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Liu S, Yu F, Yang Z, Wang T, Xiong H, Chang C, Yu W, Li N. Establishment of Dimethyl Labeling-based Quantitative Acetylproteomics in Arabidopsis. Mol Cell Proteomics 2018; 17:1010-1027. [PMID: 29440448 DOI: 10.1074/mcp.ra117.000530] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/18/2018] [Indexed: 12/19/2022] Open
Abstract
Protein acetylation, one of many types of post-translational modifications (PTMs), is involved in a variety of biological and cellular processes. In the present study, we applied both CsCl density gradient (CDG) centrifugation-based protein fractionation and a dimethyl-labeling-based 4C quantitative PTM proteomics workflow in the study of dynamic acetylproteomic changes in Arabidopsis. This workflow integrates the dimethyl chemical labeling with chromatography-based acetylpeptide separation and enrichment followed by mass spectrometry (MS) analysis, the extracted ion chromatogram (XIC) quantitation-based computational analysis of mass spectrometry data to measure dynamic changes of acetylpeptide level using an in-house software program, named Stable isotope-based Quantitation-Dimethyl labeling (SQUA-D), and finally the confirmation of ethylene hormone-regulated acetylation using immunoblot analysis. Eventually, using this proteomic approach, 7456 unambiguous acetylation sites were found from 2638 different acetylproteins, and 5250 acetylation sites, including 5233 sites on lysine side chain and 17 sites on protein N termini, were identified repetitively. Out of these repetitively discovered acetylation sites, 4228 sites on lysine side chain (i.e. 80.5%) are novel. These acetylproteins are exemplified by the histone superfamily, ribosomal and heat shock proteins, and proteins related to stress/stimulus responses and energy metabolism. The novel acetylproteins enriched by the CDG centrifugation fractionation contain many cellular trafficking proteins, membrane-bound receptors, and receptor-like kinases, which are mostly involved in brassinosteroid, light, gravity, and development signaling. In addition, we identified 12 highly conserved acetylation site motifs within histones, P-glycoproteins, actin depolymerizing factors, ATPases, transcription factors, and receptor-like kinases. Using SQUA-D software, we have quantified 33 ethylene hormone-enhanced and 31 hormone-suppressed acetylpeptide groups or called unique PTM peptide arrays (UPAs) that share the identical unique PTM site pattern (UPSP). This CDG centrifugation protein fractionation in combination with dimethyl labeling-based quantitative PTM proteomics, and SQUA-D may be applied in the quantitation of any PTM proteins in any model eukaryotes and agricultural crops as well as tissue samples of animals and human beings.
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Affiliation(s)
- Shichang Liu
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Fengchao Yu
- §Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.,¶Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Zhu Yang
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China.,‖The Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen, Guangdong, 518057, China
| | - Tingliang Wang
- **Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hairong Xiong
- ‡‡College of Life Science, South-central University for Nationalities, Wuhan, 430074, China
| | - Caren Chang
- §§Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland 20742-5815
| | - Weichuan Yu
- §Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China; .,¶Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ning Li
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China; .,‖The Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen, Guangdong, 518057, China
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Szalonek M, Sierpien B, Rymaszewski W, Gieczewska K, Garstka M, Lichocka M, Sass L, Paul K, Vass I, Vankova R, Dobrev P, Szczesny P, Marczewski W, Krusiewicz D, Strzelczyk-Zyta D, Hennig J, Konopka-Postupolska D. Potato Annexin STANN1 Promotes Drought Tolerance and Mitigates Light Stress in Transgenic Solanum tuberosum L. Plants. PLoS One 2015; 10:e0132683. [PMID: 26172952 PMCID: PMC4501783 DOI: 10.1371/journal.pone.0132683] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 06/18/2015] [Indexed: 11/18/2022] Open
Abstract
Annexins are a family of calcium- and membrane-binding proteins that are important for plant tolerance to adverse environmental conditions. Annexins function to counteract oxidative stress, maintain cell redox homeostasis, and enhance drought tolerance. In the present study, an endogenous annexin, STANN1, was overexpressed to determine whether crop yields could be improved in potato (Solanum tuberosum L.) during drought. Nine potential potato annexins were identified and their expression characterized in response to drought treatment. STANN1 mRNA was constitutively expressed at a high level and drought treatment strongly increased transcription levels. Therefore, STANN1 was selected for overexpression analysis. Under drought conditions, transgenic potato plants ectopically expressing STANN1 were more tolerant to water deficit in the root zone, preserved more water in green tissues, maintained chloroplast functions, and had higher accumulation of chlorophyll b and xanthophylls (especially zeaxanthin) than wild type (WT). Drought-induced reductions in the maximum efficiency and the electron transport rate of photosystem II (PSII), as well as the quantum yield of photosynthesis, were less pronounced in transgenic plants overexpressing STANN1 than in the WT. This conferred more efficient non-photochemical energy dissipation in the outer antennae of PSII and probably more efficient protection of reaction centers against photooxidative damage in transgenic plants under drought conditions. Consequently, these plants were able to maintain effective photosynthesis during drought, which resulted in greater productivity than WT plants despite water scarcity. Although the mechanisms underlying this stress protection are not yet clear, annexin-mediated photoprotection is probably linked to protection against light-induced oxidative stress.
