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Marzban G, Sulaj E. Sample Preparation and Phosphopeptide Enrichment for Plant Phosphoproteomics via Label-Free Mass Spectrometry. Methods Mol Biol 2024; 2787:293-303. [PMID: 38656498 DOI: 10.1007/978-1-0716-3778-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Phosphopeptide enrichment is the main bottleneck of every phosphorylation study. Therefore, in this chapter, a general workflow tries to overbridge the hurdles of plant sample handling from sample collection to protein extraction, protein solubilization, enzymatic digestion, and enrichment step prior to mass spectrometry. The workflow provides information to perform global proteomics as well as phosphoproteomics enabling the researcher to use the protocol in both fields.
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Affiliation(s)
- Gorji Marzban
- Institute for Bioprocess Science and Engineering (IBSE), Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Eldi Sulaj
- Institute of Animal Cell Technology and Systems Biology (IACTSB), Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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Nounurai P, Afifah A, Kittisenachai S, Roytrakul S. Phosphorylation of CAD1, PLDdelta, NDT1, RPM1 Proteins Induce Resistance in Tomatoes Infected by Ralstonia solanacearum. PLANTS 2022; 11:plants11060726. [PMID: 35336608 PMCID: PMC8954572 DOI: 10.3390/plants11060726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/20/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
Abstract
Ralstonia solanacaerum is one of the most devastating bacteria causing bacterial wilt disease in more than 200 species of plants, especially those belonging to the family Solanaceae. To cope with this pathogen, plants have evolved different resistance mechanisms depending on signal transduction after perception. Phosphorylation is the central regulatory component of the signal transduction pathway. We investigated a comparative phosphoproteomics analysis of the stems of resistant and susceptible tomatoes at 15 min and 30 min after inoculation with Ralstonia solanacearum to determine the phosphorylated proteins involved in induced resistance. Phosphoprotein profiling analyses led to the identification of 969 phosphoproteins classified into 10 functional categories. Among these, six phosphoproteins were uniquely identified in resistant plants including cinnamyl alcohol dehydrogenase 1 (CAD1), mitogen-activated protein kinase kinase kinase 18 (MAPKKK18), phospholipase D delta (PLDDELTA), nicotinamide adenine dinucleotide transporter 1 (NDT1), B3 domain-containing transcription factor VRN1, and disease resistance protein RPM1 (RPM1). These proteins are typically involved in defense mechanisms across different plant species. qRT-PCR analyses were performed to evaluate the level of expression of these genes in resistant and susceptible tomatoes. This study provides useful data, leading to an understanding of the early defense mechanisms of tomatoes against R. solanacearum.
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Affiliation(s)
- Prachumporn Nounurai
- Innovative Plant Biotechnology and Precision Agriculture Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
- Correspondence: (P.N.); (S.R.); Tel.: +66-25646700 (P.N. & S.R.)
| | - Anis Afifah
- Molecular and Applied Microbiology Laboratory, Diponegoro University, Jawa Tengah 50275, Indonesia;
| | - Suthathip Kittisenachai
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
- Correspondence: (P.N.); (S.R.); Tel.: +66-25646700 (P.N. & S.R.)
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Yamashita K, Umezawa T. Phosphoproteomic Approaches to Evaluate ABA Signaling. Methods Mol Biol 2022; 2462:163-179. [PMID: 35152388 DOI: 10.1007/978-1-0716-2156-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Abscisic acid (ABA) is a major phytohormone that regulates various processes in plants (e.g., seed dormancy/germination, abiotic/biotic stress responses). As protein phosphorylation is involved in the major pathways of ABA signaling, it is necessary to elucidate the phosphosignaling pathway involved in the ABA response. Phosphoproteomics enables determination of the proteins phosphorylated in vivo, and recent studies have applied a comparative phosphoproteomic approach to analyze ABA signaling in plants. For example, ABA-responsive phosphoproteins were identified in barley embryos. Furthermore, a phosphoproteomic approach is useful for screening protein kinase substrates by comparative analysis using kinase knockout mutants. Here, some technical points regarding phosphoproteomic analyses of ABA responses in plants are described.
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Affiliation(s)
- Kota Yamashita
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan.
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan.
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Rubisco lysine acetylation occurs at very low stoichiometry in mature Arabidopsis leaves: implications for regulation of enzyme function. Biochem J 2020; 477:3885-3896. [PMID: 32959870 PMCID: PMC7557146 DOI: 10.1042/bcj20200413] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 11/23/2022]
Abstract
Multiple studies have shown ribulose-1,5-bisphosphate carboxylase/oxygenase (E.C. 4.1.1.39; Rubisco) to be subject to Lys-acetylation at various residues; however, opposing reports exist about the biological significance of these post-translational modifications. One aspect of the Lys-acetylation that has not been addressed in plants generally, or with Rubisco specifically, is the stoichiometry at which these Lys-acetylation events occur. As a method to ascertain which Lys-acetylation sites on Arabidopsis Rubisco might be of regulatory importance to its catalytic function in the Calvin–Benson cycle, we purified Rubisco from leaves in both the day and night-time and performed independent mass spectrometry based methods to determine the stoichiometry of Rubisco Lys-acetylation events. The results indicate that Rubisco is acetylated at most Lys residues, but each acetylation event occurs at very low stoichiometry. Furthermore, in vitro treatments that increased the extent of Lys-acetylation on purified Rubisco had no effect on Rubisco maximal activity. Therefore, we are unable to confirm that Lys-acetylation at low stoichiometries can be a regulatory mechanism controlling Rubisco maximal activity. The results highlight the need for further use of stoichiometry measurements when determining the biological significance of reversible PTMs like acetylation.
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Aroonluk S, Roytrakul S, Jantasuriyarat C. Identification and Characterization of Phosphoproteins in Somatic Embryogenesis Acquisition during Oil Palm Tissue Culture. PLANTS 2019; 9:plants9010036. [PMID: 31881678 PMCID: PMC7020188 DOI: 10.3390/plants9010036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/08/2019] [Accepted: 12/23/2019] [Indexed: 11/16/2022]
Abstract
Somatic embryogenesis during oil palm tissue culture is a long process. The identification of the proteins that control this process may help to shorten the time of oil palm tissue culture. We collected embryogenic callus and somatic embryos at the globular, torpedo, and cotyledon maturation stages, as well as from plantlets, for total protein extraction. An enrichment column was used to enrich the phosphoproteins, which were subjected to tryptic enzyme digestion. Each sample was analyzed with nano-liquid chromatography-tandem mass spectrometry (nano LC-MS/MS). A total of 460 phosphoproteins were identified and analyzed. The functional characterization of phosphoproteins were observed as highest in the metabolic process, protein/nucleotide/ion binding, and membrane component. The different phosphoproteins are involved in the control of vegetative growth, cellular differentiation, cell morphogenesis, and signaling roles in plants. The Quantitative Real-Time Reverse Transcription-PCR technique (qPCR) was successfully used to verify the expression of genes, and the results were consistent with the level of protein expression from nano-LC-MS/MS. The E3 ubiquitin-protein ligase and sister chromatid cohesion PDS5 were specifically expressed only in the somatic embryo and plantlet, and these could be used as protein biomarkers to determine the oil palm somatic embryo maturation stage. This study sheds light on the protein phosphorylation mechanism that regulates somatic embryogenesis transition during oil palm tissue culture.
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Affiliation(s)
- Suvichark Aroonluk
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Klong Luang, Pathumthani 12120, Thailand;
| | - Chatchawan Jantasuriyarat
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart (CASTNAR, NRU-KU), Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Kasetsart University, Bangkok 10900, Thailand
- Correspondence:
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Blanc C, Coluccia F, L'Haridon F, Torres M, Ortiz-Berrocal M, Stahl E, Reymond P, Schreiber L, Nawrath C, Métraux JP, Serrano M. The Cuticle Mutant eca2 Modifies Plant Defense Responses to Biotrophic and Necrotrophic Pathogens and Herbivory Insects. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:344-355. [PMID: 29130376 DOI: 10.1094/mpmi-07-17-0181-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We isolated previously several Arabidopsis thaliana mutants with constitutive expression of the early microbe-associated molecular pattern-induced gene ATL2, named eca (expresión constitutiva de ATL2). Here, we further explored the interaction of eca mutants with pest and pathogens. Of all eca mutants, eca2 was more resistant to a fungal pathogen (Botrytis cinerea) and a bacterial pathogen (Pseudomonas syringae) as well as to a generalist herbivorous insect (Spodoptera littoralis). Permeability of the cuticle is increased in eca2; chemical characterization shows that eca2 has a significant reduction of both cuticular wax and cutin. Additionally, we determined that eca2 did not display a similar compensatory transcriptional response, compared with a previously characterized cuticular mutant, and that resistance to B. cinerea is mediated by the priming of the early and late induced defense responses, including salicylic acid- and jasmonic acid-induced genes. These results suggest that ECA2-dependent responses are involved in the nonhost defense mechanism against biotrophic and necrotrophic pathogens and against a generalist insect by modulation and priming of innate immunity and late defense responses. Making eca2 an interesting model to characterize the molecular basis for plant defenses against different biotic interactions and to study the initial events that take place in the cuticle surface of the aerial organs.
