Plant Proteoforms Under Environmental Stress: Functional Proteins Arising From a Single Gene

. 2021 ; 12 () : 793113. [epub] 20211214

Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic-ecollection

Typ dokumentu časopisecké články, přehledy

Perzistentní odkaz   https://www.medvik.cz/link/pmid34970290

Proteins are directly involved in plant phenotypic response to ever changing environmental conditions. The ability to produce multiple mature functional proteins, i.e., proteoforms, from a single gene sequence represents an efficient tool ensuring the diversification of protein biological functions underlying the diversity of plant phenotypic responses to environmental stresses. Basically, two major kinds of proteoforms can be distinguished: protein isoforms, i.e., alterations at protein sequence level arising from posttranscriptional modifications of a single pre-mRNA by alternative splicing or editing, and protein posttranslational modifications (PTMs), i.e., enzymatically catalyzed or spontaneous modifications of certain amino acid residues resulting in altered biological functions (or loss of biological functions, such as in non-functional proteins that raised as a product of spontaneous protein modification by reactive molecular species, RMS). Modulation of protein final sequences resulting in different protein isoforms as well as modulation of chemical properties of key amino acid residues by different PTMs (such as phosphorylation, N- and O-glycosylation, methylation, acylation, S-glutathionylation, ubiquitinylation, sumoylation, and modifications by RMS), thus, represents an efficient means to ensure the flexible modulation of protein biological functions in response to ever changing environmental conditions. The aim of this review is to provide a basic overview of the structural and functional diversity of proteoforms derived from a single gene in the context of plant evolutional adaptations underlying plant responses to the variability of environmental stresses, i.e., adverse cues mobilizing plant adaptive mechanisms to diminish their harmful effects.

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Abat J. K., Deswal R. (2009). Differential modulation of S-nitrosoproteome of Brassica juncea by low temperature: change in S-nitrosylation of Rubisco is responsible for the inactivation of its carboxylase activity. Proteomics 9 4368–4380. 10.1002/pmic.200800985 PubMed DOI

Ajadi A. A., Cisse A., Ahmad S., Wang Y., Shu Y., Li S., et al. (2020). Protein phosphorylation and phosphoproteome: an overview. Rice Sci. 27 184–200. 10.1016/j.rsci.2020.04.003 DOI

Barkla B. J., Vera-Estrella R., Hernández-Coronado M., Pantoja O. (2009). Quantitative proteomics of the tonoplast reveals a role for glycolytic enzymes in salt tolerance. Plant Cell 21 4044–4058. 10.1105/tpc.109.069211 PubMed DOI PMC

Barua P., Lande N. V., Subba P., Gayen D., Pinto S., Prasad T. S. K., et al. (2019). Dehydration-responsive nuclear proteome landscape off chickpea (Cicer arietinum L.) reveals phosphorylation-mediated regulation of stress response. Plant Cell Environ. 42 230–244. 10.1111/pce.13334 PubMed DOI

Benlloch R., Lois L. M. (2018). Sumoylation in plants: mechanistic insights and its role in drought stress. J. Exp. Bot. 69 4539–4554. 10.1093/jxb/ery233 PubMed DOI

Boisson B., Giglione C., Meinnel T. (2003). Unexpected protein families including cell defense components feature in the N-myristoylome of a higher eukaryote. J. Biol. Chem. 278 43418–43429. 10.1074/jbc.M307321200 PubMed DOI

Bonhomme L., Valot B., Tardieu F., Zivy M. (2012). Phosphoproteome dynamics upon changes in plant water status reveal early events associated with rapid growth adjustment in maize leaves. Mol. Cell. Proteomics 11 957–972. 10.1074/mcp.M111.015867 PubMed DOI PMC

Brini F., Hanin M., Lumbreras V., Irar S., Pages M., Masmoudi K. (2007). Functional characterization of DHN-5, a dehydrin showing a differential phosphorylation pattern in two Tunisian durum wheat (Triticum durum Desf.) varieties with marked differences in salt and drought tolerance. Plant Sci. 172 20–28.

Bueso E., Rodriguez L., Lorenzo-Orts L., Gonzalez-Guzman M., Sayas E., Munoz-Bertomeu J., et al. (2014). The single-subunit RING-type E3 ubiquitin ligase RSL1 targets PYL4 and PYR1 ABA receptors in plasma membrane to modulate abscisic acid signaling. Plant J. 80 1057–1071. 10.1111/tpj.12708 PubMed DOI

Bustos D. M., Bustamante C. A., Iglesias A. A. (2008). Involvement of nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase in response to oxidative stress. J. Plant Physiol. 165 456–461. 10.1016/j.jplph.2007.06.005 PubMed DOI

Butturini E., Boriero D., Carcerrei de Prati A., Mariotto S. (2019). Immunoprecipitation methods to identify S-glutathionylation in target proteins. MethodsX 6 1992–1998. 10.1016/j.mex.2019.09.001 PubMed DOI PMC

