Skip to main content
SpringerLink
Log in

Modulation of Proteome and Phosphoproteome Under Abiotic Stress in Plants: An Overview

  • Chapter
  • First Online:
Recent Approaches in Omics for Plant Resilience to Climate Change

Abstract

Abiotic stress factors cause significant reduction in crop yield worldwide. Crop/plant tolerance to environmental stress is a complex trait, and it depends on the expression of specific set of stress related genes, proteins and metabolites, involved in the cascades of molecular networks, signal transduction, to cope with stress perception to alleviate the cellular damage caused by different stress factors. Application of high-throughput global omics-approaches such as transcriptomics, proteomics and metabolomics will provide comprehensive understanding of plant abiotic stress response. A comprehensive understanding of the regulation at all levels or one of these will provide better tools to improve crop plant performance under stress. A focus on combined proteome and phosphoproteome-based studies provide broader molecular understanding in a better way, and the knowledge obtained is useful for developing crop/plants with enhanced tolerance to abiotic stresses. The main aim of this review is to discuss proteome and phosphoproteome dynamic changes under different abiotic stress factors, such as drought, salinity, waterlogging, heavy metal and temperature stress. This review describes the recent studies on proteomic and phosphoproteomic approaches, which have been conducted on different crop/plants under abiotic stress conditions.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Abbreviations

2D-PAGE:

Two-dimensional polyacrylamide gel electrophoresis

DIGE:

Differential in gel electrophoresis

ESI:

Electrospray ionization

ICAT:

Isotope-coded affinity tags

IMAC:

Immobilized metal affinity chromatography

iTRAQ:

Isobaric tags for relative and absolute quantification

LC:

Liquid chromatography

LCM:

Laser capture micro-dissection

MALDI-TOF:

Matrix assisted laser desorption/ionization-time of flight

MS:

Mass spectrometry

MS/MS:

Tandem mass spectrometry

MudPit:

Multidimensional Protein Identification Technology

PTM:

Post-translational modification

SILAC:

Stable isotope labelling by amino acids in cell cultures

References

  • Aggarwal K, Choe LH, Lee KH (2006) Shotgun proteomics using the iTRAQ isobaric tags. Brief Funct Genomic Proteomic 5(2):112–120

    Article  CAS  PubMed  Google Scholar 

  • Aghaei K, Ehsanpour AA, Komatsu S (2008) Proteome analysis of potato under salt stress. J Proteome Res 7(11):4858–4868. https://doi.org/10.1021/pr800460y

    Article  CAS  PubMed  Google Scholar 

  • Ahsan N, Lee DG, Lee SH, Lee KW, Bahk JD, Lee BH (2007) A proteomic screen and identification of water logging regulated proteins in tomato roots. Plant Soil 295:37–51

    Article  CAS  Google Scholar 

  • Alam I, Lee DG, Kim KH, Park CH, Sharmin SA, Lee H, Oh KW, Yun BW, Lee BH (2010) Proteome analysis of soybean roots under waterlogging stress at an early vegetative stage. J Biosci 35:49–62

    Article  CAS  PubMed  Google Scholar 

  • Alvarez S, Berla BM, Sheffield J, Cahoon RE, Jez JM, Hicks LM (2009) Comprehensive analysis of the Brassica juncea root proteome in response to cadmium exposure by complementary proteomic approaches. Proteomics 9:2419–2431

    Article  CAS  PubMed  Google Scholar 

  • Asai T, Tena G, Plotnikova J, Willmann MR, Chiu WL, Gomez-Gomez L, Boller T, Ausubel FM, Sheen J (2002) MAP kinase signalling cascade in Arabidopsis innate immunity. Nature 415:977–983

    Article  CAS  PubMed  Google Scholar 

  • Atikur RM, Yong-Goo K, Iftekhar A, Gongshe L, Hyoshin L, Joo LJ, Byung-Hyun L (2016) Proteome analysis of alfalfa roots in response to water deficit stress. J Integr Agric 15:1275–1285

    Article  CAS  Google Scholar 

  • Bachi A, Bonaldi T (2008) Quantitative proteomics as a new piece of the systems biology puzzle. J Proteome 71:357–367

    Article  CAS  Google Scholar 

  • Barkla BJ, Vera-Estrella R, Raymond C (2016) Single-cell-type quantitative proteomic and ionomic analysis of epidermal bladder cells from the halophyte model plant Mesembryanthemum crystallinum to identify salt-responsive proteins. BMC Plant Biol 16:110. https://doi.org/10.1186/s12870-016-0797-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barua P, Lande VN, Subba P, Gayen D, Pinto S, Prasad KST, Chakraborty S, Chakraborty N (2019) Dehydration responses nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation-mediated regulation of stress response. Plant Cell Environ 42(1):230–244. https://doi.org/10.1111/pce.1334

    Article  CAS  PubMed  Google Scholar 

  • Beckett P (2012) The basics of 2-D DIGE. In: Cramer R, Westermeier R (eds) Difference gel electrophoresis (DIGE). Humana Press, New York, NY, pp 9–19

    Chapter  Google Scholar 

  • Bhargava S, Sawant K (2013) Drought stress adaptation: metabolic adjustment and regulation of gene expression. Plant Breed 132:21–32

