Functional genomics of protein kinases in plants

Briefings in Functional Genomics and Proteomics

Volumn 3, Issue 4, 2005, Pages 362-371

  Chevalier, David ^a   Walker, John C ^a  

^a UNIVERSITY OF MISSOURI   (United States)

Author keywords

Arabidopsis; Functional genomics; Plant; Protein kinase; Protein phosphorylation; Signal transduction

Indexed keywords

CYTOKININ; EPIDERMAL GROWTH FACTOR; MITOGEN ACTIVATED PROTEIN KINASE; MITOGEN ACTIVATED PROTEIN KINASE 1; MITOGEN ACTIVATED PROTEIN KINASE 3; PHOSPHOENOLPYRUVATE CARBOXYLASE; PROTEIN HISTIDINE KINASE; PROTEIN KINASE; PROTEIN KINASE (CALCIUM,CALMODULIN); PROTEIN SERINE THREONINE KINASE; PYRUVATE KINASE;

ARABIDOPSIS; ARTICLE; CELL DIVISION; CELLULAR DISTRIBUTION; FUNCTIONAL GENOMICS; GENE MUTATION; GENE SEQUENCE; GENOME ANALYSIS; IMMUNOHISTOCHEMISTRY; IN SITU HYBRIDIZATION; NONHUMAN; PLANT GENETICS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; STRESS;

ARABIDOPSIS; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; GENOMICS; MAP KINASE SIGNALING SYSTEM; MODELS, BIOLOGICAL; PLANT PROTEINS; PROTEIN KINASES; RECEPTORS, CELL SURFACE;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 16344382561     PISSN: 14739550     EISSN: None     Source Type: Journal    
DOI: 10.1093/bfgp/3.4.362     Document Type: Article

References (57)

