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Bioinformatic comparison of human and higher plant phosphatomes

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Abstract

The study presents the results of bioinformatic comparison of protein phosphatases from higher plants and human phosphatome (150 proteins). Based on sequence and profile comparison with known catalytic domains, 204 plant homologues were selected from Physcomitrella patens and Arabidopsis thaliana. Clustering of joint group of plant and animal protein phosphatases revealed fundamental differences in plant and human phosphatomes. At the same time, significant differences in the sets of protein phosphatases in P. patens, A. thaliana, Orysa sativa, and Zea mays were shown.

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References

  1. Moorhead, G.B., Trinkle-Mulcahy, L., and UlkeLemee, A., Emerging roles of nuclear protein phosphatases, Nat. Rev. Mol. Cell Biol., 2007, vol. 8, no. 3, pp. 234–244.

    Article  CAS  PubMed  Google Scholar 

  2. Kerk, D., Bulgrien, J., Smith, D.W., et al., The complement of protein phosphatase catalytic subunits encoded in the genome of Arabidopsis, Plant Physiol., 2002, vol. 129, no. 2, pp. 908–925.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  3. Burley, S.K., Almo, S.C., Bonanno, J.B., et al., Structural genomics of protein superfamilies, in Structural Bioinformatics, Gu, J. and Bourne, P.E., Eds., John Wiley and Sons, Inc., 2009, pp. 983–1018.

  4. Uhrig, R.G., Labandera, A.-M., and Moorhead, G.B., Arabidopsis PPP family of serine/threonine protein phosphatases: many targets but few engines, Trends Plant Sci., 2013, vol. 18, no. 9, pp. 505–513.

    Article  CAS  PubMed  Google Scholar 

  5. Briedis, K.M., The distribution and evolution of protein kinase and phosphatase families in the three superkingdoms of life, Dis. publ., San Diego, 2008.

    Google Scholar 

  6. Kennelly, P.J., Archaeal protein kinases and protein phosphatases: insights from genomics and biochemistry, Biochem. J., 2003, vol. 370, no. 2, pp. 373–389.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  7. Tsou, R.C. and Bence, K.K., Central regulation of metabolism by protein tyrosine phosphatases, Front. Neurosci., 2012, vol. 6, p. 192.

    PubMed Central  PubMed  Google Scholar 

  8. Kim, S.J. and Ryu, S.E., Structure and catalytic mechanism of human protein tyrosine phosphatome, BMB Rep., 2012, vol. 45, no. 12, pp. 693–699.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  9. Connor, J.H., Frederick, D., Huang, H., et al., Cellular mechanisms regulating protein phosphatase-1. A key functional interaction between inhibitor-2 and the type 1 protein phosphatase catalytic subunit, J. Biol. Chem., 2000, vol. 275, no. 25, pp. 18670–18675.

    Article  CAS  PubMed  Google Scholar 

  10. Ayaydin, F., Vissi, E., Meszaros, T., et al., Inhibition of serine/threonine-specific protein phosphatases causes premature activation of cdc2MsF kinase at G2/M transition and early mitotic microtubule organization in alfalfa, Plant J., 2000, vol. 23, no. 1, pp. 85–96.

    Article  CAS  PubMed  Google Scholar 

  11. Hunter, T., Protein phosphorylation: what does the future hold?, in Life Sciences for the 21st Century, Keinan, E., Schechtez, I., and Sela, M., Eds., Hoboken: Wiley, 2004, pp. 191–223.

    Google Scholar 

  12. DeLong, A., Switching the flip: protein phosphatase roles in signaling pathways, Curr. Opin. Plant Biol., 2006, vol. 9, no. 5, pp. 470–477.

    Article  CAS  PubMed  Google Scholar 

  13. Takemiya, A., Kinoshita, T., Asanuma, M., and Shimazaki, K., Protein phosphatase 1 positively regulates stomatal opening in response to blue light in Vicia faba, Proc. Nat. Acad. Sci. USA, 2006, vol. 103, no. 36, pp. 13549–13554.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  14. Almo, S.C., Bonanno, J.B., Sauder, J.M., et al., Structural genomics of protein phosphatases, J. Struct. Funct. Genom., 2007, vol. 8, pp. 121–140.

    Article  CAS  Google Scholar 

  15. Wolstencroft, K., Lord, P., Tabernero, L., et al., Protein classification using ontology classification, Bioinformatics, 2006, vol. 22, no. 14, pp. 530–538.

