Plant Molecular Biology

, Volume 60, Issue 2, pp 293–319 | Cite as

Genome-Wide Analysis and Experimentation of Plant Serine/ Threonine/Tyrosine-Specific Protein Kinases

  • Parvathi Rudrabhatla
  • Mamatha M. Reddy
  • Ram RajasekharanEmail author


Protein tyrosine phosphorylation plays an important role in cell growth, development and oncogenesis. No classical protein tyrosine kinase has hitherto been cloned from plants. Does protein tyrosine kinase exist in plants? To address this, we have performed a genomic survey of protein tyrosine kinase motifs in plants using the delineated tyrosine phosphorylation motifs from the animal system. The Arabidopsis thaliana genome encodes 57 different protein kinases that have tyrosine kinase motifs. Animal non-receptor tyrosine kinases, SRC, ABL, LYN, FES, SEK, KIN and RAS have structural relationship with putative plant tyrosine kinases. In an extended analysis, animal receptor and non-receptor kinases, Raf and Ras kinases, mixed lineage kinases and plant serine/threonine/tyrosine (STY) protein kinases, form a well-supported group sharing a common origin within the superfamily of STY kinases. We report that plants lack bona fide tyrosine kinases, which raise an intriguing possibility that tyrosine phosphorylation is carried out by dual-specificity STY protein kinases in plants. The distribution pattern of STY protein kinase families on Arabidopsis chromosomes indicates that this gene family is partly a consequence of duplication and reshuffling of the Arabidopsis genome and of the generation of tandem repeats. Genome-wide analysis is supported by the functional expression and characterization of At2g24360 and phosphoproteomics of Arabidopsis. Evidence for tyrosine phosphorylated proteins is provided by alkaline hydrolysis, anti-phosphotyrosine immunoblotting, phosphoamino acid analysis and peptide mass fingerprinting. These results report the first comprehensive survey of genome-wide and tyrosine phosphoproteome analysis of plant STY protein kinases.


abiotic stress dual-specificity protein kinase molecular modeling phylogeny tyrosine kinase in plants 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

