1,345
Views
16
CrossRef citations to date
0
Altmetric
Research Paper

Evolutionary history of mitogen-activated protein kinase (MAPK) genes in Lotus, Medicago, and Phaseolus

, , , &
Article: e27189 | Received 24 Sep 2013, Accepted 13 Nov 2013, Published online: 02 Dec 2013

References

  • Ichimura K, Shinozaki K, Tena G, Sheen J, Henry Y, Champion A, Kreis M, Zhang SQ, Hirt H, Wilson C, et al. MAPK Group. Mitogen-activated protein kinase cascades in plants: a new nomenclature. Trends Plant Sci 2002; 7:301 - 8; http://dx.doi.org/10.1016/S1360-1385(02)02302-6; PMID: 12119167
  • Jonak C, Okrész L, Bögre L, Hirt H. Complexity, cross talk and integration of plant MAP kinase signalling. Curr Opin Plant Biol 2002; 5:415 - 24; http://dx.doi.org/10.1016/S1369-5266(02)00285-6; PMID: 12183180
  • Tena G, Asai T, Chiu WL, Sheen J. Plant mitogen-activated protein kinase signaling cascades. Curr Opin Plant Biol 2001; 4:392 - 400; http://dx.doi.org/10.1016/S1369-5266(00)00191-6; PMID: 11597496
  • Hamel LP, Nicole MC, Sritubtim S, Morency MJ, Ellis M, Ehlting J, Beaudoin N, Barbazuk B, Klessig D, Lee J, et al. Ancient signals: comparative genomics of plant MAPK and MAPKK gene families. Trends Plant Sci 2006; 11:192 - 8; http://dx.doi.org/10.1016/j.tplants.2006.02.007; PMID: 16537113
  • Chen L, Hu W, Tan S, Wang M, Ma Z, Zhou S, Deng X, Zhang Y, Huang C, Yang G, et al. Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon.. PLoS ONE 2012; 7:e46744; http://dx.doi.org/10.1371/journal.pone.0046744; PMID: 23082129
  • Neupane A, Nepal MP, Piya S, Subramanian S, Rohila JS, Reese RN, Benson BV. Identification, nomenclature, and evolutionary relationships of mitogen-activated protein kinase (MAPK) genes in soybean. Evol Bioinform Online 2013; 9:363 - 86; PMID: 24137047
  • Asai T, Tena G, Plotnikova J, Willmann MR, Chiu WL, Gomez-Gomez L, Boller T, Ausubel FM, Sheen J. MAP kinase signalling cascade in Arabidopsis innate immunity. Nature 2002; 415:977 - 83; http://dx.doi.org/10.1038/415977a; PMID: 11875555
  • Miya A, Albert P, Shinya T, Desaki Y, Ichimura K, Shirasu K, Narusaka Y, Kawakami N, Kaku H, Shibuya N. CERK1, a LysM receptor kinase, is essential for chitin elicitor signaling in Arabidopsis.. Proc Natl Acad Sci USA 2007; 104:19613 - 8; http://dx.doi.org/10.1073/pnas.0705147104; PMID: 18042724
  • Ren D, Liu Y, Yang KY, Han L, Mao G, Glazebrook J, Zhang S. A fungal-responsive MAPK cascade regulates phytoalexin biosynthesis in Arabidopsis.. Proc Natl Acad Sci USA 2008; 105:5638 - 43; http://dx.doi.org/10.1073/pnas.0711301105; PMID: 18378893
  • Ren D, Yang H, Zhang S. Cell death mediated by MAPK is associated with hydrogen peroxide production in Arabidopsis.. J Biol Chem 2002; 277:559 - 65; http://dx.doi.org/10.1074/jbc.M109495200; PMID: 11687590
  • Kishi-Kaboshi M, Okada K, Kurimoto L, Murakami S, Umezawa T, Shibuya N, Yamane H, Miyao A, Takatsuji H, Takahashi A, et al. A rice fungal MAMP-responsive MAPK cascade regulates metabolic flow to antimicrobial metabolite synthesis. Plant J 2010; 63:599 - 612; http://dx.doi.org/10.1111/j.1365-313X.2010.04264.x; PMID: 20525005
