Computational identification and phylogenetic analysis of the MAPK gene family in Oryza sativa

Plant Physiology and Biochemistry - Tập 45 - Trang 6-14 - 2007
Qingpo Liu1, Qingzhong Xue1
1Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, No 268, Kaixuan Road, Hangzhou, Zhejiang 310029, China

Tài liệu tham khảo

Agrawal, 2003, Rice MAPKs, Biochem. Biophy. Res. Commun., 302, 171, 10.1016/S0006-291X(03)00174-8 2000, Arabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature, 408, 796, 10.1038/35048692 Biondi, 2003, Signalling specificity of Ser/Thr protein kinases through docking-site-mediated interactions, Biochem. J., 372, 1, 10.1042/bj20021641 Blanc, 2003, A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome, Genome Res., 13, 137, 10.1101/gr.751803 Bowers, 2003, Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events, Nature, 422, 433, 10.1038/nature01521 Chang, 2002, Crystal structures of MAP kinases p38 complexed to the docking sites on its nuclear substrate MEF2A and activator MKK3b, Mol. Cell, 9, 1241, 10.1016/S1097-2765(02)00525-7 Decroocq-Ferrant, 1995, A homologue of the MAP/ERK family of protein kinase genes is expressed in vegetative and in female reproductive organs of Petunia hybrida, Plant Mol. Biol., 27, 339, 10.1007/BF00020188 Fu, 2002, Transcriptional regulation of a rice mitogen-activated protein kinase gene, OsMAPK4, in response to environmental stresses, Plant Cell Physiol., 43, 958, 10.1093/pcp/pcf111 Gustin, 1998, MAP kinase pathways in the yeast Saccharomyces cerevisiae, Micro-biol. Mol. Biol. Rev., 62, 1264, 10.1128/MMBR.62.4.1264-1300.1998 Guyot, 2004, Ancestral genome duplication in rice, Genome, 47, 610, 10.1139/g04-016 He, 1999, BWMK1, a novel MAP kinase induced by fungal infection and mechanical wounding in rice, Mol. Plant-Microb. Interact., 12, 1064, 10.1094/MPMI.1999.12.12.1064 Holland, 1999, Protein modification: docking sites for kinases, Curr. Biol., 9, 329, 10.1016/S0960-9822(99)80205-X Huang, 2002, Expression of Oryza sativa MAP kinase gene is developmentally regulated and stress-responsive, Physiol. Plant., 114, 572, 10.1034/j.1399-3054.2002.1140410.x Huttly, 1995, Gibberellin-regulated expression in oat aleurone cells of two kinases that show homology to MAP kinase and a ribosomal protein kinase, Plant Mol. Biol., 27, 1043, 10.1007/BF00037031 Ichimura, 2002, Mitogen-activated protein kinase cascades in plants: a new nomenclature, Trends Plant Sci., 7, 301, 10.1016/S1360-1385(02)02302-6 International Rice Genome Sequencing Project, 2005, The map-based sequence of the rice genome, Nature, 436, 793, 10.1038/nature03895 Jonak, 1999, MAP kinases in plant signal transduction, Cell Mol. Life Sci., 55, 204, 10.1007/s000180050285 Knetsch, 1996, Abscisic acid induces mitogen-activated protein kinase activation in barley aleuron protoplasts, Plant Cell, 8, 1061, 10.1105/tpc.8.6.1061 Lalle, 2005, ZmMPK6, a novel maize MAP kinase that interacts with 14-3-3 proteins, Plant Mol. Biol., 59, 713, 10.1007/s11103-005-0862-x Lieberherr, 2005, A sphingolipid elicitor-inducible mitogen-activated protein kinase is regulated by the small GTPase OsRac1 and heterotrimeric G-protein in rice, Plant Physiol., 138, 1644, 10.1104/pp.104.057414 Marenda, 2006, MAP kinase subcellular localization controls both pattern and proliferation in the developing Drosophila wing, Development, 133, 43, 10.1242/dev.02168 Mizoguchi, 1993, ATMPKs: a gene family of plant MAP kinases in Arabidopsis thaliana, FEBS Lett., 336, 440, 10.1016/0014-5793(93)80852-L Mizoguchi, 1997, Environmental stress response in plants: the role of mitogen-activated protein kinase, Trends Biotechnol., 15, 15, 10.1016/S0167-7799(96)10074-3 Ohno, 1970 Schaeffer, 1999, Mitogen-activated protein kinases: specific messages from ubiquitous messengers, Mol. Cell Biol., 19, 2435, 10.1128/MCB.19.4.2435 Schauser, 2005, Evolution of NIN-like proteins in Arabidopsis, rice and Lotus japonicus, J. Mol. Evol., 60, 229, 10.1007/s00239-004-0144-2 Schmidt, 2002, TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartet and parallel computing, Bioinformatics, 18, 502, 10.1093/bioinformatics/18.3.502 Sharrocks, 2000, Docking domains and substrate-specificity determination for MAP kinases, Trends Biochem. Sci., 25, 448, 10.1016/S0968-0004(00)01627-3 Song, 2002, OsBIMK1, a rice MAP kinase gene involved in disease resistance responses, Planta, 215, 997, 10.1007/s00425-002-0794-5 Takezawa, 1999, Elicitor- and A23187-induced expression of WCK-1, a gene encoding mitogen-activated protein kinase in wheat, Plant Mol. Biol., 40, 921, 10.1023/A:1006263607135 Tanoue, 2000, A conserved docking motif in MAP kinases common to substrates, activators and regulators, Nat. Cell Biol., 2, 110, 10.1038/35000065 Tanoue, 2001, Identification of a docking groove on ERK and p38 MAP kinases that regulates the specificity of docking interactions, EMBO J., 20, 466, 10.1093/emboj/20.3.466 Wang, 2005, Duplication and DNA segmental loss in the rice genome: implications for diploidization, New Phytol., 165, 937, 10.1111/j.1469-8137.2004.01293.x Wilson, 1995, Molecular cloning, functional expression in Escherichia coli, and characterization of multiple mitogen-activated protein kinases from tobacco, Eur. J. Biochem., 233, 249, 10.1111/j.1432-1033.1995.249_1.x Wilson, 1996, Crystal structure of p38 mitogen-activated protein kinase, J. Biol. Chem., 271, 27696, 10.1074/jbc.271.44.27696 Wu, 2005, The WRKY family of transcription factors in rice and Arabidopsis and their origins, DNA Res., 12, 9, 10.1093/dnares/12.1.9 Yu, 2005, The genomes of Oryza sativa: a history of duplications, PLOS Biol., 3, 266, 10.1371/journal.pbio.0030038 Zhang, 2005, Two ancient rounds of polyploidy in rice genome, J. Zhejiang Univ. SCI., 6B, 87, 10.1631/jzus.2005.B0087 Zhang, 2006, Molecular cloning and characterization of a novel MAP kinase gene in Chorispora bungeana, Plant Physiol. Biochem., 44, 78, 10.1016/j.plaphy.2006.01.001