Camejo D., Romero-Puertas M. D., Rodríguez-Serrano M., Sandalio L. M., Lázaro J. J., Jiménez A., et al. (2013). Salinity-induced changes in S-nitrosylation of pea mitochondrial proteins. J. Proteomics 79 87–99. 10.1016/j.jprot.2012.12.003 PubMed DOI

Carlson S. M., Gozani O. (2014). Emerging technologies to map the protein methylome. J. Mol. Biol. 426 3350–3362. 10.1016/j.jmb.2014.04.024 PubMed DOI PMC

Cieśla A., Mitula F., Misztal L., Fedorowicz-Stronska O., Janicka S., Tajdel-Zielinska M., et al. (2016). A role for barley calcium-dependent protein kinase CPK2a in the response to drought. Front. Plant Sci. 7:1550. 10.3389/fpls.2016.01550 PubMed DOI PMC

Close T. J. (1997). Dehydrins: a commonalty in the response of plants to dehydration and low temperature. Physiol. Plant. 100 291–296. 10.1111/j.1399-3054.1997.tp04785.x DOI

Diaz-Vivancos P., De Simone A., Kiddle G., Foyer C. H. (2015). Glutathione – linking cell proliferation to oxidative stress. Free Radic. Biol. Med. 89 1154–1164. 10.1016/j.freeradbiomed.2015.09.023 PubMed DOI

Dietz K. J. (2016). Thiol-based peroxidases and ascorbate peroxidases: why plantsrely on multiple peroxidase systems in the photosynthesizing chloroplast? Mol. Cells 39 20–25. 10.14348/molcells.2016.2324 PubMed DOI PMC

Ding L., Yang R., Yang G., Cao J., Li P., Zhou Y. (2016). Identification of putative phosphoproteins in wheat spikes induced by Fusarium graminearum. Planta 243 719–731. 10.1007/s00425-015-2441-y PubMed DOI PMC

Ding Y., Fromm M., Avramova Z. (2012). Multiple exposures to drought “train” transcriptional responses in Arabidopsis. Nat. Commun. 3:740. 10.1038/ncomms1732 PubMed DOI

Fang Y., Deng X., Lu X., Zheng J., Jiang H., Rao Y., et al. (2019). Differential phosphoproteome study of the response to cadmium stress in rice. Ecotoxicol. Environ. Saf. 180 780–788. 10.1016/j.ecoenv.2019.05.068 PubMed DOI

Feng B., Liu C., Shan L., He P. (2016). Protein ADP-ribosylation takes control in plant-bacterium interactions. PLoS Pathog. 12:e1005941. 10.1371/journal.ppat.1005941 PubMed DOI PMC

Feng J., Chen L., Zuo J. (2019). Protein S-nitrosylation in plants: current progresses and challenges. J. Integr. Plant Biol. 61 1206–1223. 10.1111/jipb.12780 PubMed DOI

Fíla J., Honys D. (2012). Enrichment techniques employed in phosphoproteomics. Amino Acids 43 1025–1047. 10.1007/s00726-011-1111-z PubMed DOI PMC

Ghimire S., Tang X., Zhang N., Liu W., Qi X., Fu X., et al. (2020). Genomic analysis of the SUMO-conjugating enzyme and genes under abiotic stress in potato (Solanum tuberosum L.). Int. J. Genomics 2020:9703638. 10.1155/2020/9703638 PubMed DOI PMC

Glover N. M., Redestig H., Dessimoz C. (2016). Homoeologs: what are they and how do we infer them? Trends Plant Sci. 21 609–621. 10.1016/j.tplants.2016.02.005 PubMed DOI PMC

Gnad F., Gunawardena J., Mann M. (2011). PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res. 39 D253–D260. 10.1093/nar/gkq1159 PubMed DOI PMC

Gough C., Sadanandom A. (2021). Understanding and exploiting post-translational modifications for plant disease resistance. Biomolecules 11:1122. 10.3390/biom11081122 PubMed DOI PMC

Guerra D., Crosatti C., Khoshro H. H., Mastrangelo A. M., Mica E., Mazzucotelli E. (2015). Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider’s web of mechanisms. Front. Plant Sci. 6:57. 10.3389/fpls.2015.00057 PubMed DOI PMC

Hashiguchi A., Komatsu S. (2016). Impact of post-translational modifications of crop proteins under abiotic stress. Proteomes 4:42. 10.3390/proteomes4040042 PubMed DOI PMC

Hayashi M., Inoue S., Takahashi K., Kinoshita T. (2011). Immunochemical detection of blue light-induced phosphorylation of the plasma membrane H+-ATPase in stomatal guard cells. Plant Cell Physiol. 52 1238–1248. 10.1093/pcp/pcr072 PubMed DOI

