Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis
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Ptashne M: How eukaryotic transcriptional activators work. Nature. 1988, 335: 683-689. 10.1038/335683a0.
Klempnauer KH, Gonda TJ, Bishop JM: Nucleotide sequence of the retroviral leukemia gene v-myb and its cellular progenitor c-MYB: the architecture of a transduced oncogene. Cell. 1982, 31: 453-463. 10.1016/0092-8674(82)90138-6.
Weston K: Myb proteins in life, death and differentiation. Curr Opin Genet Dev. 1998, 8: 76-81. 10.1016/S0959-437X(98)80065-8.
Lipsick JS: One billion years of Myb. Oncogene. 1996, 13: 223-235.
Paz-Ares J, Ghosal D, Wienand U, Peterson P, Saedler H: The regulatory c1 locus of Zea mays encodes a protein with homology to MYB oncogene products and with structural similarities to transcriptional activators. EMBO J. 1987, 6: 3553-3558.
Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu G: Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science. 2000, 290: 2105-2110. 10.1126/science.290.5499.2105.
Martin C, Paz-Ares J: MYB transcription factors in plants. Trends Genet. 1997, 13: 67-73. 10.1016/S0168-9525(96)10049-4.
Kranz H, Scholz K, Weisshaar B: c-MYB oncogene-like genes encoding three MYB repeats occur in all major plant lineage. Plant J. 2000, 21: 231-235. 10.1046/j.1365-313x.2000.00666.x.
Yanhui C, Xiaoyuan Y, Kun H, Meihua L, Jigang L, Zhaofeng G, Zhiqiang L, Yunfei Z, Xiaoxiao W, Xiaoming Q, Yunping S, Li Z, Xiaohui D, Jingchu L, Xing-Wang D, Zhangliang C, Hongya G, Li-Jia Q: The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol Biol. 2006, 60: 107-124. 10.1007/s11103-005-2910-y.
Pasquali G, Biricolti S, Locatelli F, Baldoni E, Mattana M: OsMYB4 expression improves adaptive responses to drought and cold stress in transgenic apples. Plant Cell Rep. 2008, 27: 1677-1686. 10.1007/s00299-008-0587-9.
Li-Jia Q, Zhu Y-X: Transcription factor families in Arabidopsis: major progress and outstanding issues for future research. Curr Opin Plant Biol. 2006, 9: 544-549. 10.1016/j.pbi.2006.07.005.
Feller A, Machemer K, Braun EL, Grotewold E: Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Plant J. 2011, 66 (1): 94-116. 10.1111/j.1365-313X.2010.04459.x.
Kanei-Ishii C, Sarai A, Sawazaki T, Nakagoshi H, He DN, Ogata K, Nishimura Y, Ishii S: The tryptophan cluster: a hypothetical structure of the DNA-binding domain of the myb protooncogene product. J Biol Chem. 1990, 265: 19990-19995.
Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T, Kanai H, Sarai A, Ishii S, Nishimura Y: Solution structure of a specific DNA complex of the MYB DNA-binding domain with cooperative recognition helices. Cell. 1994, 79: 639-648. 10.1016/0092-8674(94)90549-5.
Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L: MYB transcription factors in Arabidopsis. Trends Plant Sci. 2010, 15: 1360-1385.
Jiang C, Gu J, Chopra S, Gu X, Peterson T: Ordered origin of the typical two- and three-repeat Myb genes. Gene. 2004, 326: 13-22.
Rosinski JA, Atchley WR: Molecular evolution of the Myb family of transcription factors: evidence for polyphyletic origin. J Mol Evol. 1998, 46: 74-83. 10.1007/PL00006285.
Allan AC, Hellens RP, Laing WA: MYB transcription factors that colour our fruit. Cell. 2008, 13: 99-102.
Cominelli E, Tonelli C: A new role for plant R2R3-MYB transcription factors in cell cycle regulation. Cell Res. 2009, 19: 1231-1232. 10.1038/cr.2009.123.
Agarwal M, Hao Y, Kapoor A, Dong CH, Fujii H, Zheng X, Zhu JK: A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance. J Biol Chem. 2006, 281: 37636-37645. 10.1074/jbc.M605895200.
Ma Q, Dai X, Xu Y, Guo J, Liu Y, Chen N, Xiao J, Zhang D, Xu Z, Zhang X, Chong K: Enhanced tolerance to chilling stress in OsMYB3R-2 transgenic rice is mediated by alteration in cell cycle and ectopic expression of stress genes. Plant Physiol. 2009, 150: 244-256. 10.1104/pp.108.133454.
