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Jiang X, Lao Y, Spicer V, Zahedi RP. Improved Coverage of the N-Terminome by Combining ChaFRADIC with Alternative Proteases. Methods Mol Biol 2023; 2718:99-110. [PMID: 37665456 DOI: 10.1007/978-1-0716-3457-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Many proteolytic cleavage events cannot be covered with conventional trypsin-based N-terminomics workflows. These typically involve the derivatization of protein N-termini and Lys residues as an initial step, such that trypsin will cleave C-terminal of arginine but not lysine residues (ArgC-like cleavage). From 20,422 reviewed human protein sequences in Uniprot, 3597 have known N-terminal signal peptides. An in silico ArgC-like digestion of the corresponding 3597 mature protein sequences reveals that-even for these well-known and well-studied proteolytic events-trypsin-based N-terminomics workflows may miss up to 50% of signaling cleavage events as the corresponding neo-N-terminal peptides will have an unfavorable length of <7 (875 peptides) or >30 (911 peptides) amino acids. In this chapter, we provide a protocol that can be applied to all kinds of samples to improve access to this "inaccessible" N-terminome, by making use of the alternative, broad-specificity protease subtilisin for fast and reproducible digestion of proteins.
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Affiliation(s)
- Xuehui Jiang
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Ying Lao
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - René P Zahedi
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada.
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada.
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
- CancerCare Manitoba Research Institute, Winnipeg, MB, Canada.
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Song L, Zhan H, Wang Y, Lin Z, Li B, Shen L, Jiao Y, Li Y, Wang F, Yang J. Cross-Talk of Protein Expression and Lysine Acetylation in Response to TMV Infection in Nicotiana benthamiana. ACS OMEGA 2022; 7:32496-32511. [PMID: 36120045 PMCID: PMC9475610 DOI: 10.1021/acsomega.2c03917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Lysine acetylation (Kac), a reversible PTM, plays an essential role in various biological processes, including those involving metabolic pathways, pathogen resistance, and transcription, in both prokaryotes and eukaryotes. TMV, the major factor that causes the poor quality of Solanaceae crops worldwide, directly alters many metabolic processes in tobacco. However, the extent and function of Kac during TMV infection have not been determined. The validation test to detect Kac level and viral expression after TMV infection and Nicotinamide (NAM) treatment clarified that acetylation was involved in TMV infection. Furthermore, we comprehensively analyzed the changes in the proteome and acetylome of TMV-infected tobacco (Nicotiana benthamiana) seedlings via LC-MS/MS in conjunction with highly sensitive immune-affinity purification. In total, 2082 lysine-acetylated sites on 1319 proteins differentially expressed in response to TMV infection were identified. Extensive bioinformatic studies disclosed changes in acetylation of proteins engaged in cellular metabolism and biological processes. The vital influence of Kac in fatty acid degradation and alpha-linolenic acid metabolism was also revealed in TMV-infected seedlings. This study first revealed Kac information in N. benthamiana under TMV infection and expanded upon the existing landscape of acetylation in pathogen infection.
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Affiliation(s)
- Liyun Song
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Huaixu Zhan
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- Graduate
School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yujie Wang
- Luoyang
Branch of Henan Tobacco Company, Luoyang 471000, China
| | - Zhonglong Lin
- Yunnan
Tobacco Company of the China National Tobacco Corporation, Kunming 650011, China
| | - Bin Li
- Sichuan
Tobacco Company, Chengdu 610017, China
| | - Lili Shen
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Yubing Jiao
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Ying Li
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Fenglong Wang
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Jinguang Yang
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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Mintoo M, Chakravarty A, Tilvawala R. N-Terminomics Strategies for Protease Substrates Profiling. Molecules 2021; 26:molecules26154699. [PMID: 34361849 PMCID: PMC8348681 DOI: 10.3390/molecules26154699] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 01/02/2023] Open
Abstract
Proteases play a central role in various biochemical pathways catalyzing and regulating key biological events. Proteases catalyze an irreversible post-translational modification called proteolysis by hydrolyzing peptide bonds in proteins. Given the destructive potential of proteolysis, protease activity is tightly regulated. Dysregulation of protease activity has been reported in numerous disease conditions, including cancers, neurodegenerative diseases, inflammatory conditions, cardiovascular diseases, and viral infections. The proteolytic profile of a cell, tissue, or organ is governed by protease activation, activity, and substrate specificity. Thus, identifying protease substrates and proteolytic events under physiological conditions can provide crucial information about how the change in protease regulation can alter the cellular proteolytic landscape. In recent years, mass spectrometry-based techniques called N-terminomics have become instrumental in identifying protease substrates from complex biological mixtures. N-terminomics employs the labeling and enrichment of native and neo-N-termini peptides, generated upon proteolysis followed by mass spectrometry analysis allowing protease substrate profiling directly from biological samples. In this review, we provide a brief overview of N-terminomics techniques, focusing on their strengths, weaknesses, limitations, and providing specific examples where they were successfully employed to identify protease substrates in vivo and under physiological conditions. In addition, we explore the current trends in the protease field and the potential for future developments.
