1
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Hanna R, Rozenberg A, Saied L, Ben-Yosef D, Lavy T, Kleifeld O. In-Depth Characterization of Apoptosis N-terminome Reveals a Link Between Caspase-3 Cleavage and Post-Translational N-terminal Acetylation. Mol Cell Proteomics 2023:100584. [PMID: 37236440 PMCID: PMC10362333 DOI: 10.1016/j.mcpro.2023.100584] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 05/28/2023] Open
Abstract
The N-termini of proteins contain information about their biochemical properties and functions. These N-termini can be processed by proteases, and can undergo other co- or post-translational modifications. We have developed LATE (LysN Amino Terminal Enrichment), a method that uses selective chemical derivatization of α-amines to isolate the N-terminal peptides, in order to improve N-terminome identification in conjunction with other enrichment strategies. We applied LATE alongside another N-terminomic method to study caspase-3 mediated proteolysis both in vitro and during apoptosis in cells. This has enabled us to identify many unreported caspase-3 cleavages, some of which cannot be identified by other methods. Moreover, we have found direct evidence that neo-N-termini generated by caspase-3 cleavage can be further modified by Nt-acetylation. Some of these neo-Nt-acetylation events occur in the early phase of the apoptotic process and may have a role in translation inhibition. This has provided a comprehensive overview of the caspase-3 degradome and has uncovered previously unrecognized crosstalk between post-translational Nt-acetylation and caspase proteolytic pathways.
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Affiliation(s)
- Rawad Hanna
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Layla Saied
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Daniel Ben-Yosef
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Tali Lavy
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Oded Kleifeld
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel.
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2
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Wang R, Wang Z, Lu H. Separation methods for system-wide profiling of protein terminome. Proteomics 2023; 23:e2100374. [PMID: 35997653 DOI: 10.1002/pmic.202100374] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022]
Abstract
Protein N- and C-termini have specific biochemical properties and functions. They play vital roles in various biological processes, such as protein stability and localization. In addition, post-translational modifications and proteolytic processing generate different proteoforms at protein termini. In recent years, terminomics has attracted significant attention, and numerous strategies have been developed to achieve high-throughput and global terminomics analysis. This review summarizes the recent protein N-termini and C-termini enrichment methods and their application in different samples. We also look ahead further application of terminomics in profiling protease substrates and discovery of disease biomarkers and therapeutic targets.
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Affiliation(s)
- Rui Wang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Zhongjie Wang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China.,Department of Chemistry and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai, People's Republic of China
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3
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Chen W, Ji G, Wu R, Fang C, Lu H. Mass spectrometry-based candidate substrate and site identification of PTM enzymes. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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4
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Fernandez B, Armengaud J, Subra G, Enjalbal C. MALDI‐MS/MS of N‐Terminal TMPP‐Acyl Peptides: A Worthwhile Tool to Decipher Protein N‐Termini. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bernard Fernandez
- IBMM Université de Montpellier, CNRS, ENSCM 34293 Montpellier France
- Université Paris-Saclay, CEA, INRAE Département Médicaments et Technologies pour la Santé (DMTS) SPI 30200 Bagnols-sur-Cèze France
- Present address: CIRAD, UMR ASTRE 34398 Montpellier France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE Département Médicaments et Technologies pour la Santé (DMTS) SPI 30200 Bagnols-sur-Cèze France
| | - Gilles Subra
- IBMM Université de Montpellier, CNRS, ENSCM 34293 Montpellier France
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5
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Deep N-terminomics of Mycobacterium tuberculosis H37Rv extensively correct annotated encoding genes. Genomics 2021; 114:292-304. [PMID: 34915127 DOI: 10.1016/j.ygeno.2021.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/28/2021] [Accepted: 12/09/2021] [Indexed: 11/24/2022]
Abstract
Mycobacterium tuberculosis (MTB) is a severe causing agent of tuberculosis (TB). Although H37Rv, the type strain of M. tuberculosis was sequenced in 1998, annotation errors of encoding genes have been frequently reported in hundreds of papers. This phenomenon is particularly severe at the 5' end of the genes. Here, we applied a TMPP [(N-Succinimidyloxycarbonylmethyl) tris (2,4,6-trimethoxyphenyl) phosphonium bromide] labeling combined with StageTip separating strategy on M. tuberculosis H37Rv to characterize the N-terminal start sites of its annotated encoding genes. Totally, 1047 proteins were identified with 2058 TMPP labeled N-terminal peptides from all the 2625 mass spectrometer (MS) sequenced proteins. Comparative genomics analysis allowed the re-annotation of 43 proteins' N-termini in H37Rv and 762 proteins in Mycobacteriaceae. All revised N-termini start sites were distributed in 5'-UTR of annotated genes due to over-annotation of previous N-terminal initiation codon, especially the ATG. In addition, we identified and verified a novel gene Rv1078A in +3 frame different from the annotated gene Rv1078 in +2 frame. Altogether, our findings contribute to the better understanding of N-terminal of H37Rv and other species from Mycobacteriaceae that can assist future studies on biological study.
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6
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Koudelka T, Winkels K, Kaleja P, Tholey A. Shedding light on both ends: An update on analytical approaches for N- and C-terminomics. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119137. [PMID: 34626679 DOI: 10.1016/j.bbamcr.2021.119137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/27/2021] [Accepted: 09/06/2021] [Indexed: 02/04/2023]
Abstract
Though proteases were long regarded as nonspecific degradative enzymes, over time, it was recognized that they also hydrolyze peptide bonds very specifically with a limited substrate pool. This irreversible posttranslational modification modulates the fate and activity of many proteins, making proteolytic processing a master switch in the regulation of e.g., the immune system, apoptosis and cancer progression. N- and C-terminomics, the identification of protein termini, has become indispensable in elucidating protease substrates and therefore protease function. Further, terminomics has the potential to identify yet unknown proteoforms, e.g. formed by alternative splicing or the recently discovered alternative ORFs. Different strategies and workflows have been developed that achieve higher sensitivity, a greater depth of coverage or higher throughput. In this review, we summarize recent developments in both N- and C-terminomics and include the potential of top-down proteomics which inherently delivers information on both ends of analytes in a single analysis.
