated peptides) differentially secreted from cultured skeletal muscle tissues of db/db mice. Analysis of relative molecular mass (Mr), isoelectric point (pI) and distribution of Mr vs pI of differentially secreted peptides presented the general feature. Furthermore, Gene ontology (GO) and pathway analyses for the parent proteins made a comprehensive functional assessment of these differential peptides, indicating the enrichment in glycolysis/gluconeogenesis and striated muscle contraction processes. Intercellular location analysis pointed out most precursor proteins of peptides were cytoplasmic or cytoskeletal. Additionally, cleavage site analysis revealed that Lysine (N-terminal)-Alanine (C-terminal) and Lysine (N-terminal)-Leucine (C-terminal) represents the preferred cleavage sites for identified peptides and proceeding peptides respectively. Mapped to the precursors' sequences, most identified peptides were observed cleaved from creatine kinase m-type (KCRM) and fructose-bisphosphate aldolase A (Aldo A). Based on UniProt and Pfam database for specific domain structure or motif, 44 peptides out of total were positioned in the functional motif or domain from their parent proteins. Using C2C12 myotubes as cell model in vitro, we found several candidate peptides displayed promotive or inhibitory effects on insulin and mitochondrial-related pathways by an autocrine manner. Taken together, this study will encourage us to investigate the biologic functions and the potential regulatory mechanism of these secreted peptides from skeletal muscle tissues, thus representing a promising strategy to treat insulin resistance as well as the associated metabolic disorders.
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Affiliation(s)
- Yanting Wu
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- Affiliated Maternity and Child Health Care Hospital of Nantong University, NanTong, China
| | - Mei Han
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yan Wang
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yao Gao
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xianwei Cui
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Pengfei Xu
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Chenbo Ji
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Tianying Zhong
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Lianghui You
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- *Correspondence: Lianghui You
| | - Yu Zeng
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- Yu Zeng
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18
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Vizovišek M, Vidmar R, Drag M, Fonović M, Salvesen GS, Turk B. Protease Specificity: Towards In Vivo Imaging Applications and Biomarker Discovery. Trends Biochem Sci 2018; 43:829-844. [PMID: 30097385 DOI: 10.1016/j.tibs.2018.07.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/05/2018] [Accepted: 07/12/2018] [Indexed: 02/06/2023]
Abstract
Proteases are considered of major importance in biomedical research because of their crucial roles in health and disease. Their ability to hydrolyze their protein and peptide substrates at single or multiple sites, depending on their specificity, makes them unique among the enzymes. Understanding protease specificity is therefore crucial to understand their biology as well as to develop tools and drugs. Recent advancements in the fields of proteomics and chemical biology have improved our understanding of protease biology through extensive specificity profiling and identification of physiological protease substrates. There are growing efforts to transfer this knowledge into clinical modalities, but their success is often limited because of overlapping protease features, protease redundancy, and chemical tools lacking specificity. Herein, we discuss the current trends and challenges in protease research and how to exploit the growing information on protease specificities for understanding protease biology, as well as for development of selective substrates, cleavable linkers, and activity-based probes and for biomarker discovery.
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Affiliation(s)
- Matej Vizovišek
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; These authors contributed equally to this work
| | - Robert Vidmar
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; These authors contributed equally to this work
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marko Fonović
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Guy S Salvesen
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Boris Turk
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, SI-1000 Ljubljana, Slovenia.
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19
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Savickas S, Auf dem Keller U. Targeted degradomics in protein terminomics and protease substrate discovery. Biol Chem 2017; 399:47-54. [PMID: 28850541 DOI: 10.1515/hsz-2017-0187] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023]
Abstract
Targeted degradomics integrates positional information into mass spectrometry (MS)-based targeted proteomics workflows and thereby enables analysis of proteolytic cleavage events with unprecedented specificity and sensitivity. Rapid progress in the establishment of protease-substrate relations provides extensive degradomics target lists that now can be tested with help of selected and parallel reaction monitoring (S/PRM) in complex biological systems, where proteases act in physiological environments. In this minireview, we describe the general principles of targeted degradomics, outline the generic experimental workflow of the methodology and highlight recent and future applications in protease research.