supp.doc (1.8 mb)
Supplementary material


  1. Ali, N., Halfter, U., Chua, N.H. 1994Cloning and biochemical characterization of a plant protein kinase that phosphorylates serine, threonine and tyrosineJ. Biol. Chem.2693162631629PubMedGoogle Scholar
  2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J. 1990Basic local alignment search toolJ. Mol. Biol.215403410PubMedCrossRefGoogle Scholar
  3. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J. 1997Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Res.2533893402PubMedCrossRefGoogle Scholar
  4. Arabidopsis Genome Initiative2000Analysis of the genome of the flowering plant Arabidopsis thalianaNature408820826Google Scholar
  5. Aravind, L., Koonin, E.V. 1999Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searchesJ. Mol. Biol.28710231040PubMedCrossRefGoogle Scholar
  6. Asai, T., Tena, G., Plotnikova, J., Willmann, M.R., Chiu, W.L., Gomez-Gomez, L., Boller, T., Ausubel, F.M., Sheen, J. 2002MAP kinase signalling cascade in Arabidopsis innate immunityNature415977983PubMedCrossRefGoogle Scholar
  7. Barizza, E., Lo Schiavo, F., Terzi, M, Filippini, F. 1999Evidence suggesting protein tyrosine phosphorylation in plants depends on the developmental conditionsFEBS Lett.447191194PubMedCrossRefGoogle Scholar
  8. Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Howe, K.L., Sonnhammer, E.L. 2000The Pfam protein families databaseNucleic Acids Res.28263266PubMedCrossRefGoogle Scholar
  9. Bennett, V., Chen, L. 2001Ankyrins and cellular targeting of diverse membrane proteins to physiological sitesCurr. Opin. Cell Biol.16167Google Scholar
  10. Binari, R., Perrimon, N. 1994Stripe-specific regulation of pair-rule genes by hopscotch, a putative Jak family tyrosine kinase in DrosophilaGenes Dev.8300312PubMedGoogle Scholar
  11. Bourassa, C., Chapdelaine, A., Roberts, K.D., Chevalier, S. 1988Enhancement of the detection of alkali-resistant phosphoproteins in polyacrylamide gelsAnal. Biochem.169356362PubMedCrossRefGoogle Scholar
  12. Burge, C., Karlin, S. 1997Prediction of complete gene structures in human genomic DNAJ. Mol. Biol.2687894PubMedCrossRefGoogle Scholar
  13. Carpi, A., Maira, G.D., Vedovato, M., Rossi, V., Naccari, T., Floriduz, M., Terzi, M., Filippini, F. 2002Comparative proteome bioinformatics: identification of a whole complement of putative protein tyrosine kinases in the model flowering plant Arabidopsis thalianaProteomics214941503PubMedCrossRefGoogle Scholar
  14. Chan, A.M., King, H.W., Deakin, E.A., Tempest, P.R., Hilkens, J., Kroezen, V., Edwards, D.R., Wills, A.J., Brookes, P., Cooper, C.S. 1988Characterization of the mouse met proto-oncogeneOncogene2593599PubMedGoogle Scholar
  15. Chinchilla, D., Merchan, F., Megias, M., Kondorosi, A., Sousa, C., Crespi, M. 2003Ankyrin protein kinases: a novel type of plant kinase gene whose expression is induced by osmotic stressPlant Mol. Biol.51555566PubMedCrossRefGoogle Scholar
  16. Cloutier, J.F., Veillette, A. 1996Association of inhibitory tyrosine protein kinase p50csk with protein tyrosine phosphatase PEP in T cells and other hemopoietic cellsEMBO J.1549094918PubMedGoogle Scholar
  17. Felsenstein, J. 1996Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methodsMethods Enzymol.266418426PubMedGoogle Scholar
  18. Feng, X.H., Zhao, Y., Bottino, P.J., Kung, S.D. 1993Cloning and characterization of a novel member of protein kinase family from soybeanBiochim. Biophys. Acta1172200204PubMedGoogle Scholar
  19. Fordham-Skelton, A.P., Skipsey, M., Evans, I.M., Edwards, R., Gatehouse, J.A. 1999Higher plant tyrosine-specific protein phosphatases (PTPs) contain novel amino-terminal domains: expression during embryogenesisPlant Mol. Biol.39593605PubMedCrossRefGoogle Scholar
  20. Frank, G.D., Saito, S., Motley, E.D., Sasaki, T., Ohba, M., Kuroki, T., Inagami, T., Eguchi, S. 2002Requirement of Ca2+ and PKCdelta for Janus kinase 2 activation by angiotensin II: involvement of PYK2Mol. Endocrinol.16367377PubMedCrossRefGoogle Scholar
  21. Frye, C.A., Tang, D., Innes, R.W. 2001Negative regulation of defense responses in plants by a conserved MAPKK kinaseProc. Natl. Acad. Sci. USA98373378PubMedCrossRefGoogle Scholar