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Affiliation(s)
- Tomas Koudelka
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Konrad Winkels
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Patrick Kaleja
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
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7
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Bagal D, Gibson BW. Identification of Proteolysis Products in Protein Therapeutics through TMPP N-Terminal Tagging and Electron Transfer Dissociation Product Triggered Collisional Induced Dissociation Fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1936-1944. [PMID: 33534996 DOI: 10.1021/jasms.0c00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Thorough characterization of protein therapeutics is often challenging due to the heterogeneity arising from primary sequence variants, post-translational modifications, proteolytic clipping, or incomplete processing of the signal peptide. Modern mass spectrometry (MS) techniques are now routinely used to characterize such heterogeneous protein populations. Here, we present an LC-MS/MS method using (N-succinimidyloxycarbonylmethyl)-tris (2,4,6-trimethoxyphenyl) phosphonium bromide (TMPP-Ac-OSu) to label any free N-terminal α-amines to rapidly and selectively identify proteolytic clipping events. Electron transfer dissociation (ETD) fragmentation of these chemically tagged peptides generates two unique TMPP product ions, TMPP+ and TMPP-Ac-NH2/c0. The presence of these signature ions following ETD is used to trigger subsequent collisional induced dissociation (CID) fragmentation of the precursor ion. This results in a small subset of CID tandem MS spectra that are used in a customized database search. Using a purified fusion monoclonal antibody (mAb) as an example, we demonstrate how TMPP labeling followed by ETD product ion triggered CID fragmentation is used to accurately identify two undesired clipping sites.
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Affiliation(s)
- Dhanashri Bagal
- Amgen Discovery Research, Discovery Attribute Sciences, South San Francisco, California 94080, United States
| | - Bradford W Gibson
- Amgen Discovery Research, Discovery Attribute Sciences, South San Francisco, California 94080, United States
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8
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Zaikin VG, Borisov RS. Options of the Main Derivatization Approaches for Analytical ESI and MALDI Mass Spectrometry. Crit Rev Anal Chem 2021; 52:1287-1342. [PMID: 33557614 DOI: 10.1080/10408347.2021.1873100] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The inclusion of preliminary chemical labeling (derivatization) in the analysis process by such powerful and widespread methods as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a popular and widely used methodological approach. This is due to the need to remove some fundamental limitations inherent in these powerful analytic methods. Although a number of special reviews has been published discussing the utilization of derivatization approaches, the purpose of the present critical review is to comprehensively summarize, characterize and evaluate most of the previously developed and practically applied, as well as recently proposed representative derivatization reagents for ESI-MS and MALDI-MS platforms in their mostly sensitive positive ion mode and frequently hyphenated with separation techniques. The review is focused on the use of preliminary chemical labeling to facilitate the detection, identification, structure elucidation, quantification, profiling or MS imaging of compounds within complex matrices. Two main derivatization approaches, namely the introduction of permanent charge-fixed or highly proton affinitive residues into analytes are critically evaluated. In situ charge-generation, charge-switch and charge-transfer derivatizations are considered separately. The potential of using reactive matrices in MALDI-MS and chemical labeling in MS-based omics sciences is given.
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Affiliation(s)
- Vladimir G Zaikin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
| | - Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
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9
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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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10
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Abstract
INTRODUCTION The N-terminus of a protein can encode several protein features, including its half-live and its localization. As the proteomics field remains dominated by bottom-up approaches and as N-terminal peptides only account for a fraction of all analyzable peptides, there is a need for their enrichment prior to analysis. COFRADIC, TAILS, and the subtiligase method were among the first N-terminomics methods developed, and several variants and novel methods were introduced that often reduce processing time and/or the amount of material required. AREAS COVERED We present an overview of how the field of N-terminomics developed, including a discussion of the founding methods, several updates made to these and introduce newer methods such as TMPP-labeling, biotin-based methods besides some necessary improvements in data analysis. EXPERT OPINION N-terminomic methods remain being used and improved methods are published however, more efficient use of contemporary mass spectrometers, promising data-independent approaches, and mass spectrometry-free single peptide or protein sequences may threat the N-terminomics field.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
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11
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Marcus K, Lelong C, Rabilloud T. What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World? Proteomes 2020; 8:proteomes8030017. [PMID: 32781532 PMCID: PMC7563651 DOI: 10.3390/proteomes8030017] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis depth is of critical importance, for many others, two-dimensional gel electrophoresis-based proteomics still has a lot to offer. This is because of its robustness, its ability to separate proteoforms, and its easy interface with many powerful biochemistry techniques (including western blotting). This paper reviews where and why two-dimensional gel electrophoresis-based proteomics can still be profitably used. It emerges that, rather than being a thing of the past, two-dimensional gel electrophoresis-based proteomics is still highly valuable for many studies. Thus, its use cannot be dismissed on simple fashion arguments and, as usual, in science, the tree is to be judged by the fruit.
