AJMB  Vol.2 No.1 , January 2012
DOF transcription factors in developing peanut (Arachis hypogaea) seeds
Abstract: DNA binding with one finger (DOF) transcription factors play important roles in storage material accumulation and morphogenesis of developing seeds. Oil and protein contents varied in different cultivars in important oil crop peanut. DOF proteins have not been studied in this crop. In this paper, we analyzed all the DOF genes expressed in developing seeds from a cDNA library with 20,000 transcripts, cloned and compared similar genes of GW391729 from eight peanut cultivars, and analyzed similar genes expressed in root and leave with control and inoculated with Ralstonia solanacearum. The results indicate that total eight types of DOF genes were expressed in developing seeds of cultivar 063103. Most of DOF transcription factors expressed involved in developmental process in a complicated way. Among them, GW391729 is possible related to the seed number in fruit, and also is possible related to leafspot resistance. Detailed function of these DOF proteins need to be further studied.
Cite this paper: Yan, H. , Huang, J. , Liao, B. , Lan, X. , Luo, Q. and Tang, J. (2012) DOF transcription factors in developing peanut (Arachis hypogaea) seeds. American Journal of Molecular Biology, 2, 60-71. doi: 10.4236/ajmb.2012.21007.

[1]   Yanagisawa, S. (2002) The Dof family of plant transcription factors. Trends in Plant Science, 7, 555-560. doi:10.1016/S1360-1385(02)02362-2

[2]   Lijavetzky, D., Carbonero, P. and Vicente-Carbajosa, J. (2003) Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families. BMC Evolutionary Biology, 3, 17-27. doi:10.1186/1471-2148-3-17

[3]   Umemura, Y., Ishiduka, T., Yamamoto, R. and Esaka, M. (2004) The Dof domain, a zinc finger DNA-binding domain conserved only in higher plants, truly functions as a Cys2/Cys2 n finger domain. Plant Journal, 37, 741-749. doi:10.1111/j.1365-313X.2003.01997.x

[4]   Yang, X., Tuskan, G.A. and Cheng, Z. (2006) Divergence of the Dof gene families in poplar,arabidopsis, and rice suggests multiple modes of gene evolution after duplication. Plant Physiology, 142, 820-830. doi:10.1104/pp.106.083642

[5]   Wang, H., Zhang, B., Hao, Y., Huang, J., Tian, A., Liao, Y., Zhang, J. and Chen, S. (2007) The soybean Dof-type transcription factor genes, GmDof4 and GmDof11, enhance lipid content in the seeds of transgenic Arabidopsis plants. Plant Journal, 52, 716-729. doi:10.1111/j.1365-313X.2007.03268.x

[6]   Yanagisawa, S. (1995) A novel DNA-binding domain that may form a single zinc finger motif. Nucleic Acids Research, 23, 3403-3410. doi:10.1093/nar/23.17.3403

[7]   Yanagisawa S. (1997) Dof DNA-binding domains of plant transcription factors contribute to multiple protein-protein interactions. European Journal of Biochemistry, 250, 403-410. doi:10.1111/j.1432-1033.1997.0403a.x

[8]   Yanagisawa, S. and Schmidt, R.J. (1999) Diversity and similarity among recognition sequences of Dof transcription factors. Plant Journal, 17, 209-214. doi:10.1046/j.1365-313X.1999.00363.x

[9]   Vicente-Carbajosa, J., Moose, S.P., Parsons, R.L., Parsons R.L. and Schmidt R.J.( 1997) A maize zinc-finger protein binds the prolamin box in zein gene promoters and interacts with the basic leucine zipper transcriptional activator Opaque2. Proceedings of the National Academy of Sciences of the United States of America, 94, 7685-7690. doi:10.1073/pnas.94.14.7685

[10]   Diaz, I., Vicente-Carbajosa, J., Abraham, Z., Martínez, M., Isabel-La, Moneda, I. and Carbonero, P. (2002) The GAMYB protein from barley interacts with the DOF transcription factor BPBF and activate endosperm-specific genes during seed germination. Plant Journal, 29, 453-464. doi:10.1046/j.0960-7412.2001.01230.x

[11]   Albani, D., Hammond-Kosack, M.C.U., Smith, C., Con- lan, S., Colot, V., Holdsworth, M. and Bevan, M.W. (1997) The wheat transcription activator SPA. A seed-specific bZIP protein that recognizesthe GCN4-like motif in the bifactorial endosperm box of prolamin genes. Plant Cell, 9, 171-184.

[12]   Vicente-Carbajosa, J., Onate, L., Lara, P., Diaz, I. and Carbonero, P. (1998) Barley BLZ1: A bZIP transcriptional activator that interacts with endosperm-specific gene promoters. Plant Journal, 13, 629-640. doi:10.1111/j.1365-313X.1998.00068.x

[13]   Dong, G.Q., Ni, Z.F., Yao, Y.Y., Nie, X.L. and Sun, Q.X. (2007) Wheat Dof transcription factor WPBF interacts with TaQM and activates transcription of an alpha-gliadin gene during wheat seed development. Plant Molecular Biology, 63, 73-84. doi:10.1007/s11103-006-9073-3

[14]   Zhang, B., Chen, W., Foley, R.C., Buttner, M. and Singh, K.B. (1995) Interaction between distinct types of DNA binding proteins enhance binding to ocs element promoter sequences. Plant Cell, 7, 2241-2252.