1. Arabidopsis Genome Initiative. (2000), 'Analysis of the genome sequence of the flowering plant Arabidopsis thaliana', Nature Vol. 408, pp. 796-815.
2. Yu, J., Hu, S., Wang, J. et al. (2002), 'A draft sequence of the rice genome (Oryza sativa L. ssp. indica)', Science, Vol. 296, pp. 79-92.
3. Goff, S. A., Ricke, D., Lan, T. H. et al. (2002), 'A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)', Science, Vol. 296, pp. 92-100.
4. Shiu, S. H. and Bleecker, A. B. (2001), 'Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases', Proc. Natl. Acad. Sci. USA, Vol. 98, pp. 10763-10768.
5. Tchieu, J. H., Fana, F., Fink, J. L. et al. (2003), 'The PlantsP and PlantsT Functional Genomics Databases', Nucleic Acids Res., Vol. 31, pp. 342-344.
6. Gribskov, M., Fana, F., Harper, J. et al. (2001), 'PlantsP: A functional genomics database for plant phosphorylation', Nucleic Acids Res., Vol. 29, pp. 111-113.
7. Wang, D., Harper, J. F. and Gribskov, M. (2003), 'Systematic trans-genomic comparison of protein kinases between Arabidopsis and Saccharomyces cerevisiae', Plant Physiol., Vol. 132, pp. 2152-2165.
8. Garcia-Hernandez, M., Berardini, T. Z., Chen, G. et al. (2002), 'TAIR: A resource for integrated Arabidopsis data', Funct. Integr. Genomics, Vol. 2, pp. 239-253.
9. Rhee, S. Y., Beavis, W., Berardini, T. Z. et al. (2003), 'The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community', Nucleic Acids Res., Vol. 31, pp. 224-228.
10. Alonso, J. M., Stepanova, A. N., Leisse, T. J. et al. (2003), 'Genome-wide insertional mutagenesis of Arabidopsis thaliana', Science, Vol. 301, pp. 653-657.
11. Sussman, M. R., Amasino, R. M., Young, J. C. et al. (2000), 'The Arabidopsis knockout facility at the University of Wisconsin-Madison', Plant Physiol., Vol. 124, pp. 1465-1467.
12. Sessions, A., Burke, E., Presting, G. et al. (2002), 'A high-throughput Arabidopsis reverse genetics system', Plant Cell Vol. 14, pp. 2985-2994.
13. Till, B. J., Colbert, T., Tompa, R. et al. (2003), 'High-throughput TILLING for functional genomics', Methods Mol. Biol. Vol. 236, pp. 205-220.
14. Henikoff, S., Till, B. J. and Comai, L. (2004), 'TILLING. Traditional mutagenesis meets functional genomics', Plant Physiol., Vol. 135, pp. 630-636.
15. Till, B. J., Reynolds, S. H., Greene, E. A. et al. (2003), 'Large-scale discovery of induced point mutations with high-throughput TILLING', Genome Res., Vol. 13, pp. 524-530.
16. Johnson, L. N., Noble, M. E. and Owen, D. J. (1996), 'Active and inactive protein kinases: Structural basis for regulation', Cell Vol. 85, pp. 149-158.
17. Nuhse, T. S., Stensballe, A., Jensen, O. N. and Peck, S. C. (2003), 'Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry', Mol. Cell. Proteomics, Vol. 2, pp. 1234-1243.
18. Nuhse, T. S., Stensballe, A., Jensen, O. N. and Peck, S. C. (2004), 'Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database', Plant Cell, Vol. 16, pp. 2394-2405.
19. Champion, A., Kreis, M., Mockaitis, K. et al. (2004), 'Arabidopsis kinome: After the casting', Funct. Integr. Genomics Vol. 4, pp. 163-187.
20. Asai, T., Tena, G., Plotnikova, J. et al. (2002), 'MAP kinase signalling cascade in Arabidopsis innate immunity', Nature, Vol. 415, pp. 977-983.
21. Soyano, T., Nishihama, R., Morikiyo, K. et al. (2003), 'NQK1/NtMEK1 is a MAPKK that acts in the NPK1 MAPKKK-mediated MAPK cascade and is required for plant cytokinesis', Genes Dev., Vol. 17, pp. 1055-1067.
22. Krysan, P. J., Jester, P. J., Gottwald, J. R. and Sussman, M. R. (2002), 'An Arabidopsis mitogen-activated protein kinase kinase kinase gene family encodes essential positive regulators of cytokinesis', Plant Cell, Vol. 14, pp. 1109-1120.
23. Hrabak, E. M., Chan, C. W., Gribskov, M. et al. (2003), 'The Arabidopsis CDPK-SnRK superfamily of protein kinases', Plant Physiol., Vol. 132, pp. 666-680.
24. Hanks, S. K. and Hunter, T. (1995), 'Protein kinases 6. The eukaryotic protein kinase superfamily: Kinase (catalytic) domain structure and classification', FASEB J., Vol. 9, pp. 576-596.
25. Hardie, D. G. (1999), 'Plant protein serine threonine kinases: Classification and functions', Annu. Rev. Plant Physiol., Vol. 50, pp. 97-131.
26. Hardie, D. G. (2000), 'Plant protein-serine/threonine kinases: 'Classification into subfamilies and overview of function', Adv. Bot. Res., Vol. 32, pp. 1-44.
27. Zhang, X. S. and Choi, J. H. (2001), 'Molecular evolution of calmodulin-like domain protein kinases (CDPKs) in plants and protists', J. Mol. Evol., Vol. 53, pp. 214-224.
28. Cheng, S. H., Willmann, M. R., Chen, H. C. and Sheen, J. (2002), 'Calcium signaling through protein kinases. The Arabidopsis calcium-dependent protein kinase gene family', Plant Physiol., Vol. 129, pp. 469-485.
29. Dammann, C., Ichida, A., Hong, B. et al. (2003), 'Subcellular targeting of nine calcium-dependent protein kinase isoforms from Arabidopsis', Plant Physiol., Vol. 132, pp. 1840-1848.
30. Charrier, B., Champion, A., Henry, Y. and Kreis, M. (2002), 'Expression profiling of the whole Arabidopsis shaggy-like kinase multigene family by real-time reverse transcriptase-polymerase chain reaction', Plant Physiol., Vol. 130, pp. 577-590.