    Article  CAS  Google Scholar 

  • Bhaskara BG, Nguyen TT, Yang HT, Verslues EP (2017) Comparative analysis of phosphoproteome re-modelling after short term water stress and ABA treatments versus longer term water stress acclimation. Front Plant Sci 8:523. https://doi.org/10.3389/fpls.2017.00523

    Article  PubMed  PubMed Central  Google Scholar 

  • Carrão H, Naumann G, Barbosa P (2016) Mapping global patterns of drought risk: an empirical framework based on sub-national estimates of hazard, exposure and vulnerability. Glob Environ Chang 39:108–124

    Article  Google Scholar 

  • 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 stress. Plant Sci 185:131–142

    Article  PubMed  CAS  Google Scholar 

  • Chen X, Ronald PC (2011) Innate immunity in rice. Trends Plant Sci 16:451–459

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen X, Zhang W, Zhang B, Zhou J, Wang Y, Yang Q, Ke Y, He H (2011) Phosphoprotein regulated by heat stress in rice leaves. Proteome Sci 9:37–48

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen C, Song Y, Zhuang K, Li L, Xia Y, Shen Z (2015) Proteomic analysis of copper-binding proteins in excess copper-stressed roots of two rice (Oryza sativa L.) varieties with different cu tolerances. PLoS One 10(4):e0125367

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen XG, Zhen MS, Liu LY, Yan X, Zhang M, Yan MY (2017) In vivo phosphoproteome characterization reveals key starch granules-binding phosphoproteins involved in wheat water-deficit response. BMC Plant Biol 17(168):2–13. https://doi.org/10.1186/s12870-017-1118-z

    Article  CAS  Google Scholar 

  • Cheng WZ, Chen YZ, Yan K, Bian WY, Deng X, Yan MY (2017) Integrated physiological and proteomic analysis reveals underlying response and defense mechanisms of Brachypodium distachyon seedling leaves under osmotic stress, cadmium and their combined stresses. J Proteome 170:1–13. https://doi.org/10.1016/j.jprot.2017.09.015

    Article  CAS  Google Scholar 

  • Chitteti RB, Peng Z (2007) Proteome and phosphoproteome differential expression under salinity stress in rice (Oryza sativa) roots. J Proteome Res 6:1718–1727

    Article  CAS  PubMed  Google Scholar 

  • Cho HY, Wen TN, Wang YT, Shih MC (2016) Quantitative phosphoproteomics of protein kinase SnRK1 regulated protein phosphorylation in Arabidopsis under submergence. J Exp Bot 67(9):2745–2760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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. https://doi.org/10.1186/1471-2229-11-163

    Article  PubMed  PubMed Central  Google Scholar 

  • Cui D, Wu D, Liu J, Xu C, Li S, Li P, Zhang H, Jiang C, Wang L, Chen T, Chen H, Zhao L (2015) Proteomic analysis of seedling roots of two maize inbred lines that differ significantly in the salt stress response. PLoS One 10(2):e0116697. https://doi.org/10.1371/journal.pone.0116697

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cushman GC, Bohnert HJ (2000) Genomic approaches to plant stress tolerance. Curr Opin Plant Biol 3:117–124

    Article  CAS  PubMed  Google Scholar 

  • Dias AS, Barreiro MG, Campos PS, Ramalho JC, Lidon FC (2010) Wheat cellular membrane thermotolerance under heat stress. J Agron Crop Sci 196(2):100–108

    Article  CAS  Google Scholar 

  • Dumont E, Bahrmana N, Goulasa E, Valotc B, Sellier H, Hilberta JL, Vuylstekera C, Lejeune-Hénautb I, Delbreila BA (2011) Proteomic approach to decipher chilling response from cold acclimation in pea (Pisum sativum L.). Plant Sci 180:86–98

    Article  CAS  PubMed  Google Scholar 

  • Faghani F, Gharechahi J, Komatsu S, Mirzaei M, Khavarinejad AR, Najafi F, Farsad KL, Salekdeh HG (2015) Comparative physiology and proteomic analysis of two wheat genotypes contrasting in drought tolerance. J Proteome 114:1–15. https://doi.org/10.1016/j.jprot.2014.10.018

    Article  CAS  Google Scholar 

  • FAO (2002) Statistical database of food and agriculture organization. URL: http://www.fao.org/waicent/FAOINFO/AGRICULT/agl/agll/gaez/nav.html

    Google Scholar 

  • Farooq M, Wahid A, Kobayashi N, Fujita D, Basra SMA (2009) Plant drought stress: effects, mechanisms and management. Agron Sustain Dev 29:185–212

    Article  Google Scholar 

  • Gao L, Yan X, Li X, Guo G, Hu Y, Ma W, Yan Y (2011) Proteome analysis of wheat leaf under salt stress by two-dimensional difference gel electrophoresis (2D-DIGE). Phytochemistry 72:1180–1191

    Article  CAS  PubMed  Google Scholar 

  • Gao J, Zhang S, He DW, Shao HX, Li YC, Wei RY, Deng MG, Kuang BR, Hu HC, Yi JG, Yang SQ (2017) Comparative phosphoproteomics reveals an important role of mkk2 in banana (musa spp.) cold signal network. Sci Rep 7:40852. https://doi.org/10.1038/srep40852

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gavin A-C, Bösche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon A-M, Cruciat C-M, Remor M, Höfert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141–147