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Affiliation(s)
- Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty & Medical Proteome Analysis, Center for Proteindiagnostics (PRODI) Ruhr-University Bochum Gesundheitscampus, 4 44801 Bochum, Germany;
| | - Cécile Lelong
- CBM UMR CNRS5249, Université Grenoble Alpes, CEA, CNRS, 17 rue des Martyrs, CEDEX 9, 38054 Grenoble, France;
| | - Thierry Rabilloud
- Laboratory of Chemistry and Biology of Metals, UMR 5249, Université Grenoble Alpes, CNRS, 38054 Grenoble, France
- Correspondence: ; Tel.: +33-438-783-212
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12
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Bons J, Macron C, Aude-Garcia C, Vaca-Jacome SA, Rompais M, Cianférani S, Carapito C, Rabilloud T. A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level. Mol Cell Proteomics 2019; 18:1085-1095. [PMID: 31154437 PMCID: PMC6553941 DOI: 10.1074/mcp.ra118.001269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/14/2019] [Indexed: 12/19/2022] Open
Abstract
All but thirteen mammalian mitochondrial proteins are encoded by the nuclear genome, translated in the cytosol and then imported into the mitochondria. For a significant proportion of the mitochondrial proteins, import is coupled with the cleavage of a presequence called the transit peptide, and the formation of a new N-terminus. Determination of the neo N-termini has been investigated by proteomic approaches in several systems, but generally in a static way to compile as many N-termini as possible. In the present study, we have investigated how the mitochondrial proteome and N-terminome react to chemical stimuli that alter mitochondrial metabolism, namely zinc ions and rapamycin. To this end, we have used a strategy that analyzes both internal and N-terminal peptides in a single run, the dN-TOP approach. We used these two very different stressors to sort out what could be a generic response to stress and what is specific to each of these stressors. Rapamycin and zinc induced different changes in the mitochondrial proteome. However, convergent changes to key mitochondrial enzymatic activities such as pyruvate dehydrogenase, succinate dehydrogenase and citrate synthase were observed for both treatments. Other convergent changes were seen in components of the N-terminal processing system and mitochondrial proteases. Investigations into the generation of neo-N-termini in mitochondria showed that the processing system is robust, as indicated by the lack of change in neo N-termini under the conditions tested. Detailed analysis of the data revealed that zinc caused a slight reduction in the efficiency of the N-terminal trimming system and that both treatments increased the degradation of mitochondrial proteins. In conclusion, the use of this combined strategy allowed a detailed analysis of the dynamics of the mitochondrial N-terminome in response to treatments which impact the mitochondria.
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Affiliation(s)
- Joanna Bons
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Charlotte Macron
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Catherine Aude-Garcia
- §Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS UMR5249, CEA, BIG-LCBM, 38000 Grenoble, France
| | - Sebastian Alvaro Vaca-Jacome
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Magali Rompais
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Sarah Cianférani
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Christine Carapito
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France;
| | - Thierry Rabilloud
- §Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS UMR5249, CEA, BIG-LCBM, 38000 Grenoble, France
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13
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Kaushal P, Kwon Y, Ju S, Lee C. An SDS-PAGE based proteomic approach for N-terminome profiling. Analyst 2019; 144:7001-7009. [DOI: 10.1039/c9an01616c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Schematic diagram of the SDS-PAGE based N-termini enrichment (GelNrich) workflow.
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Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
| | - Yumi Kwon
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Shinyeong Ju
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Cheolju Lee
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
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14
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Bhagwat SR, Hajela K, Kumar A. Proteolysis to Identify Protease Substrates: Cleave to Decipher. Proteomics 2018; 18:e1800011. [DOI: 10.1002/pmic.201800011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 04/03/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Sonali R. Bhagwat
- Discipline of Biosciences and Biomedical Engineering; Indian Institute of Technology; Indore 453552 Simrol India
| | - Krishnan Hajela
- School of Life Sciences; Devi Ahilya Vishwavidyalaya; Indore 452001 India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering; Indian Institute of Technology; Indore 453552 Simrol India
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15
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N-terminome and proteogenomic analysis of the Methylobacterium extorquens DM4 reference strain for dichloromethane utilization. J Proteomics 2018; 179:131-139. [DOI: 10.1016/j.jprot.2018.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/28/2018] [Accepted: 03/16/2018] [Indexed: 12/29/2022]
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16
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Li Y, Wang Z, Zhou W, Zhang K, Ma J, Wu F, Ji J, Hong X, Deng Z, He S, Xu P. A rapid and easy protein N-terminal profiling strategy using (N
-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) labeling and StageTip. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600481] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/21/2017] [Accepted: 06/03/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Yanchang Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Zhiqiang Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing P. R. China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals; State Key Laboratory of Virology; Wuhan University School of Pharmaceutical Sciences; Wuhan P. R. China
| | - Wenjing Zhou
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology; CAS; Beijing P. R. China
| | - Kun Zhang
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology; CAS; Beijing P. R. China
| | - Jie Ma
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Feilin Wu
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Jianguo Ji
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences; Peking University; Beijing P. R. China
| | - Xuechuan Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals; State Key Laboratory of Virology; Wuhan University School of Pharmaceutical Sciences; Wuhan P. R. China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals; State Key Laboratory of Virology; Wuhan University School of Pharmaceutical Sciences; Wuhan P. R. China
| | - Simin He
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology; CAS; Beijing P. R. China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing P. R. China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals; State Key Laboratory of Virology; Wuhan University School of Pharmaceutical Sciences; Wuhan P. R. China
- Anhui Medical University; Hefei P. R. China
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17
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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: 4.4] [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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18
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Westermann B, Jacome ASV, Rompais M, Carapito C, Schaeffer-Reiss C. Doublet N-Terminal Oriented Proteomics for N-Terminomics and Proteolytic Processing Identification. Methods Mol Biol 2017; 1574:77-90. [PMID: 28315244 DOI: 10.1007/978-1-4939-6850-3_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The study of the N-terminome and the precise identification of proteolytic processing events are key in biology. Dedicated methodologies have been developed as the comprehensive characterization of the N-terminome can hardly be achieved by standard proteomics methods. In this context, we have set up a trimethoxyphenyl phosphonium (TMPP) labeling approach that allows the characterization of both N-terminal and internal digestion peptides in a single experiment. This latter point is a major advantage of our strategy as most N-terminomics methods rely on the enrichment of N-terminal peptides and thus exclude internal peptides.We have implemented a double heavy/light TMPP labeling and an automated data validation workflow that make our doublet N-terminal oriented proteomics (dN-TOP) strategy efficient for high-throughput N-terminome analysis.
