Abstract
Abiotic stresses, including drought and salt, are among the most devastating threats for modern agriculture. Overcoming these threats by modern breeding technologies requires an intricate understanding of underlying signaling mechanisms in plants. This book chapter summarizes major achievements and novel technologies and approaches to elucidate plant abiotic stress responses using proteomics and phosphoproteomics. Proteomic and phosphoproteomic studies of drought and salt stress in model and major crop plants have seen a boost over recent years, as mass spectrometry-based techniques advanced and were more widely available to plant scientists. The key proteins and mechanisms identified in these studies present leads for successful breeding of abiotic stress tolerance in plants.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Aghaei K, Ehsanpour AA, Shah AH, Komatsu S (2009) Proteome analysis of soybean hypocotyl and root under salt stress. Amino Acids 36(1):91–98
Agrawal GK, Jwa NS, Jung YH, Kim ST, Kim DW, Cho K, Shibato J, Rakwal R (2013) Rice proteomic analysis: sample preparation for protein identification. Methods Mol Biol 956:151–184. doi:10.1007/978-1-62703-194-3_12
Alpert AJ (2008) Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides. Anal Chem 80(1):62–76. doi:10.1021/ac070997p
Arabidopsis Genome I (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408(6814):796–815. doi:10.1038/35048692
Bae MS, Cho EJ, Choi EY, Park OK (2003) Analysis of the Arabidopsis nuclear proteome and its response to cold stress. Plant J 36(5):652–663
Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S (2008) Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320(5878):938–941. doi:10.1126/science.1157956
Bailey CM, Sweet SM, Cunningham DL, Zeller M, Heath JK, Cooper HJ (2009) SLoMo: automated site localization of modifications from ETD/ECD mass spectra. J Proteome Res 8(4):1965–1971. doi:10.1021/pr800917p
Barkla BJ, Castellanos-Cervantes T, de Leon JL, Matros A, Mock HP, Perez-Alfocea F, Salekdeh GH, Witzel K, Zorb C (2013a) Elucidation of salt stress defense and tolerance mechanisms of crop plants using proteomics—current achievements and perspectives. Proteomics 13(12–13):1885–1900. doi:10.1002/pmic.201200399
Barkla BJ, Vera-Estrella R, Pantoja O (2013b) Progress and challenges for abiotic stress proteomics of crop plants. Proteomics 13(12–13):1801–1815. doi:10.1002/pmic.201200401
Batistic O, Kudla J (2009) Plant calcineurin B-like proteins and their interacting protein kinases. Biochim Biophys Acta 1793(6):985–992. doi:10.1016/j.bbamcr.2008.10.006
Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 24(10):1285–1292. doi:10.1038/nbt1240
Benschop JJ, Mohammed S, O'Flaherty M, Heck AJ, Slijper M, Menke FL (2007) Quantitative phosphoproteomics of early elicitor signaling in Arabidopsis. Mol Cell Proteomics 6(7):1198–1214. doi:10.1074/mcp.M600429-MCP200
Böhmer M, Romeis T (2007) A chemical-genetic approach to elucidate protein kinase function in planta. Plant Mol Biol 65(6):817–827. doi:10.1007/s11103-007-9245-9
Böhmer M, Schroeder JI (2011) Quantitative transcriptomic analysis of abscisic acid-induced and reactive oxygen species-dependent expression changes and proteomic profiling in Arabidopsis suspension cells. Plant J 67(1):105–118. doi:10.1111/j.1365-313X.2011.04579.x
Böhmer M, Kurth J, Witte CP, Romeis T (2006) Function of plant calcium-dependent protein kinases in the activation of abiotic and pathogen-related stress responses and its potential application in the generation of stress-resistant plants. In: da Silva JA T (ed) Floriculture, ornamental and plant biotechnology: advances and topical issues , vol 3, 1st edn. Global science books, London, pp 367–372