    Article  CAS  PubMed  Google Scholar 

  • Ghaffari M, Toorchi M, Valizadeh M, Komatsu S (2013) Differential response of root proteome to drought stress in drought sensitive and tolerant. Funct Plant Biol 40:609–617

    Article  CAS  PubMed  Google Scholar 

  • Ghosh D, Xu J (2014) Abiotic stress responses in plant roots: a proteomics perspective. Front Plant Sci 5:6. https://doi.org/10.3389/fpls.2014.00006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guerrier L, Righetti PG, Boschetti E (2008) Reduction of dynamic protein concentration range of biological extracts for the discovery of low-abundance proteins by means of hexapeptide ligand library. Nat Protoc 3:883–890

    Article  CAS  PubMed  Google Scholar 

  • Guo R, Yu F, Gao Z et al (2011) GhWRKY3, a novel cotton (Gossypium hirsutum L.) WRKY gene, is involved in diverse stress responses. Mol Biol Rep 38(11):49–58

    Article  CAS  PubMed  Google Scholar 

  • Guo M, Gao W, Li L, Li H, Xu Y, Zhou C (2014) Proteomic and phosphoproteomic analysis of NaCl stress-responsive proteins in Arabidopsis roots. J Plant Interact 9(1):396–401

    Article  CAS  Google Scholar 

  • Guo Y, Wang Z, Guan X, Hu Z, Zhang Z, Zheng J, Lu Y (2017) Proteomic analysis of Potentilla fruticosa L. leaves by iTRAQ reveals response to heat stress. PLoS One 12(8):e0182917

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994–999

    Article  CAS  PubMed  Google Scholar 

  • Harb A, Krishnan A, Ambavaram MM, Pereira A (2010) Molecular and physiological analysis of drought stress in Arabidopsis reveals early responses leading to acclimation in plant growth. Plant Physiol 154:1254–1271

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hashiguchi A, Ahsan N, Komatsu S (2010) Proteomics application of crops in the context of climatic changes. Food Res Int 43:1803–1813. https://doi.org/10.1016/j.foodres.2009.07.033

    Article  CAS  Google Scholar 

  • Hashimoto M, Toorchi M, Matsushita K, Iwasaki Y, Komatsu S (2009) Proteome analysis of rice root plasma membrane and detection of cold stress responsive proteins. Protein Pept Lett 16:685–697

    Article  CAS  PubMed  Google Scholar 

  • Helmy M, Tomita M, Ishihama Y (2012a) Peptide identification by searching large-scale tandem mass spectra against large databases: bioinformatics methods in proteogenomics. Gene Genome Genomics 6:76–85

    Google Scholar 

  • Helmy M, Sugiyama N, Tomita M, Ishihama Y (2012b) Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics. Cell Mech 17:633–644. https://doi.org/10.1111/j.1365-2443.2012.01615.x

    Article  CAS  Google Scholar 

  • Hopff D, Wienkoop S, Luthje S (2013) The plasma membrane proteome of maize roots grown under low and high iron conditions. J Proteome 6:1–14

    Google Scholar 

  • Hsu LJ, Wang YL, Wan YL, Wang SY, Lin CH, Ho KC, Shi FK, Chang F (2009) Functional phosphoproteomic profiling of phosphorylation sites in membrane fractions of salt-stressed Arabidopsis thaliana. Proteome Sci 7:42. https://doi.org/10.1186/1477-5956-7-42

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu X, Wu L, Zhao F, Zhang D, Li N, Zhu G, Li C, Wang W (2015) Phosphoproteomic analysis of the response of maize leaves to drought heat and their combination stress. Front Plant Sci 6:298. https://doi.org/10.3389/fpls.2015.00298

    Article  PubMed  PubMed Central  Google Scholar 

  • Hubbard MJ, Cohen P (1993) On target with a new mechanism for the regulation of protein phosphorylation. Trends Biochem Sci 18:172–177. https://doi.org/10.1016/0968-0004(93)90109-Z

    Article  CAS  PubMed  Google Scholar 

  • Jun YZ, Fei G, Feng XL, Jun Z, Fa GZ (2010) Alternations in phosphoproteome under salt stress in Thellungiella roots. Plant Genetics 55(32):3673–3679

    Google Scholar 

  • Kamal MHA, Rashid H, Sakata K, Komatsu S (2015) Gel-free quantitative proteomic approach to identify cotyledon proteins in soybean under flooding stress. J Proteome 112:1–13

    Article  CAS  Google Scholar 

  • Ke Y, Han G, He H, Li J (2009) Differential regulation of proteins and phosphoproteins in rice under drought stress. Biochem Biophys Res Commun 379:133–138

    Article  CAS  PubMed  Google Scholar 

  • Kersten B, Agrawal GK, Durek P, Neigenfind J, Schulze W, Walther D et al (2009) Plant phosphoproteomics: an update. Proteomics 9:964–988. https://doi.org/10.1002/pmic.200800548

    Article  CAS  PubMed  Google Scholar 

  • Khan MN, Komatsu S (2016) Proteomic analysis of soybean root including hypocotyl during recovery from drought stress. J Proteome 144:39–50

    Article  CAS  Google Scholar 

  • Komatsu S, Hossain Z (2013) Organ-specific proteome analysis for identification of abiotic stress response mechanism in crop. Front Plant Sci 4:71. https://doi.org/10.3389/fpls.2013.00071