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Affiliation(s)
- Benoit Westermann
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, CNRS-UdS, UMR 7178, University of Strasbourg, 25, rue Becquerel, 67087, Strasbourg, France
| | - Alvaro Sebastian Vaca Jacome
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, CNRS-UdS, UMR 7178, University of Strasbourg, 25, rue Becquerel, 67087, Strasbourg, France
| | - Magali Rompais
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, CNRS-UdS, UMR 7178, University of Strasbourg, 25, rue Becquerel, 67087, Strasbourg, France
| | - Christine Carapito
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, CNRS-UdS, UMR 7178, University of Strasbourg, 25, rue Becquerel, 67087, Strasbourg, France
| | - Christine Schaeffer-Reiss
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, CNRS-UdS, UMR 7178, University of Strasbourg, 25, rue Becquerel, 67087, Strasbourg, France.
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19
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Kullolli M, Rock DA, Ma J. Immuno-affinity Capture Followed by TMPP N-Terminus Tagging to Study Catabolism of Therapeutic Proteins. J Proteome Res 2016; 16:911-919. [DOI: 10.1021/acs.jproteome.6b00863] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Majlinda Kullolli
- Department
of Pharmacokinetics and Drug Metabolism, Amgen Inc., South San Francisco, California 94080, United States
| | - Dan A. Rock
- Department
of Pharmacokinetics and Drug Metabolism, Amgen Inc., South San Francisco, California 94080, United States
| | - Ji Ma
- Department
of Pharmacokinetics and Drug Metabolism, Amgen Inc., South San Francisco, California 94080, United States
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20
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Rhiel M, Bittl V, Tribensky A, Charnaud SC, Strecker M, Müller S, Lanzer M, Sanchez C, Schaeffer-Reiss C, Westermann B, Crabb BS, Gilson PR, Külzer S, Przyborski JM. Trafficking of the exported P. falciparum chaperone PfHsp70x. Sci Rep 2016; 6:36174. [PMID: 27824087 PMCID: PMC5099922 DOI: 10.1038/srep36174] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/07/2016] [Indexed: 01/20/2023] Open
Abstract
Plasmodium falciparum extensively modifies its chosen host cell, the mature human erythrocyte. This remodelling is carried out by parasite-encoded proteins that are exported into the host cell. To gain access to the human red blood cell, these proteins must cross the parasitophorous vacuole, a membrane bound compartment surrounding the parasite that is generated during the invasion process. Many exported proteins carry a so-called PEXEL/HT signal that directs their transport. We recently reported the unexpected finding of a species-restricted parasite-encoded Hsp70, termed PfHsp70x, which is exported into the host erythrocyte cytosol. PfHsp70x lacks a classical PEXEL/HT motif, and its transport appears to be mediated by a 7 amino acid motif directly following the hydrophobic N-terminal secretory signal. In this report, we analyse this short targeting sequence in detail. Surprisingly, both a reversed and scrambled version of the motif retained the capacity to confer protein export. Site directed mutagenesis of glutamate residues within this region leads to a block of protein trafficking within the lumen of the PV. In contrast to PEXEL-containing proteins, the targeting signal is not cleaved, but appears to be acetylated. Furthermore we show that, like other exported proteins, trafficking of PfHsp70x requires the vacuolar translocon, PTEX.
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Affiliation(s)
- Manuel Rhiel
- Parasitology, FB Biology, Philipps University Marburg, Karl von Frisch Strasse 8, 35043 Marburg, Germany.,Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Verena Bittl
- Parasitology, FB Biology, Philipps University Marburg, Karl von Frisch Strasse 8, 35043 Marburg, Germany
| | - Anke Tribensky
- Parasitology, FB Biology, Philipps University Marburg, Karl von Frisch Strasse 8, 35043 Marburg, Germany
| | - Sarah C Charnaud
- Burnet Institute, Melbourne, Vic. 3004, Australia.,Monash University, Melbourne, Vic. 3800, Australia
| | - Maja Strecker
- Parasitology, FB Biology, Philipps University Marburg, Karl von Frisch Strasse 8, 35043 Marburg, Germany
| | - Sebastian Müller
- Parasitology, FB Biology, Philipps University Marburg, Karl von Frisch Strasse 8, 35043 Marburg, Germany
| | - Michael Lanzer
- Zentrum für Infektiologie, Parasitologie, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Cecilia Sanchez
- Zentrum für Infektiologie, Parasitologie, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR 7178, Strasbourg, France
| | - Benoit Westermann
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR 7178, Strasbourg, France
| | - Brendan S Crabb
- Burnet Institute, Melbourne, Vic. 3004, Australia.,Monash University, Melbourne, Vic. 3800, Australia.,University of Melbourne, Melbourne, Vic. 3010, Australia
| | - Paul R Gilson
- Burnet Institute, Melbourne, Vic. 3004, Australia.,Monash University, Melbourne, Vic. 3800, Australia
| | - Simone Külzer
- Parasitology, FB Biology, Philipps University Marburg, Karl von Frisch Strasse 8, 35043 Marburg, Germany.,Research School of Biology, ANU, Acton, ACT 2601, Australia
| | - Jude M Przyborski
- Parasitology, FB Biology, Philipps University Marburg, Karl von Frisch Strasse 8, 35043 Marburg, Germany
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21
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Abstract
Omics approaches have become popular in biology as powerful discovery tools, and currently gain in interest for diagnostic applications. Establishing the accurate genome sequence of any organism is easy, but the outcome of its annotation by means of automatic pipelines remains imprecise. Some protein-encoding genes may be missed as soon as they are specific and poorly conserved in a given taxon, while important to explain the specific traits of the organism. Translational starts are also poorly predicted in a relatively important number of cases, thus impacting the protein sequence database used in proteomics, comparative genomics, and systems biology. The use of high-throughput proteomics data to improve genome annotation is an attractive option to obtain a more comprehensive molecular picture of a given organism. Here, protocols for reannotating prokaryote genomes are described based on shotgun proteomics and derivatization of protein N-termini with a positively charged reagent coupled to high-resolution tandem mass spectrometry.