Boyer JS (1982) Plant productivity and environment. Science 218(4571):443–448. doi:10.1126/science.218.4571.443
Campostrini N, Areces LB, Rappsilber J, Pietrogrande MC, Dondi F, Pastorino F, Ponzoni M, Righetti PG (2005) Spot overlapping in two-dimensional maps: a serious problem ignored for much too long. Proteomics 5(9):2385–2395. doi:10.1002/pmic.200401253
Carpentier SC, Panis B, Vertommen A, Swennen R, Sergeant K, Renaut J, Laukens K, Witters E, Samyn B, Devreese B (2008) Proteome analysis of non-model plants: a challenging but powerful approach. Mass Spectrom Rev 27(4):354–377. doi:10.1002/mas.20170
Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP (2008) Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci U S A 105(52):21034–21038. doi:10.1073/pnas.0811066106
Chang IF, Hsu JL, Hsu PH, Sheng WA, Lai SJ, Lee C, Chen CW, Hsu JC, Wang SY, Wang LY, Chen CC (2012) Comparative phosphoproteomic analysis of microsomal fractions of Arabidopsis thaliana and Oryza sativa subjected to high salinity. Plant Sci 185–186:131–142. doi:10.1016/j.plantsci.2011.09.009
Chen Y, Hoehenwarter W, Weckwerth W (2010) Comparative analysis of phytohormone-responsive phosphoproteins in Arabidopsis thaliana using TiO2-phosphopeptide enrichment and mass accuracy precursor alignment. Plant J 63(1):1–17. doi:10.1111/j.1365-313X.2010.04218.x
Cheng Y, Qi Y, Zhu Q, Chen X, Wang N, Zhao X, Chen H, Cui X, Xu L, Zhang W (2009) New changes in the plasma-membrane-associated proteome of rice roots under salt stress. Proteomics 9(11):3100–3114
Chitteti BR, Peng Z (2007) Proteome and phosphoproteome differential expression under salinity stress in rice (Oryza sativa) roots. J Proteome Res 6(5):1718–1727
Choudhary MK, Basu D, Datta A, Chakraborty N, Chakraborty S (2009) Dehydration-responsive nuclear proteome of rice (Oryza sativa L.) illustrates protein network, novel regulators of cellular adaptation, and evolutionary perspective. Mol Cell Proteomics 8(7):1579–1598. doi:10.1074/mcp. M800601-MCP200
Ciais P, Reichstein M, Viovy N, Granier A, Ogee J, Allard V, Aubinet M, Buchmann N, Bernhofer C, Carrara A, Chevallier F, De Noblet N, Friend AD, Friedlingstein P, Grunwald T, Heinesch B, Keronen P, Knohl A, Krinner G, Loustau D, Manca G, Matteucci G, Miglietta F, Ourcival JM, Papale D, Pilegaard K, Rambal S, Seufert G, Soussana JF, Sanz MJ, Schulze ED, Vesala T, Valentini R (2005) Europe-wide reduction in primary productivity caused by the heat and drought in 2003. Nature 437(7058):529–533. doi:10.1038/Nature03972
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. doi:10.1038/nbt.1511
Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K (2011) Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol 11:163. doi:10.1186/1471-2229-11-163
Dinneny JR, Long TA, Wang JY, Jung JW, Mace D, Pointer S, Barron C, Brady SM, Schiefelbein J, Benfey PN (2008) Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science 320(5878):942–945. doi:10.1126/science.1153795
Dissmeyer N, Schnittger A (2011) The age of protein kinases. Methods Mol Biol 779:7–52. doi:10.1007/978-1-61779-264-9_2
Dubiella U, Seybold H, Durian G, Komander E, Lassig R, Witte CP, Schulze WX, Romeis T (2013) Calcium-dependent protein kinase/NADPH oxidase activation circuit is required for rapid defense signal propagation. Proc Natl Acad Sci U S A 110(21):8744–8749. doi:10.1073/pnas.1221294110
Durek P, Schmidt R, Heazlewood JL, Jones A, MacLean D, Nagel A, Kersten B, Schulze WX (2010) PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Res 38(Database issue):D828–834. doi:10.1093/nar/gkp810
Engelsberger WR, Erban A, Kopka J, Schulze WX (2006) Metabolic labeling of plant cell cultures with K(15)NO3 as a tool for quantitative analysis of proteins and metabolites. Plant Methods 2:14. doi:10.1186/1746-4811-2-14
