Abstract
The transmembrane receptor kinase family is the largest protein kinase family in Arabidopsis. Many members of this family play critical roles in plant signaling pathways. However, many of these kinases have yet uncharacterized functions and very little is known about the direct substrates of these kinases. We have developed the “ShortPhos” method, an efficient and simple mass spectrometry (MS)-based phosphoproteomics protocol to perform comparative phosphopeptide profiling of knockout mutants of receptor-like kinases. Through this method, we are able to better understand the functional roles of plant kinases in the context of their signaling networks.
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References
Zulawski M, Schulze G, Braginets R et al (2014) The Arabidopsis kinome: phylogeny and evolutionary insights into functional diversification. BMC Genomics 15(1):548
Zulawski M, Schulze WX (2015) The plant kinome. Methods Mol Biol 1306:1–23. https://doi.org/10.1007/978-1-4939-2648-0_1
Schweighofer A, Meskiene I (2015) Phosphatases in plants. Methods Mol Biol 1306:25–46. https://doi.org/10.1007/978-1-4939-2648-0_2
Kim J, Choi JN, John KM et al (2012) GC-TOF-MS- and CE-TOF-MS-based metabolic profiling of cheonggukjang (fast-fermented bean paste) during fermentation and its correlation with metabolic pathways. J Agric Food Chem 60(38):9746–9753. https://doi.org/10.1021/jf302833y
Kim TW, Guan S, Sun Y et al (2009) Brassinosteroid signal transduction from cell-surface receptor kinases to nuclear transcription factors. Nat Cell Biol 11(10):1254–1260
Marshall A, Aalen RB, Audenaert D et al (2012) Tackling drought stress: receptor-like kinases present new approaches. Plant Cell 24(6):2262–2278
Osakabe Y, Yamaguchi-Shinozaki K, Shinozaki K et al (2013) Sensing the environment: key roles of membrane-localized kinases in plant perception and response to abiotic stress. J Exp Bot 64(2):445–458
Wang X, Kota U, He K et al (2008) Sequential transphosphorylation of the BRI1/BAK1 receptor kinase complex impacts early events in brassinosteroid signaling. Dev Cell 15(2):220–235. https://doi.org/10.1016/j.devcel.2008.06.011
Wang ZY, Nakano T, Gendron J et al (2002) Nuclear-localized BZR1 mediates brassinosteroid-induced growth and feedback suppression of brassinosteroid biosynthesis. Dev Cell 2(4):505–513
Ryu H, Kim K, Cho H et al (2010) Predominant actions of cytosolic BSU1 and nuclear BIN2 regulate subcellular localization of BES1 in brassinosteroid signaling. Mol Cells 29(3):291–296. https://doi.org/10.1007/s10059-010-0034-y
Pascual J, Canal MJ, Escandon M et al (2017) Integrated physiological, proteomic, and metabolomic analysis of ultra violet (UV) stress responses and adaptation mechanisms in Pinus radiata. Mol Cell Proteomics 16(3):485–501. https://doi.org/10.1074/mcp.M116.059436
Schwacke R, Ponce-Soto GY, Krause K et al (2019) MapMan4: a refined protein classification and annotation framework applicable to multi-omics data analysis. Mol Plant 12(6):879–892. https://doi.org/10.1016/j.molp.2019.01.003
Wu XN, Sanchez Rodriguez C, Pertl-Obermeyer H et al (2013) Sucrose-induced receptor kinase SIRK1 regulates a plasma membrane aquaporin in Arabidopsis. Mol Cell Proteomics 12(10):2856–2873. https://doi.org/10.1074/mcp.M113.029579
Niittylä T, Fuglsang AT, Palmgren MG et al (2007) Temporal analysis of sucrose-induced phosphorylation changes in plasma membrane proteins of Arabidopsis. Mol Cell Proteomics 6(10):1711–1726
Tran HT, Plaxton WC (2008) Proteomic analysis of alterations in the secretome of Arabidopsis thaliana suspension cells subjected to nutritional phosphate deficiency. Proteomics 8. https://doi.org/10.1002/pmic.200800292