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22
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Armengaud J. Power of positive thinking in quantitative proteomics. Proteomics 2016; 15:2898-900. [PMID: 26227558 DOI: 10.1002/pmic.201500307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 07/24/2015] [Indexed: 01/20/2023]
Abstract
Derivatization of proteins with specific isotope reagents has been widely explored for quantitative proteomics where the relative abundances of proteins present in different complex samples are compared by MS. This represents an interesting arena for innovation, where protein chemistry and MS are associated for the best of both worlds. Among the numerous reagents developed, those that introduce a permanent positive charge, such as (N-succinimidyloxycarbonylmethyl)-tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP), increase the ionizability of their targets and thus improve the sensitivity of the approach. TMPP labeling also modifies the hydrophobicity and changes the peptide fragmentation pattern. Because TMPP reacts preferably with the N-termini of proteins and peptides, its use has been explored for proteogenomics and de novo protein sequencing. In this issue of Proteomics, Shen et al. (Proteomics 2015, 15, 2903-2909) show that accurate quantitation of proteins can be obtained with light/heavy TMPP-labeling of peptides, which can be easily prepared and desalted in a homemade C8-SCX-C8 stagetip, and then monitored by nano-LC-MS/MS analysis. Their results demonstrate enhanced sequence coverage compared with other approaches. Combined with an efficient enrichment procedure, the higher sensitivity of this "positive attitude" reagent may facilitate much deeper investigations into the quantitative proteomics of complex samples.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory "Innovative technologies for Detection and Diagnostics", Bagnols-sur-Cèze, France
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23
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Vizovišek M, Vidmar R, Fonović M, Turk B. Current trends and challenges in proteomic identification of protease substrates. Biochimie 2016; 122:77-87. [DOI: 10.1016/j.biochi.2015.10.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/23/2015] [Indexed: 10/22/2022]
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24
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Locard-Paulet M, Pible O, Gonzalez de Peredo A, Alpha-Bazin B, Almunia C, Burlet-Schiltz O, Armengaud J. Clinical implications of recent advances in proteogenomics. Expert Rev Proteomics 2016; 13:185-99. [DOI: 10.1586/14789450.2016.1132169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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25
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Abstract
In the past decade, proteogenomics has emerged as a valuable technique that contributes to the state-of-the-art in genome annotation; however, previous proteogenomic studies were limited to bottom-up mass spectrometry and did not take advantage of top-down approaches. We show that top-down proteogenomics allows one to address the problems that remained beyond the reach of traditional bottom-up proteogenomics. In particular, we show that top-down proteogenomics leads to the discovery of previously unannotated genes even in extensively studied bacterial genomes and present SpectroGene, a software tool for genome annotation using top-down tandem mass spectra. We further show that top-down proteogenomics searches (against the six-frame translation of a genome) identify nearly all proteoforms found in traditional top-down proteomics searches (against the annotated proteome). SpectroGene is freely available at http://github.com/fenderglass/SpectroGene .
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Affiliation(s)
- Mikhail Kolmogorov
- Department of Computer Science and Engineering, UCSD, 9500 Gilman Drive, La Jolla, CA, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, IUPUI, 719 Indiana Ave, Suite 304, Indianapolis, IN, USA
| | - Pavel A. Pevzner
- Department of Computer Science and Engineering, UCSD, 9500 Gilman Drive, La Jolla, CA, USA
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26
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Berry IJ, Steele JR, Padula MP, Djordjevic SP. The application of terminomics for the identification of protein start sites and proteoforms in bacteria. Proteomics 2015; 16:257-72. [DOI: 10.1002/pmic.201500319] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/21/2015] [Accepted: 09/30/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Iain J. Berry
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Joel R. Steele
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Matthew P. Padula
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Steven P. Djordjevic
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
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27
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Arsène-Ploetze F, Bertin PN, Carapito C. Proteomic tools to decipher microbial community structure and functioning. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:13599-13612. [PMID: 25475614 PMCID: PMC4560766 DOI: 10.1007/s11356-014-3898-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/20/2014] [Indexed: 06/04/2023]
Abstract
Recent advances in microbial ecology allow studying microorganisms in their environment, without laboratory cultivation, in order to get access to the large uncultivable microbial community. With this aim, environmental proteomics has emerged as an appropriate complementary approach to metagenomics providing information on key players that carry out main metabolic functions and addressing the adaptation capacities of living organisms in situ. In this review, a wide range of proteomic approaches applied to investigate the structure and functioning of microbial communities as well as recent examples of such studies are presented.
