TABLE 3.
Overview of high-throughput proteomic studies focused on PTMome analysis in stress-treated plants.
| Plant species | Stress treatment | Method | Differentially abundant proteins with PTM | References |
| Phosphorylation | ||||
| Arabidopsis thaliana Col—4 week old plants | Salinity (200 mM NaCl, 3 day) | Zr4+-IMAC beads PP enrichment; LC-MS/MS | 15 phosphoproteins in membrane fraction: aquaporins PIP2;1, PIP2;4; 14-3-3 interacting protein AHA-I | Hsu et al., 2009 |
| Arabidopsis thaliana—12 day old seedlings | 800 mM mannitol, 100 μM ABA (30 min.) | Phosphopeptide enrichment with PolyMAC-Ti, nanoLC HPLC, LTQ-Orbitrap | 1,850 quantified phosphopeptides, 468 differentially regulated: MAPK, CKII, SnRK2.1, SnRK2.4, SnRK2.5, SnRK2.10 | Xue et al., 2013 |
| Chickpea (Cicer arietinum) cv. JG-62 |
Drought | 2-DE Pro-Q Diamond staining; immunoblots (anti-phosphoserine, antiphospho-threonine, antiphospho-tyrosine antibodies | Regulatory and functional proteins: photosynthesis (OEE1, CA, ATP synthase subunit α) and photorespiration, stress and defense, molecular chaperones, ion transport—CaDREPP1—plasma membrane polypeptide family protein | Subba et al., 2013 |
| TMT labeling and TiO2 phosphopeptide enrichment | Kinases, phosphatases, spliceosome components | Barua et al., 2019 | ||
| Common bean VAX1 root tip | Osmotic stress (PEG-6000) | 2DE ProQ Diamond staining | 10 PPs: Ser/Thr-specific PP2A; PRK; DHN; actin; lactoylglutathione lyase; | Yang et al., 2013 |
| Soybean cv. Enrei root tip—nuclei—2 day old seedlings | Flooding: 3 h | Polymer-based metal ion affinity phosphopeptide enrichment; nanoLC-MS/MS | ABA-responsive proteins: zinc finger/BTB domain containing protein 47, GRP, rRNA processing protein Rrp5 | Yin and Komatsu, 2015 |
| Brachypodium distachyon Bd21 at 3-leaf stage | Osmotic stress (20% PEG-6000 in Hoagland solution) 48 h | TiO2 IMAC beads enrichment; LC-MS/MS |
Signaling (MAPK cascade, SnRK2, CDPK, PP2C), TFs (NF-Y, Hsf), ion transport (PIP, NIP, H+-ATPase in plasma membrane), stress (DHN3-like, HSP90) | Yuan et al., 2016 |
| Barley cv. Haruna-nijyo | Salinity (200 mM NaCl) 24 h | qRT-PCR | 10 HvPIP aquaporins (HvPIP2) | Horie et al., 2011 |
| Einkorn wheat (Triticum monococcum) 3-leaf stage | Salinity (0, 80, 320 mM NaCl) | 2-DE and Pro-Q Diamond phosphoprotein staining MALDI-TOF/TOF |
20 phosphoproteins identified: cp31BHv, betaine-aldehyde dehydrogenase, leucine aminopeptidase 2, redox enzymes (Cu/Zn-SOD, 2-Cys Prx BAS1), chaperone (CPN60α), photosynthesis (OEE), ATP synthesis (ATP synthase CF1β) | Lv et al., 2016 |
| Wheat (Triticum aestivum) Zhongmai 175 | Drought | Pro-Q Diamond phosphoprotein staining, 2-DE, MALDI-TOF/TOF | Wheat flag leaf: photosynthesis-related (LHCII), dephosphorylation of RCA under drought; Phosphorylation of glycolysis enzymes (FBA, GAPDH, ENO), TCA cycle |
Luo et al., 2018 |
| Zhengmai 366 | Salinity (180 mM NaCl) 24 h | 2-DE and Pro-Q Diamond phosphoprotein staining | Wheat embryo and endosperm: 14 PPs in embryo, 6 PPs in endosperm: COR, 27K protein, SOD | Luo et al., 2019 |
| Hanxuan 10, Ningchun 47—3-leaf stage | Osmotic stress (20% PEG-6000) | TiO2 beads microcolumn enrichment, LC-MS/MS | Wheat seedling leaves: 31 PPs involved in RNA transcription/processing, stress and defense, signal transduction | Zhang et al., 2014a |