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Affiliation(s)
- Catherine Blanc
- 1 Department of Biology, University of Fribourg. Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Fania Coluccia
- 1 Department of Biology, University of Fribourg. Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Floriane L'Haridon
- 1 Department of Biology, University of Fribourg. Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Martha Torres
- 2 Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62209, Cuernavaca, Morelos, México
| | - Marlene Ortiz-Berrocal
- 2 Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62209, Cuernavaca, Morelos, México
- 3 Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Elia Stahl
- 3 Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Philippe Reymond
- 3 Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Lukas Schreiber
- 4 Institute of Cellular and Molecular Botany, Department of Ecophysiology, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | - Christiane Nawrath
- 3 Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jean-Pierre Métraux
- 1 Department of Biology, University of Fribourg. Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Mario Serrano
- 2 Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62209, Cuernavaca, Morelos, México
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Significant and unique changes in phosphorylation levels of four phosphoproteins in two apple rootstock genotypes under drought stress. Mol Genet Genomics 2017; 292:1307-1322. [PMID: 28710562 DOI: 10.1007/s00438-017-1348-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/03/2017] [Indexed: 01/09/2023]
Abstract
Drought stress is a major problem around the world and there is still little molecular mechanism about how fruit crops deal with moderate drought stress. Here, the physiological and phosphoproteomic responses of drought-sensitive genotype (M26) and drought-tolerant genotype (MBB) under moderate drought stress were investigated. Our results of the physiology analysis indicated that the MBB genotype could produce more osmosis-regulating substances. Furthermore, phosphoproteins from leaves of both genotypes under moderate drought stress were analyzed using the isobaric tags for relative and absolute quantification technology. A total of 595 unique phosphopeptides, 682 phosphorylated sites, and 446 phosphoproteins were quantitatively analyzed in the two genotypes. Five and thirty-five phosphoproteins with the phosphorylation levels significantly changed (PLSC) were identified in M26 and MBB, respectively. Among these, four PLSC phosphoproteins were common to both genotypes, perhaps indicating a partial overlap of the mechanisms to moderate drought stress. Gene ontology analyses revealed that the PLSC phosphoproteins represent a unique combination of metabolism, transcription, translation, and protein processing, suggesting that the response in apple to moderate drought stress encompasses a new and unique homeostasis of major cellular processes. The basic trend was an increase in protein and organic molecules abundance related to drought. These increases were higher in MBB than in M26. Our study is the first to address the phosphoproteome of apple rootstocks in response to moderate drought stress, and provide insights into the molecular regulation mechanisms of apple rootstock under moderate drought stress.
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Qiu J, Hou Y, Tong X, Wang Y, Lin H, Liu Q, Zhang W, Li Z, Nallamilli BR, Zhang J. Quantitative phosphoproteomic analysis of early seed development in rice (Oryza sativa L.). PLANT MOLECULAR BIOLOGY 2016; 90:249-265. [PMID: 26613898 DOI: 10.1007/s11103-015-0410-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 11/23/2015] [Indexed: 06/05/2023]
Abstract
Rice (Oryza sativa L.) seed serves as a major food source for over half of the global population. Though it has been long recognized that phosphorylation plays an essential role in rice seed development, the phosphorylation events and dynamics in this process remain largely unknown so far. Here, we report the first large scale identification of rice seed phosphoproteins and phosphosites by using a quantitative phosphoproteomic approach. Thorough proteomic studies in pistils and seeds at 3, 7 days after pollination resulted in the successful identification of 3885, 4313 and 4135 phosphopeptides respectively. A total of 2487 proteins were differentially phosphorylated among the three stages, including Kip related protein 1, Rice basic leucine zipper factor 1, Rice prolamin box binding factor and numerous other master regulators of rice seed development. Moreover, differentially phosphorylated proteins may be extensively involved in the biosynthesis and signaling pathways of phytohormones such as auxin, gibberellin, abscisic acid and brassinosteroid. Our results strongly indicated that protein phosphorylation is a key mechanism regulating cell proliferation and enlargement, phytohormone biosynthesis and signaling, grain filling and grain quality during rice seed development. Overall, the current study enhanced our understanding of the rice phosphoproteome and shed novel insight into the regulatory mechanism of rice seed development.
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Affiliation(s)
- Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Yuxuan Hou
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Haiyan Lin
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Qing Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Wen Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Babi R Nallamilli
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China.
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Screening of kinase substrates using kinase knockout mutants. Methods Mol Biol 2015; 1306:59-69. [PMID: 25930693 DOI: 10.1007/978-1-4939-2648-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Protein kinases are widely known to be major regulators of various signaling processes, particularly in eukaryotes, including plants. To understand their role in signal transduction pathways, it is necessary to determine which proteins are phosphorylated by these enzymes. Recent studies have applied a comparative phosphoproteomic approach to identify protein kinase substrates in plants. The results demonstrated that kinase knockout mutants are useful for screening protein kinase substrates via such a comparative analysis. Here some technical points are described for the experimental design and comparative analysis using kinase knockout mutants.
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Abstract
Cereals are the most important crop plant supplying staple food throughout the world. The economic importance and continued breeding of crop plants such as rice, maize, wheat, or barley require a detailed scientific understanding of adaptive and developmental processes. Protein phosphorylation is one of the most important regulatory posttranslational modifications and its analysis allows deriving functional and regulatory principles in plants. This minireview summarizes the current knowledge of phosphoproteomic studies in cereals.
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Affiliation(s)
- Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuchang Moshan, Wuhan, 430074, China,
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Cheng H, Deng W, Wang Y, Ren J, Liu Z, Xue Y. dbPPT: a comprehensive database of protein phosphorylation in plants. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau121. [PMID: 25534750 PMCID: PMC4273206 DOI: 10.1093/database/bau121] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
As one of the most important protein post-translational modifications, the reversible phosphorylation is critical for plants in regulating a variety of biological processes such as cellular metabolism, signal transduction and responses to environmental stress. Numerous efforts especially large-scale phosphoproteome profiling studies have been contributed to dissect the phosphorylation signaling in various plants, while a large number of phosphorylation events were identified. To provide an integrated data resource for further investigations, here we present a comprehensive database of dbPPT (database of Phosphorylation site in PlanTs, at http://dbppt.biocuckoo.org), which contains experimentally identified phosphorylation sites in proteins from plants. The phosphorylation sites in dbPPT were manually curated from the literatures, whereas datasets in other public databases were also integrated. In total, there were 82 175 phosphorylation sites in 31 012 proteins from 20 plant organisms in dbPPT, presenting a larger quantity of phosphorylation sites and a higher coverage of plant species in comparison with other databases. The proportions of residue types including serine, threonine and tyrosine were 77.99, 17.81 and 4.20%, respectively. All the phosphoproteins and phosphorylation sites in the database were critically annotated. Since the phosphorylation signaling in plants attracted great attention recently, such a comprehensive resource of plant protein phosphorylation can be useful for the research community. Database URL:http://dbppt.biocuckoo.org
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Affiliation(s)
- Han Cheng
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Wankun Deng
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Yongbo Wang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jian Ren
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Zexian Liu
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Yu Xue
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
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Proteomic Analysis of the Defense Response of Wheat to the Powdery Mildew Fungus, Blumeria graminis f. sp. tritici. Protein J 2014; 33:513-24. [DOI: 10.1007/s10930-014-9583-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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13
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Phospho-proteomic analysis of developmental reprogramming in the moss Physcomitrella patens. J Proteomics 2014; 108:284-94. [DOI: 10.1016/j.jprot.2014.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/12/2014] [Accepted: 05/19/2014] [Indexed: 12/31/2022]
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14
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Slade WO, Werth EG, Chao A, Hicks LM. Phosphoproteomics in photosynthetic organisms. Electrophoresis 2014; 35:3441-51. [PMID: 24825726 DOI: 10.1002/elps.201400154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 04/18/2014] [Accepted: 04/29/2014] [Indexed: 02/04/2023]
Abstract
As primarily sessile organisms, photosynthetic species survive in dynamic environments by using elegant signaling pathways to manifest molecular responses to extracellular cues. These pathways exploit phosphorylation of specific amino acids (e.g. serine, threonine, tyrosine), which impact protein structure, function, and localization. Despite substantial progress in implementation of phosphoproteomics to understand photosynthetic organisms, researchers still struggle to translate a biological question into an experimental strategy and vice versa. This review evaluates the current status of phosphoproteomics in photosynthetic organisms and concludes with recommendations based on current knowledge.