Feuillet C, Leach JE, Rogers J, Schnable PS, Eversole K (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci 16(2):77–88. doi:10.1016/j.tplants.2010.10.005
Franz S, Ehlert B, Liese A, Kurth J, Cazalé A-C, Romeis T (2013) Calcium-dependent protein kinase CPK21 functions in abiotic stress response in Arabidopsis thaliana. Mol Plant 6(270):rs8. doi:10.1093/mp/ssq064
Gao J, Agrawal GK, Thelen JJ, Xu D (2009) P3DB: a plant protein phosphorylation database. Nucleic Acids Res 37(Database issue):D960–962. doi:10.1093/nar/gkn733
Garces-Restrepo C, Muñoz G (2007) Irrigation management transfer, vol 32. Water reports. Food and Agriculture Organization of the United Nations
Ge P, Ma C, Wang S, Gao L, Li X, Guo G, Ma W, Yan Y (2012) Comparative proteomic analysis of grain development in two spring wheat varieties under drought stress. Anal Bioanal Chem 402(3):1297–1313. doi:10.1007/s00216-011-5532-z
Geng Y, Wu R, Wee CW, Xie F, Wei X, Chan PM, Tham C, Duan L, Dinneny JR (2013) A spatio-temporal understanding of growth regulation during the salt stress response in Arabidopsis. Plant Cell 25(6):2132–2154. doi:10.1105/tpc.113.112896
Gorg A, Drews O, Luck C, Weiland F, Weiss W (2009) 2-DE with IPGs. Electrophoresis 30(Suppl 1):S122–132. doi:10.1002/elps.200900051
Guo M, Gao W, Li L, Li H, Xu Y, Zhou C (2013) Proteomic and phosphoproteomic analyses of NaCl stress-responsive proteins in Arabidopsis roots. J Plant Interact 9(6):396–401. doi:10.1080/17429145.2013.845262
He H, Li J (2008) Proteomic analysis of phosphoproteins regulated by abscisic acid in rice leaves. Biochem Biophys Res Commun 371(4):883–888. doi:10.1016/j.bbrc.2008.05.001
Heazlewood JL, Durek P, Hummel J, Selbig J, Weckwerth W, Walther D, Schulze WX (2008) PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Res 36(Database issue):D1015–1021. doi:10.1093/nar/gkm812
Helmy M, Tomita M, Ishihama Y (2011) OryzaPG-DB: rice proteome database based on shotgun proteogenomics. BMC Plant Biol 11(1):63. doi:10.1186/1471-2229-11-63
Hirayama T, Shinozaki K (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J 61(6):1041–1052. doi:10.1111/j.1365-313X.2010.04124.x
Hoehenwarter W, van Dongen JT, Wienkoop S, Steinfath M, Hummel J, Erban A, Sulpice R, Regierer B, Kopka J, Geigenberger P, Weckwerth W (2008) A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment. Proteomics 8(20):4214–4225. doi:10.1002/pmic.200701047
Hoehenwarter W, Larhlimi A, Hummel J, Egelhofer V, Selbig J, van Dongen JT, Wienkoop S, Weckwerth W (2011) MAPA distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber. J Proteome Res 10(7):2979–2991. doi:10.1021/Pr101109a
Hsu JL, Wang LY, Wang SY, Lin CH, Ho KC, Shi FK, Chang IF (2009) Functional phosphoproteomic profiling of phosphorylation sites in membrane fractions of salt-stressed Arabidopsis thaliana. Proteome Sci 7(1):42. doi:10.1186/1477-5956-7-42
Hu G, Houston NL, Pathak D, Schmidt L, Thelen JJ, Wendel JF (2011) Genomically biased accumulation of seed storage proteins in allopolyploid cotton. Genetics 189(3):1103–1115. doi:10.1534/genetics.111.132407
Huang C, Verrillo F, Renzone G, Arena S, Rocco M, Scaloni A, Marra M (2011) Response to biotic and oxidative stress in Arabidopsis thaliana: analysis of variably phosphorylated proteins. J Proteomics 74(10):1934–1949. doi:10.1016/j.jprot.2011.05.016
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436(7052):793–800
Jacoby RP, Millar AH, Taylor NL (2010) Wheat mitochondrial proteomes provide new links between antioxidant defense and plant salinity tolerance. J Proteome Res 9(12):6595–6604. doi:10.1021/pr1007834
Jiang Y, Yang B, Harris NS, Deyholos MK (2007) Comparative proteomic analysis of NaCl stress-responsive proteins in Arabidopsis roots. J Exp Bot 58(13):3591–3607. doi:10.1093/jxb/erm207
Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K, Gruissem W, Baginsky S, Schmidt R, Schulze WX, Sun Q, van Wijk KJ, Egelhofer V, Wienkoop S, Weckwerth W, Bruley C, Rolland N, Toyoda T, Nakagami H, Jones AM, Briggs SP, Castleden I, Tanz SK, Millar AH, Heazlewood JL (2011) MASCP gator: an aggregation portal for the visualization of Arabidopsis proteomics data. Plant Physiol 155(1):259–270. doi:10.1104/pp. 110.168195
Ke Y, Han G, He H, Li J (2009) Differential regulation of proteins and phosphoproteins in rice under drought stress. Biochem Biophys Res Commun 379(1):133–138. doi:10.1016/j.bbrc.2008.12.067
Kerk D, Bulgrien J, Smith DW, Barsam B, Veretnik S, Gribskov M (2002) The complement of protein phosphatase catalytic subunits encoded in the genome of Arabidopsis. Plant Physiol 129(2):908–925. doi:10.1104/pp. 004002
Kersten B, Agrawal GK, Durek P, Neigenfind J, Schulze W, Walther D, Rakwal R (2009) Plant phosphoproteomics: an update. Proteomics 9(4):964–988. doi:10.1002/pmic.200800548
Khan M, Takasaki H, Komatsu S (2005) Comprehensive phosphoproteome analysis in rice and identification of phosphoproteins responsive to different hormones/stresses. J Proteome Res 4(5):1592–1599. doi:10.1021/pr0501160
Kim T-H, Hauser F, Ha T, Xue S, Böhmer M, Nishimura N, Munemasa S, Hubbard K, Peine N, B-h L, Lee S, Robert N, Parker JE, Schroeder JI (2011) Chemical genetics reveals negative regulation of abscisic acid signaling by a plant immune response pathway. Curr Biol 21(11):990–997. doi:10.1016/j.cub.2011.04.045
Kline KG, Barrett-Wilt GA, Sussman MR (2010) In planta changes in protein phosphorylation induced by the plant hormone abscisic acid. Proc Natl Acad Sci U S A 107(36):15986–15991. doi:10.1073/pnas.1007879107
Kline-Jonakin KG, Barrett-Wilt GA, Sussman MR (2011) Quantitative plant phosphoproteomics. Curr Opinion Plant Biol 14(5):507–511. doi:10.1016/j.pbi.2011.06.008
Komatsu S, Tanaka N (2005) Rice proteome analysis: a step toward functional analysis of the rice genome. Proteomics 5(4):938–949. doi:10.1002/pmic.200401040
Kosova K, Vitamvas P, Prasil IT, Renaut J (2011) Plant proteome changes under abiotic stress—contribution of proteomics studies to understanding plant stress response. J Proteomics 74(8):1301–1322. doi:10.1016/j.jprot.2011.02.006
Lee S, Lee EJ, Yang EJ, Lee JE, Park AR, Song WH, Park OK (2004) Proteomic identification of annexins, calcium-dependent membrane binding proteins that mediate osmotic stress and abscisic acid signal transduction in Arabidopsis. Plant Cell 16(6):1378–1391. doi:10.1105/tpc.021683
Li XJ, Yang MF, Chen H, Qu LQ, Chen F, Shen SH (2010) Abscisic acid pretreatment enhances salt tolerance of rice seedlings: proteomic evidence. Biochim Biophys Acta 1804(4):929–940
Lilley KS, Dupree P (2006) Methods of quantitative proteomics and their application to plant organelle characterization. J Exp Bot 57(7):1493–1499. doi:10.1093/jxb/erj141
Lim H, Eng J, Yates JR 3rd, Tollaksen SL, Giometti CS, Holden JF, Adams MW, Reich CI, Olsen GJ, Hays LG (2003) Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry. J Am Soc Mass Spectrom 14(9):957–970
Liu CW, Hsu YK, Cheng YH, Yen HC, Wu YP, Wang CS, Lai CC (2012) Proteomic analysis of salt-responsive ubiquitin-related proteins in rice roots. Rapid Commun Mass Spectrom 26(15):1649–1660
Luan S (2009) The CBL-CIPK network in plant calcium signaling. Trends Plant Sci 14(1):37–42
May P, Wienkoop S, Kempa S, Usadel B, Christian N, Rupprecht J, Weiss J, Recuenco-Munoz L, Ebenhoh O, Weckwerth W, Walther D (2008) Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics 179(1):157–166. doi:10.1534/genetics.108.088336