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Affiliation(s)
- Simonas Savickas
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, CH-8093 Zurich, Switzerland
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej, Building 301, DK-2800 Kgs. Lyngby, Denmark
| | - Ulrich Auf dem Keller
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, CH-8093 Zurich, Switzerland
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej, Building 301, DK-2800 Kgs. Lyngby, Denmark
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20
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Engineering peptide ligase specificity by proteomic identification of ligation sites. Nat Chem Biol 2017; 14:50-57. [PMID: 29155430 PMCID: PMC5726896 DOI: 10.1038/nchembio.2521] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 10/04/2017] [Indexed: 11/08/2022]
Abstract
Enzyme-catalyzed peptide ligation is a powerful tool for site-specific protein bioconjugation, but stringent enzyme–substrate specificity limits its utility. Here, we present an approach for comprehensive characterization of peptide ligase specificity for N termini using proteome-derived peptide libraries. We used this strategy to characterize the ligation efficiency for >25,000 enzyme–substrate pairs in the context of the engineered peptide ligase subtiligase and identified a family of 72 mutant subtiligases with activity toward N-terminal sequences that were previously recalcitrant to modification. We applied these mutants individually for site-specific bioconjugation of purified proteins including antibodies, and in algorithmically selected combinations for sequencing of the cellular N terminome with reduced sequence bias. We also developed a web application to enable algorithmic selection of the most efficient subtiligase variant(s) for bioconjugation to user-defined sequences. These studies provide a new toolbox of enzymes for site-specific protein modification and a general approach for rapidly defining and engineering peptide ligase specificity.
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21
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Dufresne J, Hoang T, Ajambo J, Florentinus-Mefailoski A, Bowden P, Marshall J. Freeze-dried plasma proteins are stable at room temperature for at least 1 year. Clin Proteomics 2017; 14:35. [PMID: 29093647 PMCID: PMC5659006 DOI: 10.1186/s12014-017-9170-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/11/2017] [Indexed: 12/23/2022] Open
Abstract
Thirty human EDTA plasma samples from male and female subjects ranging in age from 24 to 74 years were collected on ice, processed ice cold and stored frozen at -80 °C, in liquid nitrogen (LN2), or freeze dried and stored at room temperature in a desiccator (FDRT) or freeze dried and stored at -20 °C for 1 year (FD-20). In a separate experiment, EDTA plasma samples were collected onto ice, processed ice cold and maintained on ice ± protease inhibitors versus incubated at room temperature for up to 96 h. Random and independent sampling by liquid chromatography and tandem mass spectrometry (LC-ESI-MS/MS), as correlated by the MASCOT, OMSSA, X!TANDEM and SEQUEST algorithms, showed that tryptic peptides from complement component 4B (C4B) were rapidly released in plasma at room temperature. Random sampling by LC-ESI-MS/MS showed that peptides from C4B were undetectable on ice, but peptides were cleaved from the mature C4B protein including NGFKSHALQLNNR within as little as 1 h at room temperature. The frequency and intensity of precursors within ± 3 m/z of the C4B peptide NGFKSHALQLNNR was confirmed by automated targeted analysis where the precursors from MS/MS spectra that correlated to the target sequence were analyzed in SQL/R. The C4B preproprotein was processed at the N terminus to release the mature chain that was cleaved on the carboxyl side of the isoprene C2 domain within a polar C terminal sequence of the mature C4B protein, to reveal the thioester reaction site, consistent with LC-ESI-MS/MS and Western blot. Random sampling showed that proteolytic peptides from complement component C4B were rarely observed with long term storage at - 80 °C in a freezer or in liquid nitrogen (LN2), freeze drying with storage at - 20 °C (FD-20 °C) or freeze drying and storage at room temperature (FDRT). Plasma samples maintained at room temperature (RT) showed at least 10-fold to 100-fold greater frequency of peptide correlation to C4B and measured peptide intensity compared to samples on ice for up to 72 h or stored at - 80 °C, LN2, FDRT or FD-20 °C for up to a year.
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Affiliation(s)
- Jaimie Dufresne
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - Trung Hoang
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - Juliet Ajambo
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | | | - Peter Bowden
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada
| | - John Marshall
- Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3 Canada.,Integrated BioBank of Luxembourg, 6 r. Nicolas-Ernest Barblé, 1210 Luxembourg, Luxembourg
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22
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Abstract
The formation of well-defined protein bioconjugates is critical for many studies and technologies in chemical biology. Tried-and-true methods for accomplishing this typically involve the targeting of cysteine residues, but the rapid growth of contemporary bioconjugate applications has required an expanded repertoire of modification techniques. One very powerful set of strategies involves the modification of proteins at their N termini, as these positions are typically solvent exposed and provide chemically distinct sites for many protein targets. Several chemical techniques can be used to modify N-terminal amino acids directly or convert them into unique functional groups for further ligations. A growing number of N-terminus-specific enzymatic ligation strategies have provided additional possibilities. This Perspective provides an overview of N-terminal modification techniques and the chemical rationale governing each. Examples of specific N-terminal protein conjugates are provided, along with their uses in a number of diverse biological applications.