Vannini C, Locatelli F, Bracale M, Magnani E, Marsoni M, Osnato M, Mattana M, Baldoni E, Coraggio I: Overexpression of the rice OsMYB4 gene increases chilling and freezing tolerance of Arabidopsis thaliana plants. Plant J. 2004, 37: 115-127. 10.1046/j.1365-313X.2003.01938.x.
Seo PJ, Xiang F, Qiao M, Park JY, Lee YN, Kim SG, Lee YH, Park WJ, Park CM: The MYB96 transcription factor mediates abscisic acid signaling during drought stress response in Arabidopsis. Plant Physiol. 2009, 151: 275-289. 10.1104/pp.109.144220.
Ding Z, Li S, An X, Liu X, Qin H, Wang D: Transgenic expression of MYB15 confers enhanced sensitivity to abscisic acid and improved drought tolerance in Arabidopsis thaliana. Cell Res. 2008, 18: 1047-1060. 10.1038/cr.2008.280.
Ito M, Araki S, Matsunaga S, Itoh T, Nishihama R, Machida Y, Doonan JH, Watanabe A: G2/M-phase-specific transcription during the plant cell cycle is mediated by c-MYB-like transcription factors. Plant Cell. 2001, 13: 1891-1905.
Araki S, Ito M, Soyano T, Nishihama R, Machida Y: Mitotic cyclins stimulate the activity of c-MYB-like factors for transactivation of G2/M phase-specific genes in tobacco. J Biol Chem. 2004, 279: 32979-32988. 10.1074/jbc.M403171200.
Dai X, Xu Y, Ma Q, Xu W, Wang T, Xue Y, Chong K: Overexpression of an R1R2R3 MYB Gene, OsMYB3R-2, increases tolerance to freezing, drought, and salt stress in transgenic Arabidopsis. Plant Physiol. 2007, 143: 1739-1751. 10.1104/pp.106.094532.
Haga N, Kato K, Murase M, Araki S, Kubo M, Demura T, Suzuki K, Muller I, Voss U, Jurgens G, Ito M: R1R2R3-MYB proteins positively regulate cytokinesis through activation of KNOLLE transcription in Arabidopsis thaliana. Development. 2007, 134: 1101-1110. 10.1242/dev.02801.
Allen RS, Li J, Stalhe MI, Dubroue A, Gubler F, Millar A: Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family. Proc. Natl. Acad. Sci. USA. 2007, 104: 16371-16376. 10.1073/pnas.0707653104.
Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ: Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Current Biol. 2008, 18: 758-762. 10.1016/j.cub.2008.04.042.
Stracke R, Werber M, Weisshaar B: The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol. 2001, 4: 447-456. 10.1016/S1369-5266(00)00199-0.
Shinozaki K, Yamaguchi-Shinozaki K, Urao T, Koizumi M: Nucleotide sequence of a gene from Arabidopsis thaliana encoding a MYB homologue. Plant Mol Biol. 1992, 19: 493-499. 10.1007/BF00023398.
Romero I, Fuertes A, Benito MJ, Malpical JM, Leyva A, Paz-Ares J: More than 80 R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana. Plant J. 1998, 14: 273-284. 10.1046/j.1365-313X.1998.00113.x.
Kranz HD, Denekamp M, Greco R, Jin H, Leyva A, Meissner RC, Petroni K, Urzainqui A, Bevan M, Martin C: Towards functional characterization of the members of the R2R3-MYB gene family from Arabidopsis thaliana. Plant J. 1998, 16: 263-276. 10.1046/j.1365-313x.1998.00278.x.
Karamysheva ZN, Surovtseva YV, Vespa L, Shakirov EV, Shippen DE: A C-terminal Myb extension domain defines a novel family of double-strand telomeric DNA-binding proteins in Arabidopsis. J Biol Chem. 2004, 279: 47799-47807. 10.1074/jbc.M407938200.
Jin H, Martin C: Multifunctionality and diversity within the plant MYB-gene family. Plant Mol Biol. 1999, 41: 577-585. 10.1023/A:1006319732410.
Lu SX, Knowles SM, Andronis C, Ong MS, Tobin EM: CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis. Plant Physiol. 2009, 150: 834-843. 10.1104/pp.108.133272.
Simon M: Distinct and overlapping roles of single-repeat MYB genes in root epidennal patterning. Dev Biol. 2007, 311: 566-578. 10.1016/j.ydbio.2007.09.001.
Dubos C: MYBL2 is a new regulator of flavonoid biosynthesis in Arabidopsis thaliana. Plant J. 2008, 55: 940-953. 10.1111/j.1365-313X.2008.03564.x.