Moller IS, Tester M (2007) Salinity tolerance of Arabidopsis: a good model for cereals? Trends Plant Sci 12(12):534–540. doi:10.1016/j.tplants.2007.09.009
Munns R (2002) Comparative physiology of salt and water stress. Plant Cell Environ 25(2):239–250
Munns R, Tester M (2008) Mechanisms of salinity tolerance. Annu Rev Plant Biol 59:651–681. doi:10.1146/annurev.arplant.59.032607.092911
Nakagami H, Pitzschke A, Hirt H (2005) Emerging MAP kinase pathways in plant stress signalling. Trends Plant Sci 10(7):339–346. doi:10.1016/j.tplants.2005.05.009
Nakagami H, Sugiyama N, Mochida K, Daudi A, Yoshida Y, Toyoda T, Tomita M, Ishihama Y, Shirasu K (2010) Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants. Plant Physiol 153(3):1161–1174. doi:10.1104/pp. 110.157347
Nam MH, Huh SM, Kim KM, Park WJ, Seo JB, Cho K, Kim DY, Kim BG, Yoon IS (2012) Comparative proteomic analysis of early salt stress-responsive proteins in roots of SnRK2 transgenic rice. Proteome Sci 10(1)
Neilson KA, Ali NA, Muralidharan S, Mirzaei M, Mariani M, Assadourian G, Lee A, van Sluyter SC, Haynes PA (2011) Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 11(4):535–553. doi:10.1002/pmic.201000553
Ng DW, Zhang C, Miller M, Shen Z, Briggs SP, Chen ZJ (2012) Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors. Heredity 108(4):419–430. doi:10.1038/hdy.2011.92
Nohzadeh Malakshah S, Habibi Rezaei M, Heidari M, Salekdeh GH (2007) Proteomics reveals new salt responsive proteins associated with rice plasma membrane. Biosci Biotechnol Biochem 71(9):2144–2154
Nühse T, Stensballe A, Jensen O, Peck S (2004) Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database. Plant Cell 16(9):2394–2405
Nühse TS, Bottrill AR, Jones AME, Peck SC (2007) Quantitative phosphoproteomic analysis of plasma membrane proteins reveals regulatory mechanisms of plant innate immune responses. Plant J 51(5):931–9400. doi:10.1111/j.1365-313X.2007.03192.x
Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127(3):635–648. doi:10.1016/j.cell.2006.09.026
Pang Q, Chen S, Dai S, Chen Y, Wang Y, Yan X (2010) Comparative proteomics of salt tolerance in Arabidopsis thaliana and Thellungiella halophila. J Proteome Res 9(5):2584–2599. doi:10.1021/pr100034f
Pechanova O, Takac T, Samaj J, Pechan T (2013) Maize proteomics: an insight into the biology of an important cereal crop. Proteomics 13(3–4):637–662. doi:10.1002/pmic.201200275
Peng Z, Wang M, Li F, Lv H, Li C, Xia G (2009) A proteomic study of the response to salinity and drought stress in an introgression strain of bread wheat. Mol Cell Proteomics 8(12):2676–2686
Piques M, Schulze WX, Hohne M, Usadel B, Gibon Y, Rohwer J, Stitt M (2009) Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Mol Syst Biol 5:314. doi:10.1038/msb.2009.68
Potato Genome Sequencing Consortium, Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti SK, Patil VU, Skryabin KG, Kuznetsov BB, Ravin NV, Kolganova TV, Beletsky AV, Mardanov AV, Di Genova A, Bolser DM, Martin DM, Li G, Yang Y, Kuang H, Hu Q, Xiong X, Bishop GJ, Sagredo B, Mejia N, Zagorski W, Gromadka R, Gawor J, Szczesny P, Huang S, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Zhang Y, Xie B, Du Y, Qu D, Bonierbale M, Ghislain M, Herrera Mdel R, Giuliano G, Pietrella M, Perrotta G, Facella P, O'Brien K, Feingold SE, Barreiro LE, Massa GA, Diambra L, Whitty BR, Vaillancourt B, Lin H, Massa AN, Geoffroy M, Lundback S, DellaPenna D, Buell CR, Sharma SK, Marshall DF, Waugh R, Bryan GJ, Destefanis M, Nagy I, Milbourne D, Thomson SJ, Fiers M, Jacobs JM, Nielsen KL, Sonderkaer M, Iovene M, Torres GA, Jiang J, Veilleux RE, Bachem CW, de Boer J, Borm T, Kloosterman B, van Eck H, Datema E, Hekkert B, Goverse A, van Ham RC, Visser RG (2011) Genome sequence and analysis of the tuber crop potato. Nature 475(7355):189–195. doi:10.1038/nature10158