| Henong 341—flag leaf and grains at 28 day after flowering | Drought (decreased SWC) | TiO2 beads microcolumn enrichment, LC-MS/MS | Wheat grain: 63 PPs—signaling (LRR-receptor kinases, casein kinase I, CDK, CDK-like); chaperones (HSPs), starch biosynthesis | Zhang et al., 2014b |
| Yangmai 18—spike | Fusarium graminearum | 2-DE, immunoblots (anti-phosphoserine, anti-phosphothreonine, anti-phosphotyrosine antibodies), MALDI-TOF MS | 28 PPs: signaling (receptor protein kinase PERK1-like); RING-finger E3 ubiquitin ligase; dnaJ-like protein; ADP ribosylation factor; metabolism (PGK; cinnamoyl-CoA reductase, isochorismate synthase); transport (ABC transporter); stress/defense (cytochrome P450) | Ding et al., 2016 |
| Rice (cv. Nipponbare) | Salinity | 2-DE ProQ Diamond | Up: Putative ribosomal protein S29, HSP70, MRL Down: ATP synthase β, glucan endo-1,3-β-glucosidase |
Chitteti and Peng, 2007 |
| Drought | 10 PPs: NAD-MDH, ribosomal protein, r40c1 protein, S-like ribonuclease, ethylene-inducible protein, GLP1, ABA-inducible protein | Ke et al., 2009 | ||
| Rice cv. Zhong Jiazao-17 indica rice—12 day seedlings | 10, 100 μM CdCl2*2.5 H2O | TiO2-IMAC enrichment, LC-MS/MS | 1,244 PPs, 392↑—Cd: ABA signaling (PP2C30, PP2C66), CDPK signaling, MAPK signaling; WRKY TFs, 14-3-3 like, NADH dehydrogenase, LHCB | Zhong et al., 2017 |
| D69 (S), D28 (T)—3-leaf stage | 0.1 mmol dm–3 Cd | 2-DE MALDI-TOF/TOF | Carbon metabolism, proteolytic enzymes, F-box containing TFs, zinc-finger, MYB TFs, DEAD-box ATP-dependent RNA helicase 37 | Fang et al., 2019 |
| Maize cv. Zhengdan 958—5-leaf stage | Drought (PEG -−0.7 MPa, 8 h), heat (42°C, 1 h) and combined stress | TiO2-IMAC beads PP enrichment; iTRAQ, nano LC-MS/MS | Stress proteins: HSPs; Receptor proteins: Ca-dependent receptor, gibberellin receptor GID1 |
Hu et al., 2015b |
| Maize mutant vp5 (ABA deficient)—2 week old | Osmotic stress (−0.7 MPa PEG6000, 8 h) | TiO2-IMAC beads PP enrichment; iTRAQ, nanoLC-MS/MS | 4,052 phosphopeptides—3,017 phosphoproteins; 14 categories: signaling (receptor-like protein kinase; tpa: protein kinase superfamily protein, leucine-rich repeat protein kinase, CDPK); chloroplast PPs (CPN60β; stresschloroplastic like X2 isoform); E3 ubiquitin protein ligase | Hu et al., 2015a |
| Maize inbred line B73—5-leaf stage | Drought (mild and severe water deficits) and recovery (5–60 min) | TiO2-IMAC beads PP enrichment; nano LC-MS/MS | Identified phosphoproteins: cell division and expansion related (GAP, USP, Golgi SNARE12), carbohydrate metabolism (SuSy3), chromatin remodeling (histone deacetylase 2b, HDT2), ABC-transporter, DEAD-box ATP-dependent RNA helicase 52C, BZIP, RING finger protein 126 | Bonhomme et al., 2012 |
| Sugarbeet monosomic addition line M14—3 week | Salinity (0, 200, 400 mM NaCl, 10, 30, 60, 90 min.) | Nutip PP enrichment; LC-MS/MS | Signaling: CDPK, MAPK, 14-3-3; calcium binding protein CML35; Ras-related smallGTP binding protein | Yu et al., 2016 |
| Okra (Abelmoschus esculentus) cv. Wufu leaves | Salinity (300 mM NaCl, 48 h) | Affinity enrichment, TMT kit, LC-MS/MS | Photosynthesis antenna proteins (LHCII), RNA degradation | Yu et al., 2019 |
| N-glycosylation | ||||
