Genome-Wide Identification and Analysis of MAPK and MAPKK Gene Families in Brachypodium distachyon

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Chen, Lihong ^a   Hu, Wei ^a   Tan, Shenglong ^a   Wang, Min ^a   Ma, Zhanbing ^a   Zhou, Shiyi ^a   Deng, Xiaomin ^a   Zhang, Yang ^a   Huang, Chao ^a   Yang, Guangxiao ^a   He, Guangyuan ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MITOGEN ACTIVATED PROTEIN KINASE; MITOGEN ACTIVATED PROTEIN KINASE KINASE; VEGETABLE PROTEIN;

ARABIDOPSIS; ARTICLE; BDMKK1 GENE; BDMKK10 1 GENE; BDMKK10 2 GENE; BDMKK10 3 GENE; BDMKK10 4 GENE; BDMKK10 5 GENE; BDMKK3 1 GENE; BDMKK3 2 GENE; BDMKK3 3 GENE; BDMKK4 GENE; BDMKK5 GENE; BDMKK6 GENE; BDMPK11 GENE; BDMPK14 GENE; BDMPK16 GENE; BDMPK17 GENE; BDMPK20 1 GENE; BDMPK20 3 GENE; BDMPK20 4 GENE; BDMPK20 5 GENE; BDMPK21 1 GENE; BDMPK21 2 GENE; BDMPK3 GENE; BDMPK4 GENE; BDMPK6 GENE; BDMPK7 1 GENE; BDMPK7 2 GENE; BRACHYPODIUM; CONTROLLED STUDY; EXON; GENE ACTIVITY; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; INTRON; MAPK GENE; MAPKK GENE; MOLECULAR EVOLUTION; NONHUMAN; PLANT GENE; PROTEIN MOTIF; RICE; SIGNAL TRANSDUCTION; SPECIES DIFFERENTIATION; SYNTENY; AMINO ACID SEQUENCE; CHEMISTRY; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; LIGHT; METABOLISM; MOLECULAR GENETICS; MULTIGENE FAMILY; NOMENCLATURE; PHYLOGENY; PHYSIOLOGICAL STRESS; PLANT CHROMOSOME; PLANT GENOME; PROMOTER REGION; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE; RADIATION EXPOSURE; SEQUENCE ALIGNMENT; TEMPERATURE;

AMINO ACID SEQUENCE; ARABIDOPSIS; BRACHYPODIUM; CHROMOSOMES, PLANT; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; LIGHT; MITOGEN-ACTIVATED PROTEIN KINASE KINASES; MITOGEN-ACTIVATED PROTEIN KINASES; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; ORYZA SATIVA; PHYLOGENY; PLANT PROTEINS; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; STRESS, PHYSIOLOGICAL; SYNTENY; TEMPERATURE; TERMINOLOGY AS TOPIC;

EID: 84867640565     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0046744     Document Type: Article

References (56)