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23
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Marshall NC, Finlay BB, Overall CM. Sharpening Host Defenses during Infection: Proteases Cut to the Chase. Mol Cell Proteomics 2017; 16:S161-S171. [PMID: 28179412 PMCID: PMC5393396 DOI: 10.1074/mcp.o116.066456] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/03/2017] [Indexed: 01/14/2023] Open
Abstract
The human immune system consists of an intricate network of tightly controlled pathways, where proteases are essential instigators and executioners at multiple levels. Invading microbial pathogens also encode proteases that have evolved to manipulate and dysregulate host proteins, including host proteases during the course of disease. The identification of pathogen proteases as well as their substrates and mechanisms of action have empowered significant developments in therapeutics for infectious diseases. Yet for many pathogens, there remains a great deal to be discovered. Recently, proteomic techniques have been developed that can identify proteolytically processed proteins across the proteome. These “degradomics” approaches can identify human substrates of microbial proteases during infection in vivo and expose the molecular-level changes that occur in the human proteome during infection as an operational network to develop hypotheses for further research as well as new therapeutics. This Perspective Article reviews how proteases are utilized during infection by both the human host and invading bacterial pathogens, including archetypal virulence-associated microbial proteases, such as the Clostridia spp. botulinum and tetanus neurotoxins. We highlight the potential knowledge that degradomics studies of host–pathogen interactions would uncover, as well as how degradomics has been successfully applied in similar contexts, including use with a viral protease. We review how microbial proteases have been targeted in current therapeutic approaches and how microbial proteases have shaped and even contributed to human therapeutics beyond infectious disease. Finally, we discuss how, moving forward, degradomics research can greatly contribute to our understanding of how microbial pathogens cause disease in vivo and lead to the identification of novel substrates in vivo, and the development of improved therapeutics to counter these pathogens.
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Affiliation(s)
- Natalie C Marshall
- From the ‡Department of Microbiology & Immunology.,§Michael Smith Laboratories
| | - B Brett Finlay
- From the ‡Department of Microbiology & Immunology.,§Michael Smith Laboratories.,¶Department of Biochemistry & Molecular Biology
| | - Christopher M Overall
- ¶Department of Biochemistry & Molecular Biology, .,**Department of Oral Biological & Medical Sciences, Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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24
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Calvo SE, Julien O, Clauser KR, Shen H, Kamer KJ, Wells JA, Mootha VK. Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast. Mol Cell Proteomics 2017; 16:512-523. [PMID: 28122942 DOI: 10.1074/mcp.m116.063818] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 01/06/2017] [Indexed: 01/08/2023] Open
Abstract
The majority of mitochondrial proteins are encoded in the nuclear genome, translated in the cytoplasm, and directed to the mitochondria by an N-terminal presequence that is cleaved upon import. Recently, N-proteome catalogs have been generated for mitochondria from yeast and from human U937 cells. Here, we applied the subtiligase method to determine N-termini for 327 proteins in mitochondria isolated from mouse liver and kidney. Comparative analysis between mitochondrial N-termini from mouse, human, and yeast proteins shows that whereas presequences are poorly conserved at the sequence level, other presequence properties are extremely conserved, including a length of ∼20-60 amino acids, a net charge between +3 to +6, and the presence of stabilizing amino acids at the N-terminus of mature proteins that follow the N-end rule from bacteria. As in yeast, ∼80% of mouse presequence cleavage sites match canonical motifs for three mitochondrial peptidases (MPP, Icp55, and Oct1), whereas the remainder do not match any known peptidase motifs. We show that mature mitochondrial proteins often exist with a spectrum of N-termini, consistent with a model of multiple cleavage events by MPP and Icp55. In addition to analysis of canonical targeting presequences, our N-terminal dataset allows the exploration of other cleavage events and provides support for polypeptide cleavage into two distinct enzymes (Hsd17b4), protein cleavages key for signaling (Oma1, Opa1, Htra2, Mavs, and Bcs2l13), and in several cases suggests novel protein isoforms (Scp2, Acadm, Adck3, Hsdl2, Dlst, and Ogdh). We present an integrated catalog of mammalian mitochondrial N-termini that can be used as a community resource to investigate individual proteins, to elucidate mechanisms of mammalian mitochondrial processing, and to allow researchers to engineer tags distally to the presequence cleavage.