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Affiliation(s)
- Florence Arsène-Ploetze
- Génétique moléculaire, Génomique et Microbiologie, Université de Strasbourg, UMR7156 CNRS, Strasbourg, France,
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28
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Lai ZW, Gomez-Auli A, Keller EJ, Mayer B, Biniossek ML, Schilling O. Enrichment of protein N-termini by charge reversal of internal peptides. Proteomics 2015; 15:2470-8. [DOI: 10.1002/pmic.201500023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 04/01/2015] [Accepted: 05/21/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Zon W. Lai
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
| | - Alejandro Gomez-Auli
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
- Faculty of Biology; University of Freiburg; Freiburg Germany
- Spemann Graduate School of Biology and Medicine; University of Freiburg; Freiburg Germany
| | - Eva J. Keller
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
| | - Bettina Mayer
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
| | - Martin L. Biniossek
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
- Spemann Graduate School of Biology and Medicine; University of Freiburg; Freiburg Germany
- BIOSS Centre for Biological Signaling Studies; University of Freiburg; Freiburg Germany
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29
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Shen H, An M, Zou X, Zhao X, Wang Q, Xing G, Ji J. Evaluation of the accuracy of protein quantification using isotope TMPP-labeled peptides. Proteomics 2015; 15:2903-9. [DOI: 10.1002/pmic.201400495] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 03/12/2015] [Accepted: 04/28/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Hongyan Shen
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Mingrui An
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Xiao Zou
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Xuyang Zhao
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Qingsong Wang
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Guowen Xing
- Institute of Organic Chemistry; College of Chemistry; Beijing Normal University; Beijing P. R. China
| | - Jianguo Ji
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
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30
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Vaca Jacome AS, Rabilloud T, Schaeffer-Reiss C, Rompais M, Ayoub D, Lane L, Bairoch A, Van Dorsselaer A, Carapito C. N-terminome analysis of the human mitochondrial proteome. Proteomics 2015; 15:2519-24. [DOI: 10.1002/pmic.201400617] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/10/2015] [Accepted: 04/30/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Alvaro Sebastian Vaca Jacome
- BioOrganic Mass Spectrometry Laboratory (LSMBO); Université de Strasbourg; IPHC; Strasbourg France
- IPHC, CNRS; UMR7178; Strasbourg France
| | - Thierry Rabilloud
- Laboratoire de Chimie et Biologie des Métaux; UMR CNRS-CEA-UGA 5249; iRTSV/LCBM, CEA Grenoble Grenoble France
| | - Christine Schaeffer-Reiss
- BioOrganic Mass Spectrometry Laboratory (LSMBO); Université de Strasbourg; IPHC; Strasbourg France
- IPHC, CNRS; UMR7178; Strasbourg France
| | - Magali Rompais
- BioOrganic Mass Spectrometry Laboratory (LSMBO); Université de Strasbourg; IPHC; Strasbourg France
- IPHC, CNRS; UMR7178; Strasbourg France
| | - Daniel Ayoub
- BioOrganic Mass Spectrometry Laboratory (LSMBO); Université de Strasbourg; IPHC; Strasbourg France
- IPHC, CNRS; UMR7178; Strasbourg France
| | - Lydie Lane
- CALIPHO Group; SIB-Swiss Institute of Bioinformatics; Geneva Switzerland
- Department of Human Protein Sciences; Faculty of Medicine; Geneva Switzerland
| | - Amos Bairoch
- CALIPHO Group; SIB-Swiss Institute of Bioinformatics; Geneva Switzerland
- Department of Human Protein Sciences; Faculty of Medicine; Geneva Switzerland
| | - Alain Van Dorsselaer
- BioOrganic Mass Spectrometry Laboratory (LSMBO); Université de Strasbourg; IPHC; Strasbourg France
- IPHC, CNRS; UMR7178; Strasbourg France
| | - Christine Carapito
- BioOrganic Mass Spectrometry Laboratory (LSMBO); Université de Strasbourg; IPHC; Strasbourg France
- IPHC, CNRS; UMR7178; Strasbourg France
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31
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Koniev O, Wagner A. Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation. Chem Soc Rev 2015; 44:5495-551. [PMID: 26000775 DOI: 10.1039/c5cs00048c] [Citation(s) in RCA: 397] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioconjugation methodologies have proven to play a central enabling role in the recent development of biotherapeutics and chemical biology approaches. Recent endeavours in these fields shed light on unprecedented chemical challenges to attain bioselectivity, biocompatibility, and biostability required by modern applications. In this review the current developments in various techniques of selective bond forming reactions of proteins and peptides were highlighted. The utility of each endogenous amino acid-selective conjugation methodology in the fields of biology and protein science has been surveyed with emphasis on the most relevant among reported transformations; selectivity and practical use have been discussed.
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Affiliation(s)
- Oleksandr Koniev
- Laboratory of Functional Chemo-Systems (UMR 7199), Labex Medalis, University of Strasbourg, 74 Route du Rhin, 67401 Illkirch-Graffenstaden, France.
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32
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Abstract
Determination of a protein's N-terminal sequence can be important for the characterization of protein processing. To increase the confidence of protein N-terminal identification, chemical derivatization of the N-terminal amine group by (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) or dimethyl labeling followed by mass spectrometric analysis is commonly performed. Using this approach, proteins can be separated by SDS-PAGE, and the protein N-terminus of interest is labeled by TMPP or dimethyl in-gel before tryptic digestion and LC-MS analysis. The N-terminus of a protein can thus be easily identified because the N-terminal tryptic peptides are preferentially labeled. Peptides with N-terminal derivatization produce a better fragmentation pattern during tandem mass spectrometric analysis, which significantly facilitates sequencing of these peptides.
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33
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Kucharova V, Wiker HG. Proteogenomics in microbiology: taking the right turn at the junction of genomics and proteomics. Proteomics 2014; 14:2360-675. [PMID: 25263021 DOI: 10.1002/pmic.201400168] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/18/2014] [Accepted: 09/23/2014] [Indexed: 12/14/2022]
Abstract
High-accuracy and high-throughput proteomic methods have completely changed the way we can identify and characterize proteins. MS-based proteomics can now provide a unique supplement to genomic data and add a new level of information to the interpretation of genomic sequences. Proteomics-driven genome annotation has become especially relevant in microbiology where genomes are sequenced on a daily basis and limitations of an in silico driven annotation process are well recognized. In this review paper, we outline different strategies on how one can design a proteogenomic experiment, for example on genome-sequenced (synonymous proteogenomics) versus unsequenced organisms (ortho-proteogenomics) or with the aid of other "omic" data such as RNA-seq. We touch upon many challenges that are encountered during a typical proteogenomic study, mostly concerning bioinformatics methods and downstream data analysis, but also related to creation and use of sequence databases. A large list of proteogenomic case studies of different microorganisms is provided to illustrate the mapping of MS/MS-derived peptide spectra to genomic DNA sequences. These investigations have led to accurate determination of translational initiation sites, pointed out eventual read-throughs or programmed frameshifts, detected signal peptide processing or other protein maturation events, removed questionable annotation assignments, and provided evidence for predicted hypothetical proteins.
