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He M, Wang J, Herold S, Xi L, Schulze WX. A Rapid and Universal Workflow for Label-Free-Quantitation-Based Proteomic and Phosphoproteomic Studies in Cereals. Curr Protoc 2022; 2:e425. [PMID: 35674286 DOI: 10.1002/cpz1.425] [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: 06/15/2023]
Abstract
Proteomics and phosphoproteomics are robust tools to analyze dynamics of post-transcriptional processes during growth and development. A variety of experimental methods and workflows have been published, but most of them were developed for model plants and have not been adapted to high-throughput platforms. Here, we describe an experimental workflow for proteome and phosphoproteome studies tailored to cereal crop tissues. The workflow consists of two parallel parts that are suitable for analyzing protein/phosphoprotein from total proteins and the microsomal membrane fraction. We present phosphoproteomic data regarding quantification coverage and analytical reproducibility for example preparations from maize root and shoot, wheat leaf, and a microsomal protein preparation from maize leaf. To enable users to adjust for tissue specific requirements, we provide two different methods of protein clean-up: traditional ethanol precipitation (PC) and a recently developed technology termed single-pot, solid-phase-enhanced sample preparation (SP3). Both the PC and SP3 methods are effective in the removal of unwanted substances in total protein crude extracts. In addition, two different methods of phosphopeptide enrichment are presented: a TiO2 -based method and Fe(III)-NTA cartridges on a robotized platform. Although the overall number of phosphopeptides is stable across protein clean-up and phosphopeptide enrichment methods, there are differences in the preferred phosphopeptides in each enrichment method. The preferred protocol depends on laboratory capabilities and research objective. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Total protein crude extraction Basic Protocol 2: Total protein clean-up with ethanol precipitation Alternate Protocol 1: Total protein clean-up with SP3 method Basic Protocol 3: Microsomal fraction protein extraction Basic Protocol 4: Protein concentration determination by Bradford assay Basic Protocol 5: In-solution digestion with trypsin Basic Protocol 6: Phosphopeptide enrichment with TiO2 Alternate Protocol 2: Phosphopeptide enrichment with Fe(III)-NTA cartridges Basic Protocol 7: Peptide desalting with C18 material Basic Protocol 8: LC-MS/MS analysis of (phospho)peptides and spectrum matching.
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Affiliation(s)
- Mingjie He
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Jiahui Wang
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sandra Herold
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
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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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Zhang Z, Gong J, Wang B, Li X, Ding Y, Yang B, Zhu C, Liu M, Zhang W. Regrowth strategies of Leymus chinensis in response to different grazing intensities. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02113. [PMID: 32112460 DOI: 10.1002/eap.2113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/07/2020] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
In temperate grassland ecosystems, grazing can affect plant growth by foraging, trampling, and excretion. The ability of dominant plant species to regrow after grazing is critical, since it allows the regeneration of photosynthetic tissues to support growth. We conducted a field experiment to evaluate the effects of different grazing intensities (control, light, medium, and heavy) on the physiological and biochemical responses of Leymus chinensis and the carbon (C) sources utilized during regrowth. Light grazing promoted regrowth and photoassimilate storage of L. chinensis, by increasing the net photosynthetic rate (Pn ), photosynthetic quenching, light interception, sugar accumulation, sucrose synthase activities, and fructose supply from stems. At medium grazing intensity, L. chinensis had low Pn , light interception, and sugar accumulation, but higher expression of a sucrose transporter gene (LcSUT1) and water-use efficiency, which reflected a tendency to store C in belowground to promote survival. This strategy was associated with regulation by abscisic acid (ABA), jasmonate, and salicylic acid (SA) signaling. However, L. chinensis tolerated heavy grazing by increased ABA and jasmonate-induced promotion of C assimilation and osmotic adjustment, combined with photoprotection against photo-oxidation, suggesting a strategy based on regrowth. In addition, stems were the main C source organs and energy supply rather than roots. Simultaneously, SA represented a weaker defense than ABA and jasmonate. Therefore, L. chinensis adopted different strategies for regrowth under different grazing intensities, and light grazing promoted regrowth the most. Our results demonstrate the regulation of C reserves utilization by phytohormones, and this regulation provides an explanation for recent results about grazing responses.
