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Motif-Based Prediction of Plant Tubulin Phosphorylation Sites Associated with Calcium-Dependent Protein Kinases in Arabidopsis thaliana

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Abstract

New motifs for phosphorylation sites associated with calcium-dependent protein kinases were developed using 494 sites experimentally proved in mammalians. Subsequent motif-based search revealed consensus regions in α-, β-, and γ-tubulin from Arabidopsis thaliana. The analysis of selected candidate sites and comparison of sequences and structures of homological mammalian and plant protein kinases were performed. Bioinformatic analysis reveals Arabidopsis protein kinases CPK20 (At2g38910), CPK21 (AT4G04720), and GRIK2 (At5g60550) as probable contributors of the plant tubulin code.

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REFERENCES

  1. Wloga, D. and Gaertig, J., Post-translational modifications of microtubules, J. Cell Sci., 2010, vol. 123, no. 20, pp. 3447–3455. doi 10.1242/jcs.063727

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  2. Blume, Ya., Yemets, A., Sulimenko, V., Sulimenko, T., Chan, J., Lloyd, C., and Draber, P., Tyrosine phosphorylation of plant tubulin, Planta, 2008, vol. 229, no. 1, pp. 143–150. doi 10.1007/s00425-008-0816-z

    Article  PubMed  CAS  Google Scholar 

  3. Fisher, D., Gilroy, S., and Cyr, R., Evidence for opposing effects of calmodulin on cortical microtubules, Plant Physiol., 1996, vol. 112, no. 3, pp. 1079–1087.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  4. Karpov, P.A., Nadezhdina, E.S., Yemets, A.I., Matusov, V.G., Nyporko, A.Yu., Shashina, N.Yu., and Blume, Ya.B., Bioinformatic search of plant microtubule- and cell cycle related serine-threonine protein kinases, BMC Genomics, 2010, vol. 11, suppl. 1, p. S14. doi 10.1186/1471-2164-11-S1-S14

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  5. Karpov, P.A., Nadezhdina, E.S., Yemets, A.I., and Blume, Ya.B., Results of the clusterization of human microtubule and cel-cycle related serine/threonine protein kinases and their plant homologues, Moscow Univ. Biol. Sci. Bull., 2010, vol. 65, no. 4, pp. 213–216. doi 10.3103/S0096392510040267

    Article  Google Scholar 

  6. Goodman, D.B., Rasmussen, H., DiBella, F., and Guthrow, C.E., Cyclic adenosine 3':5'-monophosphate-stimulated phosphorylation of isolated neurotubule subunits, Proc. Natl. Acad. Sci. U. S. A., 1970, vol. 67, no. 2, pp. 652–659.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  7. Eipper, B.A., Rat brain microtubule protein: purification and determination of covalently bound phosphate and carbohydrate, Proc. Natl. Acad. Sci. U. S. A., 1972, vol. 69, no. 8, pp. 2283–2287.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Alvarado-Kristensson, M., Rodriguez, M.J., Silio, V., Valpuesta, J.M., and Carrera, A.C., SADB phosphorylation of gamma-tubulin regulates centrosome duplication, Nat. Cell Biol., 2009, vol. 11, pp. 1081–1092. doi doi 10.1038/ncb1921

    Article  PubMed  CAS  Google Scholar 

  9. McKenney, K.M., McKenney, R.J., Huang, H.H., Li, T., Meltzer, S., Jan, L.Y., Vale, R.D., Wiita, A.P., and Jan, Y.N., Phosphorylation of β-tubulin by the down syndrome kinase, minibrain/DYRK1a, regulates microtubule dynamics and dendrite morphogenesis, Neuron, 2016, vol. 90, no. 3, pp. 551–563. doi 10.1016/j.neuron.2016.03.027

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  10. Boscán, B.E., Uzcanga, G.L., Calabokis, M., Camargo, R., Aponte, F., and Bubis, J., Interaction of tubulin and protein kinase CK2 in Trypanosoma equiperdum, Z. Naturforsch. C, 2017, vol. 72, nos. 11–12, pp. 459–4565. doi 10.1515/znc-2017-0019

  11. Goldenring, J.R., Gonzalez, B., McGuire, J.S., Jr., and DeLorenzo, R.J., Purification and characterization of a calmodulin-dependent kinase from rat brain cytosol able to phosphorylate tubulin and microtubule-associated proteins, J. Biol. Chem., 1983, vol. 258, no. 20, pp. 12632–12640.

