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Chen Y, Wang Y, Yang J, Zhou W, Dai S. Exploring the diversity of plant proteome. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1197-1210. [PMID: 33650765 DOI: 10.1111/jipb.13087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/25/2021] [Indexed: 05/10/2023]
Abstract
The tremendous functional, spatial, and temporal diversity of the plant proteome is regulated by multiple factors that continuously modify protein abundance, modifications, interactions, localization, and activity to meet the dynamic needs of plants. Dissecting the proteome complexity and its underlying genetic variation is attracting increasing research attention. Mass spectrometry (MS)-based proteomics has become a powerful approach in the global study of protein functions and their relationships on a systems level. Here, we review recent breakthroughs and strategies adopted to unravel the diversity of the proteome, with a specific focus on the methods used to analyze posttranslational modifications (PTMs), protein localization, and the organization of proteins into functional modules. We also consider PTM crosstalk and multiple PTMs temporally regulating the life cycle of proteins. Finally, we discuss recent quantitative studies using MS to measure protein turnover rates and examine future directions in the study of the plant proteome.
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Affiliation(s)
- Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Wenbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
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Chen Y, Weckwerth W. Mass Spectrometry Untangles Plant Membrane Protein Signaling Networks. TRENDS IN PLANT SCIENCE 2020; 25:930-944. [PMID: 32359835 DOI: 10.1016/j.tplants.2020.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Plasma membranes (PMs) act as primary cellular checkpoints for sensing signals and controlling solute transport. Membrane proteins communicate with intracellular processes through protein interaction networks. Deciphering these signaling networks provides crucial information for elucidating in vivo cellular regulation. Large-scale proteomics enables system-wide characterization of the membrane proteome, identification of ligand-receptor pairs, and elucidation of signals originating at membranes. In this review we assess recent progress in the development of mass spectrometry (MS)-based proteomic pipelines for determining membrane signaling pathways. We focus in particular on current techniques for the analysis of membrane protein phosphorylation and interaction, and how these proteins may be connected to downstream changes in gene expression, metabolism, and physiology.
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Affiliation(s)
- Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS), University of Vienna, Vienna, 1090, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Vienna, 1090, Austria.
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Renvoisé M, Bonhomme L, Davanture M, Zivy M, Lemaire C. Phosphoproteomic Analysis of Isolated Mitochondria in Yeast. Methods Mol Biol 2017; 1636:283-299. [PMID: 28730486 DOI: 10.1007/978-1-4939-7154-1_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mitochondria play a central role in cellular energy metabolism and cell death. Deregulation of mitochondrial functions is associated with several human pathologies (neurodegenerative diseases, neuromuscular diseases, type II diabetes, obesity, cancer). The steadily increasing number of identified mitochondrial phosphoproteins, kinases, and phosphatases in recent years suggests that reversible protein phosphorylation plays an important part in the control of mitochondrial processes. In addition, many mitochondrial phosphoproteins probably still remain to be identified, considering that 30% of proteins are expected to be phosphorylated in eukaryotes. In this chapter, we describe two procedures for the analysis of the mitochondrial phosphoproteome. The first one is a qualitative method that combines blue native and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (2D-BN/SDS-PAGE) and specific phosphoprotein staining. The second one is a quantitative approach that associates mitochondrial peptide labeling, phosphopeptide enrichment, and mass spectrometry.
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Affiliation(s)
- Margaux Renvoisé
- UMR 9198 CNRS, Institute for Integrative Biology of the Cell (I2BC), B3S, LPSM-CEA Saclay, 91191, Gif-sur-Yvette cedex, France
| | - Ludovic Bonhomme
- INRA/UCA UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 63039, Clermont-Ferrand, France
| | - Marlène Davanture
- GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, UniversitÕ Paris-Saclay, Ferme du Moulon, 91191, Gif-sur-Yvette, France
| | - Michel Zivy
- GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, UniversitÕ Paris-Saclay, Ferme du Moulon, 91191, Gif-sur-Yvette, France
| | - Claire Lemaire
- UMR 9198 CNRS, Institute for Integrative Biology of the Cell (I2BC), B3S, LPSM-CEA Saclay, 91191, Gif-sur-Yvette cedex, France.