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Affiliation(s)
- Veronika Kucharova
- Department of Clinical Science, The Gade Research Group for Infection and Immunity, University of Bergen, Norway
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34
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Boichenko AP, Govorukhina N, Klip HG, van der Zee AGJ, Güzel C, Luider TM, Bischoff R. A panel of regulated proteins in serum from patients with cervical intraepithelial neoplasia and cervical cancer. J Proteome Res 2014; 13:4995-5007. [PMID: 25232869 DOI: 10.1021/pr500601w] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We developed a discovery-validation mass-spectrometry-based pipeline to identify a set of proteins that are regulated in serum of patients with cervical intraepithelial neoplasia (CIN) and squamous cell cervical cancer using iTRAQ, label-free shotgun, and targeted mass-spectrometric quantification. In the discovery stage we used a "pooling" strategy for the comparative analysis of immunodepleted serum and revealed 15 up- and 26 down-regulated proteins in patients with early- (CES) and late-stage (CLS) cervical cancer. The analysis of nondepleted serum samples from patients with CIN, CES, an CLS and healthy controls showed significant changes in abundance of alpha-1-acid glycoprotein 1, alpha-1-antitrypsin, serotransferrin, haptoglobin, alpha-2-HS-glycoprotein, and vitamin D-binding protein. We validated our findings using a fast UHPLC/MRM method in an independent set of serum samples from patients with cervical cancer or CIN and healthy controls as well as serum samples from patients with ovarian cancer (more than 400 samples in total). The panel of six proteins showed 67% sensitivity and 88% specificity for discrimination of patients with CIN from healthy controls, a stage of the disease where current protein-based biomarkers, for example, squamous cell carcinoma antigen (SCCA), fail to show any discrimination. Additionally, combining the six-protein panel with SCCA improves the discrimination of patients with CES and CLS from healthy controls.
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Affiliation(s)
- Alexander P Boichenko
- Department of Analytical Biochemistry, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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35
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Hartmann EM, Armengaud J. N-terminomics and proteogenomics, getting off to a good start. Proteomics 2014; 14:2637-46. [PMID: 25116052 DOI: 10.1002/pmic.201400157] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 04/23/2014] [Accepted: 08/08/2014] [Indexed: 12/11/2022]
Abstract
Proteogenomics consists of the annotation or reannotation of protein-coding nucleic acid sequences based on the empirical observation of their gene products. While functional annotation of predicted genes is increasingly feasible given the multiplicity of genomes available for many branches of the tree of life, the accurate annotation of the translational start sites is still a point of contention. Extensive coverage of the proteome, including specifically the N-termini, is now possible, thanks to next-generation mass spectrometers able to record data from thousands of proteins at once. Efforts to increase the peptide coverage of protein sequences and to detect low abundance proteins are important to make proteomic and proteogenomic studies more comprehensive. In this review, we present the panoply of N-terminus-oriented strategies that have been developed over the last decade.
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Affiliation(s)
- Erica M Hartmann
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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Carapito C, Burel A, Guterl P, Walter A, Varrier F, Bertile F, Van Dorsselaer A. MSDA, a proteomics software suite for in-depth Mass Spectrometry Data Analysis using grid computing. Proteomics 2014; 14:1014-9. [DOI: 10.1002/pmic.201300415] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 01/15/2014] [Accepted: 01/15/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique; IPHC; Université de Strasbourg; CNRS; UMR7178 Strasbourg France
| | - Alexandre Burel
- Laboratoire de Spectrométrie de Masse BioOrganique; IPHC; Université de Strasbourg; CNRS; UMR7178 Strasbourg France
| | - Patrick Guterl
- Laboratoire de Spectrométrie de Masse BioOrganique; IPHC; Université de Strasbourg; CNRS; UMR7178 Strasbourg France
| | - Alexandre Walter
- Laboratoire de Spectrométrie de Masse BioOrganique; IPHC; Université de Strasbourg; CNRS; UMR7178 Strasbourg France
| | - Fabrice Varrier
- Laboratoire de Spectrométrie de Masse BioOrganique; IPHC; Université de Strasbourg; CNRS; UMR7178 Strasbourg France
| | - Fabrice Bertile
- Laboratoire de Spectrométrie de Masse BioOrganique; IPHC; Université de Strasbourg; CNRS; UMR7178 Strasbourg France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique; IPHC; Université de Strasbourg; CNRS; UMR7178 Strasbourg France
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Bland C, Hartmann EM, Christie-Oleza JA, Fernandez B, Armengaud J. N-Terminal-oriented proteogenomics of the marine bacterium roseobacter denitrificans Och114 using N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) labeling and diagonal chromatography. Mol Cell Proteomics 2014; 13:1369-81. [PMID: 24536027 DOI: 10.1074/mcp.o113.032854] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Given the ease of whole genome sequencing with next-generation sequencers, structural and functional gene annotation is now purely based on automated prediction. However, errors in gene structure are frequent, the correct determination of start codons being one of the main concerns. Here, we combine protein N termini derivatization using (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP Ac-OSu) as a labeling reagent with the COmbined FRActional DIagonal Chromatography (COFRADIC) sorting method to enrich labeled N-terminal peptides for mass spectrometry detection. Protein digestion was performed in parallel with three proteases to obtain a reliable automatic validation of protein N termini. The analysis of these N-terminal enriched fractions by high-resolution tandem mass spectrometry allowed the annotation refinement of 534 proteins of the model marine bacterium Roseobacter denitrificans OCh114. This study is especially efficient regarding mass spectrometry analytical time. From the 534 validated N termini, 480 confirmed existing gene annotations, 41 highlighted erroneous start codon annotations, five revealed totally new mis-annotated genes; the mass spectrometry data also suggested the existence of multiple start sites for eight different genes, a result that challenges the current view of protein translation initiation. Finally, we identified several proteins for which classical genome homology-driven annotation was inconsistent, questioning the validity of automatic annotation pipelines and emphasizing the need for complementary proteomic data. All data have been deposited to the ProteomeXchange with identifier PXD000337.