    PubMed  CAS  Google Scholar 

  12. Karpov, P.A., Yemets, A.I., Matusov, V.G., Nyporko, A.Yu., Nadezhdina, E.S., and Blume, Ya.B., Bioinformatic search for plant homologs of Ste20-like serine/threonine protein kinases, Cytol. Genet., 2009, vol. 43, no. 6, pp. 68–77.

    CAS  Google Scholar 

  13. Karpov, P., Raevsky, A., Korablyov, M., and Blume, Ya., Identification of plant homologues of dual specificity Yak1-related kinases, Comput. Biol. J., 2014. doi 10.1155/2014/909268

  14. Bryantseva, S.A., Gavryushina, E.S., Yemets, A.I., Karpov, P.A., Blume, Ya.B., Drygin, Yu.F., and Nadezhdina, E.S., MAST2-like protein kinase from grape Vitis vinifera: cloning of catalytic domain cDNA, Cytol. Genet., 2010, vol. 44, no. 4, pp. 227–232. doi 10.3103/S0095452710040079

    Article  Google Scholar 

  15. Chudinova, E.M., Karpov, P.A., Fokin, A.I., Yemets, A.I., Lytvyn, D.I., Nadezhdina, E.S., and Blume, Y.B., MAST-like protein kinase IREH1 from Arabidopsis thaliana co-localizes with the centrosome when expressed in animal cells, Planta, 2017, vol. 246, no. 5, pp. 959–969. doi 10.1007/s00425-017-2742-4

    Article  PubMed  CAS  Google Scholar 

  16. Sheremet, Ya.A., Yemets, A.I., Vissenberg, K., Verbelen, J.P., and Blume, Ya.B., Effects of inhibitors of serine/threonine protein kinases on Arabidopsis thaliana root morphology and microtubule organization in its cells, Cell Tissue Biol., 2010, vol. 4, no. 4, pp. 399–409. doi 10.1134/S1990519X10040139

    Article  Google Scholar 

  17. Blume, Ya.B., Lloyd, C.W., and Yemets, A.I., Plant tubulin phosphorylation and its role in cell cycle progression, in The Plant Cytoskeleton: A Key Tool for Agro-Biotechnology, 2008, pp. 145–59. doi 10.1007/978-1-4020-8843-8_7

  18. Sathyanarayanan, P. and Poovaiah, B., Decoding Ca2+ signals in plants, Crit. Rev. Plant Sci., 2004, vol. 23, no. 1, pp. 1–11. org/ doi 10.1080/07352680490273310

  19. Harmon, A.C., Calcium-regulated protein kinases of plants, Gravitat. Space Biol. Bull., 2003, vol. 16, no. 2, pp. 83–90.

    Google Scholar 

  20. Hrabak, E.M., Chan, C.W., Gribskov, M., Harper, J.F., Choi, J.H., Halford, N., Kudla, J., Luan, S., Nimmo, H.G., Sussman, M.R., Thomas, M., Walker-Simmons, K., Zhu, J.K., and Harmon, A.C., The Arabidopsis CDPK-SnRK superfamily of protein kinases, Plant Physiol., 2003, vol. 132, no. 2, pp. 666–680. doi 10.1104/pp.102.011999

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Novozhylov, D.O., Karpov, P.A., and Blume, Ya.B., Bioinformatic search for Ca2+- and calmodulin-dependent protein kinases potentially associated with the regulation of plant cytoskeleton, Cytol. Genet., 2017, vol. 51, no. 4, pp. 239–246. doi 10.3103/S0095452717040053

    Article  Google Scholar 

  22. Baratier, J., Peris, L., Brocard, J., Gory-Faure, S., Dufour, F., Bosc, C., Fourest-Lieuvin, A., Blanchoin, L., Salin, P., Job, D., and Andrieux, A., Phosphorylation of microtubule-associated protein STOP by calmodulin kinase II, J. Biol. Chem., 2006, vol. 281, no. 28, pp. 19561–19569. doi 10.1074/jbc.m509602200

    Article  PubMed  CAS  Google Scholar 

  23. Wandosell, F., Serrano, L., Hernandez, M.A., and Avila, J., Phosphorylation of tubulin by a calmodulin-dependent protein kinase, J. Biol. Chem., 1986, vol. 261, no. 22, pp. 10332–10339.