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El Rassi Z, Puangpila C. Liquid-phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis-An update covering the period 2014-2016. Electrophoresis 2016; 38:150-161. [DOI: 10.1002/elps.201600413] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/03/2016] [Accepted: 10/04/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Ziad El Rassi
- Department of Chemistry; Oklahoma State University; Stillwater OK USA
| | - Chanida Puangpila
- Department of Chemistry, Faculty of Science; Chiang Mai University; Chiang Mai Thailand
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Quantitative phosphoproteomics reveals the role of the AMPK plant ortholog SnRK1 as a metabolic master regulator under energy deprivation. Sci Rep 2016; 6:31697. [PMID: 27545962 PMCID: PMC4992866 DOI: 10.1038/srep31697] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/25/2016] [Indexed: 01/11/2023] Open
Abstract
Since years, research on SnRK1, the major cellular energy sensor in plants, has tried to define its role in energy signalling. However, these attempts were notoriously hampered by the lethality of a complete knockout of SnRK1. Therefore, we generated an inducible amiRNA::SnRK1α2 in a snrk1α1 knock out background (snrk1α1/α2) to abolish SnRK1 activity to understand major systemic functions of SnRK1 signalling under energy deprivation triggered by extended night treatment. We analysed the in vivo phosphoproteome, proteome and metabolome and found that activation of SnRK1 is essential for repression of high energy demanding cell processes such as protein synthesis. The most abundant effect was the constitutively high phosphorylation of ribosomal protein S6 (RPS6) in the snrk1α1/α2 mutant. RPS6 is a major target of TOR signalling and its phosphorylation correlates with translation. Further evidence for an antagonistic SnRK1 and TOR crosstalk comparable to the animal system was demonstrated by the in vivo interaction of SnRK1α1 and RAPTOR1B in the cytosol and by phosphorylation of RAPTOR1B by SnRK1α1 in kinase assays. Moreover, changed levels of phosphorylation states of several chloroplastic proteins in the snrk1α1/α2 mutant indicated an unexpected link to regulation of photosynthesis, the main energy source in plants.
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Fíla J, Radau S, Matros A, Hartmann A, Scholz U, Feciková J, Mock HP, Čapková V, Zahedi RP, Honys D. Phosphoproteomics Profiling of Tobacco Mature Pollen and Pollen Activated in vitro. Mol Cell Proteomics 2016; 15:1338-50. [PMID: 26792808 PMCID: PMC4824859 DOI: 10.1074/mcp.m115.051672] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 11/02/2015] [Indexed: 11/06/2022] Open
Abstract
Tobacco mature pollen has extremely desiccated cytoplasm, and is metabolically quiescent. Upon re-hydration it becomes metabolically active and that results in later emergence of rapidly growing pollen tube. These changes in cytoplasm hydration and metabolic activity are accompanied by protein phosphorylation. In this study, we subjected mature pollen, 5-min-activated pollen, and 30-min-activated pollen to TCA/acetone protein extraction, trypsin digestion and phosphopeptide enrichment by titanium dioxide. The enriched fraction was subjected to nLC-MS/MS. We identified 471 phosphopeptides that carried 432 phosphorylation sites, position of which was exactly matched by mass spectrometry. These 471 phosphopeptides were assigned to 301 phosphoproteins, because some proteins carried more phosphorylation sites. Of the 13 functional groups, the majority of proteins were put into these categories: transcription, protein synthesis, protein destination and storage, and signal transduction. Many proteins were of unknown function, reflecting the fact that male gametophyte contains many specific proteins that have not been fully functionally annotated. The quantitative data highlighted the dynamics of protein phosphorylation during pollen activation; the identified phosphopeptides were divided into seven groups based on the regulatory trends. The major group comprised mature pollen-specific phosphopeptides that were dephosphorylated during pollen activation. Several phosphopeptides representing the same phosphoprotein had different regulation, which pinpointed the complexity of protein phosphorylation and its clear functional context. Collectively, we showed the first phosphoproteomics data on activated pollen where the position of phosphorylation sites was clearly demonstrated and regulatory kinetics was resolved.