  22. Garg, R., Oliver, P.M., Maeda, N., Pandey, K.N. 2002Genomic structure, organization, and promoter region analysis of murine guanylyl cyclase/atrial natriuretic peptide receptor-A geneGene291123133PubMedCrossRefGoogle Scholar
  23. Goddard, J.M., Weiland, J.J., Capecchi, M.R. 1986Isolation and characterization of Caenorhabditis elegans DNA sequences homologous to the v-abl oncogeneProc. Natl. Acad. Sci. USA821722176Google Scholar
  24. Gotoh, I., Adachi, M., Nishida, E. 2001Identification and characterization of a novel MAP kinase kinase, MLTKJ. Biol. Chem.27642764286PubMedCrossRefGoogle Scholar
  25. Gribskov, M., Fana, F., Harper, J., Hope Harmon, D.A. A.C., Smith, D.W., Tax, F.E., Zhang, G. 2001PlantsP: a functional genomics database for plant phosphorylationNucleic Acids Res.29111113PubMedCrossRefGoogle Scholar
  26. Guex, N., Peitsch, M.C. 1997SWISS-MODEL and the Swiss-Pdbviewer: an environment for comparative protein modellingElectrophoresis1827142723PubMedCrossRefGoogle Scholar
  27. Gupta, R., Huang, Y., Kieber, J., Luan, S. 1998Identification of a dual-specificity protein phosphatase that inactivates a MAP kinase from ArabidopsisPlant J.16581589PubMedCrossRefGoogle Scholar
  28. Hanks, S.K. 1987Homology probing identification of cDNA clones encoding members of the protein-serine kinase familyProc. Natl. Acad. Sci. USA84388392PubMedGoogle Scholar
  29. Hanks, S.K., Quinn, A.M. 1991Protein kinase catalytic domain sequence database: identification of conserved features of primary structure and classification of family membersMethods Enzymol.2003862PubMedGoogle Scholar
  30. Hanks, S.K., Quinn, A.M., Hunter, T. 1988The protein kinase family: conserved features and deduced phylogeny of the catalytic domainsScience2414251PubMedGoogle Scholar
  31. Hirayama, T., Oka, A. 1992Novel protein kinase of Arabidopsis thaliana (APK1) that phosphorylates tyrosine, serine and threoninePlant Mol. Biol.20653662PubMedCrossRefGoogle Scholar
  32. Holtrich, U., Brauninger, A., Strebhardt, K., Rubsamen-Waigmann, H. 1991Two additional protein-tyrosine kinases expressed in human lung: fourth member of the fibroblast growth factor receptor family and an intracellular protein-tyrosine kinaseProc. Natl. Acad. Sci. USA881041110415PubMedGoogle Scholar
  33. Honys, D., Twell, D. 2003Comparative analysis of the Arabidopsis pollen transcriptomePlant Physiol.132640652PubMedCrossRefGoogle Scholar
  34. Huang, H.J., Lin, Y.M., Huang, D.D., Takahashi, T., Sugiyama, M. 2003Protein tyrosine phosphorylation during phytohormone-stimulated cell proliferation in Arabidopsis hypocotylsPlant Cell Physiol.44770775PubMedCrossRefGoogle Scholar
  35. Hunter, T. 1987A thousand and one protein kinasesCell50823829PubMedCrossRefGoogle Scholar
  36. Ichimura, K., Mizoguchi, T., Shinozaki, K. 1997ATMRK1, an Arabidopsis protein kinase related to mammal mixed-lineage kinases and Raf protein kinasesPlant Sci.130171179CrossRefGoogle Scholar
  37. Innes, R.W. 2001Mapping out the roles of MAP kinases in plant defenseTrends Plant Sci.6392394PubMedCrossRefGoogle Scholar
  38. Katzen, A.L, Montarras, D., Jackson, J., Paulson, R.F., Kornberg, T., Bishop, J.M. 1991A gene related to the proto-oncogene fps/fes is expressed at diverse times during the life cycle of Drosophila melanogasterMol. Cell Biol.11226239PubMedGoogle Scholar
  39. Kumar, S., Tamura, K., Jakobsen, I.B., Nei, M. 2001MEGA2: Molecular Evolutionary Genetics Analysis Software Arizona State UniversityTempeGoogle Scholar
  40. Kyte, J., Doolittle, R. 1982A simple method for displaying the hydropathic character of a proteinJ. Mol. Biol.157105132PubMedCrossRefGoogle Scholar
  41. Lamers, M.B., Antson, A.A., Hubbard, R.E., Scott, R.K., Williams, D.H. 1999Structure of the protein tyrosine kinase domain of C-terminal Src kinase (CSK) in complex with staurosporineJ. Mol. Biol.285713725PubMedCrossRefGoogle Scholar
  42. Lazar, S., Galiani, D., Dekel, N. 2002cAMP-Dependent PKA negatively regulates polyadenylation of c-mos mRNA in rat oocytesMol. Endocrinol.16331341PubMedCrossRefGoogle Scholar
  43. Lindberg, R.A., Quinn, A.M., Hunter, T. 1992Dual-specificity protein kinases: will any hydroxyl do?Trends Biochem. Sci.17114119PubMedCrossRefGoogle Scholar