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Affiliation(s)
- Sarah E Calvo
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114; .,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115.,¶Broad Institute, Cambridge, Massachusetts 02141
| | | | | | - Hongying Shen
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Kimberli J Kamer
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - James A Wells
- **Departments of Pharmaceutical Chemistry and.,§§Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143
| | - Vamsi K Mootha
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
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26
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Kawano Y, Takahashi W, Eto M, Kamba T, Miyake H, Fujisawa M, Kamai T, Uemura H, Tsukamoto T, Azuma H, Matsubara A, Nishimura K, Nakamura T, Ogawa O, Naito S. Prognosis of metastatic renal cell carcinoma with first-line interferon-α therapy in the era of molecular-targeted therapy. Cancer Sci 2016; 107:1013-7. [PMID: 27089226 PMCID: PMC4946720 DOI: 10.1111/cas.12951] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/20/2016] [Accepted: 04/15/2016] [Indexed: 12/27/2022] Open
Abstract
The RCC‐SELECT study showed the correlation between single nucleotide polymorphisms (SNP) in STAT3 gene and survival in metastatic renal cell carcinoma (mRCC) patients with first‐line interferon‐α (IFN‐α). In that study, even patients with STAT3 SNP linked to shorter overall survival (OS) exhibited remarkably improved prognosis. All 180 patients evaluated in the above study were further analyzed for correlation between OS and demographics/clinicopathological parameters. OS was estimated using the Kaplan–Meier method. Associations between OS and potential prognostic factors were assessed using the log‐rank test and the Cox proportional hazards model. The median OS was 42.8 months. Univariate analysis showed that worse Eastern Cooperative Oncology Group‐performance status (ECOG‐PS), high T stage, regional lymph node metastasis, distant metastasis, higher grade, infiltrative growth pattern, the presence of microscopic vascular invasion (MVI), hypercalcemia, anemia, thrombocytopenia and elevated C‐reactive protein were significantly associated with OS. Multivariate analysis revealed that ECOG‐PS (hazard ratio [HR] = 3.665, P = 0.0004), hypercalcemia (HR = 6.428, P = 0.0005) and the presence of MVI (HR = 2.668, P = 0.0109) were jointly significant poor prognostic factors. This is the first study analysing prognostic factors of mRCC patients with first‐line IFN‐α using large cohort of the prospective study. The present study suggests that first‐line IFN‐α is still a useful therapy for mRCC even in the era of molecular targeted therapy.
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Affiliation(s)
- Yoshiaki Kawano
- Department of Urology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Wataru Takahashi
- Department of Urology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Masatoshi Eto
- Department of Urology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.,Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomomi Kamba
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hideaki Miyake
- Division of Urology, Department of Surgery Related, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masato Fujisawa
- Division of Urology, Department of Surgery Related, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takao Kamai
- Department of Urology, Dokkyo Medical University, Shimotsuka- gun, Tochigi, Japan
| | - Hirotsugu Uemura
- Department of Urology, Kinki University School of Medicine, Osaka-Sayama, Japan
| | - Taiji Tsukamoto
- Department of Urologic Surgery and Andrology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Haruhito Azuma
- Department of Urology, Osaka Medical College, Takatsuki, Japan
| | - Akio Matsubara
- Department of Urology, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuo Nishimura
- Department of Urology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Tsuyoshi Nakamura
- Graduate School of Science and Engineering, Chuo University, Tokyo, Japan
| | - Osamu Ogawa
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seiji Naito
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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27
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Eckhard U, Marino G, Butler GS, Overall CM. Positional proteomics in the era of the human proteome project on the doorstep of precision medicine. Biochimie 2016; 122:110-8. [DOI: 10.1016/j.biochi.2015.10.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/28/2015] [Indexed: 12/30/2022]
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28
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Jordal PL, Dyrlund TF, Winge K, Larsen MR, Danielsen EH, Wells JA, Otzen DE, Enghild JJ. Detection of proteolytic signatures for Parkinson's disease. FUTURE NEUROLOGY 2016. [DOI: 10.2217/fnl.16.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To investigate if idiopathic Parkinson's disease (IPD) is associated with distinct proteolytic signatures relative to non-neurodegenerative controls (NND) and patients with multiple system atrophy (MSA). Materials & methods: A subtiligase-based N-terminomics screening method was exploited for semiquantitative comparison of protein N-termini in cerebrospinal fluid for pooled samples of IPD (n = 6) and NND (n = 8) individuals. Subsequently, targeted selected reaction monitoring mass spectrometry measured the relative concentration of the proteolytic signature peptides in individual IPD (n = 22), NND (n = 11) and MSA (n = 18) samples. Results: The discovery screen detected 300 N-termini for 156 proteins. Selected reaction monitoring analysis revealed that two of these peptides differentiate IPD from NND while three peptides differentiate IPD from MSA. Conclusion: IPD is associated with distinct proteolytic signatures.