    Article  PubMed  PubMed Central  Google Scholar 

  • Komatsu S, Konishi H, Shen S, Yang G (2003) Rice proteomics: a step toward functional analysis of the rice genome. Mol Cell Proteomics 2:2–10

    Article  CAS  PubMed  Google Scholar 

  • Komatsu S, Kobayashi Y, Nishizawa K, Nanjo Y, Frukawa K (2010) Comparative proteomics analysis of differentially expressed proteins in soybean cell wall during flooding stress. Amino Acids 39:1435–1449

    Article  CAS  PubMed  Google Scholar 

  • Kumar A, Majeti NVP (2014) Proteomic responses to lead-induced oxidative stress in Talinum triangulareJacq. (Willd.) roots, identification of key biomarkers related to glutathione metabolisms. Environ Sci Pollut Res 21:8750–8764

    Article  CAS  Google Scholar 

  • Kumari GJ, Surabhi GK, Thippeswamy M, Annapurnadevi A, Naik ST, Sudhakar C (2007) Effect of salinity on growth and proteomic changes in two cultivars of mulberry (Morus alba L.) with contrasting salt tolerance. Indian J Biotechnol 6:508–518

    CAS  Google Scholar 

  • Lan P, Li W, Wen NT, Schmidt W (2012) Quantitative phosphoproteome profiling of iron deficient Arabidopsis roots. Plant Physiol 159:403–417

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lassowskat I, Böttcher C, Eschen-Lippold L et al (2014) Sustained mitogen-activated protein kinase activation reprograms defense metabolism and phosphoprotein profile in Arabidopsis thaliana. Front Plant Sci 5:554. https://doi.org/10.3389/fpls.2014.00554

    Article  PubMed  PubMed Central  Google Scholar 

  • Lee DG, Ahsan N, Lee SH, Lee JJ, Bahk JD, Kang KY, Lee BH (2009) Chilling stress-induced proteomic changes in rice roots. J Plant Physiol 166:1–11

    Article  CAS  PubMed  Google Scholar 

  • Leopold AC (1990) Coping with desiccation. In: Alscher RG, Cumming JR (eds) Stress response in plants, adaptation and acclimation mechanisms. Wiley, New York, NY, pp 37–56

    Google Scholar 

  • Li W, Zhao F, Fang W, Xie D, Hou J, Yang X, Zhao Y, Tang Z, Nie L, Lv S (2015) Identification of early salt stress responsive proteins in seedling roots of upland cotton (Gossypium hirsutum L.) employing iTRAQ-based proteomic technique. Front Plant Sci 6:732. https://doi.org/10.3389/fpls.2015.00732

    Article  PubMed  PubMed Central  Google Scholar 

  • Li GK, Gao J, Peng H, Shen YO, Ding HP, Zhang ZM, Pan GT, Lin HJ (2016) Proteomic change in maize as a response to heavy metal (lead) stress revealed by iTRAQ quantitative proteomics. Genet Mol Res 15(1). https://doi.org/10.4238/gmr.15017254

  • Li NA, Zhang S, Liang Y, Qi Y, Chen J, Zhu W, Zhang L (2018a) Label-free quantitative proteomic analysis of drought-stress responsive late embryogenesis abundant proteins in the seedling leaves of two wheat (Triticum aestivum L.) genotypes. J Proteome 172:122–142. https://doi.org/10.1016/j.jprot.2017.09.016

    Article  CAS  Google Scholar 

  • Li X, Rehman US, Yamaguchi H, Hitachi K, Tsuchida K, Yamaguchi T, Sunohara Y, Matsumoto H, Komatsu S (2018b) Proteomic analysis of the effect of plant-derived smoke on soybean during recovery from flooding stress. J Proteome 181:238–248

    Article  CAS  Google Scholar 

  • Liu WJ, Chen YE, Tian WJ, Du JB, Zhang ZW, Xu F, Zhang F, Yuan S, Lin HH (2009) Dephosphorylation of photosystem II proteins and phosphorylation of CP29 in barley photosynthetic membranes as a response to water stress. Biochim Biophys Acta 1787(10):1238–1245

    Article  CAS  PubMed  Google Scholar 

  • Liu T, Shen C, Wang Y, Huang C, Shi J (2014) New insights into regulation of proteome and polysaccharide in cell wall of Elsholtzia splendens in response to copper stress. PLoS One 9(10):e109573. https://doi.org/10.1371/journal.pone.0109573

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu D, Estiarte M, Ogaya R, Yang X, Peñuelas J (2017) Shift in community structure in an early-successional Mediterranean shrubland driven by long-term experimental warming and drought and natural extreme droughts. Glob Chang Biol 23:4267–4279

    Article  PubMed  Google Scholar 

  • Lv WD, Subburaj JS, Cao M, Yan X, Li X, Appels R, Sun FD, Ma W, Yan MY (2014) Proteome and phosphoproteome characterization reveals new response and defense mechanisms of Brachypodium distachyon leaves under salt stress. Am Soc Biochem Mol Biol 13:1–21

    Google Scholar 

  • Magdeldin S, Enany S, Yoshida Y, Xu B, Zhang Y, Zureena Z, Lokamani I, Yaoita E, Yamamoto T (2014) Basics and recent advances of two dimensional-polyacrylamide gel electrophoresis. Clin Proteomics 11:16–30