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Affiliation(s)
- Zihe Zhang
- Key Laboratory of Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
- Beijing Key Laboratory of Traditional Chinese Medicine Protection and Utilization, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Jirui Gong
- Key Laboratory of Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
- Beijing Key Laboratory of Traditional Chinese Medicine Protection and Utilization, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Biao Wang
- Key Laboratory of Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Xiaobing Li
- Key Laboratory of Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Yong Ding
- Grassland Research Institute of Chinese Academic of Agricultural Science, Hohhot, Inner Mongolia, 010021, China
| | - Bo Yang
- Key Laboratory of Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Chenchen Zhu
- Key Laboratory of Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Min Liu
- Key Laboratory of Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Wei Zhang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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Yang M, Deng W, Cao X, Wang L, Yu N, Zheng Y, Wu J, Wu R, Yue X. Quantitative Phosphoproteomics of Milk Fat Globule Membrane in Human Colostrum and Mature Milk: New Insights into Changes in Protein Phosphorylation during Lactation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4546-4556. [PMID: 32208690 DOI: 10.1021/acs.jafc.9b06850] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phosphorylation is a widespread posttranslational protein modification and is important in various biological processes. However, milk fat globule membrane (MFGM) phosphoproteins have not been explored systematically in human milk. Here, we used quantitative phosphoproteomics to analyze phosphorylation sites in human MFGM proteins and their differences at different stages of lactation; 305 phosphorylation sites on 170 proteins and 269 phosphorylation sites on 170 proteins were identified in colostrum and mature MFGM, respectively. Among these, 71 phosphorylation sites on 48 proteins were differentially expressed between the different stages of lactation. Osteopontin in human MFGM was the most heavily phosphorylated protein, with a total of 39 identified phosphorylation sites. Our results shed light on phosphorylation sites, composition, and biological functions of MFGM phosphoproteins in human colostrum and mature milk, and provide novel insights into the crucial roles of protein phosphorylation during infant development.
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Affiliation(s)
- Mei Yang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Wei Deng
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Xueyan Cao
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Lijie Wang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Na Yu
- Liaoning General Fair Testing Company, Ltd, Shenyang 110026, China
| | - Yan Zheng
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
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Cooper B, Beard HS, Garrett WM, Campbell KB. Benzothiadiazole Conditions the Bean Proteome for Immunity to Bean Rust. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:600-611. [PMID: 31999214 DOI: 10.1094/mpmi-09-19-0250-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The common bean rust fungus reduces harvests of the dry, edible common bean. Natural resistance genes in the plant can provide protection until a fungal strain that breaks resistance emerges. In this study, we demonstrate that benzo(1,2,3)thiadiazole-7-carbothioic acid S-methyl ester (BTH) sprayed on susceptible beans induces resistance to common bean rust. Protection occurred as soon as 72 h after treatment and resulted in no signs of disease 10 days after inoculation with rust spores. By contrast, the susceptible control plants sustained heavy infections and died. To understand the effect BTH has on the bean proteome, we measured the changes of accumulation for 3,973 proteins using mass spectrometry. The set of 409 proteins with significantly increased accumulation in BTH-treated leaves included receptor-like kinases SOBIR1, CERK1, and LYK5, which perceive pathogens, and EDS1, a regulator of the salicylic acid defense pathway. Other proteins that likely contributed to resistance included pathogenesis-related proteins, a full complement of enzymes that catalyze phenylpropanoid biosynthesis, and protein receptors, transporters, and enzymes that modulate other defense responses controlled by jasmonic acid, ethylene, brassinosteroid, abscisic acid, and auxin. Increases in the accumulation of proteins required for vesicle-mediated protein secretion and RNA splicing occurred as well. By contrast, more than half of the 168 decreases belonged to chloroplast proteins and proteins involved in cell expansion. These results reveal a set of proteins needed for rust resistance and reaffirm the utility of BTH to control disease by amplifying the natural immune system of the bean plant.