31. Li, J., Nam, K. H., Vafeados, D. and Chory, J. (2001), 'BIN2, a new brassinosteroid-insensitive locus in Arabidopsis', Plant Physiol., Vol. 127, pp. 14-22.
32. Li, J. and Nam, K. H. (2002), 'Regulation of brassinosteroid signaling by a GSK3/SHAGGY-like kinase', Science, Vol. 295, pp. 1299-1301.
33. Perez-Perez, J. M., Ponce, M. R. and Micol, J. L. (2002), 'The UCU1 Arabidopsis gene encodes a SHAGGY/GSK3-like kinase required for cell expansion along the proximodistal axis', Dev. Biol. Vol. 242, pp. 161-173.
34. Piao, H. L., Lim, J. H., Kim, S. J. et al. (2001), 'Constitutive over-expression of AtGSK1 induces NaCl stress responses in the absence of NaCl stress and results in enhanced NaCl tolerance in Arabidopsis', Plant J., Vol. 27, pp. 305-314.
35. Dornelas, M. C., Wittich, P., von Recklinghausen, I. et al. (1999), 'Characterization of three novel members of the Arabidopsis SHAGGY-related protein kinase (ASK) multigene family', Plant Mol. Biol., Vol. 39, pp. 137-147.
36. Torii, K. U., Mitsukawa, N., Oosumi, T. et al. (1996), 'The Arabidopsis ERECTA gene encodes a putative receptor protein kinase with extracellular leucine-rich repeats', Plant Cell, Vol. 8, pp. 735-746.
37. Shpak, E. D., Lakeman, M. B. and Torii, K. U. (2003), 'Dominant-negative receptor uncovers redundancy in the Arabidopsis ERECTA leucine-rich repeat receptor-like kinase signaling pathway that regulates organ shape', Plant Cell, Vol. 15, pp. 1095-1110.
38. Shpak, E. D., Berthiaume, C. T., Hill, E. J. and Torii, K. U. (2004), 'Synergistic interaction of three ERECTA-family receptor-like kinases controls Arabidopsis organ growth and flower development by promoting cell proliferation', Development, Vol. 131, pp. 1491-1501.
39. Verica, J. A. and He, Z. H. (2002), 'The cell wall-associated kinase (WAK) and WAK-like kinase gene family', Plant Physiol., Vol. 129, pp. 455-459.
40. Verica, J. A., Chae, L., Tong, H. et al. (2003), 'Tissue-specific and developmentally regulated expression of a cluster of tandemly arrayed cell wall-associated kinase-like kinase genes in Arabidopsis', Plant Physiol., Vol. 133, pp. 1732-1746.
41. He, Z. H., Fujiki, M. and Kohorn, B. D. (1996), 'A cell wall-associated, receptor-like protein kinase', J. Biol. Chem., Vol. 271, pp. 19789-19793.
42. Wagner, T. A. and Kohorn, B. D. (2001), 'Wall-associated kinases are expressed throughout plant development and are required for cell expansion', Plant Cell, Vol. 13, pp. 303-318.
43. Lally, D., Ingmire, P., Tong, H. Y. and He, Z. H. (2001), 'Antisense expression of a cell wall-associated protein kinase, WAK4, inhibits cell elongation and alters morphology', Plant Cell, Vol. 13, pp. 1317-1331.
44. Lohrmann, J. and Harter, K. (2002), 'Plant two-component signaling systems and the role of response regulators', Plant Physiol. Vol. 128, pp. 363-369.
45. Grefen, C. and Harter, K. (2004), 'Plant two-component systems: Principles, functions, complexity and cross talk', Planta, Vol. 219, pp. 733-742.
46. Urao, T., Yakubov, B., Satoh, R. et al. (1999), 'A transmembrane hybrid-type histichne kinase in Arabidopsis functions as an osmosensor', Plant Cell, Vol. 11, pp. 1743-1754.
47. Hejatko, J., Pernisova, M., Eneva, T. et al. (2003), 'The putative sensor histidine kinase CKI1 is involved in female gametophyte development in Arabidopsis', Mol. Genet. Genomics, Vol. 269, pp. 443-453.
48. Pischke, M. S., Jones, L. G., Otsuga, D. et al. (2002), 'An Arabidopsis histidine kinase is essential for megagametogenesis', Proc. Natl. Acad. Sci. USA, Vol. 99, pp. 15800-15805.
49. Guo, H. and Ecker, J. R. (2004), 'The ethylene signaling pathway: New insights', Curr. Opin. Plant Biol., Vol. 7, pp. 40-49.
50. Bleecker, A. B. and Kende, H. (2000), 'Ethylene: A gaseous signal molecule in plants', Annu. Rev. Cell Dev. Biol., Vol. 16, pp. 1-18.
51. Chang, C. and Stadler, R. (2001), 'Ethylene hormone receptor action in Arabidopsis', Bioessays, Vol. 23, pp. 619-627.
52. Hua, J. and Meyerowitz, E. M. (1998), 'Ethylene responses are negatively regulated by a receptor gene family in Arabidopsis thaliana', Cell, Vol. 94, pp. 261-271.
53. Wang, W., Hall, A. E., O'Malley, R. and Bleecker, A. B. (2003), 'Canonical histidine kinase activity of the transmitter domain of the ETR1 ethylene receptor from Arabidopsis is not required for signal transmission', Proc. Natl. Acad. Sci. USA, Vol. 100, pp. 352-357.
54. Zhao, X. C., Qu, X., Mathews, D. E. and Schaller, G. E. (2002), 'Effect of ethylene pathway mutations upon expression of the ethylene receptor ETR1 from Arabidopsis', Plant Physiol., Vol. 130, pp. 1983-1991.
55. Gamble, R. L., Coonfield, M. L. and Schaller, G. E. (1998), 'Histidine kinase activity of the ETR1 ethylene receptor from Arabidopsis', Proc. Natl. Acad. Sci. USA, Vol. 95, pp. 7825-7829.
56. Inoue, T., Higuchi, M., Hashimoto, Y. et al. (2001), 'Identification of CRE1 as a cytokinin receptor from Arabidopsis', Nature, Vol. 409, pp. 1060-1063.
57. Higuchi, M., Pischke, M. S., Mahonen, A. P. et al. (2004), 'In planta functions of the Arabidopsis cytokinin receptor family', Proc. Natl. Acad. Sci. USA, Vol. 101, pp. 8821-8826.