    Article  Google Scholar 

  16. Zhang, W. and Shi, L., Evolution of the ppm-family protein phosphatases in streptomyces: duplication of catalytic domain and lateral recruitment of additional sensory domains, Microbiology, 2004, vol. 150, no. 12, pp. 4189–4197.

    Article  CAS  PubMed  Google Scholar 

  17. Cohen, P.T.W., Overview of protein serine/threonine phosphatases and their classification, in Protein Phosphatases, Arino, J. and Alexander, D.R., Eds., Berlin: Springer-Verlag, 2004, pp. 1–20.

    Chapter  Google Scholar 

  18. Gohla, A., Birkenfeld, J., and Bokoch, G.M., Chronophin, a novel HAD-type serine protein phosphatase, regulates cofilin-dependent actin dynamics, Nat. Cell Biol., 2005, vol. 7, no. 1, pp. 21–29.

    Article  CAS  PubMed  Google Scholar 

  19. Shi, Y., Serine/threonine phosphatases: mechanism through structure, Cell, 2009, vol. 139, no. 3, pp. 468–484.

    Article  CAS  PubMed  Google Scholar 

  20. Rayapureddi, J.P., Kattamuri, C., Steinmetz, B.D., et al., Eyes absent represents a class of protein tyrosine phosphatases, Nature, 2003, vol. 426, no. 6964, pp. 295–298.

    Article  CAS  PubMed  Google Scholar 

  21. Alonso, A., Sasin, J., Bottini, N., et al., Protein tyrosine phosphatases in the human genome, Cell, 2004, vol. 117, pp. 699–711.

    Article  CAS  PubMed  Google Scholar 

  22. Kerk, D., Templeton, G., and Moorhead, G.B.G., Evolutionary radiation pattern of novel protein phosphatases revealed by analysis of protein data from the completely sequenced genomes of humans, green algae, and higher plants, Plant Physiol., 2008, vol. 146, pp. 351–367.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  23. Bohmer, F., Szedlacsek, S., Tabernero, L., et al., Protein tyrosine phosphatase structure-function relationships in regulation and pathogenesis, FEBS J., 2012, vol. 280, no. 2, pp. 413–431.

    Article  PubMed  Google Scholar 

  24. Moorhead, G.B., De Wever, V., Templeton, G., and Kerk, D., Evolution of protein phosphatases in plants and animals, Biochem. J., 2009, vol. 417, no. 2, pp. 401–409.

    Article  CAS  PubMed  Google Scholar 

  25. Greg, B., Trinkle-Mulcahy, I., and Ulke-Lemé, A., Emerging roles of nuclear protein phosphatases, Nature Rev. Mol. Cell Biol., 2007, vol. 8, pp. 234–244.

    Article  Google Scholar 

  26. Charbonneau, H. and Tonks, N.K., 1002 protein phosphatases?, Annu. Rev. Cell Biol., 1992, vol. 8, pp. 463–493.

    Article  CAS  PubMed  Google Scholar 

  27. Forrest, A.R.R., Ravasi, T., Taylor, D., et al., Phosphoregulators: protein kinases and protein phosphatases of mouse, Genome Res., 2003, vol. 13, no. 6, pp. 1443–1454.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  28. Wu, J.Q., Guo, J.Y., Tang, W., et al., PP1-mediated dephosphorylation of phosphoproteins at mitotic exit is controlled by inhibitor-1 and PP1 phosphorylation, Nat. Cell Biol., 2009, vol. 11, no. 5, pp. 644–651.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  29. Koh, C.G., Oon, S.H., and Brenner, S., Serine/threonine phosphatases of the pufferfish, Fugu rubripes, Gene, 1997, vol. 198, nos. 1/2, pp. 223–228.

    Article  CAS  PubMed  Google Scholar 

  30. Smith, R.D. and Walker, J.C., Plant protein phosphatases, Annu. Rev. Plant Physiol. Plant Mol. Biol., 1996, vol. 47, pp. 101–125.

    Article  CAS  PubMed  Google Scholar 

  31. Luan, S., Protein phosphatases in plants, Annu. Rev. Plant Biol., 2003, vol. 54, pp. 63–92.

    Article  CAS  PubMed  Google Scholar 

  32. Wang, H., Larue, C., Chevalier, D., et al., The protein phosphatases and protein kinases of Arabidopsis thaliana, Arabidopsis Book, 2007, vol. 5, p. e0106.

  33. Templeton, G.W., Nimick, M., Morrice, N., et al., Identification and characterization of AtI-2, an Arabidopsis homologue of an ancient protein phosphatase 1 (PP1) regulatory subunit, Biochem. J., 2011, vol. 435, no. 1, pp. 73–83.