1. Romeis T, (2001) Protein kinases in the plant defence response. Curr Opin Plant Biol 4: 407-414.
2. Tena G, Asai T, Chiu WL, Sheen J, (2001) Plant mitogen-activated protein kinase signaling cascades. Curr Opin Plant Biol 4: 392-400.
3. Zhang S, Klessig DF, (2001) MAPK cascades in plant defense signaling. Trends Plant Sci 6: 520-527.
4. Pitzschke A, Schikora A, Hirt H, (2009) MAPK cascade signalling networks in plant defence. Curr Opin Plant Biol 12: 421-426.
5. Colcombet J, Hirt H, (2008) Arabidopsis MAPKs: a complex signalling network involved in multiple biological processes. Biochem J 413: 217-226.
6. Teige M, Scheikl E, Eulgem T, Doczi R, Ichimura K, et al. (2004) The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis. Mol Cell 15: 141-152.
7. Gao M, Liu J, Bi D, Zhang Z, Cheng F, et al. (2008) MEKK1, MKK1/MKK2 and MPK4 function together in a mitogen-activated protein kinase cascade to regulate innate immunity in plants. Cell Res 18: 1190-1198.
8. Qiu JL, Zhou L, Yun BW, Nielsen HB, Fiil BK, et al. (2008b) Arabidopsis mitogen-activated protein kinase kinases MKK1 and MKK2 have overlapping functions in defense signaling mediated by MEKK1, MPK4, and MKS1. Plant Physiol 148: 212-222.
9. Chen T, Zhu H, Ke D, Cai K, Wang C, et al. (2012) A MAP kinase kinase interacts with SymRK and regulates nodule organogenesis in Lotus japonicus. Plant Cell 24: 823-838.
10. Takahashi F, Yoshida R, Ichimura K, Mizoguchi T, Seo S, et al. (2007) The mitogen-activated protein kinase cascade MKK3-MPK6 is an important part of the jasmonate signal transduction pathway in Arabidopsis. Plant Cell 19: 805-818.
11. Asai T, Tena G, Plotnikova J, Willmann MR, Chiu WL, et al. (2002) MAP kinase signalling cascade in Arabidopsis innate immunity. Nature 415: 977-983.
12. Wang H, Ngwenyama N, Liu Y, Walker JC, Zhang S, (2007) Stomatal development and patterning are regulated by environmentally responsive mitogen-activated protein kinases in Arabidopsis. Plant Cell 19: 63-73.
13. Lee SK, Kim BG, Kwon TR, Jeong MJ, Park SR, et al. (2011) Overexpression of the mitogen-activated protein kinase gene OsMAPK33 enhances sensitivity to salt stress in rice (Oryza sativa L.). J Biosci 36: 139-151.
14. Boudsocq M, Lauriere C, (2005) Osmotic signaling in plants: multiple pathways mediated by emerging kinase families. Plant Physiol 138: 1185-1194.
15. Meszaros T, Helfer A, Hatzimasoura E, Magyar Z, Serazetdinova L, et al. (2006) The Arabidopsis MAP kinase kinase MKK1 participates in defence responses to the bacterial elicitor flagellin. Plant J 48: 485-498.
16. Qiu JL, Fiil BK, Petersen K, Nielsen HB, Botanga CJ, et al. (2008a) Arabidopsis MAP kinase 4 regulates gene expression through transcription factor release in the nucleus. EMBO J 27: 2214-2221.
17. Wilson C, Voronin V, Touraev A, Vicente O, Heberle-Bors E, (1997) A developmentally regulated MAP kinase activated by hydration in tobacco pollen. Plant Cell 9: 2093-2100.
18. Gudesblat GE, Iusem ND, Morris PC, (2007) Guard cell-specific inhibition of Arabidopsis MPK3 expression causes abnormal stomatal responses to abscisic acid and hydrogen peroxide. New Phytol 173: 713-721.
19. Hamel LP, Nicole MC, Sritubtim S, Morency MJ, Ellis M, et al. (2006) Ancient signals: comparative genomics of plant MAPK and MAPKK gene families. Trends Plant Sci 11: 192-198.
20. Xu J, Li Y, Wang Y, Liu H, Lei L, et al. (2008) Activation of MAPK kinase 9 induces ethylene and camalexin biosynthesis and enhances sensitivity to salt stress in Arabidopsis. J Biol Chem 283: 26996-27006.
21. Yoo SD, Sheen J, (2008) MAPK signaling in plant hormone ethylene signal transduction. Plant Signal Behav 3: 848-849.
22. Zhou C, Cai Z, Guo Y, Gan S, (2009) An Arabidopsis mitogen-activated protein kinase cascade, MKK9-MPK6, plays a role in leaf senescence. Plant Physiol 150: 167-177.
23. Beck M, Komis G, Muller J, Menzel D, Samaj J, (2010) Arabidopsis homologs of nucleus- and phragmoplast-localized kinase 2 and 3 and mitogen-activated protein kinase 4 are essential for microtubule organization. Plant Cell 22: 755-771.
24. Beck M, Komis G, Ziemann A, Menzel D, Samaj J, (2010) Mitogen-activated protein kinase 4 is involved in the regulation of mitotic and cytokinetic microtubule transitions in Arabidopsis thaliana. New Phytol 189: 1069-1083.
25. Zeng Q, Chen JG, Ellis BE, (2011) AtMPK4 is required for male-specific meiotic cytokinesis in Arabidopsis. Plant J 67: 895-906.