    PubMed  CAS  Google Scholar 

  24. Holmfeldt, P., Zhang, X., Stenmark, S., Walczak, C.E., and Gullberg, M., CaMKIIgamma-mediated inactivation of the Kin I kinesin MCAK is essential for bipolar spindle formation, EMBO J., 2005, vol. 24, no. 6, pp. 1255–1266. doi 10.1038/sj.emboj.7600601

    Article  CAS  Google Scholar 

  25. Hoffman, L., Farley, M.M., and Waxham, M.N., Calcium-calmodulin-dependent protein kinase II isoforms differentially impact the dynamics and structure of the actin cytoskeleton, Biochemistry, 2013, vol. 52, no. 7, pp. 1198–1207. doi 10.1021/bi3016586

    Article  PubMed  CAS  Google Scholar 

  26. Zhao, J.W., Gao, Z.L., Ji, Q.Y., Wang, H., Zhang, H.Y., Yang, Y.D., Xing, F.J., Meng, L.J., and Wang, Y., Regulation of cofilin activity by CaMKII and calcineurin, Am. J. Med. Sci., 2012, vol. 344, no. 6, pp. 462–72. doi 10.1097/MAJ.0b013e318244745b

    Article  PubMed  Google Scholar 

  27. Easley, C.A., Faison, M.O., Kirsch, T.L., Lee, J.A., Seward, M.E., and Tombes, R.M., Laminin ctivates CaMK-II to stabilize nascent embryonic axons, Brain Res., 2006, vol. 1092, no. 1, pp. 59–68. doi 10.1016/ j.brainres.2006.03.099

    Article  PubMed  CAS  Google Scholar 

  28. The UniProt Consortium UniProt: the universal protein knowledgebase, Nucleic Acids Res., 2018, vol. 46, no. 5, p. 2699. org/ doi 10.1093/nar/gky092

  29. Lee, M.M., Chan, M.K., and Bundschuh, R., SIBBLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches, Nucleic Acids Res., 2009, vol. 37, nos. 1–2, pp. W53–W56. doi 10.1093/nar/gkp301

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  30. Korf, I., Yandell, M., and Bedell, J., BLAST, Sebastopol: O’Reilly and Associates, Inc., 2003.

    Google Scholar 

  31. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J., Higgins, D.G., and Clustal, W., Clustal X., version 2.0, Bioinformatics, 2007, vol. 23, no. 21, pp. 2947–2948. doi 10.1093/bioinformatics/btm404

    Article  PubMed  CAS  Google Scholar 

  32. Hornbeck, P.V., Zhang, B., Murray, B., Kornhauser, J.M., Latham, V., and Skrzypek, E., PhosphoSitePlus, 2014: mutations, PTMs and recalibrations, Nucleic Acids Res., 2014, vol. 43, pp. D512–D520. doi 10.1093/nar/gku1267

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Crooks, G.E., Hon, G., Chandonia, J.M., and Brenner, S.E., WebLogo: A sequence logo generator, Genome Res., 2004, vol. 14, no. 6, pp. 1188–1190. doi 10.1101/gr.849004

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Sigrist, C.J.A., de Castro, E., Cerutti, L., Cuche, B.A., Hulo, N., Bridge, A., Bougueleret, L., and Xenarios, I., New and continuing developments at PROSITE, Nucleic Acids Res., 2013, vol. 41, pp. D344–D347. doi 10.1093/nar/gks1067

    Article  PubMed  CAS  Google Scholar 

  35. Atteson, K., The performance of neighbor-joining algorithms of phylogeny reconstruction, Lecture Notes Comp. Sci., 1997, vol. 1276, pp. 101–110.