He D., Li M., Damaris R. N., Bu C., Xue J., Yang P. (2020). Quantitative ubiquitylomics approach for characterizing the dynamic change and extensive modulation of ubiquitylation in rice seed germination. Plant J. 101 1430–1447. 10.1111/tpj.14593 PubMed DOI

Heinemann B., Künzler P., Eubel H., Braun H. P., Hildebrandt T. M. (2020). Estimating the number of protein molecules in a plant cell: protein and amino acid homeostasis during drought. Plant Physiol. 185 385–404. 10.1093/plphys/kiaa050 PubMed DOI PMC

Hershko A., Ciechanover A., Varshavsky A. (2000). The ubiquitin system. Nat. Med. 6 1073–1081. 10.1038/80384 PubMed DOI

Hilser V. J., Anderson J. A., Motlagh H. N. (2015). Allostery vs. “allokairy“. Proc. Natl. Acad. Sci. U.S.A. 112 11430–11431. 10.1073/pnas.1515239112 PubMed DOI PMC

Hirschey M. D., Zhao Y. (2015). Metabolic regulation by lysine malonylation, succinylation, and glutarylation. Mol. Cell. Proteomics 14 2308–2315. 10.1074/mcp.R114.046664 PubMed DOI PMC

Horie T., Kaneko T., Sugimoto G., Sasano S., Panda S. K., Shibasaka M., et al. (2011). Mechanisms of water transport mediated by PIP aquaporins and their regulation via phosphorylation events under salinity stress in barley roots. Plant Cell Physiol. 52 663–675. 10.1093/pcp/pcr027 PubMed DOI

Hornbeck P. V., Zhang B., Murray B., Kornhauser J. M., Latham V., Skrzypek E. (2015). PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 43 D512–D520. 10.1093/nar/gku1267 PubMed DOI PMC

Hsu J. L., Wang L. Y., Wang S. Y., Lin C. H., Ho K. C., Shi F. K., et al. (2009). Functional phosphoproteomic profiling of phosphorylation sites in membrane fractions of salts-stressed Arabidopsis thaliana. Proteome Sci. 7:42. 10.1186/1477-5956-7-42 PubMed DOI PMC

Hu X., Wu L., Zhao F., Zhang D., Li N., Zhu G., et al. (2015b). Phosphoproteomic analysis of the response of maize leaves to drought, heat and their combination stress. Front. Plant Sci. 6:298. 10.3389/fpls.2015.00298 PubMed DOI PMC

Hu X., Li N., Wu L., Li C., Zhang L., Liu T., et al. (2015a). Quantitative iTRAQ-based proteomic analysis of phosphoproteins and ABA-regulated phosphoproteins in maize leaves under osmotic stress. Sci. Rep. 5:15626. 10.1038/srep15626 PubMed DOI PMC

Huang C. H., Su M. G., Kao H. J., Jhong J. H., Weng S. L., Lee T. Y. (2016). UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines. BMC Syst. Biol. 10:S6. PubMed PMC

Chaki M., Carreras A., López-Jaramillo J., Begara-Morales J. C., Sánchez-Calvo B., Valderrama R., et al. (2013). Tyrosine nitration provokes inhibition of sunflower carbonic anhydrase (β-CA) activity under high temperature stress. Nitric Oxide 29 30–33. 10.1016/j.niox.2012.12.003 PubMed DOI

Chaki M., Valderrama R., Fernandez-Ocana A. M., Carreras A., Gomez-Rodriguez M. V., Lopez-Jaramillo J., et al. (2011). High temperature triggers the metabolism of S.nitrosothiols in sunflower mediating a process of nitrosative stress which provokes the inhibition of ferredoxin-NADP reductase by tyrosine nitration. Plant Cell Environ. 34 1803–1818. 10.1111/j.1365-3040.2011.02376.x PubMed DOI

Chen Y., Liu P., Hoehenwarter W., Lin J. (2012). Proteomic and phosphoproteomic analysis of Picea wilsonii pollen development under nutrient limitation. J. Proteome Res. 11 4180–4190. 10.1021/pr300295m PubMed DOI

Chitteti B. R., Peng Z. (2007). Proteome and phosphoproteome differential expression under salinity stress in rice (Oryza sativa) roots. J. Proteome Res. 6 1718–1727. 10.1021/pr060678z PubMed DOI

Ishitani M., Liu J., Halfter U., Kim C. S., Shi W., Zhu J. K. (2000). SOS3 function in plant salt tolerance requires N-myristoylation and calcium binding. Plant Cell 12 1667–1677. 10.1105/tpc.12.9.1667 PubMed DOI PMC

Jaffrey S. R., Snyder S. H. (2001). The biotin switch method for the detection of S-nitrosylated proteins. Sci. STKE 86:pl1. 10.1126/stke.2001.86.pl1 PubMed DOI