Engelsberger WR, Schulze WX (2012) Nitrate and ammonium lead to distinct global dynamic phosphorylation patterns when resupplied to nitrogen starved Arabidopsis seedlings. Plant J 69(6):978–995
Lan P, Li W, Wen TN et al (2012) Quantitative phosphoproteome profiling of iron-deficient Arabidopsis roots. Plant Physiol 159(1):403–417
Douglas P, Morrice N, MacKintosh C (1995) Identification of a regulatory phosphorylation site in the hinge 1 region of nitrate reductase from spinach (Spinacea oleracea) leaves. FEBS Lett 377(2):113–117
Wu X, Sanchez-Rodriguez C, Pertl-Obermeyer H et al (2013) Sucrose-induced receptor kinase SIRK1 regulates a plasma membrane aquaporin in Arabidopsis. Mol Cell Proteomics 12(10):2856–2873
Wu X, Sklodowski K, Encke B et al (2014) A kinase-phosphatase signaling module with BSK8 and BSL2 involved in regulation of sucrose-phosphate synthase. J Proteome Res 13(7):3397–3409
Benschop JJ, Mohammed S, O’Flaherty M et al (2007) Quantitative phospho-proteomics of early elicitor signalling in Arabidopsis. Mol Cell Proteomics 6(7):1705–1713
Reiland S, Finazzi G, Endler A et al (2011) Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF). Proc Natl Acad Sci U S A 108(31):12955–12960
Reiland S, Messerli G, Baerenfäller K et al (2009) Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiol 150(2):889–903
Chen Y, Höhenwarter W, Weckwerth W (2010) Comparative analysis of phytohormone-responsive phosphoproteins in Arabidopsis thaliana using TiO2-phosphopeptide enrichment and MAPA. Plant J 63(1):1–17
Zhang H, Zhou H, Berke L et al (2013) Quantitative phosphoproteomics after auxin-stimulated lateral root induction identifies an SNX1 protein phosphorylation site required for growth. Mol Cell Proteomics 12(5):1158–1169
Durek P, Schmidt R, Heazlewood JL et al (2010) PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Res 38:D828–D834
Heazlewood JL, Durek P, Hummel J et al (2008) PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Res 36:D1015–D1021
Duan G, Walther D, Schulze WX (2013) Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana. Front Plant Sci 4:540
Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2(8):1896–1906. https://doi.org/10.1038/nprot.2007.261
Morandell S, Grosstessner-Hain K, Roitinger E et al (2010) QIKS-quantitative identification of kinase substrates. Proteomics 10:2015–2025
Wu XN, Xi L, Pertl-Obermeyer H et al (2017) Highly efficient single-step enrichment of low abundance phosphopeptides from plant membrane preparations. Front Plant Sci 8:1673. https://doi.org/10.3389/fpls.2017.01673
Rappsilber J, Ishihama Y, Mann M (2003) Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem 75(3):663–670
Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26(12):1367–1372. https://doi.org/10.1038/nbt.1511
Su W, Huber SC, Crawford NM (1996) Identification in vitro of a post-translational regulatory site in the hinge 1 region of Arabidopsis nitrate reductase. Plant Cell 8(3):519–527. https://doi.org/10.1105/tpc.8.3.519
Tyanova S, Temu T, Sinitcyn P et al (2016) The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods 13(9):731–740. https://doi.org/10.1038/nmeth.3901
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Lu, D., Gao, T., Xi, L., Krall, L., Wu, X.N. (2021). Phosphoproteomics Profiling of Receptor Kinase Mutants. In: Wu, X.N. (eds) Plant Phosphoproteomics. Methods in Molecular Biology, vol 2358. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1625-3_4
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DOI: https://doi.org/10.1007/978-1-0716-1625-3_4
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