  44. Liu, T.C., Huang, C.J., Chu, Y.C., Wei, C.C., Chou, C.C., Chou, M.Y., Chou, C.K., Yang, J.J. 2000Cloning and expression of ZAK, a mixed lineage kinase-like protein containing a leucine-zipper and a sterile-alpha motifBiochem. Biophys. Res. Commun.274811816PubMedGoogle Scholar
  45. Lukashin, A.V., Borodovsky, M. 1998GeneMark.hmm: new solutions for gene findingNucleic Acid Res.2611071115PubMedGoogle Scholar
  46. McCafferty, D.M., Craig, A.W., Senis, Y.A., Greer, P.A. 2002Absence of Fer protein-tyrosine kinase exacerbates leukocyte recruitment in response to endotoxinJ. Immunol.16849304935PubMedGoogle Scholar
  47. Mizoguchi, T., Irie, K., Hirayama, T., Hayashida, N., Yamaguchi-Shinozaki, K., Matsumoto, K., Shinozaki, K. 1996A gene encoding a mitogen-activated protein kinase kinase kinase is induced simultaneously with genes for a mitogen-activated protein kinase and an S6 ribosomal protein kinase by touch, cold, and water stress in Arabidopsis thalianaProc. Natl. Acad. Sci. USA93765769PubMedCrossRefGoogle Scholar
  48. Morgan, D.O., Bondt, H.L. 1994Protein kinase regulation: insights from crystal structure analysisCurr. Opin. Cell Biol.6239246PubMedCrossRefGoogle Scholar
  49. Morgan, W.R., Greenwald, I. 1993Two novel transmembrane protein tyrosine kinases expressed during Caenorhabditis elegans hypodermal developmentMol. Cell Biol.1371337143PubMedGoogle Scholar
  50. Munoz, G.E., Marshall, S.H. 1994Selective phosphoamino acid enrichment by organic solvent fractionationBiotechniques1710441046PubMedGoogle Scholar
  51. Murashige, T., Skoog, F. 1962A revised medium for rapid growth and bioassays with tobacco tissue culturesPlant Physiol.15473497Google Scholar
  52. Noiman, S., Shaul, Y. 1995Detection of histidine-phosphoproteins in animal tissuesFEBS Lett.3646366PubMedCrossRefGoogle Scholar
  53. Nuckolls, G.H., Osherov, N., Loomis, W.F., Spudich, J.A. 1996The Dictyostelium dual-specificity kinase splA is essential for spore differentiationDevelopment12232953305PubMedGoogle Scholar
  54. Okada, M., Nada, S., Yamanashi, Y., Yamamoto, T., Nakagawa, H. 1991CSK: a protein-tyrosine kinase involved in regulation of src family kinasesJ. Biol. Chem.26624249242452PubMedGoogle Scholar
  55. Page, R.D.M. 1996TREEVIEW: an application to display phylogenetic trees on personal computersComput. Appl. Biosci.12357358PubMedGoogle Scholar
  56. Ponting, C.P., Aravind, L. 1997PAS: a multifunctional domain family comes to lightCurr. Biol.77477CrossRefGoogle Scholar
  57. Rider, L.G., Raben, N., Miller, L., Jelsema, C. 1994The cDNAs encoding two forms of the LYN protein tyrosine kinase are expressed in rat mast cells and human myeloid cellsGene138219222PubMedCrossRefGoogle Scholar
  58. Roy, F., Therrien, M. 2002MAP kinase module: the Ksr connectionCurr. Biol.12325327CrossRefGoogle Scholar
  59. Rudrabhatla, P., Rajasekharan, R. 2002Developmentally regulated dual-specificity kinase that is induced by abiotic stressesPlant Physiol.130380390PubMedCrossRefGoogle Scholar
  60. Rudrabhatla, P., Rajasekharan, R. 2003Mutational analysis of stress-responsive peanut dual specificity kinase: identification of tyrosine residues involved in protein kinase activityJ. Biol. Chem.2781732817335PubMedCrossRefGoogle Scholar
  61. Rudrabhatla, P., Rajasekharan, R. 2004Functional characterization of peanut STY kinase Molecular docking and inhibition kinetics with tyrosine kinase inhibitorsBiochemistry431212312132PubMedCrossRefGoogle Scholar
  62. Ryals Lawton, J. K.A., Delaney, T.P., Friedrich, L., Kessmann, H., Neuenschwander, U., Uknes, S., Vernooij, B., Weymann, K. 1995Signal transduction in systemic acquired resistanceProc. Natl. Acad. Sci. USA9242024205Google Scholar
  63. Saitou, N., Nei, M. 1987The neighbor joining method: a new method for reconstructing phylogenetic treesMol. Biol. Evol.4406425PubMedGoogle Scholar
  64. Sayle, R., Milner-White, E.J. 1995RasMol: biomolecular graphics for allTrends Biochem. Sci.20374PubMedCrossRefGoogle Scholar
  65. Schoof, H., Zaccaria, P., Gundlach, H., Lemcke, K., Rudd, S., Kolesov, G., Arnold, R., Mewes, H.W., Mayer, K.F.X. 2002MIPS Arabidopsis thaliana database (MAtDB): an integrated biological knowledge resource based on the first complete plant genomeNucleic Acids Res.309193PubMedCrossRefGoogle Scholar