Janská A., Aprile A., Zámeèník J., Cattivelli L., Ovesná J. (2011). Transcriptional responses of winter barley to cold indicate nucleosome remodelling as a specific feature of crown tissues. Funct. Integr. Genomics 11 307–325. 10.1007/s10142-011-0213-8 PubMed DOI PMC

Job C., Rajjou L., Lovigny Y., Belghazi M., Job D. (2005). Patterns of protein oxidation in Arabidopsis seeds and during germination. Plant Physiol. 138 790–802. 10.1104/pp.105.062778 PubMed DOI PMC

Johansson E., Olsson O., Nyström T. (2004). Progression and specificity of protein oxidation in the life cycle of Arabidopsis thaliana. J. Biol. Chem. 279 22204–22208. 10.1074/jbc.M402652200 PubMed DOI

Jurado-Flores A., Romero L. C., Gotor C. (2021). Label-free quantitative proteomic analysis of nitrogen stravation in Arabidopsis root reveals new aspects of H2S signaling by protein persulfidation. Antioxidants 10:508. 10.3390/antiox10040508 PubMed DOI PMC

Kang J. S., Frank J., Kang C. H., Kajiura H., Vikram M., Ueda A., et al. (2008). Salt tolerance of Arabidopsis thaliana requires maturation of N-glycosylated proteins in the Golgi apparatus. Proc. Natl. Acad. Sci. U.S.A. 105 5933–5938. 10.1073/pnas.0800237105 PubMed DOI PMC

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. 10.1016/j.bbrc.2008.12.067 PubMed DOI

Kijima S. T., Staiger C. J., Katoh K., Nagasaki A., Ito K., Uyeda T. Q. P. (2018). Arabidopsis vegetative actin isoforms, AtACT2 and AtACT7, generate distinct filament arrays in living plant cells. Sci. Rep. 8:4381. 10.1038/s41598-018-22707-w PubMed DOI PMC

Knox A. K., Dhillon T., Cheng H., Tondelli A., Pecchioni N., Stockinger E. J. (2010). CBF gene copy number variation at frost resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals. Theor. Appl. Genet. 121 21–35. 10.1007/s00122-010-1288-7 PubMed DOI

Komatsu S., Yamada E., Furukawa K. (2009). Cold stress changes the concanavalin A-positive glycosylation pattern of proteins expressed in the basal parts of rice leaf sheaths. Amino Acids 36 115–123. 10.1007/s00726-008-0039-4 PubMed DOI

Kosová K., Prášil I. T., Vítámvás P. (2011). “Role of dehydrins in plant stress response,” in Handbook of Plant and Crop Stress, 3rd Edn, ed. Pessarakli M. (Boca Raton, FL: CRC Press; ), 239–285.

Kosová K., Vítámvás P., Prášil I. T. (2021). “Physiological adaptations in temperate crops to environmental constraints during the growing season,” in Handbook of Plant and Crop Physiology, 4th Edn, ed. Pessarakli M. (Boca Raton, FL: Taylor and Francis; ).

Kosová K., Vítámvás P., Urban M. O., Prášil I. T., Renaut J. (2018). Plant abiotic stress proteomics: the major factors determining alterations in cellular proteome. Front. Plant Sci. 9:122. 10.3389/fpls.2018.00122 PubMed DOI PMC

Kumar S. V., Wigge P. A. (2010). H2A.Z-containing nucleosomes mediate the thermosensory response in Arabidopsis. Cell 140 136–147. 10.1016/j.cell.2009.11.006 PubMed DOI

Lee H., Guo Y., Ohta M., Xiong L. M., Stevenson B., Zhu J. K. (2002). LOS2, a genetic locus required for cold-responsive gene transcription encodes a bi-functional enolase. EMBO J. 21 2692–2702. 10.1093/emboj/21.11.2692 PubMed DOI PMC

Leutert M., Entwisle S. W., Villén J. (2021). Decoding post-translational modification crosstalk with proteomics. Mol. Cell. Proteomics 20 100129. 10.1016/j.mcpro.2021.100129 PubMed DOI PMC

Levi A., Panta G. R., Parmentier C. M., Muthalif M. M., Arora R., Shanker S., et al. (1999). Complementary DNA cloning, sequencing and expression of an unusual dehydrin from blueberry floral buds. Physiol. Plant. 107 98–109. 10.1034/j.1399-3054.1999.100114.x PubMed DOI

Levine R. L., Garland D., Oliver C. N., Amici A., Climent I., Lenz A. G., et al. (1990). Determination of carbonyl content in oxidatively modified proteins. Methods Enzymol. 186 464–478. 10.1016/0076-6879(90)86141-h PubMed DOI

Li G. X. H., Vogel C., Choi H. (2018). PTMscape: an open source tool to predict generic post-translational modifications and map modification crosstalk in protein domains and biological processes. Mol. Omics 14 197–209. 10.1039/c8mo00027a PubMed DOI PMC