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Margaria P, Abbà S, Palmano S (2013) Novel aspects of grapevine response to phytoplasma infection investigated by a proteomic and phospho-proteomic approach with data integration into functional networks. BMC Genomics 14:38. https://doi.org/10.1186/1471-2164-14-38

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR et al (2013) Integrated proteomic analysis of post-translational modifications by serial enrichment. Nat Methods 10:634–637. https://doi.org/10.1038/nmeth.2518

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mostek A, Borner A, Badowiec A, Weidner S (2015) Alterations in root proteome of salt-sensitive and tolerant barley lines under salt stress conditions. J Plant Physiol 174:166–176

    Article  CAS  PubMed  Google Scholar 

  • Muneer S, Jeong RB (2015) Proteomic analysis of salt-stress responsive proteins in roots of tomato (Lycopersicon esculentum L.) plants towards silicon efficiency. Plant Gowth Reg. https://doi.org/10.1007/s10725-015-0045-y

    Article  CAS  Google Scholar 

  • Mustafa G, Komatsu S (2014) Quantitative proteomics reveals the effect of protein glycosylation in soybean root under flooding stress. Front Plant Sci 5:1–14

    Article  Google Scholar 

  • Nakagami H, Sugiyama N, Ishihama Y, Shirasu K (2012) Shotguns in the front line: phosphoproteomics in plants. Plant Cell Physiol 53:118–124. https://doi.org/10.1093/pcp/pcr148

    Article  CAS  PubMed  Google Scholar 

  • Nam MH, Huh SM, Kim KM, Park WJ, Seo JB, Cho K et al (2012) Comparative proteomic analysis of early salt stress-responsive proteins in roots of SnRK2 transgenic rice. Proteome Sci 10:25. https://doi.org/10.1186/1477-5956-10-25

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nanjo Y, Skultety L, Ashraf Y, Komatsu S (2010) Comparative proteomic analysis of early-stage soybean seedlings responses to flooding by using gel and gel-free techniques. J Proteome Res 9:3989–4002

    Article  CAS  PubMed  Google Scholar 

  • Nanjo Y, Skultety L, Uváčková L, Klubicová K, Hajduch M, Komatsu S (2012) Mass spectrometry-based analysis of proteomic changes in the root tips of flooded soybean seedlings. J Proteome Res 11:372–385

    Article  CAS  PubMed  Google Scholar 

  • Neilson KA, Gammulla CG, Mirzaei M, Nijat Imin N, Haynes PA (2010) Proteomic analysis of temperature stress in plants. Proteomics 10:828–845

    Article  CAS  PubMed  Google Scholar 

  • Nriagu JO, Pacyna JM (1998) Quantitative assessment of worldwide contamination of air, water and soils with trace metals. Nature 333:134–139

    Article  Google Scholar 

  • Nühse TS, Stensballe A, Jensen ON, Peck SC (2003) Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol Cell Proteomics 2:1234–1243

    Article  PubMed  CAS  Google Scholar 

  • Oskuei KB, Yin X, Hasiguehi A, Bandehog A, Komatsu S (2017) Proteomic analysis of soybean seedling leaf under waterlogging stress in a time-dependent manner. Biochim Biophys Acta, Proteins Proteomics 1865(9):1167–1177. https://doi.org/10.1016/j.bbapap.2017.06.022

    Article  CAS  Google Scholar 

  • Pan Z, Zhu S, Guan R, Deng X (2010) Identification of 2,4-D-responsive proteins in embryogenic callus of Valencia sweet orange (Citrus sinensis Osbeck) following osmotic stress. Plant Cell Tissue Organ Cult 103(2):145–153

    Article  CAS  Google Scholar 

  • Pan D, Wang L, Tan F, Lu S, Zayrab M, Cheng LC, Chen S, Chen W (2018) Phosphoproteomics unveils stable energy supply as key to flooding tolerance in Kandelia candel. J Proteome 176:1–12

    Article  CAS  Google Scholar 

  • Paul S, Gayen D, Datta SK, Datta K (2015) Dissecting root proteome of transgenic rice cultivars unreveils metabolic alterations and accumulation of novel stress responsive proteins under drought stress. Plant Sci 234:133–143

    Article  CAS  PubMed  Google Scholar 

  • Pawson T, Scott JD (1997) Signaling through scaffold, anchoring, and adaptor proteins. Science 278:2075–2080

    Article  CAS  PubMed  Google Scholar 

  • Pi Z, Zhao M, Peng JX, Shen HS (2017) Phosphoproteomic analysis of paper mulberry reveals phosphorylation functions in chilling tolerance. J Proteome Res 16(5):1944–1961. https://doi.org/10.1021/acs.jproteome.6b01016

    Article  CAS  PubMed  Google Scholar 

  • Pi E, Zhu C, Fan W, Huang Y, Qu L, Li Y, Zhao Q, Ding F, Qiu L, Wang H, Poovaiah BW, Du L (2018) Quantitative phosphoproteomic and metabonomic analysis reveal GmMYB173 optimises flavonoid metabolism in soybean under salt stress. Mol Cell Proteomics 117:1–48