Matsui K: AtMYBL2, a protein with a single MYB domain, act as negative regulator of anthocyanin biosynthesis in Arabidopsis. Plant J. 2008, 55: 954-967. 10.1111/j.1365-313X.2008.03565.x.
Pesch M, Hulskamp M: One, two, thee. Models for trichome patterning in Arabidopsis. Curr. Opin. Plant Biol. 2009, 12: 587-592. 10.1016/j.pbi.2009.07.015.
Kyte J, Doolittle RF: A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982, 157: 105-132. 10.1016/0022-2836(82)90515-0.
Ramachandran S, Hiratsuka K, Chua NH: Transcription factors in plant growth and development. Curr Opin Genet Dev. 1994, 4 (5): 642-646. 10.1016/0959-437X(94)90129-Q.
Borevitz JO, Xia Y, Blount J, Dixon RA, Lamb C: Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant Cell. 2000, 12: 2383-2394.
Nesi N, Jond C, Debeaujon I, Caboche M, Lepiniec L: The Arabidopsis TT2 gene encodes an R2R3 MYB domain protein that acts as a key determinant for proanthocyanidin accumulation in developing seed. Plant Cell. 2001, 13: 2099-2114.
Baudry A, Heim MA, Dubreucq B, Caboche M, Weisshaar B, Lepiniec L: TT2, TT8, and TTG1 synergistically specify the expression of BANYULS and proanthocyanidin biosynthesis in Arabidopsis thaliana. Plant J. 2004, 39: 366-380. 10.1111/j.1365-313X.2004.02138.x.
Lee MM, Schiefelbein J: WEREWOLF, a MYB-related protein in Arabidopsis, is a position-dependent regulator of epidermal cell patterning. Cell. 1999, 99: 473-483. 10.1016/S0092-8674(00)81536-6.
Lee MM, Schiefelbein J: Developmentally distinct MYB genes encode functionally equivalent proteins in Arabidopsis. Development. 2001, 12: 1539-1546.
Higginson T, Li SF, Parish RW: AtMYB103 regulates tapetum and trichome development in Arabidopsis thaliana. Plant J. 2003, 35: 177-192. 10.1046/j.1365-313X.2003.01791.x.
Ito M: Conservation and diversification of three-repeat MYB transcription factor in plants. J Plant Res. 2005, 118: 61-69. 10.1007/s10265-005-0192-8.
Jin H, Cominelli E, Bailey P, Parr A, Mehrtens F, Jones J, Tonelli C, Weisshaar B, Martin C: Transcriptional repression by AtMYB4 controls production of UV-protecting sunscreens in Arabidopsis. EMBO J. 2000, 19: 6150-6161. 10.1093/emboj/19.22.6150.
Hemm MR, Herrmann KM, Chapple C: AtMYB4: a transcription factor general in the battle against UV. Trends Plant Sci. 2001, 6: 135-136. 10.1016/S1360-1385(01)01915-X.
Walker JC: Receptor-like protein kinase genes of Arabidopsis thaliana. Plant J. 1993, 3: 451-456. 10.1111/j.1365-313X.1993.tb00164.x.
Bender J, Fink GR: A MYB homologue, ATR1, activates tryptophan gene expression in Arabidopsis. Proc. Natl. Acad. Sci. USA. 1998, 95: 5655-5660. 10.1073/pnas.95.10.5655.
Kim JH, Lee BW, Schroeder FC, Jander G: Identification of indoleglucosinolate breakdown products with antifeedant effects on Myzus persicae (green peach aphid). Plant J. 2008, 54: 1015-1026. 10.1111/j.1365-313X.2008.03476.x.
Kirik V, Lee MM, Wester K, Herrmann U, Zheng Z, Oppenheimer D, Schiefelbein J, Hulskamp M: Functional diversification of MYB23 and GL1 genes in trichome morphogenesis and initiation. Development. 2005, 132: 1477-1485. 10.1242/dev.01708.
Kaundal R, Saini R, Zhao PX: Combining Machine Learning and Homology-based Approaches to Accurately Predict Subcellular Localization in Arabidopsis. Plant Physiol. 2010, 154 (1): 36-54. 10.1104/pp.110.156851.
Jain M, Khurana P, Tyagi AK, Khurana JP: Genome-wide analysis of intronless genes in rice and Arabidopsis. Funct Integr Genomics. 2008, 8: 69-78. 10.1007/s10142-007-0052-9.
Li J, Li X, Guo L, Lu F, Feng X, He K, Wei L, Chen Z, Qu LJ, Gu H: A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice. J Exp Bot. 2006, 57 (6): 1263-1273. 10.1093/jxb/erj094.