    Article  Google Scholar 

  36. Kumar, S., Stecher, G., and Tamura, K., MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets, Mol. Biol. Evol., 2016, vol. 33, no. 7, pp. 1870–1874. doi 10.1093/molbev/msw054

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  37. Letunic, I., Doerks, T., and Bork, P., SMART: recent updates, new developments and status in 2015, Nucleic Acids Res., 2015, vol. 43, pp. D257–D60. doi 10.1093/nar/gku949

    Article  PubMed  CAS  Google Scholar 

  38. Finn, R.D., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Mistry, J., Mitchell, A.L., Potter, S.C., Punta, M., Qureshi, M., Sangrador-Vegas, A., Salazar, G.A., Tate, J., and Bateman, A., The Pfam protein families database: towards a more sustainable future, Nucleic Acids Res., 2016, vol. 44, no. D1, pp. D279–D285. doi 10.1093/nar/gkv1344

    Article  PubMed  CAS  Google Scholar 

  39. DeCastro, E., Sigrist, C.J.A., Gattiker, A., Bulliard, V., Langendijk-Genevaux, P.S., Gasteiger, E., Bairoch, A., and Hulo, N., ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins, Nucleic Acids Res., 2006, vol. 34, pp. W362–W365. doi 10.1093/nar/gkl124

    Article  CAS  Google Scholar 

  40. Finn, R.D., Attwood, T.K., Babbitt, P.C., Bateman, A., Bork, P., Bridge, A.J., Chang, H.Y., Dosztnyi, Z., El-Gebali, S., Fraser, M., Gough, J., Haft, D., Holliday, G.L., Huang, H., Huang, X., Letunic, I., Lopez, R., Lu, S., Marchler-Bauer, A., Mi, H., Mistry, J., Natale, D.A., Necci, M., Nuka, G., Orengo, C.A., Park, Y., Pesseat, S., Piovesan, D., Potter, S.C., Rawlings, N.D., Redaschi, N., Richardson, L., Rivoire, C., Sangrador-Vegas, A., Sigrist, C., Sillitoe, I., Smithers, B., Squizzato, S., Sutton, G., Thanki, N., Thomas, P.D., Tosatto, S.C., Wu, C.H., Xenarios, I., Yeh, L.S., Young, S.Y., and Mitchell, A.L., InterPro in 2017-beyond protein family and domain annotations, Nucleic Acids Res., 2017, vol. 45, no. D1, pp. D190–D199. doi 10.1093/nar/gkw1107

    Article  PubMed  CAS  Google Scholar 

  41. Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., and Zhang, Y., The I-TASSER Suite: protein structure and function prediction, Nature Meth., 2015, vol. 12, no. 1, pp. 7–8. doi 10.1038/nmeth.3213

    Article  CAS  Google Scholar 

  42. Lee, J.-Y., Yoo, B.-C., and Harmon, A.C., Kinetic and calcium-binding properties of three calcium-dependent protein kinase isoenzymes from soybean, Biochemistry, 1998, vol. 37, no. 19, pp. 6801–6809. doi 10.1021/bi980062q

    Article  PubMed  CAS  Google Scholar 

  43. Bachmann, M., Shiraishi, N., Campbell, W.H., Yoo, B.-C., Harmon, A.C., and Huber, S.C., Identification of Ser-543 as the major regulatory phosphorylation site in spinach leaf nitrate reductase, Plant Cell., 1996, vol. 8, no. 3, pp. 505–517. doi 10.1105/tpc.8.3.505

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Huang, J.-Z., Hardin, S.C., and Huber, S.C., Identification of a novel phosphorylation motif for CDPKs: phosphorylation of synthetic peptides lacking basic residues at P-3/P-4, Arch. Biochem. Biophys., 2001, vol. 393, no. 1, pp. 61–66. doi 10.1006/abbi.2001.2476

    Article  PubMed  CAS  Google Scholar 

  45. Sebastia, C.H., Hardin, S.C., Clouse, S.D., Kieber, J.J., and Huber, S.C., Identification of a new motif for CDPK phosphorylation in vitro that suggests ACC synthase may be a CDPK substrate, Arch. Biochem. Biophys., 2004, vol. 428, no. 1, pp. 81–91. doi 10.1016/ j.abb.2004.04.025

    Article  CAS  Google Scholar 

  46. Harmon, A.C., Gribskov, M., Gubrium, E., and Harper, J.F., The CDPK superfamily of protein kinases, New Phytol., 2001, vol. 151, no. 1, pp. 175–183. org/ doi 10.1046/j.1469-8137.2001.00171.x

  47. McCurdy, D.W. and Harmon, A.C., Calcium-dependent protein kinase in the green alga Chara, Planta, 1992, vol. 188, no. 1, pp. 54–61. doi 10.1007/BF00198939