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Affiliation(s)
- Jan Fíla
- From the ‡Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, v.v.i., Rozvojova 263, 165 00 Praha 6, Czech Republic
| | - Sonja Radau
- §Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straβe 6b, 44227 Dortmund, Germany
| | - Andrea Matros
- ¶Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetic and Crop Plant Research, Corrensstraβe 3, 06466 Gatersleben, Germany
| | - Anja Hartmann
- ¶Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetic and Crop Plant Research, Corrensstraβe 3, 06466 Gatersleben, Germany
| | - Uwe Scholz
- ‖Department of Breeding Research, Leibniz Institute of Plant Genetic and Crop Plant Research, Corrensstraβe 3, 06466 Gatersleben, Germany
| | - Jana Feciková
- From the ‡Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, v.v.i., Rozvojova 263, 165 00 Praha 6, Czech Republic
| | - Hans-Peter Mock
- ¶Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetic and Crop Plant Research, Corrensstraβe 3, 06466 Gatersleben, Germany
| | - Věra Čapková
- From the ‡Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, v.v.i., Rozvojova 263, 165 00 Praha 6, Czech Republic
| | - René Peiman Zahedi
- §Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straβe 6b, 44227 Dortmund, Germany
| | - David Honys
- From the ‡Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, v.v.i., Rozvojova 263, 165 00 Praha 6, Czech Republic;
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Ramalingam A, Kudapa H, Pazhamala LT, Weckwerth W, Varshney RK. Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement. FRONTIERS IN PLANT SCIENCE 2015; 6:1116. [PMID: 26734026 PMCID: PMC4689856 DOI: 10.3389/fpls.2015.01116] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/25/2015] [Indexed: 05/19/2023]
Abstract
The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these "omics" approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs.
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Affiliation(s)
- Abirami Ramalingam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Lekha T Pazhamala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India; School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
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Nagler M, Nukarinen E, Weckwerth W, Nägele T. Integrative molecular profiling indicates a central role of transitory starch breakdown in establishing a stable C/N homeostasis during cold acclimation in two natural accessions of Arabidopsis thaliana. BMC PLANT BIOLOGY 2015; 15:284. [PMID: 26628055 PMCID: PMC4667452 DOI: 10.1186/s12870-015-0668-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 11/23/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND The variation of growth and cold tolerance of two natural Arabidopsis accessions, Cvi (cold sensitive) and Rschew (cold tolerant), was analysed on a proteomic, phosphoproteomic and metabolomic level to derive characteristic information about genotypically distinct strategies of metabolic reprogramming and growth maintenance during cold acclimation. RESULTS Growth regulation before and after a cold acclimation period was monitored by recording fresh weight of leaf rosettes. Significant differences in the shoot fresh weight of Cvi and Rschew were detected both before and after acclimation to low temperature. During cold acclimation, starch levels were found to accumulate to a significantly higher level in Cvi compared to Rschew. Concomitantly, statistical analysis revealed a cold-induced decrease of beta-amylase 3 (BAM3; AT4G17090) in Cvi but not in Rschew. Further, only in Rschew we observed an increase of the protein level of the debranching enzyme isoamylase 3 (ISA3; AT4G09020). Additionally, the cold response of both accessions was observed to severely affect ribosomal complexes, but only Rschew showed a pronounced accumulation of carbon and nitrogen compounds. The abundance of the Cold Regulated (COR) protein COR78 (AT5G52310) as well as its phosphorylation was observed to be positively correlated with the acclimation state of both accessions. In addition, transcription factors being involved in growth and developmental regulation were found to characteristically separate the cold sensitive from the cold tolerant accession. Predicted protein-protein interaction networks (PPIN) of significantly changed proteins during cold acclimation allowed for a differentiation between both accessions. The PPIN revealed the central role of carbon/nitrogen allocation and ribosomal complex formation to establish a new cold-induced metabolic homeostasis as also observed on the level of the metabolome and proteome. CONCLUSION Our results provide evidence for a comprehensive multi-functional molecular interaction network orchestrating growth regulation and cold acclimation in two natural accessions of Arabidopsis thaliana. The differential abundance of beta-amylase 3 and isoamylase 3 indicates a central role of transitory starch degradation in the coordination of growth regulation and the development of stress tolerance. Finally, our study indicates naturally occurring differential patterns of C/N balance and protein synthesis during cold acclimation.
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Affiliation(s)
- Matthias Nagler
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
| | - Ella Nukarinen
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
| | - Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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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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