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Affiliation(s)
- Michal Szalonek
- Plant Pathogenesis Lab, Institute of Biochemistry and Biophysics Polish Academy of Science, Warsaw, Poland
| | - Barbara Sierpien
- Plant Pathogenesis Lab, Institute of Biochemistry and Biophysics Polish Academy of Science, Warsaw, Poland
| | - Wojciech Rymaszewski
- Plant Pathogenesis Lab, Institute of Biochemistry and Biophysics Polish Academy of Science, Warsaw, Poland
| | | | - Maciej Garstka
- Department of Metabolic Regulation, University of Warsaw, Warsaw, Poland
| | - Malgorzata Lichocka
- Plant Pathogenesis Lab, Institute of Biochemistry and Biophysics Polish Academy of Science, Warsaw, Poland
| | - Laszlo Sass
- Laboratory of Molecular Stress and Photobiology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Kenny Paul
- Laboratory of Molecular Stress and Photobiology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Imre Vass
- Laboratory of Molecular Stress and Photobiology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Radomira Vankova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany AS CR, Praha, Czech Republic
| | - Peter Dobrev
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany AS CR, Praha, Czech Republic
| | - Pawel Szczesny
- Plant Pathogenesis Lab, Institute of Biochemistry and Biophysics Polish Academy of Science, Warsaw, Poland
| | - Waldemar Marczewski
- Department of Potato Genetics and Parental Lines, Plant Breeding and Acclimatization Institute—National Research Institute, Mlochow, Poland
| | - Dominika Krusiewicz
- Department of Potato Genetics and Parental Lines, Plant Breeding and Acclimatization Institute—National Research Institute, Mlochow, Poland
| | - Danuta Strzelczyk-Zyta
- Department of Potato Genetics and Parental Lines, Plant Breeding and Acclimatization Institute—National Research Institute, Mlochow, Poland
| | - Jacek Hennig
- Plant Pathogenesis Lab, Institute of Biochemistry and Biophysics Polish Academy of Science, Warsaw, Poland
| | - Dorota Konopka-Postupolska
- Plant Pathogenesis Lab, Institute of Biochemistry and Biophysics Polish Academy of Science, Warsaw, Poland
- * E-mail:
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Pedreschi R, Lurie S, Hertog M, Nicolaï B, Mes J, Woltering E. Post-harvest proteomics and food security. Proteomics 2013; 13:1772-83. [PMID: 23483703 DOI: 10.1002/pmic.201200387] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 10/27/2012] [Accepted: 11/11/2012] [Indexed: 12/12/2022]
Abstract
To guarantee sufficient food supply for a growing world population, efforts towards improving crop yield and plant resistance should be complemented with efforts to reduce post-harvest losses. Post-harvest losses are substantial and occur at different stages of the food chain in developed and developing countries. In recent years, a substantially increasing interest can be seen in the application of proteomics to understand post-harvest events. In the near future post-harvest proteomics will be poised to move from fundamental research to aiding the reduction of food losses. Proteomics research can help in reducing food losses through (i) identification and validation of gene products associated to specific quality traits supporting marker-assisted crop improvement programmes, (ii) delivering markers of initial quality that allow optimisation of distribution conditions and prediction of remaining shelf-life for decision support systems and (iii) delivering early detection tools of physiological or pathogen-related post-harvest problems. In this manuscript, recent proteomics studies on post-harvest and stress physiology are reviewed and discussed. Perspectives on future directions of post-harvest proteomics studies aiming to reduce food losses are presented.