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Affiliation(s)
- Peter Lüttge Jordal
- Section for Medical Biotechnology, Danish Technological Institute, 8000 Aarhus C, Denmark
- Department of Molecular Biology & Genetics, Aarhus University, 8000 Aarhus C, Denmark
- iNANO, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Thomas F Dyrlund
- Department of Molecular Biology & Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Kristian Winge
- Bispebjerg Movement Disorders Biobank, Department of Neurology, Bispebjerg University Hospital, 2400, Copenhagen NV, Denmark
| | - Martin R Larsen
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Erik H Danielsen
- Department of Neurology, Aarhus University Hospital, 8000 Aarhus C, Denmark
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Daniel E Otzen
- Department of Molecular Biology & Genetics, Aarhus University, 8000 Aarhus C, Denmark
- iNANO, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Jan J Enghild
- Department of Molecular Biology & Genetics, Aarhus University, 8000 Aarhus C, Denmark
- iNANO, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
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29
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Pu J, Chronis I, Ahn D, Dickinson BC. A Panel of Protease-Responsive RNA Polymerases Respond to Biochemical Signals by Production of Defined RNA Outputs in Live Cells. J Am Chem Soc 2015; 137:15996-9. [PMID: 26652972 DOI: 10.1021/jacs.5b10290] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA is an attractive biomolecule for biosensing and engineering applications due to its information storage capacity and ability to drive gene expression or knockdown. However, methods to link chemical signals to the production of specific RNAs are lacking. Here, we develop protease-responsive RNA polymerases (PRs) as a strategy to encode multiple specific proteolytic events in defined sequences of RNA in live mammalian cells. This work demonstrates that RNAP-based molecular recording devices can be deployed for multimodal analyses of biochemical activities or to trigger gene circuits using measured signaling events.
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Affiliation(s)
- Jinyue Pu
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Ian Chronis
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Daniel Ahn
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
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30
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Anania VG, Lill JR. Proteomic tools for the characterization of cell death mechanisms in drug discovery. Proteomics Clin Appl 2015; 9:671-83. [DOI: 10.1002/prca.201400151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 01/28/2015] [Accepted: 02/18/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Veronica G. Anania
- Department of Biomarker Development; Genentech, Inc; South San Francisco CA USA
| | - Jennie R. Lill
- Department of Protein Chemistry; Genentech, Inc. South San Francisco CA USA
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31
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One-step site-specific modification of native proteins with 2-pyridinecarboxyaldehydes. Nat Chem Biol 2015; 11:326-31. [PMID: 25822913 DOI: 10.1038/nchembio.1792] [Citation(s) in RCA: 236] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/06/2015] [Indexed: 01/01/2023]
Abstract
The chemical modification of proteins is an enabling technology for many scientific fields, including chemical biology, biophysics, bioengineering and materials science. These methods allow the attachment of strategically selected detection probes, polymers, drug molecules and analysis platforms. However, organic reactions that can proceed under conditions mild enough to maintain biomolecular function are limited. Even more rare are chemical strategies that can target a single site, leading to products with uniform properties and optimal function. We present a versatile method for the selective modification of protein N termini that does not require any genetic engineering of the protein target. This reaction is demonstrated for 12 different proteins, including the soluble domain of the human estrogen receptor. The function of this protein was confirmed through the binding of a fluorescent estrogen mimic, and the modified protein was explored as a prototype for the detection of endocrine-disrupting chemicals in water.