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Affiliation(s)
- William O Slade
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Chen X, Chan WL, Zhu FY, Lo C. Phosphoproteomic analysis of the non-seed vascular plant model Selaginella moellendorffii. Proteome Sci 2014; 12:16. [PMID: 24628833 PMCID: PMC4022089 DOI: 10.1186/1477-5956-12-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 03/06/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Selaginella (Selaginella moellendorffii) is a lycophyte which diverged from other vascular plants approximately 410 million years ago. As the first reported non-seed vascular plant genome, Selaginella genome data allow comparative analysis of genetic changes that may be associated with land plant evolution. Proteomics investigations on this lycophyte model have not been extensively reported. Phosphorylation represents the most common post-translational modifications and it is a ubiquitous regulatory mechanism controlling the functional expression of proteins inside living organisms. RESULTS In this study, polyethylene glycol fractionation and immobilized metal ion affinity chromatography were employed to isolate phosphopeptides from wild-growing Selaginella. Using liquid chromatography-tandem mass spectrometry analysis, 1593 unique phosphopeptides spanning 1104 non-redundant phosphosites with confirmed localization on 716 phosphoproteins were identified. Analysis of the Selaginella dataset revealed features that are consistent with other plant phosphoproteomes, such as the relative proportions of phosphorylated Ser, Thr, and Tyr residues, the highest occurrence of phosphosites in the C-terminal regions of proteins, and the localization of phosphorylation events outside protein domains. In addition, a total of 97 highly conserved phosphosites in evolutionary conserved proteins were identified, indicating the conservation of phosphorylation-dependent regulatory mechanisms in phylogenetically distinct plant species. On the other hand, close examination of proteins involved in photosynthesis revealed phosphorylation events which may be unique to Selaginella evolution. Furthermore, phosphorylation motif analyses identified Pro-directed, acidic, and basic signatures which are recognized by typical protein kinases in plants. A group of Selaginella-specific phosphoproteins were found to be enriched in the Pro-directed motif class. CONCLUSIONS Our work provides the first large-scale atlas of phosphoproteins in Selaginella which occupies a unique position in the evolution of terrestrial plants. Future research into the functional roles of Selaginella-specific phosphorylation events in photosynthesis and other processes may offer insight into the molecular mechanisms leading to the distinct evolution of lycophytes.
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Affiliation(s)
- Xi Chen
- School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China.,Wuhan Institute of Biotechnology, Wuhan, Hubei, China
| | - Wai Lung Chan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China
| | - Fu-Yuan Zhu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China
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López-Pedrouso M, Alonso J, Zapata C. Evidence for phosphorylation of the major seed storage protein of the common bean and its phosphorylation-dependent degradation during germination. PLANT MOLECULAR BIOLOGY 2014; 84:415-28. [PMID: 24142381 DOI: 10.1007/s11103-013-0141-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/06/2013] [Indexed: 05/22/2023]
Abstract
Phaseolin is the major seed storage protein of common bean, Phaseolus vulgaris L., accounting for up to 50 % of the total seed proteome. The regulatory mechanisms responsible for the synthesis, accumulation and degradation of phaseolin in the common bean seed are not yet sufficiently known. Here, we report on a systematic study in dormant and 4-day germinating bean seeds from cultivars Sanilac (S) and Tendergreen (T) to explore the presence and dynamics of phosphorylated phaseolin isoforms. High-resolution two-dimensional electrophoresis in combination with the phosphoprotein-specific Pro-Q Diamond phosphoprotein fluorescent stain and chemical dephosphorylation by hydrogen fluoride-pyridine enabled us to identify differentially phosphorylated phaseolin polypeptides in dormant and germinating seeds from cultivars S and T. Phosphorylated forms of the two subunits of type α and β that compose the phaseolin were identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and MALDI-TOF/TOF tandem MS. In addition, we found that the levels of phosphorylation of the phaseolin changed remarkably in the seed transition from dormancy to early germination stage. Temporal changes in the extent of phosphorylation in response to physiological and metabolic variations suggest that phosphorylated phaseolin isoforms have functional significance. In particular, this prospective study supports the hypothesis that mobilization of the phaseolin in germinating seeds occurs through the degradation of highly phosphorylated isoforms. Taken together, our results indicate that post-translational phaseolin modifications through phosphorylations need to be taken into consideration for a better understanding of the molecular mechanisms underlying its regulation.
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Affiliation(s)
- María López-Pedrouso
- Department of Genetics, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
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17
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Preparation and loading buffer study of polyvinyl alcohol-based immobilized Ti4+
affinity chromatography for phosphopeptide enrichment. J Sep Sci 2013; 36:3563-70. [DOI: 10.1002/jssc.201300622] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 09/02/2013] [Accepted: 09/03/2013] [Indexed: 11/07/2022]
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18
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Hu Y, Guo S, Li X, Ren X. Comparative analysis of salt-responsive phosphoproteins in maize leaves using Ti4+-IMAC enrichment and ESI-Q-TOFMS. Electrophoresis 2013; 34:485-92. [DOI: 10.1002/elps.201200381] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 10/09/2012] [Accepted: 10/11/2012] [Indexed: 11/05/2022]
Affiliation(s)
- Yufeng Hu
- Department of Environmental Sciences & Engineering, College of Resources and Environmental Sciences; China Agricultural University; Beijing; P. R. China
| | - Shuangxi Guo
- Department of Plant Nutrition; College of Resources and Environmental Sciences; China Agricultural University; Beijing; P. R. China
| | - Xuexian Li
- Department of Plant Nutrition; College of Resources and Environmental Sciences; China Agricultural University; Beijing; P. R. China
| | - Xueqin Ren
- Department of Environmental Sciences & Engineering, College of Resources and Environmental Sciences; China Agricultural University; Beijing; P. R. China
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19
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Abstract
The tubulin-like FtsZ protein initiates assembly of the bacterial and plastid division machineries. In bacteria, phosphorylation of FtsZ impairs GTPase activity, polymerization and interactions with other division proteins. Using a proteomics approach, we have shown that AtFtsZ2 is phosphorylated in vivo in Arabidopsis and that PGK1 (phosphoglycerate kinase 1) interacts with AtFtsZ2 in planta, suggesting a possible role in FtsZ phosphorylation.
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20
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Guo G, Lv D, Yan X, Subburaj S, Ge P, Li X, Hu Y, Yan Y. Proteome characterization of developing grains in bread wheat cultivars (Triticum aestivum L.). BMC PLANT BIOLOGY 2012. [PMID: 22900893 DOI: 10.86/1471-2229-12-147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND The analyses of protein synthesis, accumulation and regulation during grain development in wheat are more complex because of its larger genome size compared to model plants such as Arabidopsis and rice. In this study, grains from two wheat cultivars Jimai 20 and Zhoumai 16 with different gluten quality properties were harvested at five development stages, and were used to displayed variable expression patterns of grain proteins. RESULTS Proteome characterization during grain development in Chinese bread wheat cultivars Jimai 20 and Zhoumai 16 with different quality properties was investigated by 2-DE and tandem MALDI-TOF/TOF-MS. Identification of 117 differentially accumulated protein spots representing 82 unique proteins and five main expression patterns enabled a chronological description of wheat grain formation. Significant proteome expression differences between the two cultivars were found; these included 14 protein spots that accumulated in both cultivars but with different patterns and 27 cultivar-different spots. Among the cultivar-different protein spots, 14 accumulated in higher abundance in Jimai 20 than in Zhoumai 16, and included NAD-dependent isocitrate dehydrogenase, triticin precursor, LMW-s glutenin subunit and replication factor C-like protein. These proteins are likely to be associated with superior gluten quality. In addition, some proteins such as class II chitinase and peroxidase 1 with isoforms in developing grains were shown to be phosphorylated by Pro-Q Diamond staining and phosphorprotein site prediction. Phosphorylation could have important roles in wheat grain development. qRT-PCR analysis demonstrated that transcriptional and translational expression patterns of many genes were significantly different. CONCLUSIONS Wheat grain proteins displayed variable expression patterns at different developmental stages and a considerable number of protein spots showed differential accumulation between two cultivars. Differences in seed storage proteins were considered to be related to different quality performance of the flour from these wheat cultivars. Some proteins with isoforms were phosphorylated, and this may reflect their importance in grain development. Our results provide new insights into proteome characterization during grain development in different wheat genotypes.