  • Ding X, Richter T, Chen M, Fujii H, Seo YS, Xie M, Zheng X, Kanrar S, Stevenson RA, Dardick C, et al. A rice kinase-protein interaction map. Plant Physiol 2009; 149:1478 - 92; http://dx.doi.org/10.1104/pp.108.128298; PMID: 19109415
  • Jung KH, Cao P, Seo YS, Dardick C, Ronald PC. The Rice Kinase Phylogenomics Database: a guide for systematic analysis of the rice kinase super-family. Trends Plant Sci 2010; 15:595 - 9; http://dx.doi.org/10.1016/j.tplants.2010.08.004; PMID: 20832349
  • Krisak L, Strich R, Winters RS, Hall JP, Mallory MJ, Kreitzer D, Tuan RS, Winter E. SMK1, a developmentally regulated MAP kinase, is required for spore wall assembly in Saccharomyces cerevisiae.. Genes Dev 1994; 8:2151 - 61; http://dx.doi.org/10.1101/gad.8.18.2151; PMID: 7958885
  • Wagner M, Briza P, Pierce M, Winter E. Distinct steps in yeast spore morphogenesis require distinct SMK1 MAP kinase thresholds. Genetics 1999; 151:1327 - 40; PMID: 10101160
  • Breitkreutz A, Boucher L, Tyers M. MAPK specificity in the yeast pheromone response independent of transcriptional activation. Curr Biol 2001; 11:1266 - 71; http://dx.doi.org/10.1016/S0960-9822(01)00370-0; PMID: 11525741
  • Elion EA, Satterberg B, Kranz JE. FUS3 phosphorylates multiple components of the mating signal transduction cascade: evidence for STE12 and FAR1. Mol Biol Cell 1993; 4:495 - 510; http://dx.doi.org/10.1091/mbc.4.5.495; PMID: 8334305
  • Herskowitz I. MAP kinase pathways in yeast: for mating and more. Cell 1995; 80:187 - 97; http://dx.doi.org/10.1016/0092-8674(95)90402-6; PMID: 7834739
  • Chang F, Herskowitz I. Identification of a gene necessary for cell cycle arrest by a negative growth factor of yeast: FAR1 is an inhibitor of a G1 cyclin, CLN2. Cell 1990; 63:999 - 1011; http://dx.doi.org/10.1016/0092-8674(90)90503-7; PMID: 2147873
  • Chen RE, Thorner J. Function and regulation in MAPK signaling pathways: lessons learned from the yeast Saccharomyces cerevisiae. Biochim Biophys Acta 2007; 1773:1311-40;PMID: 17604854
  • Madhani HD, Fink GR. The riddle of MAP kinase signaling specificity. Trends Genet 1998; 14:151 - 5; http://dx.doi.org/10.1016/S0168-9525(98)01425-5; PMID: 9594663
  • Truckses DM, Garrenton LS, Thorner J. Jekyll and Hyde in the microbial world. Science 2004; 306:1509 - 11; http://dx.doi.org/10.1126/science.1104677; PMID: 15567850
  • Sabbagh W Jr., Flatauer LJ, Bardwell AJ, Bardwell L. Specificity of MAP kinase signaling in yeast differentiation involves transient versus sustained MAPK activation. Mol Cell 2001; 8:683 - 91; http://dx.doi.org/10.1016/S1097-2765(01)00322-7; PMID: 11583629
  • Levin DE. Cell wall integrity signaling in Saccharomyces cerevisiae.. Microbiol Mol Biol Rev 2005; 69:262 - 91; http://dx.doi.org/10.1128/MMBR.69.2.262-291.2005; PMID: 15944456
  • Dihazi H, Kessler R, Eschrich K. High osmolarity glycerol (HOG) pathway-induced phosphorylation and activation of 6-phosphofructo-2-kinase are essential for glycerol accumulation and yeast cell proliferation under hyperosmotic stress. J Biol Chem 2004; 279:23961 - 8; http://dx.doi.org/10.1074/jbc.M312974200; PMID: 15037628