Blanc G, Wolfe KH: Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell. 2004, 16: 1679-1691. 10.1105/tpc.021410.
Thomas BC, Pedersen B, Freeling M: Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res. 2006, 16: 934-946. 10.1101/gr.4708406.
Rabinowicz PD, Braun EL, Wolfe AD, Bowen B, Grotewold E: Maize R2R3 MYB genes: sequence analysis reveals amplification in higher plants. Genetics. 1999, 153: 427-444.
Braun EL, Grotewold E: Diversification of the R2R3 MYB gene family and the segmental allotetraploid origin of the maize genome. Maize Genet Coop Newsl. 1999, 73: 26-27.
Lenka SK, Katiyar A, Chinnusamy V, Bansal KC: Comparative analysis of drought responsive transcriptome in Indica rice genotypes with contrasting drought tolerance. Plant Biotechnol J. 2011, 9 (3): 315-327. 10.1111/j.1467-7652.2010.00560.x.
Lenka SK, Lohia B, Kumar A, Chinnusamy V, Bansal KC: Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes. Plant Mol Biol. 2009, 69: 261-271. 10.1007/s11103-008-9423-4.
Wang ZY, Kenigsbuch D, Sun L, Harel E, Ong MS, Tobin EM: A Myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene. Plant Cell. 2007, 9: 491-507.
Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay S, Chory J: Diurnal and circadian expression profiling, model-based pattern matching and promoter analysis. Cold Spring Harb Symp Quant Biol. 2007, 72: 353-363. 10.1101/sqb.2007.72.006.
Boguski MS, Lowe TM, Tolstoshev CM: dbEST–database for "expressed sequence tags". Nat Genet. 1993, 4: 332-333. 10.1038/ng0893-332.
Zeng H, Luo L, Zhang W, Zhou J, Li Z, Liu H, Zhu T, Feng X, Zhong Y: PlantQTL-GE: a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information. Nucleic Acids Res. 2007, 35: D879-D882. 10.1093/nar/gkl814.
Zimmermann P, Hoffmann MH, Hennig L, Gruissem W: GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 2004, 136: 2621-2632. 10.1104/pp.104.046367.
Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P: Genevestigator V3: A Reference Expression Database for the Meta-Analysis of Transcriptomes. Adv Bioinformatics. 2008, 2008: 420747-
Yang A, Dai X, Zhang WH: A R2R3-type MYB gene, OsMYB2, is involved in salt, cold, and dehydration tolerance in rice. J Exp Bot. 2012, 63 (7): 2541-56. 10.1093/jxb/err431.
Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, Lin H, Hamilton J, Haas B, Sultana R, Cheung F, Wortman J, Buell CR: The institute for genomic research Osa1 rice genome annotation database. Plant Physiol. 2005, 138: 18-26. 10.1104/pp.104.059063.
Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR: The TIGR rice Ggenome annotation resource: improvements and new features. Nucleic Acids Res. 2007, 35: D883-D887. 10.1093/nar/gkl976.
Chen R, Ni Z, Nie X, Qin Y, Dong G, Sun Q: Isolation and characterization of genes encoding Myb transcription factor in wheat (Triticum aestivem L.). Plant Sci. 2005, 169: 1146-1154. 10.1016/j.plantsci.2005.07.018.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics. 2007, 23: 2947-2948. 10.1093/bioinformatics/btm404.
Li J, Clegg MT, Jiang T: Evolutionary Dynamics of the DNA-Binding Domains in Putative R2R3-MYB Genes Identified from Rice Subspecies indica and japonica Genomes. Plant Physiol. 2004, 135: 575-585.
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, Deweese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH: CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 2011, 39: D225-D229. 10.1093/nar/gkq1189.
Finn RD, Tate J, Mistry J, Coggill PC, Sammut JS, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A: The Pfam protein families database. Nucleic Acids Res. 2008, 36: D281-D288. 10.1093/nar/gkn226.
Bailey TL, Williams N, Misleh C, Li WW: MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 2006, 34: W369-W373. 10.1093/nar/gkl198.
Higo K, Ugawa Y, Iwamoto M, Korenaga T: Plant cis-acting regulatory DNA elements (PLACE) database. Nucleic Acids Res. 1999, 27: 297-300. 10.1093/nar/27.1.297.
Papadopoulos JS, Agarwala R: COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics. 2007, 23: 1073-1079. 10.1093/bioinformatics/btm076.
Voorrips RE: MapChart: Software for the graphical presentation of linkage maps and QTLs. J Hered. 2002, 93 (1): 77-78. 10.1093/jhered/93.1.77.
Poole RL: The TAIR database. Methods Mol Biol. 2007, 406: 179-212.