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Affiliation(s)
- Guangfang Guo
- College of Life Science, Capital Normal University, Beijing 100048, China
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21
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Guo G, Lv D, Yan X, Subburaj S, Ge P, Li X, Hu Y, Yan Y. Proteome characterization of developing grains in bread wheat cultivars (Triticum aestivum L.). BMC PLANT BIOLOGY 2012; 12:147. [PMID: 22900893 PMCID: PMC3480910 DOI: 10.1186/1471-2229-12-147] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 08/16/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND The analyses of protein synthesis, accumulation and regulation during grain development in wheat are more complex because of its larger genome size compared to model plants such as Arabidopsis and rice. In this study, grains from two wheat cultivars Jimai 20 and Zhoumai 16 with different gluten quality properties were harvested at five development stages, and were used to displayed variable expression patterns of grain proteins. RESULTS Proteome characterization during grain development in Chinese bread wheat cultivars Jimai 20 and Zhoumai 16 with different quality properties was investigated by 2-DE and tandem MALDI-TOF/TOF-MS. Identification of 117 differentially accumulated protein spots representing 82 unique proteins and five main expression patterns enabled a chronological description of wheat grain formation. Significant proteome expression differences between the two cultivars were found; these included 14 protein spots that accumulated in both cultivars but with different patterns and 27 cultivar-different spots. Among the cultivar-different protein spots, 14 accumulated in higher abundance in Jimai 20 than in Zhoumai 16, and included NAD-dependent isocitrate dehydrogenase, triticin precursor, LMW-s glutenin subunit and replication factor C-like protein. These proteins are likely to be associated with superior gluten quality. In addition, some proteins such as class II chitinase and peroxidase 1 with isoforms in developing grains were shown to be phosphorylated by Pro-Q Diamond staining and phosphorprotein site prediction. Phosphorylation could have important roles in wheat grain development. qRT-PCR analysis demonstrated that transcriptional and translational expression patterns of many genes were significantly different. CONCLUSIONS Wheat grain proteins displayed variable expression patterns at different developmental stages and a considerable number of protein spots showed differential accumulation between two cultivars. Differences in seed storage proteins were considered to be related to different quality performance of the flour from these wheat cultivars. Some proteins with isoforms were phosphorylated, and this may reflect their importance in grain development. Our results provide new insights into proteome characterization during grain development in different wheat genotypes.
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Affiliation(s)
- Guangfang Guo
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Dongwen Lv
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Xing Yan
- College of Life Science, Capital Normal University, Beijing 100048, China
| | | | - Pei Ge
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Xiaohui Li
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Yingkao Hu
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing 100048, China
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22
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Comparative proteomic and phosphoproteomic analysis of the silkworm (Bombyx mori) posterior silk gland under high temperature treatment. Mol Biol Rep 2012; 39:8447-56. [PMID: 22707192 DOI: 10.1007/s11033-012-1698-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 06/06/2012] [Indexed: 10/28/2022]
Abstract
The proteins from the posterior silk gland of silkworm hybrids and their parents reared under high temperatures were studied by using comparative proteomic and phosphoproteomic analysis. A total of 82.07, 6.17 and 11.76 % protein spots showed additivity, overdominance and underdominance patterns, respectively. Fifteen differentially expressed protein spots were identified by peptide mass fingerprinting. Among these, four spots, including sHSPs and prohibitin protein that were directly relevant to heat response, were identified. Eleven protein spots were found to play an important role in silk synthesis, and nine protein spots expressed phosphorylation states. According to Gene ontology and KEGG pathway analysis, these nine spots played an important role in stress-induced signal transduction. Expression of most silk synthesis-related proteins was reduced, whereas stress-responsive proteins increased with heat exposure time in three breeds. Furthermore, most proteins showed under- or overdominance in the hybrids compared to the parents. The results suggested that high temperature could alter the expression of proteins related to silk synthesis and heat response in silkworm. Moreover, differentially expressed proteins occurring in the hybrid and its parents may be the main explanation of the observed heterosis.
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23
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Cacas JL, Furt F, Le Guédard M, Schmitter JM, Buré C, Gerbeau-Pissot P, Moreau P, Bessoule JJ, Simon-Plas F, Mongrand S. Lipids of plant membrane rafts. Prog Lipid Res 2012; 51:272-99. [PMID: 22554527 DOI: 10.1016/j.plipres.2012.04.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipids tend to organize in mono or bilayer phases in a hydrophilic environment. While they have long been thought to be incapable of coherent lateral segregation, it is now clear that spontaneous assembly of these compounds can confer microdomain organization beyond spontaneous fluidity. Membrane raft microdomains have the ability to influence spatiotemporal organization of protein complexes, thereby allowing regulation of cellular processes. In this review, we aim at summarizing briefly: (i) the history of raft discovery in animals and plants, (ii) the main findings about structural and signalling plant lipids involved in raft segregation, (iii) imaging of plant membrane domains, and their biochemical purification through detergent-insoluble membranes, as well as the existing debate on the topic. We also discuss the potential involvement of rafts in the regulation of plant physiological processes, and further discuss the prospects of future research into plant membrane rafts.
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Affiliation(s)
- Jean-Luc Cacas
- Laboratoire de Biogenèse Membranaire, UMR 5200 CNRS, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
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24
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Simon-Plas F, Perraki A, Bayer E, Gerbeau-Pissot P, Mongrand S. An update on plant membrane rafts. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:642-9. [PMID: 21903451 DOI: 10.1016/j.pbi.2011.08.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 08/12/2011] [Accepted: 08/17/2011] [Indexed: 05/18/2023]
Abstract
The dynamic segregation of membrane components within microdomains, such as the sterol-enriched and sphingolipid-enriched membrane rafts, emerges as a central regulatory mechanism governing physiological responses in various organisms. Over the past five years, plasma membrane located raft-like domains have been described in several plant species. The protein and lipid compositions of detergent-insoluble membranes, supposed to contain these domains, have been extensively characterised. Imaging methods have shown that lateral segregation of lipids and proteins exists at the nanoscale level at the plant plasma membrane, correlating detergent insolubility and membrane-domain localisation of presumptive raft proteins. Finally, the dynamic association of specific proteins with detergent-insoluble membranes upon environmental stress has been reported, confirming a possible role for plant rafts as signal transduction platforms, particularly during biotic interactions.
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Affiliation(s)
- Françoise Simon-Plas
- UMR Plante-Microbe-Environnement 1088, Institut National de la Recherche Agronomique-5184, CNRS-Université de Bourgogne, 21065 Dijon Cedex, France
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25
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Liu CC, Liu CF, Wang HX, Shen ZY, Yang CP, Wei ZG. Identification and analysis of phosphorylation status of proteins in dormant terminal buds of poplar. BMC PLANT BIOLOGY 2011; 11:158. [PMID: 22074553 PMCID: PMC3234192 DOI: 10.1186/1471-2229-11-158] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 11/11/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although there has been considerable progress made towards understanding the molecular mechanisms of bud dormancy, the roles of protein phosphorylation in the process of dormancy regulation in woody plants remain unclear. RESULTS We used mass spectrometry combined with TiO₂ phosphopeptide-enrichment strategies to investigate the phosphoproteome of dormant terminal buds (DTBs) in poplar (Populus simonii × P. nigra). There were 161 unique phosphorylated sites in 161 phosphopeptides from 151 proteins; 141 proteins have orthologs in Arabidopsis, and 10 proteins are unique to poplar. Only 34 sites in proteins in poplar did not match well with the equivalent phosphorylation sites of their orthologs in Arabidopsis, indicating that regulatory mechanisms are well conserved between poplar and Arabidopsis. Further functional classifications showed that most of these phosphoproteins were involved in binding and catalytic activity. Extraction of the phosphorylation motif using Motif-X indicated that proline-directed kinases are a major kinase group involved in protein phosphorylation in dormant poplar tissues. CONCLUSIONS This study provides evidence about the significance of protein phosphorylation during dormancy, and will be useful for similar studies on other woody plants.
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Affiliation(s)
- Chang-Cai Liu
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), 26 Hexing Road, Harbin 150040, China
- Laboratory for Chemical Defence and Microscale Analysis, P.O. Box 3, Zhijiang 443200, China
| | - Chang-Fu Liu
- Shenyang Agricultural University, Dongling Road 120, Shenyang, Liaoning 110866, China
| | - Hong-Xia Wang
- Institute of Basic Medical Sciences, National Center for Biomedical Analysis, 27 Taiping Road, Beijing 100850, China
| | - Zhi-Ying Shen
- Daqing Branch, Harbin Medical University, Daqing 163319, China
| | - Chuan-Ping Yang
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), 26 Hexing Road, Harbin 150040, China
| | - Zhi-Gang Wei
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), 26 Hexing Road, Harbin 150040, China
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26
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Xing T, Laroche A. Revealing plant defense signaling: getting more sophisticated with phosphoproteomics. PLANT SIGNALING & BEHAVIOR 2011; 6:1469-74. [PMID: 21897123 PMCID: PMC3256373 DOI: 10.4161/psb.6.10.17345] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The regulation mechanisms of any plant-pathogen interaction are complex and dynamic. A proteomic approach is necessary in understanding regulatory networks because it identifies new proteins in relation to their function and ultimately aims to clarify how their expression, accumulation and modification is controlled. One of the major control mechanisms for protein activity in plant-pathogen interactions is protein phosphorylation, and an understanding of the significance of protein phosphorylation in plant-pathogen interaction can be overwhelming. Due to the high number of protein kinases and phosphatases in any single plant genome and specific limitations of any technologies, it is extremely challenging for us to fully delineate the phosphorylation machinery. Current proteomic approaches and technology advances have demonstrated their great potential in identifying new components. Recent studies in well-developed plant-pathogen systems have revealed novel phosphorylation pathways, and some of them are off the core phosphorylation cascades. Additional phosphoproteomic studies are needed to increase our comprehension of the different mechanisms and their fine tuning involved in the host resistance response to pathogen attacks.