  • Zhou Z, Gartner A, Cade R, Ammerer G, Errede B. Pheromone-induced signal transduction in Saccharomyces cerevisiae requires the sequential function of three protein kinases. Mol Cell Biol 1993; 13:2069 - 80; PMID: 8455599
  • Grimsrud PA, den Os D, Wenger CD, Swaney DL, Schwartz D, Sussman MR, Ané JM, Coon JJ. Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes. Plant Physiol 2010; 152:19 - 28; http://dx.doi.org/10.1104/pp.109.149625; PMID: 19923235
  • Khan GA, Declerck M, Sorin C, Hartmann C, Crespi M, Lelandais-Brière C. MicroRNAs as regulators of root development and architecture. Plant Mol Biol 2011; 77:47 - 58; http://dx.doi.org/10.1007/s11103-011-9793-x; PMID: 21607657
  • Schoenbeck MA, Samac DA, Fedorova M, Gregerson RG, Gantt JS, Vance CP. The alfalfa (Medicago sativa) TDY1 gene encodes a mitogen-activated protein kinase homolog. Mol Plant Microbe Interact 1999; 12:882 - 93; http://dx.doi.org/10.1094/MPMI.1999.12.10.882; PMID: 10517028
  • Liu JZ, Horstman HD, Braun E, Graham MA, Zhang C, Navarre D, Qiu WL, Lee Y, Nettleton D, Hill JH, et al. Soybean homologs of MPK4 negatively regulate defense responses and positively regulate growth and development. Plant Physiol 2011; 157:1363 - 78; http://dx.doi.org/10.1104/pp.111.185686; PMID: 21878550
  • Fernandez-Pascual M, Lucas MM, de Felipe MR, Boscá L, Hirt H, Golvano MP. Involvement of mitogen-activated protein kinases in the symbiosis Bradyrhizobium-Lupinus.. J Exp Bot 2006; 57:2735 - 42; http://dx.doi.org/10.1093/jxb/erl038; PMID: 16868044
  • Cooper JE. Early interactions between legumes and rhizobia: disclosing complexity in a molecular dialogue. J Appl Microbiol 2007; 103:1355 - 65; http://dx.doi.org/10.1111/j.1365-2672.2007.03366.x; PMID: 17953546
  • Parniske M. Intracellular accommodation of microbes by plants: a common developmental program for symbiosis and disease?. Curr Opin Plant Biol 2000; 3:320 - 8; http://dx.doi.org/10.1016/S1369-5266(00)00088-1; PMID: 10873847
  • Herouart D, Baudouin E, Frendo P, Harrison J, Santos R, Jamet A, Van de Sype G, Touati D, Puppo A. Reactive oxygen species, nitric oxide and glutathione: a key role in the establishment of the legume-Rhizobium symbiosis?. Plant Physiol Biochem 2002; 40:619 - 24; http://dx.doi.org/10.1016/S0981-9428(02)01415-8
  • Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, et al. Genome sequence of the palaeopolyploid soybean. Nature 2010; 463:178 - 83; http://dx.doi.org/10.1038/nature08670; PMID: 20075913
  • Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M, Sasamoto S, Watanabe A, Ono A, Kawashima K, et al. Genome structure of the legume, Lotus japonicus.. DNA Res 2008; 15:227 - 39; http://dx.doi.org/10.1093/dnares/dsn008; PMID: 18511435
  • Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, Roe BA, Tabata S. Sequencing the genespaces of Medicago truncatula and Lotus japonicus.. Plant Physiol 2005; 137:1174 - 81; http://dx.doi.org/10.1104/pp.104.057034; PMID: 15824279
  • Gepts P. Phaseolus vulgaris (Beans). In: Sydney B, Jeffrey HM, eds. Encyclopedia of Genetics. New York: Academic Press, 2001:1444-5.
  • Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science 2000; 290:1151 - 5; http://dx.doi.org/10.1126/science.290.5494.1151; PMID: 11073452
  • Zhang JZ. Evolution by gene duplication: an update. Trends Ecol Evol 2003; 18:292 - 8; http://dx.doi.org/10.1016/S0169-5347(03)00033-8
  • Dufresne A, Garczarek L, Partensky F. Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol 2005; 6:R14; http://dx.doi.org/10.1186/gb-2005-6-2-r14; PMID: 15693943
  • Abada EA, Sung H, Dwivedi M, Park B-J, Lee S-K, Ahnn J. C. elegans behavior of preference choice on bacterial food. Mol Cells 2009; 28:209 - 13; http://dx.doi.org/10.1007/s10059-009-0124-x; PMID: 19756391
  • Coolon JD, Jones KL, Todd TC, Carr BC, Herman MA. Caenorhabditis elegans genomic response to soil bacteria predicts environment-specific genetic effects on life history traits. PLoS Genet 2009; 5:e1000503; http://dx.doi.org/10.1371/journal.pgen.1000503; PMID: 19503598
  • Horiuchi J, Prithiviraj B, Bais HP, Kimball BA, Vivanco JM. Soil nematodes mediate positive interactions between legume plants and rhizobium bacteria. Planta 2005; 222:848 - 57; http://dx.doi.org/10.1007/s00425-005-0025-y; PMID: 16025342
  • Schranz ME, Mitchell-Olds T. Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. Plant Cell 2006; 18:1152 - 65; http://dx.doi.org/10.1105/tpc.106.041111; PMID: 16617098
  • Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 1999; 151:1531 - 45; PMID: 10101175
  • Ohno S. Evolution by gene duplication. Berlin, New York: Springer-Verlag, 1970.
  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. Clustal W and clustal X version 2.0. Bioinformatics 2007; 23:2947 - 8; http://dx.doi.org/10.1093/bioinformatics/btm404; PMID: 17846036
  • Bailey TL, Elkan C. The value of prior knowledge in discovering motifs with MEME. Proceedings / International Conference on Intelligent Systems for Molecular Biology; ISMB International Conference on Intelligent Systems for Molecular Biology 1995; 3:21-9.
  • Petsko GA, Ringe D. Protein structure and function. Oxford: New Science Press, 2004.
  • Rost B. Twilight zone of protein sequence alignments. Protein Eng 1999; 12:85 - 94; http://dx.doi.org/10.1093/protein/12.2.85; PMID: 10195279
  • Lesk AM. Introduction to protein architecture: the structural biology of proteins. Oxford, New York: Oxford University Press, 2001.
  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731 - 9; http://dx.doi.org/10.1093/molbev/msr121; PMID: 21546353
  • Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783 - 91; http://dx.doi.org/10.2307/2408678
  • Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Heled J, Kearse M, Moir R, Stones-Havas S, Sturrock S, et al. Geneious v5.5, available from http://www.geneious.com. 2011.
  • Rambaldi D, Ciccarelli FD. FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci. Bioinformatics 2009; 25:2281 - 2; http://dx.doi.org/10.1093/bioinformatics/btp381; PMID: 19542150
  • Severin AJ, Woody JL, Bolon YT, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, et al. RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol 2010; 10:160; http://dx.doi.org/10.1186/1471-2229-10-160; PMID: 20687943
  • Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002; 30:207 - 10; http://dx.doi.org/10.1093/nar/30.1.207; PMID: 11752295
  • Nakano M, Nobuta K, Vemaraju K, Tej SS, Skogen JW, Meyers BC. Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res 2006; 34:D731 - 5; http://dx.doi.org/10.1093/nar/gkj077; PMID: 16381968
  • Battke F, Symons S, Nieselt K. Mayday--integrative analytics for expression data. BMC Bioinformatics 2010; 11:121; http://dx.doi.org/10.1186/1471-2105-11-121; PMID: 20214778

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.