    Article  CAS  PubMed  Google Scholar 

  34. Wu, C.H., Apweiler, R., Bairoch, A., et al., The universal protein resource (UniProt): an expanding universe of protein information, Nucleic Acids Res., 2006, vol. 34, pp. 187–191.

    Article  Google Scholar 

  35. The UniProt Consortium. Update on activities at the Universal Protein Resource (UniProt) in 2013, Nucl. Acids Res., 2013, vol. 41, pp. D43–D47.

  36. Korf, I., Yandell, M., and Bedell, J., BLAST, O’Reilly, Sebastopol: Media, 2003.

    Google Scholar 

  37. Letunic, I., Doerks, T., and Bork, P., SMART 7: recent updates to the protein domain annotation resource, Nucleic Acids Res., 2012, vol. 40, no. 1, pp. 302–305.

    Article  Google Scholar 

  38. Larkin, M.A., Blackshields, G., Brown, N.P., et al., Clustal W and Clustal X version 2.0, Bioinformatics, 2007, vol. 23, pp. 2947–2948.

    Article  CAS  PubMed  Google Scholar 

  39. Olson, S.A., Emboss opens up sequence analysis. European molecular biology open software suite, Brief Bioinform., 2002, vol. 3, no. 1, pp. 87–91.

    Article  PubMed  Google Scholar 

  40. Franceschini, A., Szklarczyk, D., Frankild, S., et al., STRING v9.1: protein–protein interaction networks, with increased coverage and integration, Nucleic Acids Res., 2013, vol. 41, pp. D808–D815.

  41. Atteson, K., The performance of neighbor-joining algorithms of phylogeny reconstruction, in Lecture Notes in Computer Science, Jiang, T. and Lee, D., Eds., Berlin: Springer-Verlag, 1997, vol. 1276, pp. 101–110.

    Article  Google Scholar 

  42. Nei, M. and Kumar, S., Molecular Evolution and Phylogenetics, Oxford: Univ. Press, 2000.

    Google Scholar 

  43. Huson, D.H., Richter, D.C., Rausch, C., et al., Dendroscope: an interactive viewer for large phylogenetic trees, BMC Bioinform., 2007, vol. 8, no. 460.

  44. Kumar, S., Dudley, J., Nei, M., and Tamura, K., Mega: a biologist-centric software for evolutionary analysis of DNA and protein sequences, Brief. Bioinform., 2008, vol. 9, pp. 299–306.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  45. Dickman, M.B. and Yarden, O., Serine/threonine protein kinases and phosphatases in filamentous fungi, Fungal Genet. Biol., 1999, vol. 26, no. 2, pp. 99–117.

    Article  CAS  PubMed  Google Scholar 

  46. Wang, W.Q., Sun, J.P., and Zhang, Z.Y., An overview of the protein tyrosine phosphatase superfamily, Curr. Top. Med. Chem., 2003, vol. 3, no. 7, pp. 739–748.

    Article  CAS  PubMed  Google Scholar 

  47. Zhang, Z.Y., Protein tyrosine phosphatases: structure and function, substrate specificity, and inhibitor development, Annu. Rev. Pharmacol. Toxicol., 2002, vol. 42, pp. 209–234.

    Article  CAS  PubMed  Google Scholar 

  48. Zhang, M., Liu, J., Kim, Y., et al., Structural and functional analysis of the phosphoryl transfer reaction mediated by the human small C-terminal domain phosphatase, Scp1, Protein Sci., 2010, vol. 19, no. 5, pp. 974–986.

    CAS  PubMed Central  PubMed  Google Scholar 

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Authors and Affiliations

  1. Institute of Food Biotechnology and Genomics, Osipovskogo str. 2A, Kyiv, 04123, Ukraine

    D. A. Samofalova, P. A. Karpov & Ya. B. Blume

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  1. D. A. Samofalova
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  2. P. A. Karpov
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Correspondence to D. A. Samofalova.

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Original Russian Text © D.A. Samofalova, P.A. Karpov, Ya.B. Blume, 2015, published in Tsitologiya i Genetika, 2015, Vol. 49, No. 4, pp. 3–10.

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Samofalova, D.A., Karpov, P.A. & Blume, Y.B. Bioinformatic comparison of human and higher plant phosphatomes. Cytol. Genet. 49, 207–219 (2015). https://doi.org/10.3103/S0095452715040088

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