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Affiliation(s)
- Tim Xing
- Department of Biology and Institute of Biochemistry; Carleton University; Ottawa, ON Canada
| | - André Laroche
- Agriculture and Agri-Food Canada; Lethbridge Research Center; Lethbridge, AB Canada
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27
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Mithoe SC, Menke FLH. Phosphoproteomics perspective on plant signal transduction and tyrosine phosphorylation. PHYTOCHEMISTRY 2011; 72:997-1006. [PMID: 21315387 DOI: 10.1016/j.phytochem.2010.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/25/2010] [Accepted: 12/06/2010] [Indexed: 05/14/2023]
Abstract
Plants and animal cells use intricate signaling pathways to respond to a diverse array of stimuli. These stimuli include signals from environment, such as biotic and abiotic stress signals, as well as cell-to-cell signaling required for pattern formation during development. The transduction of the signal often relies on the post-translational modification (PTM) of proteins. Protein phosphorylation in eukaryotic cells is considered to be a central mechanism for regulation and cellular signaling. The classic view is that phosphorylation of serine (Ser) and threonine (Thr) residues is more abundant, whereas tyrosine (Tyr) phosphorylation is less frequent. This review provides an overview of the progress in the plant phosphoproteomics field and how this progress has lead to a re-evaluation of the relative contribution of tyrosine phosphorylation to the plant phosphoproteome. In relation to this appreciated contribution of tyrosine phosphorylation we also discuss some of the recent progress on the role of tyrosine phosphorylation in plant signal transduction.
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Affiliation(s)
- Sharon C Mithoe
- Department of Biology, Molecular Genetics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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28
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Bond AE, Row PE, Dudley E. Post-translation modification of proteins; methodologies and applications in plant sciences. PHYTOCHEMISTRY 2011; 72:975-96. [PMID: 21353264 DOI: 10.1016/j.phytochem.2011.01.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 10/21/2010] [Accepted: 01/21/2011] [Indexed: 05/03/2023]
Abstract
Proteins have the potential to undergo a variety of post-translational modifications and the different methods available to study these cellular processes has advanced rapidly with the continuing development of proteomic technologies. In this review we aim to detail five major post-translational modifications (phosphorylation, glycosylaion, lipid modification, ubiquitination and redox-related modifications), elaborate on the techniques that have been developed for their analysis and briefly discuss the study of these modifications in selected areas of plant science.
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Affiliation(s)
- A E Bond
- Biochemistry Group, College of Medicine, Swansea University, Swansea, UK
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29
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Kaufmann K, Smaczniak C, de Vries S, Angenent GC, Karlova R. Proteomics insights into plant signaling and development. Proteomics 2011; 11:744-55. [DOI: 10.1002/pmic.201000418] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 10/29/2010] [Accepted: 11/02/2010] [Indexed: 12/11/2022]
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30
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Singh A, Giri J, Kapoor S, Tyagi AK, Pandey GK. Protein phosphatase complement in rice: genome-wide identification and transcriptional analysis under abiotic stress conditions and reproductive development. BMC Genomics 2010. [PMID: 20637108 DOI: 10.1186/1471–2164–11-435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein phosphatases are the key components of a number of signaling pathways where they modulate various cellular responses. In plants, protein phosphatases constitute a large gene family and are reportedly involved in the regulation of abiotic stress responses and plant development. Recently, the whole complement of protein phosphatases has been identified in Arabidopsis genome. While PP2C class of serine/threonine phosphatases has been explored in rice, the whole complement of this gene family is yet to be reported. RESULTS In silico investigation revealed the presence of 132-protein phosphatase-coding genes in rice genome. Domain analysis and phylogenetic studies of evolutionary relationship categorized these genes into PP2A, PP2C, PTP, DSP and LMWP classes. PP2C class represents a major proportion of this gene family with 90 members. Chromosomal localization revealed their distribution on all the 12 chromosomes, with 42 genes being present on segmentally duplicated regions and 10 genes on tandemly duplicated regions of chromosomes. The expression profiles of 128 genes under salinity, cold and drought stress conditions, 11 reproductive developmental (panicle and seed) stages along with three stages of vegetative development were analyzed using microarray expression data. 46 genes were found to be differentially expressing in 3 abiotic stresses out of which 31 were up-regulated and 15 exhibited down-regulation. A total of 82 genes were found to be differentially expressing in different developmental stages. An overlapping expression pattern was found for abiotic stresses and reproductive development, wherein 8 genes were up-regulated and 7 down-regulated. Expression pattern of the 13 selected genes was validated employing real time PCR, and it was found to be in accordance with the microarray expression data for most of the genes. CONCLUSIONS Exploration of protein phosphatase gene family in rice has resulted in the identification of 132 members, which can be further divided into different classes phylogenetically. Expression profiling and analysis indicate the involvement of this large gene family in a number of signaling pathways triggered by abiotic stresses and their possible role in plant development. Our study will provide the platform from where; the expression pattern information can be transformed into molecular, cellular and biochemical characterization of members belonging to this gene family.
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Affiliation(s)
- Amarjeet Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, India
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31
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Singh A, Giri J, Kapoor S, Tyagi AK, Pandey GK. Protein phosphatase complement in rice: genome-wide identification and transcriptional analysis under abiotic stress conditions and reproductive development. BMC Genomics 2010; 11:435. [PMID: 20637108 PMCID: PMC3091634 DOI: 10.1186/1471-2164-11-435] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 07/16/2010] [Indexed: 11/12/2022] Open
Abstract
Background Protein phosphatases are the key components of a number of signaling pathways where they modulate various cellular responses. In plants, protein phosphatases constitute a large gene family and are reportedly involved in the regulation of abiotic stress responses and plant development. Recently, the whole complement of protein phosphatases has been identified in Arabidopsis genome. While PP2C class of serine/threonine phosphatases has been explored in rice, the whole complement of this gene family is yet to be reported. Results In silico investigation revealed the presence of 132-protein phosphatase-coding genes in rice genome. Domain analysis and phylogenetic studies of evolutionary relationship categorized these genes into PP2A, PP2C, PTP, DSP and LMWP classes. PP2C class represents a major proportion of this gene family with 90 members. Chromosomal localization revealed their distribution on all the 12 chromosomes, with 42 genes being present on segmentally duplicated regions and 10 genes on tandemly duplicated regions of chromosomes. The expression profiles of 128 genes under salinity, cold and drought stress conditions, 11 reproductive developmental (panicle and seed) stages along with three stages of vegetative development were analyzed using microarray expression data. 46 genes were found to be differentially expressing in 3 abiotic stresses out of which 31 were up-regulated and 15 exhibited down-regulation. A total of 82 genes were found to be differentially expressing in different developmental stages. An overlapping expression pattern was found for abiotic stresses and reproductive development, wherein 8 genes were up-regulated and 7 down-regulated. Expression pattern of the 13 selected genes was validated employing real time PCR, and it was found to be in accordance with the microarray expression data for most of the genes. Conclusions Exploration of protein phosphatase gene family in rice has resulted in the identification of 132 members, which can be further divided into different classes phylogenetically. Expression profiling and analysis indicate the involvement of this large gene family in a number of signaling pathways triggered by abiotic stresses and their possible role in plant development. Our study will provide the platform from where; the expression pattern information can be transformed into molecular, cellular and biochemical characterization of members belonging to this gene family.
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Affiliation(s)
- Amarjeet Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, India
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32
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Hoehenwarter W, Chen Y, Recuenco-Munoz L, Wienkoop S, Weckwerth W. Functional analysis of proteins and protein species using shotgun proteomics and linear mathematics. Amino Acids 2010; 41:329-41. [PMID: 20602127 DOI: 10.1007/s00726-010-0669-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 06/16/2010] [Indexed: 12/16/2022]
Abstract
Covalent post-translational modification of proteins is the primary modulator of protein function in the cell. It greatly expands the functional potential of the proteome compared to the genome. In the past few years shotgun proteomics-based research, where the proteome is digested into peptides prior to mass spectrometric analysis has been prolific in this area. It has determined the kinetics of tens of thousands of sites of covalent modification on an equally large number of proteins under various biological conditions and uncovered a transiently active regulatory network that extends into diverse branches of cellular physiology. In this review, we discuss this work in light of the concept of protein speciation, which emphasizes the entire post-translationally modified molecule and its interactions and not just the modification site as the functional entity. Sometimes, particularly when considering complex multisite modification, all of the modified molecular species involved in the investigated condition, the protein species must be completely resolved for full understanding. We present a mathematical technique that delivers a good approximation for shotgun proteomics data.