Qiu QS, Guo Y, Dietrich MA, Schumaker KS, Zhu JK (2002) Regulation of SOS1, a plasma membrane Na+/H+ exchanger in Arabidopsis thaliana, by SOS2 and SOS3. Proc Natl Acad Sci U S A 99(12):8436–8441, Epub 2002 May 8428
Rampitsch C, Bykova NV (2012) The beginnings of crop phosphoproteomics: exploring early warning systems of stress. Front Plant Sci 3:144. doi:10.3389/fpls.2012.00144
Ray DK, Mueller ND, West PC, Foley JA (2013) Yield trends Are insufficient to double global crop production by 2050. PLoS One 8(6):e66428. doi:10.1371/journal.pone.0066428
Reiland S, Messerli G, Baerenfaller K, Gerrits B, Endler A, Grossmann J, Gruissem W, Baginsky S (2009) Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiol 150(2):889–903. doi:10.1104/pp. 109.138677
Reiland S, Finazzi G, Endler A, Willig A, Baerenfaller K, Grossmann J, Gerrits B, Rutishauser D, Gruissem W, Rochaix JD, Baginsky S (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. doi:10.1073/pnas.1104734108
Salekdeh GH, Siopongco J, Wade LJ, Ghareyazie B, Bennett J (2002) A proteomic approach to analyzing drought- and salt-responsiveness in rice. Field Crop Res 76(2–3):199–219
Saqib M, Zörb C, Schubert S (2006) Salt-resistant and salt-sensitive wheat genotypes show similar biochemical reaction at protein level in the first phase of salt stress. J Plant Nutr Soil Sci 169(4):542–548. doi:10.1002/jpln.200520557
Savitski MM, Lemeer S, Boesche M, Lang M, Mathieson T, Bantscheff M, Kuster B (2011) Confident phosphorylation site localization using the Mascot Delta Score. Mol Cell Proteomics 10(2):M110.003830. doi:10.1074/mcp.M110.003830
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh C-T, Emrich SJ, Jia Y, Kalyanaraman A, Hsia A-P, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia J-M, Deragon J-M, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956):1112–1115. doi:10.1126/science.1178534
Schulze WX (2010) Proteomics approaches to understand protein phosphorylation in pathway modulation. Curr Opin Plant Biol 13(3):280–287. doi:10.1016/j.pbi.2009.12.008
Schulze WX, Usadel B (2010) Quantitation in mass-spectrometry-based proteomics. Annu Rev Plant Biol 61:491–516. doi:10.1146/annurev-arplant-042809-112132
Shteynberg D, Deutsch E, Mendoza L, Slagel J, Lam HH, Nesvizhskii A, Moritz R (2012) PTMProphet: TPP software for validation of modified site locations on post-translationally modified peptides. Paper presented at the 60th ASMS Conference on Mass Spectrometry, Vancouver, BC, Canada, 20–24 May
Sobhanian H, Razavizadeh R, Nanjo Y, Ehsanpour AA, Jazii FR, Motamed N, Komatsu S (2010) Proteome analysis of soybean leaves, hypocotyls and roots under salt stress. Proteome Sci 8
Sugimoto M, Takeda K (2009) Proteomic analysis of specific proteins in the root of salt-tolerant barley. Biosci Biotechnol Biochem 73(12):2762–2765
Suzuki N, Koussevitzky S, Mittler R, Miller G (2012) ROS and redox signalling in the response of plants to abiotic stress. Plant Cell Environ 35(2):259–270. doi:10.1111/j.1365-3040.2011.02336.x
Taus T, Kocher T, Pichler P, Paschke C, Schmidt A, Henrich C, Mechtler K (2011) Universal and confident phosphorylation site localization using phosphoRS. J Proteome Res 10(12):5354–5362. doi:10.1021/pr200611n
Tester M, Langridge P (2010) Breeding technologies to increase crop production in a changing world. Science 327(5967):818–822. doi:10.1126/science.1183700
Tomato Genome C (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485(7400):635–641. doi:10.1038/nature11119
Umezawa T, Sugiyama N, Takahashi F, Anderson JC, Ishihama Y, Peck SC, Shinozaki K (2013) Genetics and phosphoproteomics reveal a protein phosphorylation network in the abscisic acid signaling pathway in Arabidopsis thaliana. Sci Signal 6(270):rs8. doi:10.1126/scisignal.2003509