    Google Scholar 

  • Pitzschke A, Schikora A, Hirt H (2009) MAPK cascade signalling networks in plant defence. Curr Opin Plant Biol 12:421–426

    Article  CAS  PubMed  Google Scholar 

  • Ren J, Mao J, Zuo C, Urrea CA, Dawuda MM, Zhao X, Li X, Chen B (2017) Significant and unique changes in phosphorylation levels of four phosphoproteins in two apple rootstock genotypes under drought stress. Mol Gen Genomics 292(6):1307–1322. https://doi.org/10.1007/s00438-017-1348-7

    Article  CAS  Google Scholar 

  • Robinson AA, McManus CA, Dunn MJ (2011) Two-dimensional polyacrylamide gel electrophoresis. In: Ivanov AR, Lazarev AV (eds) Sample preparation in biological mass spectrometry. Springer, Netherlands, pp 217–242

    Chapter  Google Scholar 

  • Rodziewicz P, Swarcewicz B, Chmielewska K, Wojakowska A, Stobiecki M (2014) Influence of abiotic stresses on plant proteome and metabolome changes. Acta Physiol Plant 36:1–19. https://doi.org/10.1007/s11738-013-1402-y

    Article  CAS  Google Scholar 

  • Romeo S, Trupiano D, Aniani A, Renzone G, Scalonia A, Sebastiani L (2014) Proteomic analysis of Populus×euramericana (clone I-214) roots to identify key factors involved in zinc stress response. J Plant Physiol 171:1054–1063

    Article  CAS  PubMed  Google Scholar 

  • Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3(12):1154–1169

    Article  CAS  PubMed  Google Scholar 

  • Roy A, Rushton PJ, Rohila JS (2011) The potential of proteomics technologies for crop improvement under drought conditions. Crit Rev Plant Sci 30:471–490

    Article  CAS  Google Scholar 

  • Sachs MM, Freeling M, Okimoto R (1980) The anaerobic proteins of maize. Cell 20:761–767

    Article  CAS  PubMed  Google Scholar 

  • Schutz W, Hausmann N, Krug K, Hampp R, Maceka B (2011) Extending SILAC to proteomics of plant cell lines. Plant Cell 23:1701–1705

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shafiq-ur-Rehman HPJC, Ashraf M (2005) Stress environments and their impact on crop production. In: Ashraf M, Harris PJC (eds) Abiotic stresses, plant resistance through breeding and molecular approaches. Haworth Press, New York, NY, pp 3–15

    Google Scholar 

  • Shao S, Guo T, Aebersold R (2015) Mass spectrometry-based proteomic quest for diabetes biomarkers. Biochem Biophys Acta 1854(6):519–527. https://doi.org/10.1016/j.bbapap.2014.12.012

    Article  CAS  PubMed  Google Scholar 

  • Shen Q, Fu L, Qiu L, Xue F, Zhang G, Wu D (2016) Time-course of ionic responses and proteomic analysis of Tibetan wild barley at early stage under salt stress. Plant Growth Regul. https://doi.org/10.1007/s10725-016-0180-0

    Article  CAS  Google Scholar 

  • Simova-Stoilova LP, Romero-Rodríguez MC, Sánchez-Lucas R, Navarro-Cerrillo RM, Medina-Aunon JA, Jorrín-Novo JV (2015a) 2-DE proteomics analysis of drought treated seedlings of Quercus ilex supports a root active strategy for metabolic adaptation in response to water shortage. Front Plant Sci 6:627

    Article  PubMed  PubMed Central  Google Scholar 

  • Simova-Stoilova LP, Romero-Rodríguez MC, Sánchez-Lucas R, Navarro-Cerrillo RM, Medina-Aunon JA, Jorrín-Novo JV (2015b) 2-DE proteomics analysis of drought treated seedlings of Quercus ilex supports a root active strategy for metabolic adaptation in response to water shortage. Front Plant Sci 6:627

    Article  PubMed  PubMed Central  Google Scholar 

  • Singh SK, Kakani VG, Surabhi GK, Reddy KR (2010) Cowpea (Vigna unguiculata [L.] Walp.) genotypes response to multiple abiotic stresses. J Photochem Photobiol 100:135–146

    Article  CAS  Google Scholar 

  • Singh S, Parihar P, Singh R, Singh VP, Prasad SM (2016) Heavy metal tolerance in plants: role of transcriptomics, proteomics, metabolomics, and ionomics. Front Plant Sci 6:1143. https://doi.org/10.3389/fpls.2015.01143

    Article  PubMed  PubMed Central  Google Scholar 

  • Sreenivasulu N, Sopory SK, Kishor PBK (2007) Deciphering the regulatory mechanisms of abiotic stress tolerance in plants by genomic approaches. Gene 388:1–13

    Article  CAS  PubMed  Google Scholar 

  • Subbaiah CC, Sachs MM (2003) Molecular and cellular adaptations of maize to flooding stress. Ann Bot 91:119–127

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sugiyama N, Nakagami H, Mochida K et al (2008) Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Mol Syst Biol 4:193

    Article  PubMed  PubMed Central  Google Scholar 

  • Sun H, Xia B, Wang X, Gao F, Zhou Y (2017) Quantitative phosphoproteomic analysis provides insight into the response to short-term drought stress in Ammopiptanthus mongolicus roots. Int J Mol Sci 18:2158. https://doi.org/10.3390/ijms.18102158