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Affiliation(s)
- Wolfgang Hoehenwarter
- Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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Riaño-Pachón DM, Kleessen S, Neigenfind J, Durek P, Weber E, Engelsberger WR, Walther D, Selbig J, Schulze WX, Kersten B. Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana. BMC Genomics 2010; 11:411. [PMID: 20594336 PMCID: PMC2996939 DOI: 10.1186/1471-2164-11-411] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 07/01/2010] [Indexed: 12/26/2022] Open
Abstract
Background Protein phosphorylation is an important post-translational modification influencing many aspects of dynamic cellular behavior. Site-specific phosphorylation of amino acid residues serine, threonine, and tyrosine can have profound effects on protein structure, activity, stability, and interaction with other biomolecules. Phosphorylation sites can be affected in diverse ways in members of any species, one such way is through single nucleotide polymorphisms (SNPs). The availability of large numbers of experimentally identified phosphorylation sites, and of natural variation datasets in Arabidopsis thaliana prompted us to analyze the effect of non-synonymous SNPs (nsSNPs) onto phosphorylation sites. Results From the analyses of 7,178 experimentally identified phosphorylation sites we found that: (i) Proteins with multiple phosphorylation sites occur more often than expected by chance. (ii) Phosphorylation hotspots show a preference to be located outside conserved domains. (iii) nsSNPs affected experimental phosphorylation sites as much as the corresponding non-phosphorylated amino acid residues. (iv) Losses of experimental phosphorylation sites by nsSNPs were identified in 86 A. thaliana proteins, among them receptor proteins were overrepresented. These results were confirmed by similar analyses of predicted phosphorylation sites in A. thaliana. In addition, predicted threonine phosphorylation sites showed a significant enrichment of nsSNPs towards asparagines and a significant depletion of the synonymous substitution. Proteins in which predicted phosphorylation sites were affected by nsSNPs (loss and gain), were determined to be mainly receptor proteins, stress response proteins and proteins involved in nucleotide and protein binding. Proteins involved in metabolism, catalytic activity and biosynthesis were less affected. Conclusions We analyzed more than 7,100 experimentally identified phosphorylation sites in almost 4,300 protein-coding loci in silico, thus constituting the largest phosphoproteomics dataset for A. thaliana available to date. Our findings suggest a relatively high variability in the presence or absence of phosphorylation sites between different natural accessions in receptor and other proteins involved in signal transduction. Elucidating the effect of phosphorylation sites affected by nsSNPs on adaptive responses represents an exciting research goal for the future.
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Ytterberg AJ, Jensen ON. Modification-specific proteomics in plant biology. J Proteomics 2010; 73:2249-66. [PMID: 20541636 DOI: 10.1016/j.jprot.2010.06.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 05/18/2010] [Accepted: 06/01/2010] [Indexed: 10/19/2022]
Abstract
Post-translational modifications (PTMs) are involved in the regulation of a wide range of biological processes, and affect e.g. protein structure, activity and stability. Several hundred PTMs have been described in the literature, but relatively few have been studied using mass spectrometry and proteomics. In general, methods for PTM characterization are developed to study yeast and mammalian biology and later adopted to investigate plants. Our point of view is that it is advantageous to enrich for PTMs on the peptide level as part of a quantitative proteomics strategy to not only identify the PTM, but also to determine the functional relevance in the context of regulation, response to abiotic stress etc. Protein phosphorylation is the only PTM that has been studied extensively at the proteome wide level in plants using mass spectrometry based methods. We review phosphoproteomics studies in plants and discuss the redox mediated PTMs (S-nitrosylation, tyrosine nitration and S-glutathionylation), ubiquitylation, SUMOylation, and glycosylation, including GPI anchors, and the quantitative proteomics methods that are used to study these modification in plants. Where appropriate we contrast the methods to those used for mammalian PTM characterization.
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Affiliation(s)
- A Jimmy Ytterberg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
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35
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Kim BG, Lee JH, Ahn JM, Park SK, Cho JH, Hwang D, Yoo JS, Yates JR, Ryoo HM, Cho JY. ‘Two-Stage Double-Technique Hybrid (TSDTH)’ Identification Strategy for the Analysis of BMP2-Induced Transdifferentiation of Premyoblast C2C12 Cells to Osteoblast. J Proteome Res 2009; 8:4441-54. [DOI: 10.1021/pr900231a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Byung-Gyu Kim
- Department of Biochemistry, School of Dentistry, Kyungpook National University, and 2nd BK21 program 700-422, Korea, Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92014, School of Interdisciplinary Bioscience and Bioengineering, Department of Chemical Engineering, POSTECH, Pohang, 790-784, Korea, Mass Spectrometer Development team, Korea Basic Science Institute, Daejeon, Korea, and Department of Cell and Developmental Biology, School of Dentistry, Seoul National
| | - Ji-Hyun Lee
- Department of Biochemistry, School of Dentistry, Kyungpook National University, and 2nd BK21 program 700-422, Korea, Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92014, School of Interdisciplinary Bioscience and Bioengineering, Department of Chemical Engineering, POSTECH, Pohang, 790-784, Korea, Mass Spectrometer Development team, Korea Basic Science Institute, Daejeon, Korea, and Department of Cell and Developmental Biology, School of Dentistry, Seoul National
| | - Jung-Mo Ahn
- Department of Biochemistry, School of Dentistry, Kyungpook National University, and 2nd BK21 program 700-422, Korea, Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92014, School of Interdisciplinary Bioscience and Bioengineering, Department of Chemical Engineering, POSTECH, Pohang, 790-784, Korea, Mass Spectrometer Development team, Korea Basic Science Institute, Daejeon, Korea, and Department of Cell and Developmental Biology, School of Dentistry, Seoul National
| | - Sung Kyu Park
- Department of Biochemistry, School of Dentistry, Kyungpook National University, and 2nd BK21 program 700-422, Korea, Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92014, School of Interdisciplinary Bioscience and Bioengineering, Department of Chemical Engineering, POSTECH, Pohang, 790-784, Korea, Mass Spectrometer Development team, Korea Basic Science Institute, Daejeon, Korea, and Department of Cell and Developmental Biology, School of Dentistry, Seoul National
| | - Ji-Hoon Cho
- Department of Biochemistry, School of Dentistry, Kyungpook National University, and 2nd BK21 program 700-422, Korea, Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92014, School of Interdisciplinary Bioscience and Bioengineering, Department of Chemical Engineering, POSTECH, Pohang, 790-784, Korea, Mass Spectrometer Development team, Korea Basic Science Institute, Daejeon, Korea, and Department of Cell and Developmental Biology, School of Dentistry, Seoul National
| | - Daehee Hwang
- Department of Biochemistry, School of Dentistry, Kyungpook National University, and 2nd BK21 program 700-422, Korea, Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92014, School of Interdisciplinary Bioscience and Bioengineering, Department of Chemical Engineering, POSTECH, Pohang, 790-784, Korea, Mass Spectrometer Development team, Korea Basic Science Institute, Daejeon, Korea, and Department of Cell and Developmental Biology, School of Dentistry, Seoul National
| | - Jong-Shin Yoo
- Department of Biochemistry, School of Dentistry, Kyungpook National University, and 2nd BK21 program 700-422, Korea, Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92014, School of Interdisciplinary Bioscience and Bioengineering, Department of Chemical Engineering, POSTECH, Pohang, 790-784, Korea, Mass Spectrometer Development team, Korea Basic Science Institute, Daejeon, Korea, and Department of Cell and Developmental Biology, School of Dentistry, Seoul National
| | - John R. Yates
- Department of Biochemistry, School of Dentistry, Kyungpook National University, and 2nd BK21 program 700-422, Korea, Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92014, School of Interdisciplinary Bioscience and Bioengineering, Department of Chemical Engineering, POSTECH, Pohang, 790-784, Korea, Mass Spectrometer Development team, Korea Basic Science Institute, Daejeon, Korea, and Department of Cell and Developmental Biology, School of Dentistry, Seoul National
| | - Hyun-Mo Ryoo
- Department of Biochemistry, School of Dentistry, Kyungpook National University, and 2nd BK21 program 700-422, Korea, Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92014, School of Interdisciplinary Bioscience and Bioengineering, Department of Chemical Engineering, POSTECH, Pohang, 790-784, Korea, Mass Spectrometer Development team, Korea Basic Science Institute, Daejeon, Korea, and Department of Cell and Developmental Biology, School of Dentistry, Seoul National
| | - Je-Yoel Cho
- Department of Biochemistry, School of Dentistry, Kyungpook National University, and 2nd BK21 program 700-422, Korea, Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92014, School of Interdisciplinary Bioscience and Bioengineering, Department of Chemical Engineering, POSTECH, Pohang, 790-784, Korea, Mass Spectrometer Development team, Korea Basic Science Institute, Daejeon, Korea, and Department of Cell and Developmental Biology, School of Dentistry, Seoul National
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Kersten B, Agrawal GK, Durek P, Neigenfind J, Schulze W, Walther D, Rakwal R. Plant phosphoproteomics: an update. Proteomics 2009; 9:964-88. [PMID: 19212952 DOI: 10.1002/pmic.200800548] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Phosphoproteomics involves identification of phosphoproteins, precise mapping, and quantification of phosphorylation sites, and eventually, revealing their biological function. In plants, several systematic phosphoproteomic analyses have recently been performed to optimize in vitro and in vivo technologies to reveal components of the phosphoproteome. The discovery of novel substrates for specific protein kinases is also an important issue. Development of a new tool has enabled rapid identification of potential kinase substrates such as kinase assays using plant protein microarrays. Progress has also been made in quantitative and dynamic analysis of mapped phosphorylation sites. Increased quantity of experimentally verified phosphorylation sites in plants has prompted the creation of dedicated web-resources for plant-specific phosphoproteomics data. This resulted in development of computational prediction methods yielding significantly improved sensitivity and specificity for the detection of phosphorylation sites in plants when compared to methods trained on less plant-specific data. In this review, we present an update on phosphoproteomic studies in plants and summarize the recent progress in the computational prediction of plant phosphorylation sites. The application of the experimental and computed results in understanding the phosphoproteomic networks of cellular and metabolic processes in plants is discussed. This is a continuation of our comprehensive review series on plant phosphoproteomics.