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Affiliation(s)
- Céline Bland
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
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Shen H, He Z, Yan H, Xing Z, Chen Y, Xu W, Xu W, Ma M. The fronds tonoplast quantitative proteomic analysis in arsenic hyperaccumulator Pteris vittata L. J Proteomics 2014; 105:46-57. [PMID: 24508335 DOI: 10.1016/j.jprot.2014.01.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 01/22/2014] [Accepted: 01/27/2014] [Indexed: 12/30/2022]
Abstract
UNLABELLED Pteris vittata, the first known arsenic hyperaccumulating plant, can accumulate very high concentration arsenic in its aboveground tissues, while low in roots. Previous studies have suggested that arsenic vacuole compartmentalization may play an important role in the arsenic-hyperaccumulation in P. vittata, but the mechanism(s) of arsenic transport to vacuole are largely unknown. We obtained tonoplast isolated from fronds of P. vittata sporophyte grown under minus and 1mM arsenate for 3weeks by iodixanol step gradient centrifugation method, and then used TMPP protein labeling technology followed by liquid chromatography-a linear ion trap-Orbitrap hybrid mass spectrometer analysis for the quantitative detection of proteins. And we designed and used an "artificial" database for database searching. In total, 56 tonoplast proteins were identified; more than 70% of them were transport proteins. Under arsenate treatment, one TDT transporter protein, a member of the TerC family and a PDR-like protein were upregulated differentially. While V-ATPase subunits c, E, and G, and V-PPase, were downregulated. Additionally, the identified tonoplast proteins in our present study provide an informative basis for arsenic carriers or channels and help to clarify the regulation of tonoplast arsenic transport processes in P. vittata. BIOLOGICAL SIGNIFICANCE Vacuole compartmentalization is crucial to As hyperaccumulator P. vittata, while there is limited known arsenic transport proteins involved in vacuole compartmentalization. In this paper, we obtained tonoplast of P. vittata fronds by iodixanol step gradient centrifugation method and then used TMPP protein labeling proteome technology for the quantitative detection of fronds tonoplast proteins. Our findings are the first challenge to the tonoplast proteins data mining of P. vittata which provide an informative basis for As carriers or channels. The proteomic approach in our study is suited for detecting alterations tonoplast protein and help to clarify the regulation of tonoplast transport processes. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Hongling Shen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenyan He
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Huili Yan
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zenan Xing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanshan Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxiu Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wenzhong Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Mi Ma
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Armengaud J, Trapp J, Pible O, Geffard O, Chaumot A, Hartmann EM. Non-model organisms, a species endangered by proteogenomics. J Proteomics 2014; 105:5-18. [PMID: 24440519 DOI: 10.1016/j.jprot.2014.01.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 12/24/2013] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED Previously, large-scale proteomics was possible only for organisms whose genomes were sequenced, meaning the most common model organisms. The use of next-generation sequencers is now changing the deal. With "proteogenomics", the use of experimental proteomics data to refine genome annotations, a higher integration of omics data is gaining ground. By extension, combining genomic and proteomic data is becoming routine in many research projects. "Proteogenomic"-flavored approaches are currently expanding, enabling the molecular studies of non-model organisms at an unprecedented depth. Today draft genomes can be obtained using next-generation sequencers in a rather straightforward way and at a reasonable cost for any organism. Unfinished genome sequences can be used to interpret tandem mass spectrometry proteomics data without the need for time-consuming genome annotation, and the use of RNA-seq to establish nucleotide sequences that are directly translated into protein sequences appears promising. There are, however, certain drawbacks that deserve further attention for RNA-seq to become more efficient. Here, we discuss the opportunities of working with non-model organisms, the proteomic methods that have been used until now, and the dramatic improvements proffered by proteogenomics. These put the distinction between model and non-model organisms in great danger, at least in terms of proteomics! BIOLOGICAL SIGNIFICANCE Model organisms have been crucial for in-depth analysis of cellular and molecular processes of life. Focusing the efforts of thousands of researchers on the Escherichia coli bacterium, Saccharomyces cerevisiae yeast, Arabidopsis thaliana plant, Danio rerio fish and other models for which genetic manipulation was possible was certainly worthwhile in terms of fundamental and invaluable biological insights. Until recently, proteomics of non-model organisms was limited to tedious, homology-based techniques, but today draft genomes or RNA-seq data can be straightforwardly obtained using next-generation sequencers, allowing the establishment of a draft protein database for any organism. Thus, proteogenomics opens new perspectives for molecular studies of non-model organisms, although they are still difficult experimental organisms. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France.
| | - Judith Trapp
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France; Irstea, UR MALY, F-69626 Villeurbanne, France
| | - Olivier Pible
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France
| | | | | | - Erica M Hartmann
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France
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Bland C, Bellanger L, Armengaud J. Magnetic Immunoaffinity Enrichment for Selective Capture and MS/MS Analysis of N-Terminal-TMPP-Labeled Peptides. J Proteome Res 2013; 13:668-80. [DOI: 10.1021/pr400774z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Céline Bland
- DSV,
IBEB, Lab Biochim System Perturb, CEA, Parc Technologique Marcel Boiteux, Bagnols-sur-Cèze F-30207, France
| | - Laurent Bellanger
- DSV,
IBEB, Lab Ing Cellul Biotechnol, CEA, Parc Technologique Marcel Boiteux, Bagnols-sur-Cèze F-30207, France
| | - Jean Armengaud
- DSV,
IBEB, Lab Biochim System Perturb, CEA, Parc Technologique Marcel Boiteux, Bagnols-sur-Cèze F-30207, France
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