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Affiliation(s)
- Romina Pedreschi
- Food & Biobased Research Centre, Wageningen University, Wageningen, The Netherlands.
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DeSouza LV, Siu KM. Mass spectrometry-based quantification. Clin Biochem 2013; 46:421-31. [DOI: 10.1016/j.clinbiochem.2012.10.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/16/2012] [Accepted: 10/17/2012] [Indexed: 12/25/2022]
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Clark GB, Morgan RO, Fernandez MP, Roux SJ. Evolutionary adaptation of plant annexins has diversified their molecular structures, interactions and functional roles. THE NEW PHYTOLOGIST 2012; 196:695-712. [PMID: 22994944 DOI: 10.1111/j.1469-8137.2012.04308.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/29/2012] [Indexed: 05/04/2023]
Abstract
Annexins are an homologous, structurally related superfamily of proteins known to associate with membrane lipid and cytoskeletal components. Their involvement in membrane organization, vesicle trafficking and signaling is fundamental to cellular processes such as growth, differentiation, secretion and repair. Annexins exist in some prokaryotes and all eukaryotic phyla within which plant annexins represent a monophyletic clade of homologs descended from green algae. Genomic, proteomic and transcriptomic approaches have provided data on the diversity, cellular localization and expression patterns of different plant annexins. The availability of 35 complete plant genomes has enabled systematic comparative analysis to determine phylogenetic relationships, characterize structures and observe functional specificity between and within individual subfamilies. Short amino termini and selective erosion of the canonical type 2 calcium coordinating sites in domains 2 and 3 are typical of plant annexins. The convergent evolution of alternate functional motifs such as 'KGD', redox-sensitive Cys and hydrophobic Trp/Phe residues argues for their functional relevance and contribution to mechanistic diversity in plant annexins. This review examines recent findings and advances in plant annexin research with special focus on their structural diversity, cellular and molecular interactions and their potential integrated functions in the broader context of physiological responses.
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Affiliation(s)
- Greg B Clark
- Section of Molecular Cell and Developmental Biology, University of Texas, Austin, TX, 78713, USA
| | - Reginald O Morgan
- Department of Biochemistry and Molecular Biology, Faculty of Medicine and University Institute of Biotechnology of Asturias, University of Oviedo, E-33006, Oviedo, Spain
| | - Maria-Pilar Fernandez
- Department of Biochemistry and Molecular Biology, Faculty of Medicine and University Institute of Biotechnology of Asturias, University of Oviedo, E-33006, Oviedo, Spain
| | - Stanley J Roux
- Section of Molecular Cell and Developmental Biology, University of Texas, Austin, TX, 78713, USA
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Kovanich D, Cappadona S, Raijmakers R, Mohammed S, Scholten A, Heck AJR. Applications of stable isotope dimethyl labeling in quantitative proteomics. Anal Bioanal Chem 2012; 404:991-1009. [DOI: 10.1007/s00216-012-6070-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 04/13/2012] [Accepted: 04/23/2012] [Indexed: 01/03/2023]
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Lim S, Chisholm K, Coffin RH, Peters RD, Al-Mughrabi KI, Wang-Pruski G, Pinto DM. Protein Profiling in Potato (Solanum tuberosum L.) Leaf Tissues by Differential Centrifugation. J Proteome Res 2012; 11:2594-601. [DOI: 10.1021/pr201004k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Sanghyun Lim
- Department of Plant and Animal
Sciences, Nova Scotia Agricultural College, Truro, Nova Scotia, Canada
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Kenneth Chisholm
- National Research Council Institute for Marine Biosciences, Halifax, Nova
Scotia, Canada
| | | | | | | | - Gefu Wang-Pruski
- Department of Plant and Animal
Sciences, Nova Scotia Agricultural College, Truro, Nova Scotia, Canada
| | - Devanand M. Pinto
- National Research Council Institute for Marine Biosciences, Halifax, Nova
Scotia, Canada
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Urbany C, Colby T, Stich B, Schmidt L, Schmidt J, Gebhardt C. Analysis of Natural Variation of the Potato Tuber Proteome Reveals Novel Candidate Genes for Tuber Bruising. J Proteome Res 2011; 11:703-16. [DOI: 10.1021/pr2006186] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Claude Urbany
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Thomas Colby
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Benjamin Stich
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Lysann Schmidt
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Jürgen Schmidt
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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