26. Takahashi Y, Soyano T, Kosetsu K, Sasabe M, Machida Y, (2010) HINKEL kinesin, ANP MAPKKKs and MKK6/ANQ MAPKK, which phosphorylates and activates MPK4 MAPK, constitute a pathway that is required for cytokinesis in Arabidopsis thaliana. Plant Cell Physiol 51: 1766-1776.
27. MAPK Group (2002) Mitogen-activated protein kinase cascades in plants: a new nomenclature. Trends Plant Sci 7: 301-308.
28. Rao KP, Richa T, Kumar K, Raghuram B, Sinha AK, (2010) In silico analysis reveals 75 members of mitogen-activated protein kinase kinase kinase gene family in rice. DNA Res 17: 139-153.
29. Bevan MW, Garvin DF, Vogel JP, (2010) Brachypodium distachyon genomics for sustainable food and fuel production. Curr Opin Biotechnol 21: 211-217.
30. IBI (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768.
31. Kumar S, Mohan A, Balyan HS, Gupta PK, (2009) Orthology between genomes of Brachypodium, wheat and rice. BMC Res Notes 2: 93.
32. Finn RD, Clements J, Eddy SR, (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39: W29-37.
33. Thompson JD, Higgins DG, Gibson TJ, (1994) Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
34. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
35. Bailey TL, Elkan C, (1995) The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 3: 21-29.
36. Gu Z, Cavalcanti A, Chen FC, Bouman P, Li WH, (2002) Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol 19: 256-262.
37. Higo K, Ugawa Y, Iwamoto M, Korenaga T, (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27: 297-300.
38. Jang CS, Kamps TL, Skinner DN, Schulze SR, Vencill WK, et al. (2006) Functional classification, genomic organization, putatively cis-acting regulatory elements, and relationship to quantitative trait loci, of sorghum genes with rhizome-enriched expression. Plant Physiol 142: 1148-1159.
39. Dong J, Chen C, Chen Z, (2003) Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response. Plant Mol Biol 51: 21-37.
40. Sakuma Y, Maruyama K, Qin F, Osakabe Y, Shinozaki K, et al. (2006) Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression. Proc Natl Acad Sci U S A 103: 18822-18827.
41. Ohme-Takagi M, Suzuki K, Shinshi H, (2000) Regulation of ethylene-induced transcription of defense genes. Plant Cell Physiol 41: 1187-1192.
42. Tang H, Wang X, Bowers JE, Ming R, Alam M, et al. (2008) Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res 18: 1944-1954.
43. Albrecht V, Ritz O, Linder S, Harter K, Kudla J, (2001) The NAF domain defines a novel protein-protein interaction module conserved in Ca2+-regulated kinases. EMBO J 20: 1051-1063.
44. Zhang Y, Mao L, Wang H, Brocker C, Yin X, et al. (2012) Genome-wide identification and analysis of grape aldehyde dehydrogenase (ALDH) gene superfamily. PLoS One 7: e32153.
45. Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, et al. (2009) ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 37: D868-872.
46. Wise RA, Teeter JG, Jensen RL, England RD, Schwartz PF, et al. (2007) Standardization of the single-breath diffusing capacity in a multicenter clinical trial. Chest 132: 1191-1197.
47. Jung KH, Dardick C, Bartley LE, Cao P, Phetsom J, et al. (2008) Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS One 3: e3337.
48. Sharoni AM, Nuruzzaman M, Satoh K, Shimizu T, Kondoh H, et al. (2010) Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant Cell Physiol 52: 344-360.
49. Ichimura K, Tena G, Henery Y, Champion A, Kreis M, et al. (2002) Mitogen-activated protein kinase cascades in plants: a new nomenclature. Trends Plant Sci 7: 301-308.
50. Kong F, Wang J, Cheng L, Liu S, Wu J, et al. (2012) Genome-wide analysis of the mitogen-activated protein kinase gene family in Solanum lycopersicum. Gene 499: 108-120.
51. Holub E, (2001) Arms race is ancient history in Arabidopsis, the wildflower. Nat Rev Genet 2: 516-527.
52. Ameline-Torregrosa C, Wang BB, O'Bleness MS, Deshpande S, Zhu H, et al. (2008) Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula. Plant Physiol 146: 5-21.
53. Lyons E, Pedersen B, Kane J, Alam M, Ming R, et al. (2008) Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol 148: 1772-1781.
54. Sinha AK, Jaggi M, Raghuram B, Tuteja N, (2011) Mitogen-activated protein kinase signaling in plants under abiotic stress. Plant Signal Behav 6: 196-203.
55. Lynch M, Conery JS, (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
56. Jonak C, Okresz L, Bogre L, Hirt H, (2002) Complexity, cross talk and integration of plant MAP kinase signalling. Curr Opin Plant Biol 5: 415-424.