Li G., Zhang Z. S., Gao H. Y., Liu P., Dong S. T., Zhang J. W., et al. (2012). Effects of nitrogen on photosynthetic characteristics of leaves from two different stay-green corn (Zea mays L.) varieties at the grain-filling stage. Can. J. Plant Sci. 92 671–680. 10.4141/CJPS2012-039 DOI

Liu C., Niu G., Li X., Zhang H., Chen H., Lan P., et al. (2021). Comparative label-free quantitative proteomics analysis revealed essential roles of N-glycans in salt tolerance by modulating protein abundance in Arabidopsis. Front. Plant Sci. 12:646425. 10.3389/fpls.2021.646425 PubMed DOI PMC

Liu Y., Wang M., Xi J., Luo F., Li A. (2018). PTM-ssMP: A web server for predicting different types of post-translational modification sites using novel site-specific modification profile. Int. J. Biol. Sci. 14 946–956. 10.7150/ijbs.24121 PubMed DOI PMC

Luo F., Deng X., Liu Y., Yan Y. (2018). Identification of phosphorylation proteins in response to water deficit during wheat flag leaf and grain development. Bot. Stud. 59:28. 10.1186/s40529-018-0245-7 PubMed DOI PMC

Luo X., Han C., Deng X., Zhu D., Liu Y., Yan Y. (2019). Identification of phosphorylated proteins in response to salt stress in wheat embryo and endosperm during seed germination. Cereal Res. Commun. 47 53–66. 10.1556/0806.46.02018.061 DOI

Lv D. W., Zhu G. R., Zhu D., Bian Y. W., Liang X. N., Cheng Z. W., et al. (2016). Proteomic and phosphoproteomic analysis reveals the response and defense mechanism in leaves of diploid wheat Triticum monococcum under salt stress and recovery. J. Proteomics 143 93–105. 10.1016/jprot.2016.04.013 PubMed DOI

Martinez-Seidel F., Suwanchaikasem P., Nie S., Leeming M. G., Pereira Firmino A. A., Williamson N. A., et al. (2021). Membrane-enriched proteomics link ribosome accumulation and proteome reprogramming with cold acclimation in barley root meristems. Front. Plant Sci. 12:656683. 10.3389/fpls.2021.656683 PubMed DOI PMC

Matamoros M. A., Becana M. (2021). Molecular responses of legumes to abiotic stress: post-translational modifications of proteins and redox signaling. J. Exp. Bot. 72 5876–5892. 10.1093/jxb/erab008 PubMed DOI PMC

McLaughlin S., Aderem A. (1995). The myristoyl-electrostatic switch: a modulator of reversible protein-membrane interactions. Trends Biochem. Sci. 20 272–276. 10.1016/s0968-0004(00)89042-8 PubMed DOI

Meyer Y., Reichheld J. P., Vignols F. (2005). Thioredoxins in Arabidopsis andother plants. Photosynth. Res. 86 419–433. 10.1007/s11120-005-5220-y PubMed DOI

Mock H. P., Dietz K. J. (2016). Redox proteomics for the assessment of redox-related posttranslational regulation in plants. Biochim. Biophys. Acta 1864 967–973. 10.1016/j.bbapap.2016.01.005 PubMed DOI

Mustafa G., Komatsu S. (2014). Quantitative proteomics reveals the effect of protein glycosylation in soybean root under flooding stress. Front. Plant Sci. 5:627. 10.3389/fpls.2021.656683 PubMed DOI PMC

Mustafa G., Komatsu S. (2021). Plant proteomic research for improvement of food crops under stresses: a review. Mol. Omics 10.1039/D1MOD00151E PubMed DOI

Noël L. D., Cagna G., Stuttmann J., Wirthmüller L., Betsuyaku S., Witte C. P., et al. (2007). Interaction between SGT1 and cytosolic/nuclear HSC70 chaperones regulates Arabidopsis immune responses. Plant Cell 19 4061–4076. 10.1105/tpc.107.051896 PubMed DOI PMC

Oliver S. N., Finnegan E. J., Dennis E. S., Peacock W. J., Trevaskis B. (2009). Vernalization induced flowering in cereals is associated with changes in histone methylation at the VERNALIZATION1 gene. Proc. Natl. Acad. Sci. U.S.A. 106 8386–8391. 10.1073/pnas.0903566106 PubMed DOI PMC

Pandey P., Dubey R. S. (2021). Cultivar specific oxidative modification of proteins, proteolytic activity and alterations in proteomes of rice seedlings to simultaneous water deficit and aluminum toxicity. J. Plant Growth Regul. 10.1007/s00344-021-10363-w DOI

Pierre M., Traverso J. A., Boisson B., Domenichini S., Bouchez D., Giglione C., et al. (2007). N-myristoylation regulates the SnRK1 pathway in Arabidopsis. Plant Cell 19 2804–2821. 10.1105/tpc.107.051870 PubMed DOI PMC