Unlu M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18(11):2071–2077. doi:10.1002/elps.1150181133
Vanderschuren H, Lentz E, Zainuddin I, Gruissem W (2013) Proteomics of model and crop plant species: status, current limitations and strategic advances for crop improvement. J Proteomics. doi:10.1016/j.jprot.2013.05.036
Vertommen A, Panis B, Swennen R, Carpentier SC (2011) Challenges and solutions for the identification of membrane proteins in non-model plants. J Proteomics 74(8):1165–1181. doi:10.1016/j.jprot.2011.02.016
Wang W, Vinocur B, Altman A (2003) Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218(1):1–14. doi:10.1007/s00425-003-1105-5
Wang MC, Peng ZY, Li CL, Li F, Liu C, Xia GM (2008) Proteomic analysis on a high salt tolerance introgression strain of Triticum aestivum/Thinopyrum ponticum. Proteomics 8(7):1470–1489. doi:10.1002/pmic.200700569
Wang P, Xue L, Batelli G, Lee S, Hou Y-J, Van Oosten MJ, Zhang H, Tao WA, Zhu J-K (2013) Quantitative phosphoproteomics identifies SnRK2 protein kinase substrates and reveals the effectors of abscisic acid action. Proc Natl Acad Sci U S A 110(27):11205–11210. doi:10.1073/pnas.1308974110
Witzel K, Weidner A, Surabhi GK, Börner A, Mock HP (2009) Salt stress-induced alterations in the root proteome of barley genotypes with contrasting response towards salinity. J Exp Bot 60(12):3545–3557
Yan S, Tang Z, Su W, Sun W (2005) Proteomic analysis of salt stress-responsive proteins in rice root. Proteomics 5(1):235–244. doi:10.1002/pmic.200400853
Yang Y, Thannhauser TW, Li L, Zhang S (2007) Development of an integrated approach for evaluation of 2-D gel image analysis: impact of multiple proteins in single spots on comparative proteomics in conventional 2-D gel/MALDI workflow. Electrophoresis 28(12):2080–2094. doi:10.1002/elps.200600524
Zhang L, Tian LH, Zhao JF, Song Y, Zhang CJ, Guo Y (2009) Identification of an apoplastic protein involved in the initial phase of salt stress response in rice root by two-dimensional electrophoresis. Plant Physiol 149(2):916–928
Zhang H, Han B, Wang T, Chen S, Li H, Zhang Y, Dai S (2012) Mechanisms of plant salt response: insights from proteomics. J Proteome Res 11(1):49–67. doi:10.1021/pr200861w
Zhao Q, Zhang H, Wang T, Chen S, Dai S (2013) Proteomics-based investigation of salt-responsive mechanisms in plant roots. J Proteomics 82:230–253. doi:10.1016/j.jprot.2013.01.024
Zhou YJ, Gao F, Li XF, Zhang J, Zhang GF (2010) Alterations in phosphoproteome under salt stress in Thellungiella roots. Chin Sci Bull 55(32):3673–3679. doi:10.1007/s11434-010-4116-1
Zörb C, Schmitt S, Neeb A, Karl S, Linder M, Schubert S (2004) The biochemical reaction of maize (Zea mays L.) to salt stress is characterized by a mitigation of symptoms and not by a specific adaptation. Plant Sci 167(1):91–100
Zörb C, Schmitt S, Mühling KH (2010) Proteomic changes in maize roots after short-term adjustment to saline growth conditions. Proteomics 10(24):4441–4449
Acknowledgments
Research in the author’s laboratory is funded by the Deutsche Fors-chungsgemeinschaft (BO3155-3/1) and the European Space Agency (4000109583-ESA-CORA-GBF-2013-005-Böhmer).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this chapter
Cite this chapter
Böhmer, M. (2015). Investigation of Plant Abiotic Stress Tolerance by Proteomics and Phosphoproteomics. In: Pandey, G. (eds) Elucidation of Abiotic Stress Signaling in Plants. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2211-6_3
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2211-6_3
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4939-2210-9
Online ISBN: 978-1-4939-2211-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)