    Article  PubMed Central  Google Scholar 

  • Surabhi GK (2018) Update in root proteomics with special reference to abiotic stresses: achievements and challenges. J Protein Proteomics 9(1):31–35

    CAS  Google Scholar 

  • Surabhi GK, Reddy AM, Sudhakar C (2003) NaCl effects on proline metabolism in two high yielding genotypes of mulberry (Morus alba L.) with contrasting salt tolerance. Plant Sci 165:1245–1251

    Article  CAS  Google Scholar 

  • Surabhi GK, Reddy AM, Kumari GJ Sudhakar C (2008) Modulations in key enzymes of nitrogen metabolism in two high yielding genotypes of mulberry (Morus alba L.) with differential sensitivity to salt stress. Environ Exp Bot 64:171–179

    Article  CAS  Google Scholar 

  • Suszkiw J (1994) After the flood- satellites show damage to Midwest farmlands. Agricul Res 42:20–21

    Google Scholar 

  • Thakur P, Kumar S, Malik JA, Berger JD, Nayyar H (2010) Cold stress effects on reproductive development in grain crops: an overview. Environ Exp Bot 67:429–443

    Article  CAS  Google Scholar 

  • Tyers M, Mann M (2003) From genomics to proteomics. Nature 422:193–197

    Article  CAS  PubMed  Google Scholar 

  • Umezawa T, Sugiyama N, Takahashi F, Anderson CJ, Ishihama Y, Peck CS, Shinozaki K (2013) Genetics and phosphoproteomics reveal a protein phosphorylation network in the abscisic acid signaling pathway in Arabidopsis thaliana. Research Resource (Plant Biology) 6:1–14

    Google Scholar 

  • Unlu M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18:2071–2077

    Article  CAS  PubMed  Google Scholar 

  • Veeranagamallaiah G, Jyothsnakumari G, Thippeswamy M, Reddy PCO, Surabhi GK, Sriranganayakulu G, Mahesh Y, Rajasekhar B, Madhurarekha C, Sudhakar C (2008) Proteomic analysis of salt stress responses in foxtail millet (Setaria italica L. cv. Prasad) seedlings. Plant Sci 175:631–641

    Article  CAS  Google Scholar 

  • Veeranagamallaiah G, Prasanthi J, Reddy KE, Pandurangaiah M, Babu OS, Sudhakar C (2011) Group 1 and 2 LEA protein expression correlates with a decrease in water stress induced protein aggregation in horsegram during germination and seedling growth. J Plant Physiol 168:671–677

    Article  CAS  PubMed  Google Scholar 

  • Wang W, Scali M, Vignani R, Spadafora A, Sensi E, Mazzuca S, Cresti M (2003a) Protein extraction for two-dimensional electrophoresis from olive leaf, a plant tissue containing high levels of interfering compounds. Electrophoresis 24:2369–2375

    Article  CAS  PubMed  Google Scholar 

  • Wang W, Vinocur B, Altman A (2003b) Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218:1–14

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Zhang LL, Feng R (2015) Proteomic analysis of cold stress responses in banana leaves. J Am Soc Hortic Sci 140(3):214–222

    Article  Google Scholar 

  • Wang R, Mei Y, Xu L, Zhu X, Wang Y, Guo J, Liu L (2018) Differential proteomic analysis reveals sequential heat stress-responsive regulatory network in radish (Raphanus sativus L.) taproot. Planta 247(5):1109–1122. https://doi.org/10.1007/s00425-018-2846-5

    Article  CAS  PubMed  Google Scholar 

  • Washburn MP, Wolters D, Yates JR (2001) Large scale analysis of the yeast proteome by multi-dimensional protein identification technology. Nat Biotechnol 19:242–247

    Article  CAS  PubMed  Google Scholar 

  • Wen TN, Cho HY, Wang YT, Shih MC (2016) Quantitative phosphoproteomics of protein kinase SnRK1 regulated protein phosphorylation in Arabidopsis under submergence. J Exp Bot 67(9):2745–2760

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Witzel K, Weidner A, Surabhi GK, Borner A, Mock H (2009) Salt stress-induced alterations in the root proteome of barley genotypes with contrasting response towards salinity. J Exp Bot 60:3545–3557

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Witzel K, Weidner A, Surabhi GK, Varshney RK, Kunze G, Buck-Sorlin G, Borner A, Mock HP (2010) Comparative analysis of the grain proteome fraction in barley genotypes with contrasting salinity tolerance during germination. Plant Cell Environ 33:211–222

    Article  CAS  PubMed  Google Scholar 

  • Xin C, Wang X, Cai J, Zhou Q, Liu F, Dai T (2016) Changes of transcriptome and proteome are associated with the enhanced post-anthesis high-temperature tolerance induced by pre-anthesis heat priming in wheat. Plant Growth Regul 79:135. https://doi.org/10.1007/s10725-015-0119-x

    Article  CAS  Google Scholar 

  • Xu C, Huang B (2008) Root proteomic responses to heat stress in two Agrostis grass species contrasting in heat tolerance. J Exp Bot 59:4183–4194

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xue L, Ren H, Li S, Gao M, Shi S, Chang E, Wei Y, Yao X, Jiang Z, Liu J (2015) Comparative proteomic analysis in Miscanthus sinensis exposed to antimony stress. Environ Pollut 201:150–160