Podell S., Gribskov M. (2004). Predicting N-terminal myristoylation sites in plant proteins. BMC Genomics 5:37. 10.1186/1471-2164-5-37 PubMed DOI PMC

Rabbani N., Al-Motawa M., Thornalley P. J. (2020). Protein glycation in plants - an under-researched field with much still to discover. Int. J. Mol. Sci. 21:3942. 10.3390/ijms21113942 PubMed DOI PMC

Rampitsch C., Bykova N. (2012). The beginnings of crop phosphoproteomics: exploring early warning systems of stress. Front. Plant Sci. 3:144. 10.3389/fpls.2012.00144 PubMed DOI PMC

Ricard J., Meunier J. C., Buc J. (1974). Regulatory behavior of monomeric enzymes. 1. The mnemonical enzyme concept. Eur. J. Biotechnol. 49 195–208. 10.1111/j.1432-1033.1974.tb03825.x PubMed DOI

Romero-Puertas M. C., Palma J. M., Gómez M., del Río L. A., Sandalio L. M. (2002). Cadmium causes the oxidative modification of proteins in pea plants. Plant Cell Environ. 25 677–686. 10.1046/j.1365-3040.2002.00850.x DOI

Romero-Puertas M. C., Rodriguez-Serrano M., Sandalio L. M. (2013). Protein S-nitrosylation in plants under abiotic stress: an overview. Front. Plant Sci. 4:373. 10.3389/fpls.2013.00373 PubMed DOI PMC

Ronai Z., Robinson R., Rutberg S., Lazarus P., Sardana M. (1992). Aldolase-DNA interactions in a SEWA cell system. Biochim. Biophys. Acta 1130 20–28. 10.1016/0167-4781(92)90456-A PubMed DOI

Sanchez-Barrena M. J., Fujii H., Angulo I., Martinez-Ripoll M., Zhu J. K., Albert A. (2007). The structure of the C-terminal domain of the protein kinase atsos2 bound to the calcium sensor atsos3. Mol. Cell 26 427–435. 10.1016/j.molcel.2007.04.013 PubMed DOI PMC

Sarge K. D., Park-Sarge O. K. (2009). Detection of proteins sumolyated in vivo and in vitro. Methods Mol. Biol. 590 265–277. 10.1007/978-1-603-27-378-7_17 PubMed DOI PMC

Sehrawat A., Abat J. K., Deswal R. (2013). RuBisCO depletion improved proteome coverage of cold responsive S-nitrosylated targets in Brassica juncea. Front. Plant Sci. 4:342. 10.3389/fpls.2013.00342 PubMed DOI PMC

Sehrawat A., Deswal R. (2014). S-nitrosylation analysis in Brassica juncea apoplast highlights the importance of nitric oxide in cold-stress signaling. J. Proteome Res. 13 2599–2619. 10.1021/pr500082u PubMed DOI

Shang X., Cao Y., Ma L. (2017). Alternative splicing in plant genes: a means of regulating the environmental fitness of plants. Int. J. Mol. Sci. 18:432. 10.3390/ijms18020432 PubMed DOI PMC

Sharma B., Joshi D., Yadav P. K., Gupta A. K., Bhatt T. K. (2016). Role of ubiquitin-mediated degradation system in plant biology. Front. Plant Sci. 7:806. 10.3389/fpls.2016.00806 PubMed DOI PMC

Silva-Sanchez C., Li H., Chen S. (2015). Recent advances and challenges in plant phosphoproteomics. Proteomics 15 1127–1141. 10.1002/pmic.201400410 PubMed DOI

Singh R., Green M. R. (1993). Sequence-specific binding of transfer-RNA by glyceraldehyde-3-phosphate dehydrogenase. Science 259 365–368. 10.1126/science.8420004 PubMed DOI

Smith L. M., Kelleher N. L., and The Consortium for Top Down Proteomics (2013). Proteoform: a single term describing protein complexity. Nat. Methods 10 186–187. 10.1038/nmth.2369 PubMed DOI PMC

Strasser R., Altmann F., Mach L., Glossl J., Steinkellner H. (2004). Generation of Arabidopsis thaliana plants with complex N-glycans lacking beta-1,2-linked xylose and core alpha-1,3-linked fucose. FEBS Lett. 561 132–136. 10.1016/S0014-5793(04)00150-4 PubMed DOI

Subba P., Barua P., Kumar R., Datta A., Soni K. K., Chakraborty S., et al. (2013). Phosphoproteomic dynamics of chickpea (Cicer arietinum L.) reveals shared and distinct components of dehydration response. J. Proteome Res. 12 5025–5047. 10.1021/pr400628j PubMed DOI

Sung S., Amasino R. M. (2005). Remembering winter: toward a molecular understanding of vernalization. Annu. Rev. Plant Biol. 56 491–508. 10.1146/annurev.arplant.56.032604.144307 PubMed DOI