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32
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Wysocka M, Wojtysiak A, Okońska M, Gruba N, Jarząb M, Wenta T, Lipińska B, Grzywa R, Sieńczyk M, Rolka K, Lesner A. Design and synthesis of new substrates of HtrA2 protease. Anal Biochem 2015; 475:44-52. [PMID: 25640585 DOI: 10.1016/j.ab.2015.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 01/17/2015] [Accepted: 01/19/2015] [Indexed: 11/27/2022]
Abstract
HtrA2 belongs to the HtrA (high temperature requirement A) family of ATP-independent serine proteases. The primary function of HtrA2 includes maintaining the mitochondria homeostasis, cell death (by apoptosis, necrosis, or anoikis), and contribution to the cell signaling. Several recent reports have shown involvement of HtrA2 in development of cancer and neurodegenerative disorders. Here, we describe the profiling of HtrA2 protease substrate specificity via the combinatorial chemistry approach that led to the selection of novel intramolecularly quenched substrates. For all synthesized compounds, the highest HtrA2-mediated hydrolysis efficiency and selectivity among tested HtrA family members was observed for ABZ-Ile-Met-Thr-Abu-Tyr-Met-Phe-Tyr(3-NO2)-NH2, which displayed a specificity constant kcat/KM value of 14,535M(-1)s(-1).
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Affiliation(s)
| | - Anna Wojtysiak
- Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland
| | | | - Natalia Gruba
- Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland
| | - Mirosław Jarząb
- Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland
| | - Tomasz Wenta
- Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland
| | | | - Reneta Grzywa
- Faculty of Chemistry, Wroclaw Technical University, 50-370 Wrocław, Poland
| | - Marcin Sieńczyk
- Faculty of Chemistry, Wroclaw Technical University, 50-370 Wrocław, Poland
| | - Krzysztof Rolka
- Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland
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33
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Sabino F, Hermes O, Egli FE, Kockmann T, Schlage P, Croizat P, Kizhakkedathu JN, Smola H, auf dem Keller U. In vivo assessment of protease dynamics in cutaneous wound healing by degradomics analysis of porcine wound exudates. Mol Cell Proteomics 2014; 14:354-70. [PMID: 25516628 DOI: 10.1074/mcp.m114.043414] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Proteases control complex tissue responses by modulating inflammation, cell proliferation and migration, and matrix remodeling. All these processes are orchestrated in cutaneous wound healing to restore the skin's barrier function upon injury. Altered protease activity has been implicated in the pathogenesis of healing impairments, and proteases are important targets in diagnosis and therapy of this pathology. Global assessment of proteolysis at critical turning points after injury will define crucial events in acute healing that might be disturbed in healing disorders. As optimal biospecimens, wound exudates contain an ideal proteome to detect extracellular proteolytic events, are noninvasively accessible, and can be collected at multiple time points along the healing process from the same wound in the clinics. In this study, we applied multiplexed Terminal Amine Isotopic Labeling of Substrates (TAILS) to globally assess proteolysis in early phases of cutaneous wound healing. By quantitative analysis of proteins and protein N termini in wound fluids from a clinically relevant pig wound model, we identified more than 650 proteins and discerned major healing phases through distinctive abundance clustering of markers of inflammation, granulation tissue formation, and re-epithelialization. TAILS revealed a high degree of proteolysis at all time points after injury by detecting almost 1300 N-terminal peptides in ∼450 proteins. Quantitative positional proteomics mapped pivotal interdependent processing events in the blood coagulation and complement cascades, temporally discerned clotting and fibrinolysis during the healing process, and detected processing of complement C3 at distinct time points after wounding and by different proteases. Exploiting data on primary cleavage specificities, we related candidate proteases to cleavage events and revealed processing of the integrin adapter protein kindlin-3 by caspase-3, generating new hypotheses for protease-substrate relations in the healing skin wound in vivo. The data have been deposited to the ProteomeXchange Consortium with identifier PXD001198.
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Affiliation(s)
- Fabio Sabino
- From the ‡ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Olivia Hermes
- From the ‡ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Fabian E Egli
- From the ‡ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Tobias Kockmann
- From the ‡ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Pascal Schlage
- From the ‡ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Pierre Croizat
- §Paul Hartmann AG, Paul Hartmann Strasse 12, 89522 Heidenheim, Germany
| | - Jayachandran N Kizhakkedathu
- ¶University of British Columbia, Department of Pathology and Laboratory Medicine and Department of Chemistry, Centre for Blood Research, 4.401 Life Sciences Institute, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Hans Smola
- §Paul Hartmann AG, Paul Hartmann Strasse 12, 89522 Heidenheim, Germany
| | - Ulrich auf dem Keller
- From the ‡ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland;
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34
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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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