  66. Shekhtman, A., Ghose, R., Wang, D., Cole, P.A., Cowburn, D. 2001Novel mechanism of regulation of the non-receptor tyrosine kinase Csk: insights from NMR mapping studies and site-directed mutagenesisJ Mod Biol314129138Google Scholar
  67. Shevchenko, A., Jensen, O.N., Podtelejnikov, A.V., Sagliocco, F., Wilm, M., Vorm, O., Mortensen, P., Shevchenko, A., Boucherie, H., Mann, M. 1996Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two-dimensional gelsProc. Natl. Acad. Sci. USA931444014445PubMedCrossRefGoogle Scholar
  68. Sippl, M.J. 1993Assessment of the CASP4 fold recognition categoryProteins17355362PubMedCrossRefGoogle Scholar
  69. Stanger, B.Z., Leder, P., Lee, T.H., Kim, E., Seed, B. 1995RIP: a novel protein containing a death domain that interacts with Fas/APO-1 (CD95) in yeast and causes cell deathCell81513523PubMedCrossRefGoogle Scholar
  70. Takahashi, T., Shirasawa, T. 1994Molecular cloning of rat JAK3, a novel member of the JAK family of protein tyrosine kinasesFEBS Lett.342124128PubMedCrossRefGoogle Scholar
  71. Tan, J.L., Spudich, J.A. 1990Developmentally regulated protein-tyrosine kinase genes in Dictyostelium discoideumMol. Cell Biol.1035783583PubMedGoogle Scholar
  72. Tang, D., Innes, R.W. 2002Overexpression of a kinase-deficient form of the EDR1 gene enhances powdery mildew resistance and ethylene-induced senescence in ArabidopsisPlant J.32975983PubMedCrossRefGoogle Scholar
  73. Thompson, J.D., Higgins, D.G., Gibson, T.J. 1994ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Res.2246734680PubMedGoogle Scholar
  74. Tregear, J.W., Jouannic, S., Schwebel-Dugue, N., Kreis, M. 1996An unusual protein kinase displaying characteristics of both the serine/threonine kinase and tyrosine families is encoded by the Arabidopsis thaliana gene ATN1Plant Sci.117107119CrossRefGoogle Scholar
  75. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Profeta, A.S., Weiner, P. 1984A new force field for molecular mechanical simulation of nucleic acids and proteinsJ. Am. Chem. Soc.106765784Google Scholar
  76. Wilks, A.F., Kurban, R.R. 1988Isolation and structural analysis of murine c-fes cDNA clonesOncogene3289294PubMedGoogle Scholar
  77. Xu, Q., Fu, H., Gupta, R., Luan, S. 1998Molecular characterization of a tyrosine-specific protein phosphatase encoded by a stress-responsive gene in ArabidopsisPlant Cell10849857PubMedGoogle Scholar
  78. Yang, R.B., Foster, D.C., Garbers, D.L., Fulle, H.J. 1995Two membrane forms of guanylyl cyclase found in the eyeProc. Natl. Acad. Sci. USA92602606PubMedGoogle Scholar
  79. Yarden, Y., Escobedo, J.A., Kuang, W.J., Yang-Feng, T.L., Daniel, T.O., Tremble, P.M., Chen, E.Y., Ando, M.E., Harkins, R.N., Francke, U., Fried, V.A., Ullrich, A., Williams, L.T. 1986Structure of the receptor for platelet-derived growth factor helps define a family of closely related growth factor receptorsNature323226232PubMedCrossRefGoogle Scholar
  80. Yee, K., Bishop, T.R., Mather, C., Zon, L.I. 1993Isolation of a novel receptor tyrosine kinase cDNA expressed by developing erythroid progenitorsBlood8213351343PubMedGoogle Scholar
  81. Yi, T.L., Bolen, J.B., Ihle, J.N. 1991Hematopoietic cells express two forms of lyn kinase differing by 21 amino acids in the amino terminusMol. Cell Biol.1123912398PubMedGoogle Scholar
  82. Yuryev, A., Wennogle, L.P. 1998The RAF family: an expanding network of post-translational controls and protein–protein interactionsCell Res.88198PubMedGoogle Scholar
  83. Zhang, S., Klessig, D.F. 2001MAPK cascades in plant defense signalingTrends Plant Sci.6520527PubMedCrossRefGoogle Scholar
  84. Zimmermann, P., Hirsch-Hoffman, M., Hennig, L., Gruissem, W. 2004GENEVESTIGATOR. Arabidopsis microarray database and analysis toolboxPlant Physiol.13626212632PubMedCrossRefGoogle Scholar
  85. Zhou, G., Bao, Z.Q., Dixon, J.E. 1995Components of a new human protein kinase signal transduction pathwayJ. Biol. Chem.2701266512669PubMedGoogle Scholar

Copyright information

© Springer 2006

Authors and Affiliations

  • Parvathi Rudrabhatla
    • 1
  • Mamatha M. Reddy
    • 1
  • Ram Rajasekharan
    • 1
    Email author
  1. 1.Department of BiochemistryIndian Institute of ScienceBangaloreIndia

Personalised recommendations