Suzuki Y. J., Carini M., Butterfield D. A. (2010). Protein carbonylation. Antioxid. Redox Signal. 12 323–325. 10.1089/ars.2009.2887 PubMed DOI PMC

Tanou G., Filippou P., Belghazi M., Job D., Diamantidis G., Fotopoulos V., et al. (2012). Oxidative and nitrosative-based signalling and associated post-translational modifications orchestrate the acclimation of citrus plants to salinity stress. Plant J. 72 585–599. 10.1111/j.1365-313X.2012.05100.x PubMed DOI

Tanou G., Job C., Rajjou L., Arc E., Belghazi M., Diamantidis G., et al. (2009). Proteomics reveals the overlapping roles of hydrogen peroxide and nitric oxide in the acclimation of citrus plants to salinity. Plant J. 60 795–804. 10.1111/j.1365-313X.2009.04000.x PubMed DOI

Thompson J. E., Hopkins M. T., Taylor C., Wang T. W. (2004). Regulation of senescence by eukaryotic translation initiation factor 5A: implications for plant growth and development. Trends Plant Sci. 9 174–179. 10.1016/j.tplants.2004.02.008 PubMed DOI

Tondelli A., Francia E., Barabaschi D., Pasquariello M., Pecchioni N. (2011). Inside the CBF locus in Poaceae. Plant Sci. 180 39–45. 10.1016/j.plantsci.2010.08.012 PubMed DOI

Vandiver M. S., Paul B. D., Xu R., Karuppagounder S., Rao F., Snowman A. M., et al. (2013). Sulfhydration mediates neuroprotective actions of parkin. Nat. Commun. 4:1626. 10.1038/ncomms2623 PubMed DOI PMC

Virág D., Dalmadi-Kiss B., Vékey K., Drahos L., Klebovich I., Antal I., et al. (2020). Current trends in the analysis of post-translational modifications. Chromatographia 83 1–10. 10.1007/s10337-0419-03796-9 DOI

Wang J., Ma Z., Li C., Ren P., Yao L., Li B., et al. (2021). Dynamic responses of barley root quantitative succinyl-proteome to short-term phosphate starvation and recovery. Front. Plant Sci. 12:649147. 10.3389/fpls.2021.649147 PubMed DOI PMC

Wang X., Komatsu S. (2016a). Plant subcellular proteomics: application for exploring optimal cell function in soybean. J. Proteomics 143 45–56. 10.1016/j.jprot.2016.01.011 PubMed DOI

Wang X., Komatsu S. (2016b). Gel-free/label-free proteomic analysis of endoplasmic reticulum proteins in soybean root tips under flooding and drought stresses. J. Proteome Res. 15 2211–2227. 10.1021/acs.jproteome.6b00190 PubMed DOI

Wang X., Li L., Liu B., Zhou H., Elmongy M. S., Xia Y. (2020). Combined proteome and transcriptome analysis of heat-primed azalea reveals new insights into plant heat acclimation memory. Front. Plant Sci. 11:1278. 10.3389/fpls.2020.01278 PubMed DOI PMC

Whittington A. C., Larion M., Bowler J. M., Ramsey K. M., Brüschweiler R., Miller B. G. (2015). Dual allosteric activation mechanisms in monomeric human glucokinase. Proc. Natl. Acad. Sci. U.S.A. 112 11553–11558. 10.1073/pnas.1506664112 PubMed DOI PMC

Willems P., Horne A., Van Parys T., Goormachtig S., De Smet I., Botzki A., et al. (2019). The plant PTM viewer, a central resource for exploring plant protein modifications. Plant J. 99 752–762. PubMed

Wu X., Gong F., Cao D., Hu X., Wang W. (2016). Advances in crop proteomics: PTMs of proteins under abiotic stress. Proteomics 16 847–865. 10.1002/pmic.201500301 PubMed DOI

Würschum T., Longin C. F., Hahn V., Tucker M. R., Leiser W. L. (2017). Copy number variations of CBF genes at the Fr-A2 locus are essential components of winetr hardiness in wheat. Plant J. 89 764–773. 10.1111/tpj.13424 PubMed DOI

Xiao J., Xu S., Li C., Xu Y., Xing L., Niu Y., et al. (2014). O-GlcNAc-mediated interaction between VER2 and TaGRP2 elicits TaVRN1 mRNA accumulation during vernalization in winter wheat. Nat. Commun. 5:4572. 10.1038/ncomms5572 PubMed DOI PMC

Xu W., Wan J., Zhan J., Li X., He H., Shi Z., et al. (2017). Global profiling of crotonylation on non-histone proteins. Cell Res. 27 946–949. 10.1038/cr.2017.60 PubMed DOI PMC