| Soybean (cv. Enrei) root tip—2 day old | Flooding (2 day) | SDS-PAGE and concanavalin A lectin blot | Up: glycolysis enzymes (GAPDH) Down: N-glycan synthesis enzymes (STT3) |
Mustafa and Komatsu, 2014 |
| Rice (cv. Nipponbare) leaf sheath—2 week old seedlings | Cold (5°C, 2 day) | SDS-PAGE and concanavalin A lectin blot | Up: energy metabolism (mitochondrial F1-ATPase, 6-phosphogluconate dehydrogenase, NADP-dependent malic enzyme, enolase, UDP-glucose pyrophosphorylase), chaperone (CPN60α, HSP90), signaling (calreticulin) | Komatsu et al., 2009 |
| Carbonylation | ||||
| Rice cv. Malviya-36 (S), Vandana (T) | 15% PEG-6000, 1 mM AlCl3 | 2DE, immunoblot of DNPH-derivatized proteins | Up: RubisCO LSU, OEE3, PS I subunit II, IV; CaM | Pandey and Dubey, 2021 |
| S-nitrosylation | ||||
| Brassica juncea var. Pusa Jaikisan 7 day old seedlings | Cold (4°C) for 2–96 h | 2-DE, biotin-switch | 20 S-nitrosylated proteins: RubisCO LSU, SSU; ACC synthase 4, PRX, FBA, HSP70, APX, SOD | Abat and Deswal, 2009 |
| RubisCO depletion, 2DE, biotin switch assay, nLC-MS/MS | S-nitrosylated proteins: SOD, Trx-H type; GAPDH, FBA, sedoheptulose-bisphosphatase | Sehrawat et al., 2013 | ||
| RubisCO depletion, 2DE, biotin switch assay, MALDI-TOF/TOF, nLC-MS/MS | 48 (24 GSNO-treated, 24 cold-responsive) S-nitrosoproteins: 12S globulin protein cruciferin; redox (DHAR, Cu/Zn-SOD), stress defense (lactoylglutathione lyase, GLP) | Sehrawat and Deswal, 2014 | ||
| Citrus (Citrus aurantium) mature leaves from 5-month old plants | 150 mM NaCl, 16 day | 2-DE, immunoblots (carbonylation, Tyr-nitration), biotin-switch (S-nitrosylation) | Leaves: Carbonylation: RCA, Tyr-nitration: RubisCO LSU, S-nitrosylation: PRX |
Tanou et al., 2009 |
| 150 mM NaCl, 8 day | 1-DE, immunoblots (carbonylation, Tyr-nitration), biotin-switch (S-nitrosylation) | Leaves: Fe-SOD, NOX, AOX, GSNOR, Roots: Cu/Zn-SOD, Mn-SOD, NOX, DAO, PAO, GSNOR |
Tanou et al., 2012 | |
| Continuous light, dark, heat, cold, drought, salinity | SDS-PAGE and immunoblots (biotin switch assay) | S-nitrosylation patterns enhanced by heat, cold and drought but suppressed by dark and salinity with respect to control | Ziogas et al., 2013 | |
| Pea (Pisum sativum) cv. Lincoln—leaf mitochondria | 150 mM NaCl, 14 day | SDS-PAGE, MALDI-TOF/TOF, immunoblot | ATP synthase β, HSP90, PRXIIF | Camejo et al., 2013 |
AOX, alternative oxidase; APX, ascorbate peroxidase; CA, carbonic anhydrase; CaM, calmodulin; CDK, cyclin-dependent kinase; CDPK, calcium-dependent protein kinase; CK, casein kinase; DHAR, dehydroascorbate reductase; DHN, dehydrin; ENO, enolase; FBA, fructose bisphosphate aldolase; GAP, GTPase-activating protein; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GLP, germin-like protein; GRP, glycine-rich protein; GSNO, S-nitrosoglutathione; GSNOR, S-nitrosoglutathione reductase; LHC, light-harvesting complex; MDH, malate dehydrogenase; OEE, oxygen-evolving enhancer protein; PGK, phosphoglycerate kinase; PP, protein phosphatase; PS, photosystem; PRK, pyruvate kinase; PRX, peroxiredoxin; RCA, RubisCO activase; RubisCO (LSU, SSU), ribulose bisphosphate carboxylase/oxygenase (large and small subunit); S, susceptible genotype (to a given stress); SOD, superoxide dismutase; SuSy, sucrose synthase; SWC, soil water content; T, tolerant genotype (to a given stress); Trx, thioredoxin.