    Article  PubMed  CAS  Google Scholar 

  48. Sugiyama, K., Mori, I.C., Takahashi, K., Muto, S., and Shihira-Ishikawa, I., A calcium-dependent protein kinase functions in wound healing in Ventricaria ventricosa (Chlorophyta), J. Phycol., 2000, vol. 36, pp. 1145–1152. doi 10.1046/j.1529-8817.2000.00050.x

    Article  CAS  Google Scholar 

  49. Billker, O., Lourido, S., and Sibley, L.D., Calcium-dependent signaling and kinases in Apicomplexan parasites, Cell Host Microbe, 2009, vol. 5, no. 6, pp. 612–622. doi 10.1016/j.chom.2009.05.017

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  50. Fantino, E., Segretin, M.E., Santin, F., Mirkin, F.G., and Ulloa, R.M., Analysis of the potato calciumdependent protein kinase family and characterization of StCDPK7, a member induced upon infection with Phytophthora infestans, Plant Cell Rep., 2017, vol. 36, no. 7, pp. 1137–1157. doi 10.1007/s00299-017-2144-x

    Article  PubMed  CAS  Google Scholar 

  51. Valmonte, G.R., Arthur, K., and Higgins, C.M., MacDiarmid R.M., Calcium-dependent protein kinases in plants: evolution, expression and function, Plant Cell Physiol., 2014, vol. 55, no. 3, pp. 551–569. doi 10.1093/pcp/pct200

    Article  PubMed  CAS  Google Scholar 

  52. Ren, R., Sun, Y., Zhao, Y., Geiser, D., Ma, H., and Zhou, X., Phylogenetic resolution of deep eukaryotic and fungal relationships using highly conserved low-copy nuclear genes, Genome Biol. Evol., 2016, vol. 8, no. 9, pp. 2683–2701. doi 10.1093/gbe/evw196

    Article  PubMed  PubMed Central  Google Scholar 

  53. Hey, S.J., Mayerhofer, H., Halford, N.G., and Dickinson, J.R., DNA sequences from Arabidopsis, which encode protein kinases and function as upstream regulators of Snf1 in yeast, J. Biol. Chem., 2007, vol. 282, pp. 10472–10479. doi 10.1074/jbc.M611244200

    Article  PubMed  CAS  Google Scholar 

  54. Shen, W., Reyes, M., and Hanley-Bowdoin, L., Arabidopsis protein kinases GRIK1 and GRIK2 specifically activate SnRK1 by phosphorylating its activation loop, Plant Physiol., 2009, vol. 150, no. 2, pp. 996–1005. doi 10.1104/pp.108.132787

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  55. Crozet, P., Jammes, F., Valot, B., Ambard-Bretteville, F., Nessler, S., Hodges, M., Vidal, J., and Thomas, M., Cross-phosphorylation between Arabidopsis thaliana sucrose nonfermenting 1-related protein kinase 1 (AtSnRK1) and its activating kinase (AtSnAK) determines their catalytic activities, J. Biol. Chem., 2010, vol. 285, no. 16, pp. 12071–12077. doi 10.1074/ jbc.M109.079194

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  56. Karpov, P.A., Raevsky, A.V., Krasnoperova, E.E., Isayenkov, S.V., Yemets, A.I., and Blume, Ya.B., Protein kinase KIN10 from Arabidopsis thaliana as a potential regulator of primary microtubule nucleation centers in plants, Cytol. Genet., 2017, vol. 51, no. 6, pp. 415–421. doi 10.3103/S0095452717060056

    Article  Google Scholar 

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  1. Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123, Kyiv, Ukraine

    P. A. Karpov, D. O. Novozhylov, S. V. Isayenkov & Ya. B. Blume

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  1. P. A. Karpov
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  2. D. O. Novozhylov
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Correspondence to P. A. Karpov, D. O. Novozhylov, S. V. Isayenkov or Ya. B. Blume.

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Karpov, P.A., Novozhylov, D.O., Isayenkov, S.V. et al. Motif-Based Prediction of Plant Tubulin Phosphorylation Sites Associated with Calcium-Dependent Protein Kinases in Arabidopsis thaliana. Cytol. Genet. 52, 428–439 (2018). https://doi.org/10.3103/S0095452718060038

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