Xu Y., Shen C., Ma J., Chen W., Mao J., Zhou Y., et al. (2017). Quantitative succinyl-proteome profiling of Camellia sinensis cv. ‘Anji Baicha’ during periodic albinism. Sci. Rep. 7:187. 10.1038/s41598-017-02128-x PubMed DOI PMC

Xue L., Wang P., Wang L., Renzi E., Radivojac P., Tang H., et al. (2013). Quantitative measurement of phosphoproteome response to osmotic stress in Arabidopsis based on library-assisted extracted ion chromatogram (LAXIC). Mol. Cell. Proteomics 12 2354–2369. 10.1074/mcp.O113.027284 PubMed DOI PMC

Yakubov B., Barazani O., Shachack A., Rowland L. J., Shoseyov O., Golan-Goldhirsh A. (2005). Cloning and expression of a dehydrin-like protein from Pistacia vera L. Trees 19 224–230. 10.1007/s00468-004-0385-0 DOI

Yamaguchi-Shinozaki K., Shinozaki K. (2006). Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu. Rev. Plant Biol. 57 781–803. 10.1146/annurev.arplant.57.032905.105444 PubMed DOI

Yang I., Liu Q., Liu Z., Yang H., Wang J., Li X., et al. (2015). Arabidopsis C3HC4-RING finger E3 ubiquitin ligase AtAIRP4 positively regulates stress-responsive abscisic acid signalling. J. Integr. Plant Biol. 58 67–80. 10.1111/jipb.12364 PubMed DOI

Yang Z. B., Eticha D., Führs H., Heintz D., Ajoub D., Van Dorsselaer A., et al. (2013). Proteomic and phosphoproteomic analysis of polyethylene glycol-induced osmotic stress in root tips of common bean (Phaseolus vulgaris L.). J. Exp. Bot. 64 5569–5586. 10.1093/jxb/ert328 PubMed DOI PMC

Yin X., Komatsu S. (2015). Quantitative proteomics of nuclear phosphoproteins in the root tip of soybean during the initial stages of flooding stress. J. Proteomics 119 183–195. 10.1016/j.prot.2015.02.004 PubMed DOI

Yin X., Sakata K., Komatsu S. (2014). Phosphoproteomics reveals the effect of ethylene in soybean root under flooding stress. J. Proteome Res. 13 5618–5634. 10.1021/pr500621c PubMed DOI

Yu B., Li J., Koh J., Dufresne C., Yang N., Qi S., et al. (2016). Quantitative proteomics and phosphoproteomics of sugar beet monosomic addition line M14 in response to salt stress. J. Proteomics 143 286–297. 10.1016/j.jprot.2016.04.011 PubMed DOI

Yu C., Wu Q., Sun C., Tang M., Sun J., Zhan Y. (2019). The phosphoproteomic response of okra (Abelmoschus esculentus L.) seedlings to salt stress. Int. J. Mol. Sci. 20:1262. 10.3390/ijms20061262 PubMed DOI PMC

Yuan L. L., Zhang M., Yan X., Bian Y. W., Zhen S. M., Yan Y. M. (2016). Dynamic phosphoproteome analysis of seedling leaves in Brachypodium distachyon L. reveals central phosphorylated proteins involved in the drought stress response. Sci. Rep. 6:35280. 10.1038/srep35280 PubMed DOI PMC

Zhang H., Cui F., Wu Y., Lou I., Tian M., Ning Y., et al. (2015). The Ring finger ubiquitin E3 ligase SDIR1 targets SDIR1-interacting protein 1 for degradation to modulate the salt stress response and ABA signaling in Arabidopsis. Plant Cell 27 214–227. 10.1105/tpc.114.134163 PubMed DOI PMC

Zhang M., Lv D., Ge P., Bian Y., Chen G., Zhu G., et al. (2014a). Phosphoproteome analysis reveals new drought response and defense mechanisms of seedling leaves in bread wheat (Triticum aestivum L.). J. Proteomics 109 290–308. 10.1016/j.jprot.2014.07.010 PubMed DOI

Zhang M., Ma C. Y., Lv D. W., Zhen S. M., Li X. H., Yan Y. M. (2014b). Comparative phosphoproteome analysis of the developing grains in bread wheat (Triticum aestivum L.) under well-watered and water-deficit conditions. J. Proteome Res. 13 4281–4297. 10.1021/pr500400t PubMed DOI

Zhong M., Li S. F., Huang F. L., Qiu J. H., Zhang J., Sheng Z. H., et al. (2017). The phosphoproteomic response of rice seedlings to cadmium stress. Int. J. Mol. Sci. 18:2055. 10.3390/ijms18102055 PubMed DOI PMC

Ziogas V., Tanou G., Filippou P., Diamantidis G., Vasilakakis M., Fotopoulos V., et al. (2013). Nitrosative responses in citrus plants exposed to six abiotic stress conditions. Plant Physiol. Biochem. 68 118–126. 10.1016/j.plaphy.2013.04.004 PubMed DOI

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