    Article  CAS  PubMed  Google Scholar 

  • Yang X, Feng Y, He Z, Stoffella JP (2005) Molecular mechanisms of heavy metal hyperaccumulation and phytoremediation. J Trace Elem Med Biol 18(4):339–353

    Article  CAS  PubMed  Google Scholar 

  • Yang L, Ma C, Wang L, Chen S, Li H (2012) Salt stress induced proteome and transcriptome changes in sugar beet monosomic addition line M14. J Plant Physiol 169:839–850

    Article  CAS  PubMed  Google Scholar 

  • Yin X, Komatsu S (2017) Comprehensive analysis of response and tolerant mechanisms in early-stage soybean at initial flooding stress. J Proteome 169(3):225–232

    Article  CAS  Google Scholar 

  • Yin X, Sakata K, Komatsu S (2014) Phosphoproteomics reveals the effects of ethylene in soybean root under flooding stress. J Proteome Res 9:1–66

    Google Scholar 

  • You X, Yang LT, Lu YB, Li H, Zhang SQ, Chen LS (2014) Proteomic changes of Citrus roots in response to long-term manganese toxicity. Trees 28:1383–1399

    Article  CAS  Google Scholar 

  • Yu B, Li J, Koh J, Dufresne C, Yang N, Qi S, Zhang Y, Ma C, Duong BV, Chen S, Li H (2016) Quantitative proteomic and phosphoproteomics of sugar beet monosomic addition line M14 in response to plant. J Proteome 143:286–297. https://doi.org/10.1016/j.jprot.2016.04.011

    Article  CAS  Google Scholar 

  • Yuan L, Zhang M, Yan X, Bian WY, Zhen MS, Yan MY (2016) Dynamic phosphoproteome analysis of seedling leaves in Brachylpodium distachyon L. reveals central phosphorylated proteins involved in the drought stress response. Sci Rep 6:35280. https://doi.org/10.1038/srep35280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zadraznik T, Moen A, Jacobsen EW, Meglic V, Vozlic SJ (2017) Towards a better understanding of protein changes in common bean under drought: a case study of N-glycoprotein. Plant Physiol Biochem 118:400–412. https://doi.org/10.1016/j.plaphy.2017.07.004

    Article  CAS  PubMed  Google Scholar 

  • Zhang M, Lv D, Ge P et al (2014) Phosphoproteome analysis reveals new drought response and defense mechanisms of seedling leaves in bread wheat (Triticum aestivum L.). J Proteome 109:290–308. https://doi.org/10.1016/j.jprot.2014.07.010

    Article  CAS  Google Scholar 

  • Zhang YH, Lei G, Zhou WH, He C, Liao LJ, Huang JY (2017) Quantitative iTRAQ-based proteomic analysis of rice grains to assess high night temperature stress. Proteomics 17(5). https://doi.org/10.1002/pmic.201600365

    Article  PubMed Central  CAS  Google Scholar 

  • Zhang A, Han D, Wang Y, Mu H, Zhang T, Yan X, Pan Q (2018) Transcriptomic and proteomic feature of salt stress-regulated network in Jerusalem artichoke (Helianthus tuberosus L.) root based on de novo assembly sequencing analysis. Planta 247(3):715–732. https://doi.org/10.1007/s00425-017-2818-1

    Article  CAS  PubMed  Google Scholar 

  • Zhong M, Li S, Huang F, Qiu J, Zhang J, Sheng Z, Tang S, Wei X, Hu P (2017) The phosphoproteomic response of rice seedlings to cadmium stress. Int J Mol Sci 18:1–17

    Google Scholar 

  • Zhou H, Ye M, Dong J, Han G, Jiang X, Wu R, Zou H (2008) Specific phosphopeptide enrichment with immobilized titanium ion affinity chromatography adsorbent for phosphoproteome analysis. J Proteome Res 7:3957–3967

    Article  CAS  PubMed  Google Scholar 

  • Zhu JK (2001) Cell signaling under salt, water and cold stresses. Curr Opin Plant Biol 4:401–406

    Article  CAS  PubMed  Google Scholar 

  • Zieske LR (2006) A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies. J Exp Bot 57(7):1501–1508

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

Work in the laboratory of Giridara Kumar Surabhi (GKS), supported by the Forest and Environment Department, Government of Odisha, India, is gratefully acknowledged. The authors apologize for being unable to cite all relevant papers.

Author information

Authors and Affiliations

  1. Plant Molecular Biology and ‘OMICS’ Laboratory, Regional Plant Resource Centre, Bhubaneswar, Odisha, India

    Subhankar Mohanty & Giridara Kumar Surabhi

Authors
  1. Subhankar Mohanty
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Giridara Kumar Surabhi
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Mountain Research Centre for Field Crops, Khudwani, SKUAST-Kashmir, India

    Shabir Hussain Wani

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Mohanty, S., Surabhi, G.K. (2019). Modulation of Proteome and Phosphoproteome Under Abiotic Stress in Plants: An Overview. In: Wani, S. (eds) Recent Approaches in Omics for Plant Resilience to Climate Change. Springer, Cham. https://doi.org/10.1007/978-3-030-21687-0_12

Download citation

Publish with us

Policies and ethics

Search

Navigation