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Affiliation(s)
- Birgit Kersten
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany.
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Gális I, Gaquerel E, Pandey SP, Baldwin IT. Molecular mechanisms underlying plant memory in JA-mediated defence responses. PLANT, CELL & ENVIRONMENT 2009; 32:617-27. [PMID: 18657055 DOI: 10.1111/j.1365-3040.2008.01862.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants must respond to biotic and abiotic challenges to optimize their Darwinian fitness in nature. Many of these challenges occur repeatedly during a plant's lifetime, and their sequence and timing can profoundly influence the fitness outcome of a plant's response. The ability to perceive, store and recall previous stressful events is likely useful for efficient, rapid and cost-effective responses, but we know very little about the mechanisms involved. Using jasmonate-elicited anti-herbivore defence responses as an example, we consider how 'memories' of previous attacks could be created in (1) the biosynthetic processes involved in the generation of the oxylipin bursts elicited by herbivore attacks; (2) the perception of oxylipins and their transduction into cellular events by transcription factors and transcriptional activators; and (3) the role of small RNAs in the formation of long-term stress imprints in plants.
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Affiliation(s)
- Ivan Gális
- Department of Molecular Ecology, Max-Planck-Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany
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38
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Jorrín-Novo JV, Maldonado AM, Echevarría-Zomeño S, Valledor L, Castillejo MA, Curto M, Valero J, Sghaier B, Donoso G, Redondo I. Plant proteomics update (2007–2008): Second-generation proteomic techniques, an appropriate experimental design, and data analysis to fulfill MIAPE standards, increase plant proteome coverage and expand biological knowledge. J Proteomics 2009; 72:285-314. [DOI: 10.1016/j.jprot.2009.01.026] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Stork W, Diezel C, Halitschke R, Gális I, Baldwin IT. An ecological analysis of the herbivory-elicited JA burst and its metabolism: plant memory processes and predictions of the moving target model. PLoS One 2009; 4:e4697. [PMID: 19277115 PMCID: PMC2650097 DOI: 10.1371/journal.pone.0004697] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2008] [Accepted: 01/17/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Rapid herbivore-induced jasmonic acid (JA) accumulation is known to mediate many induced defense responses in vascular plants, but little is known about how JA bursts are metabolized and modified in response to repeated elicitations, are propagated throughout elicited leaves, or how they directly influence herbivores. METHODOLOGY/PRINCIPAL FINDINGS We found the JA burst in a native population of Nicotiana attenuata to be highly robust despite environmental variation and we examined the JA bursts produced by repeated elicitations with Manduca sexta oral secretions (OS) at whole- and within-leaf spatial scales. Surprisingly, a 2(nd) OS-elicitation suppressed an expected JA burst at both spatial scales, but subsequent elicitations caused more rapid JA accumulation in elicited tissue. The baseline of induced JA/JA-Ile increased with number of elicitations in discrete intervals. Large veins constrained the spatial spread of JA bursts, leading to heterogeneity within elicited leaves. 1(st)-instar M. sexta larvae were repelled by elicitations and changed feeding sites. JA conjugated with isoleucine (JA-Ile) translates elicitations into defense production (e.g., TPIs), but conjugation efficiency varied among sectors and depended on NaWRKY3/6 transcription factors. Elicited TPI activity correlated strongly with the heterogeneity of JA/JA-Ile accumulations after a single elicitation, but not repeated elicitations. CONCLUSIONS/SIGNIFICANCE Ecologically informed scaling of leaf elicitation reveals the contribution of repeated herbivory events to the formation of plant memory of herbivory and the causes and importance of heterogeneity in induced defense responses. Leaf vasculature, in addition to transmitting long-distance damage cues, creates heterogeneity in JA bursts within attacked leaves that may be difficult for an attacking herbivore to predict. Such unpredictability is a central tenet of the Moving Target Model of defense, which posits that variability in itself is defensive.
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Affiliation(s)
- William Stork
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Jena, Germany
| | - Celia Diezel
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Jena, Germany
| | - Rayko Halitschke
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Jena, Germany
| | - Ivan Gális
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Jena, Germany
| | - Ian T. Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Jena, Germany
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40
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de la Fuente van Bentem S, Hirt H. Protein tyrosine phosphorylation in plants: More abundant than expected? TRENDS IN PLANT SCIENCE 2009; 14:71-6. [PMID: 19162527 DOI: 10.1016/j.tplants.2008.11.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2008] [Revised: 11/09/2008] [Accepted: 11/13/2008] [Indexed: 05/20/2023]
Abstract
Protein phosphorylation in eukaryotes predominantly occurs on serine (Ser) and threonine (Thr) residues, whereas phosphorylation on tyrosine (Tyr) residues is less abundant. Plants lack classic Tyr kinases, such as the epidermal growth factor receptor, that govern Tyr phosphorylation in animals. A long-standing debate questions whether plants have any Tyr-specific kinases and, although several protein kinases with both Ser/Thr and Tyr specificities exist, data supporting the existence of other such kinases are scarce. As we discuss here, mass-spectrometry-based analyses now indicate that Tyr phosphorylation is as extensive in plants as it is in animals. However, careful inspection of available data indicates that these promising mass spectrometry studies have to be interpreted with caution before current ideas on Tyr phosphorylation in plants are revised.
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Affiliation(s)
- Sergio de la Fuente van Bentem
- Department of Plant Molecular Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
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41
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Baginsky S. Plant proteomics: concepts, applications, and novel strategies for data interpretation. MASS SPECTROMETRY REVIEWS 2009; 28:93-120. [PMID: 18618656 DOI: 10.1002/mas.20183] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Proteomics is an essential source of information about biological systems because it generates knowledge about the concentrations, interactions, functions, and catalytic activities of proteins, which are the major structural and functional determinants of cells. In the last few years significant technology development has taken place both at the level of data analysis software and mass spectrometry hardware. Conceptual progress in proteomics has made possible the analysis of entire proteomes at previously unprecedented density and accuracy. New concepts have emerged that comprise quantitative analyses of full proteomes, database-independent protein identification strategies, targeted quantitative proteomics approaches with proteotypic peptides and the systematic analysis of an increasing number of posttranslational modifications at high temporal and spatial resolution. Although plant proteomics is making progress, there are still several analytical challenges that await experimental and conceptual solutions. With this review I will highlight the current status of plant proteomics and put it into the context of the aforementioned conceptual progress in the field, illustrate some of the plant-specific challenges and present my view on the great opportunities for plant systems biology offered by proteomics.
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Affiliation(s)
- Sacha Baginsky
- Institute of Plant Sciences, Swiss Federal Institute of Technology, Universitätsstrasse 2, 8092 Zurich, Switzerland.
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42
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Assmann SM, Albert R. Discrete dynamic modeling with asynchronous update, or how to model complex systems in the absence of quantitative information. Methods Mol Biol 2009; 553:207-25. [PMID: 19588107 DOI: 10.1007/978-1-60327-563-7_10] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A major aim of systems biology is the study of the inter-relationships found within and between large biological data sets. Here we describe one systems biology method, in which the tools of network analysis and discrete dynamic (Boolean) modeling are used to develop predictive models of cellular signaling in cases where detailed temporal and kinetic information regarding the propagation of the signal through the system is lacking. This approach is also applicable to data sets derived from some other types of biological systems, such as transcription factor-mediated regulation of gene expression during the control of developmental fate, or host defense responses following pathogen attack, and is equally applicable to plant and non-plant systems. The method also allows prediction of how elimination of one or more individual signaling components will affect the ultimate outcome, thus allowing the researcher to model the effects of genetic knockout or pharmacological block. The method also serves as a starting point from which more quantitative models can be developed as additional information becomes available.
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Affiliation(s)
- Sarah M Assmann
- Biology Department, Penn State University, University Park, PA, USA
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43
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Boller T, Felix G. A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. ANNUAL REVIEW OF PLANT BIOLOGY 2009; 60:379-406. [PMID: 19400727 DOI: 10.1146/annurev.arplant.57.032905.105346] [Citation(s) in RCA: 1927] [Impact Index Per Article: 128.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Microbe-associated molecular patterns (MAMPs) are molecular signatures typical of whole classes of microbes, and their recognition plays a key role in innate immunity. Endogenous elicitors are similarly recognized as damage-associated molecular patterns (DAMPs). This review focuses on the diversity of MAMPs/DAMPs and on progress to identify the corresponding pattern recognition receptors (PRRs) in plants. The two best-characterized MAMP/PRR pairs, flagellin/FLS2 and EF-Tu/EFR, are discussed in detail and put into a phylogenetic perspective. Both FLS2 and EFR are leucine-rich repeat receptor kinases (LRR-RKs). Upon treatment with flagellin, FLS2 forms a heteromeric complex with BAK1, an LRR-RK that also acts as coreceptor for the brassinolide receptor BRI1. The importance of MAMP/PRR signaling for plant immunity is highlighted by the finding that plant pathogens use effectors to inhibit PRR complexes or downstream signaling events. Current evidence indicates that MAMPs, DAMPs, and effectors are all perceived as danger signals and induce a stereotypic defense response.