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Affiliation(s)
- Bret Cooper
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, U.S.A
| | - Hunter S Beard
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, U.S.A
| | - Wesley M Garrett
- Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville, MD, U.S.A
| | - Kimberly B Campbell
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, U.S.A
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Singh S, Singh UB, Trivedi M, Sahu PK, Paul S, Paul D, Saxena AK. Seed Biopriming with Salt-Tolerant Endophytic Pseudomonas geniculata-Modulated Biochemical Responses Provide Ecological Fitness in Maize ( Zea mays L.) Grown in Saline Sodic Soil. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 17:E253. [PMID: 31905865 PMCID: PMC6981434 DOI: 10.3390/ijerph17010253] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/19/2019] [Accepted: 12/27/2019] [Indexed: 11/24/2022]
Abstract
Under changing climate, soil salinity and sodicity is a limiting factor to crop production and are considered a threat to sustainability in agriculture. A number of attempts are being made to develop microbe-based technologies for alleviation of toxic effects of salts. However, the mechanisms of salt tolerance in agriculturally important crops are not fully understood and still require in-depth study in the backdrop of emerging concepts in biological systems. The present investigation was aimed to decipher the microbe-mediated mechanisms of salt tolerance in maize. Endophytic Pseudomonas geniculate MF-84 was isolated from maize rhizosphere and tagged with green fluorescent protein for localization in the plant system. Confocal microphotographs clearly indicate that MF-84 was localized in the epidermal cells, cortical tissues, endodermis and vascular bundles including proto-xylem, meta-xylem, phloem and bundle sheath. The role of P. geniculate MF-84 in induction and bioaccumulation of soluble sugar, proline and natural antioxidants enzymes in maize plant was investigated which lead not only to growth promotion but also provide protection from salt stress in maize. Results suggested that application of P. geniculate MF-84 reduces the uptake of Na+ and increases uptake of K+ and Ca2+ in maize roots indicative of the role of MF-84 in maintaining ionic balance/homeostasis in the plant roots under higher salt conditions. It not only helps in alleviation of toxic effects of salt but also increases plant growth along with reduction in crop losses due to salinity and sodicity.
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Affiliation(s)
- Shailendra Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, MaunathBhanjan 275 103, India; (S.S.); (P.K.S.); (S.P.); (A.K.S.)
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow 227 105, India;
| | - Udai B. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, MaunathBhanjan 275 103, India; (S.S.); (P.K.S.); (S.P.); (A.K.S.)
| | - Mala Trivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow 227 105, India;
| | - Pramod Kumar Sahu
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, MaunathBhanjan 275 103, India; (S.S.); (P.K.S.); (S.P.); (A.K.S.)
| | - Surinder Paul
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, MaunathBhanjan 275 103, India; (S.S.); (P.K.S.); (S.P.); (A.K.S.)
| | - Diby Paul
- Pilgram Marpeck School of Science, Technology, Engineering and Mathematics, TruettMcConnel University, 100 Alumni Dr., Cleveland, GA 30528, USA
| | - Anil Kumar Saxena
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, MaunathBhanjan 275 103, India; (S.S.); (P.K.S.); (S.P.); (A.K.S.)
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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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Vu LD, Stes E, Van Bel M, Nelissen H, Maddelein D, Inzé D, Coppens F, Martens L, Gevaert K, De Smet I. Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves. J Proteome Res 2016; 15:4304-4317. [DOI: 10.1021/acs.jproteome.6b00348] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lam Dai Vu
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Elisabeth Stes
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Michiel Van Bel
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Hilde Nelissen
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Davy Maddelein
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Dirk Inzé
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Lennart Martens
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Kris Gevaert
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Ive De Smet
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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