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Kaushal P, Lee C. N-terminomics - its past and recent advancements. J Proteomics 2020; 233:104089. [PMID: 33359939 DOI: 10.1016/j.jprot.2020.104089] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/22/2020] [Accepted: 12/20/2020] [Indexed: 02/06/2023]
Abstract
N-terminomics is a rapidly evolving branch of proteomics that encompasses the study of protein N-terminal sequence. A proteome-wide collection of such sequences has been widely used to understand the proteolytic cascades and in annotating the genome. Over the last two decades, various N-terminomic strategies have been developed for achieving high sensitivity, greater depth of coverage, and high-throughputness. We, in this review, cover how the field of N-terminomics has evolved to date, including discussion on various sample preparation and N-terminal peptide enrichment strategies. We also compare different N-terminomic methods and highlight their relative benefits and shortcomings in their implementation. In addition, an overview of the currently available bioinformatics tools and data analysis pipelines for the annotation of N-terminomic datasets is also included. SIGNIFICANCE: It has been recognized that proteins undergo several post-translational modifications (PTM), and a number of perturbed biological pathways are directly associated with modifications at the terminal sites of a protein. In this regard, N-terminomics can be applied to generate a proteome-wide landscape of mature N-terminal sequences, annotate their source of generation, and recognize their significance in the biological pathways. Besides, a system-wide study can be used to study complicated proteolytic machinery and protease cleavage patterns for potential therapeutic targets. Moreover, due to unprecedented improvements in the analytical methods and mass spectrometry instrumentation in recent times, the N-terminomic methodologies now offers an unparalleled ability to study proteoforms and their implications in clinical conditions. Such approaches can further be applied for the detection of low abundant proteoforms, annotation of non-canonical protein coding sites, identification of candidate disease biomarkers, and, last but not least, the discovery of novel drug targets.
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Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea; KHU-KIST Department of Converging Science and Technology, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul 02447, Republic of Korea.
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Chen L, Shan Y, Yang C, Sui Z, Zhang X, Zhang L, Zhang Y. Carboxypeptidase B-Assisted Charge-Based Fractional Diagonal Chromatography for Deep Screening of C-Terminome. Anal Chem 2020; 92:8005-8009. [DOI: 10.1021/acs.analchem.0c00762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lingfan Chen
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Fujian Province New Drug Safety Evaluation Centre, Fujian Medical University, Fuzhou 350108, China
| | - Yichu Shan
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chao Yang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xiaodan Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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6
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The proteome of baker's yeast mitochondria. Mitochondrion 2017; 33:15-21. [DOI: 10.1016/j.mito.2016.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/12/2016] [Accepted: 08/13/2016] [Indexed: 01/29/2023]
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7
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Venne AS, Solari FA, Faden F, Paretti T, Dissmeyer N, Zahedi RP. An improved workflow for quantitative N-terminal charge-based fractional diagonal chromatography (ChaFRADIC) to study proteolytic events in Arabidopsis thaliana. Proteomics 2016; 15:2458-69. [PMID: 26010716 DOI: 10.1002/pmic.201500014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/28/2015] [Accepted: 05/20/2015] [Indexed: 11/11/2022]
Abstract
We applied an extended charge-based fractional diagonal chromatography (ChaFRADIC) workflow to analyze the N-terminal proteome of Arabidopsis thaliana seedlings. Using iTRAQ protein labeling and a multi-enzyme digestion approach including trypsin, GluC, and subtilisin, a total of 200 μg per enzyme, and measuring only one third of each ChaFRADIC-enriched fraction by LC-MS, we quantified a total of 2791 unique N-terminal peptides corresponding to 2249 different unique N-termini from 1270 Arabidopsis proteins. Our data indicate the power, reproducibility, and sensitivity of the applied strategy that might be applicable to quantify proteolytic events from as little as 20 μg of protein per condition across up to eight different samples. Furthermore, our data clearly reflect the methionine excision dogma as well as the N-end rule degradation pathway (NERP) discriminating into a stabilizing or destabilizing function of N-terminal amino acid residues. We found bona fide NERP destabilizing residues underrepresented, and the list of neo N-termini from wild type samples may represent a helpful resource during the evaluation of NERP substrate candidates. All MS data have been deposited in the ProteomeXchange with identifier PXD001855 (http://proteomecentral.proteomexchange.org/dataset/PXD001855).
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Affiliation(s)
- A Saskia Venne
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - Fiorella A Solari
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - Frederik Faden
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - Tomasso Paretti
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany.,Department of Molecular Medicine, Institute of Biochemistry, University of Pavia, Italy
| | - Nico Dissmeyer
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
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Pagel O, Loroch S, Sickmann A, Zahedi RP. Current strategies and findings in clinically relevant post-translational modification-specific proteomics. Expert Rev Proteomics 2015; 12:235-53. [PMID: 25955281 PMCID: PMC4487610 DOI: 10.1586/14789450.2015.1042867] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometry-based proteomics has considerably extended our knowledge about the occurrence and dynamics of protein post-translational modifications (PTMs). So far, quantitative proteomics has been mainly used to study PTM regulation in cell culture models, providing new insights into the role of aberrant PTM patterns in human disease. However, continuous technological and methodical developments have paved the way for an increasing number of PTM-specific proteomic studies using clinical samples, often limited in sample amount. Thus, quantitative proteomics holds a great potential to discover, validate and accurately quantify biomarkers in body fluids and primary tissues. A major effort will be to improve the complete integration of robust but sensitive proteomics technology to clinical environments. Here, we discuss PTMs that are relevant for clinical research, with a focus on phosphorylation, glycosylation and proteolytic cleavage; furthermore, we give an overview on the current developments and novel findings in mass spectrometry-based PTM research.
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Affiliation(s)
- Oliver Pagel
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
| | | | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
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