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Affiliation(s)
- Thomas Boller
- Botanisches Institut, Universität Basel, CH 4056 Basel, Switzerland.
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44
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Schreiber TB, Mäusbacher N, Breitkopf SB, Grundner-Culemann K, Daub H. Quantitative phosphoproteomics--an emerging key technology in signal-transduction research. Proteomics 2008; 8:4416-32. [PMID: 18837465 DOI: 10.1002/pmic.200800132] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein phosphorylation is the most important type of reversible post-translational modification involved in the regulation of cellular signal-transduction processes. In addition to controlling normal cellular physiology on the molecular level, perturbations of phosphorylation-based signaling networks and cascades have been implicated in the onset and progression of various human diseases. Recent advances in mass spectrometry-based proteomics helped to overcome many of the previous limitations in protein phosphorylation analysis. Improved isotope labeling and phosphopeptide enrichment strategies in conjunction with more powerful mass spectrometers and advances in data analysis have been integrated in highly efficient phosphoproteomics workflows, which are capable of monitoring up to several thousands of site-specific phosphorylation events within one large-scale analysis. Combined with ongoing efforts to define kinase-substrate relationships in intact cells, these major achievements have considerable potential to assess phosphorylation-based signaling networks on a system-wide scale. Here, we provide an overview of these exciting developments and their potential to transform signal-transduction research into a technology-driven, high-throughput science.
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Affiliation(s)
- Thiemo B Schreiber
- Department of Molecular Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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45
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Maathuis FJ. Conservation of protein phosphorylation sites within gene families and across species. PLANT SIGNALING & BEHAVIOR 2008; 3:1011-3. [PMID: 19704437 PMCID: PMC2633760 DOI: 10.4161/psb.6721] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Accepted: 08/04/2008] [Indexed: 05/20/2023]
Abstract
Recent large scale phosphoproteomics studies have helped identify many phosphorylation sites of both membrane and soluble proteins. In most cases the relevance of specific sites has yet to be established whereas in a small number of cases their potency in modulating protein activity is evident. With the increasing amount of data it is becoming clear that phosphosites are often conserved within protein families, pointing to generic regulatory mechanisms. In addition, such mechanisms may be conserved across species. In this addendum evidence is presented for these phenomena occurring in rice and Arabidopsis.
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46
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Towards functional phosphoproteomics by mapping differential phosphorylation events in signaling networks. Proteomics 2008; 8:4453-65. [DOI: 10.1002/pmic.200800175] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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47
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Vlad F, Turk BE, Peynot P, Leung J, Merlot S. A versatile strategy to define the phosphorylation preferences of plant protein kinases and screen for putative substrates. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 55:104-17. [PMID: 18363786 DOI: 10.1111/j.1365-313x.2008.03488.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Most signaling networks are regulated by reversible protein phosphorylation. The specificity of this regulation depends in part on the capacity of protein kinases to recognize and efficiently phosphorylate particular sequence motifs in their substrates. Sequenced plant genomes potentially encode over than 1000 protein kinases, representing 4% of the proteins, twice the proportion found in humans. This plethora of plant kinases requires the development of high-throughput strategies to identify their substrates. In this study, we have implemented a semi-degenerate peptide array screen to define the phosphorylation preferences of four kinases from Arabidopsis thaliana that are representative of the plant calcium-dependent protein kinase and Snf1-related kinase superfamily. We converted these quantitative data into position-specific scoring matrices to identify putative substrates of these kinases in silico in protein sequence databases. Our data show that these kinases display related but nevertheless distinct phosphorylation motif preferences, suggesting that they might share common targets but are likely to have specific substrates. Our analysis also reveals that a conserved motif found in the stress-related dehydrin protein family may be targeted by the SnRK2-10 kinase. Our results indicate that semi-degenerate peptide array screening is a versatile strategy that can be used on numerous plant kinases to facilitate identification of their substrates, and therefore represents a valuable tool to decipher phosphorylation-regulated signaling networks in plants.
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Affiliation(s)
- Florina Vlad
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, UPR 2355, 1 avenue de la Terrasse, Bât. 23, 91198 Gif-sur-Yvette Cedex, France
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48
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Stulemeijer IJE, Joosten MHAJ. Post-translational modification of host proteins in pathogen-triggered defence signalling in plants. MOLECULAR PLANT PATHOLOGY 2008; 9:545-60. [PMID: 18705867 PMCID: PMC6640405 DOI: 10.1111/j.1364-3703.2008.00468.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Microbial plant pathogens impose a continuous threat to global food production. Similar to animals, an innate immune system allows plants to recognize pathogens and swiftly activate defence. To activate a rapid response, receptor-mediated pathogen perception and subsequent downstream signalling depends on post-translational modification (PTM) of components essential for defence signalling. We discuss different types of PTMs that play a role in mounting plant immunity, which include phosphorylation, glycosylation, ubiquitination, sumoylation, nitrosylation, myristoylation, palmitoylation and glycosylphosphatidylinositol (GPI)-anchoring. PTMs are rapid, reversible, controlled and highly specific, and provide a tool to regulate protein stability, activity and localization. Here, we give an overview of PTMs that modify components essential for defence signalling at the site of signal perception, during secondary messenger production and during signalling in the cytoplasm. In addition, we discuss effectors from pathogens that suppress plant defence responses by interfering with host PTMs.
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Affiliation(s)
- Iris J E Stulemeijer
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
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49
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Pieroni E, de la Fuente van Bentem S, Mancosu G, Capobianco E, Hirt H, de la Fuente A. Protein networking: insights into global functional organization of proteomes. Proteomics 2008; 8:799-816. [PMID: 18297653 DOI: 10.1002/pmic.200700767] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The formulation of network models from global protein studies is essential to understand the functioning of organisms. Network models of the proteome enable the application of Complex Network Analysis, a quantitative framework to investigate large complex networks using techniques from graph theory, statistical physics, dynamical systems and other fields. This approach has provided many insights into the functional organization of the proteome so far and will likely continue to do so. Currently, several network concepts have emerged in the field of proteomics. It is important to highlight the differences between these concepts, since different representations allow different insights into functional organization. One such concept is the protein interaction network, which contains proteins as nodes and undirected edges representing the occurrence of binding in large-scale protein-protein interaction studies. A second concept is the protein-signaling network, in which the nodes correspond to levels of post-translationally modified forms of proteins and directed edges to causal effects through post-translational modification, such as phosphorylation. Several other network concepts were introduced for proteomics. Although all formulated as networks, the concepts represent widely different physical systems. Therefore caution should be taken when applying relevant topological analysis. We review recent literature formulating and analyzing such networks.
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Affiliation(s)
- Enrico Pieroni
- CRS4 Bioinformatica, c/o Parco Tecnologico POLARIS, Pula, Italy
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50
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Xu C, Huang B. Root proteomic responses to heat stress in two Agrostis grass species contrasting in heat tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:4183-94. [PMID: 19008411 PMCID: PMC2639019 DOI: 10.1093/jxb/ern258] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 09/05/2008] [Accepted: 09/26/2008] [Indexed: 05/18/2023]
Abstract
Protein metabolism plays an important role in plant adaptation to heat stress. This study was designed to identify heat-responsive proteins in roots associated with thermotolerance for two C3 grass species contrasting in heat tolerance, thermal Agrostis scabra and heat-sensitive Agrostis stolonifera L. Plants were exposed to 20 degrees C (control), 30 C (moderate heat stress), or 40 degrees C (severe heat stress) in growth chambers. Roots were harvested at 2 d and 10 d after temperature treatment. Proteins were extracted and separated by two-dimensional polyacrylamide gel electrophoresis. Seventy protein spots were regulated by heat stress in at least one species. Under both moderate and severe heat stress, more proteins were down-regulated than were up-regulated, and thermal A. scabra roots had more up-regulated proteins than A. stolonifera roots. The sequences of 66 differentially expressed protein spots were identified using mass spectrometry. The results suggested that the up-regulation of sucrose synthase, glutathione S-transferase, superoxide dismutase, and heat shock protein Sti (stress-inducible protein) may contribute to the superior root thermotolerance of A. scabra. In addition, phosphoproteomic analysis indicated that two isoforms of fructose-biphosphate aldolase were highly phosphorylated under heat stress, and thermal A. scabra had greater phosphorylation than A. stolonifera, suggesting that the aldolase phosphorylation might be involved in root thermotolerance.
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Affiliation(s)
| | - Bingru Huang
- To whom correspondence should be addressed. E-mail:
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