[15]   Yanagisawa, S. (2000) Dof1 and Dof2 transcription factors are associated with expression of multiple genes involved in carbon metabolism in maize. Plant Journal, 21, 281-288. doi:10.1046/j.1365-313x.2000.00685.x

[16]   Viquez, O.M., Konan, K.N. and Dodo, H.W. (2003) Structure and organization of the genomic clone of a major peanut allergen gene, Ara h 1. Molecular Immunology, 40, 565-571. doi:10.1016/j.molimm.2003.09.002

[17]   Viquez, O.M., Konan, K.N. and Dodo, H.W. (2004) Genomic organization of peanut allergen gene, Ara h 3. Molecular Immunology, 41, 1235-1240. doi:10.1016/j.molimm.2004.06.033

[18]   Wang, J., Yan, H.Y. and Kang, Q.S. (2005) Construction of a plant transgenic expression vector of peanut. Journal of Wuhan Botanical Research, 23, 514-518.

[19]   Day R.C., Herridge R.P., Ambrose B.A. and Macknight R.C. (2008) Transcriptome analysis of proliferating arabidopsis endosperm reveals biological implications for the control of syncytial division, cytokinin signaling, and gene expression regulation. Plant Physiology, 148, 1964-1984. doi:10.1104/pp.108.128108

[20]   Guo, Y., Qin, G., Gu, H. and Qu, L. (2009) Dof5.6/HCA2, a Dof transcription factor gene, regulates interfascicular cambium formation and vascular tissue development in arabidopsis. Plant Cell, 21, 3518-3534. doi:10.1105/tpc.108.064139

[21]   Ogawa, M., Hanada, A., Yamauchi, Y., Kuwahara, A., Kamiya, Y. and Yamaguchi, S. (2003) Gibberellin biosynthesis and response during arabidopsis seed germination. Plant Cell, 15, 1591-1604. doi:10.1105/tpc.011650

[22]   Depuydt, S., Trenkamp, S., Fernie, A.R., Elftieh, S., Renou, J., Vuylsteke, M., Holsters, M. and Vereecke, D. (2009) An integrated genomics approach to define niche establishment by Rhodococcus fascians. Plant Physiology, 149, 1366-1386. doi:10.1104/pp.108.131805

[23]   Wellmer, F., Alves-Ferreira, M., Dubois, A., Riechmann, J.L. and Meyerowitz, E.M. (2006) Genome-wide analysis of gene expression during early arabidopsis flower development. PLoS Genetics, 2, 1012-1024. doi:10.1371/journal.pgen.0020117

[24]   Fulton, L., Batoux, M., Vaddepalli, P., Yadav, R.K., Busch, W., Andersen, S.U., Jeong, S., Lohmann, J.U. and Schneitz, K. (2009) DETORQUEO, QUIRKY, and ZERZAUST represent novel components involved in organ development mediated by the receptor-like kinase STRUBBELIG in Arabidopsis thaliana. PLoS Genetics, 5, 1-22. doi:10.1371/journal.pgen.1000355

[25]   Zhao, C., Craig, J.C., Petzold, H.E., Dickerman, A.W. and Beers, E.P. (2005) The xylem and phloem transcriptomes from secondary tissues of the arabidopsis root-hypocotyl. Plant Physiology, 138, 803-818. doi:10.1104/pp.105.060202

[26]   Ward, J.M., Cufr, C.A., Denzel, M.A. and Neff, M.M. (2005) The Dof transcription factor OBP3 modulates phytochrome and cryptochrome signaling in arabidopsis. Plant Cell, 17, 475-485. doi:10.1105/tpc.104.027722

[27]   Mouhu, K., Hyt?nen, T., Folta, K., Rantanen, M., Paulin, L., Auvinen, P. and Elomaa, P. (2009)Identification of flowering genes in strawberry, a perennial SD plant. BMC Plant Biology, 9, 122-137. doi:10.1186/1471-2229-9-122

[28]   Borges, F., Gomes, G., Gardner, R., Moreno, N., McCormick, S., Feijó, J.A. and Becker, J.D. (2008) Comparative transcriptomics of arabidopsis sperm cells. Plant Physiology, 148, 1168-1181. doi:10.1104/pp.108.125229

[29]   Para, A., Farré, E.M., Imaizumi, T., Pruneda-Paz, J.L., Harmon, F.G. and Kay, S.A. (2007) PRR3 is a vascular regulator of TOC1 stability in the arabidopsis circadian clock. Plant Cell, 19, 3462-3473. doi:10.1105/tpc.107.054775

[30]   Chawade, A., Br?utigam, M., Lindl?f, A., Olsson, O. and Olsson, B. (2007) Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors. BMC Genomics, 8, 304-318. doi:10.1186/1471-2164-8-304

[31]   Kreps, J.A., Wu, Y., Chang, H., Zhu, T., Wang, X. and Harper, J.F. (2002) Transcriptome changes for arabidopsis in response to salt, osmotic, and cold stress. Plant Physiology, 130, 2129-2141. doi:10.1104/pp.008532

[32]   Budhiraja, R., Hermkes, R., Müller, S., Schmidt, J., Colby, T., Panigrahi, K., Coupland, G. and Bachmair, A. (2009) Substrates related to chromatin and to RNA-dependent processes are modified by arabidopsis SUMO isoforms that differ in a conserved residue with influence on desumoylation. Plant Physiology, 149, 1529-1540. doi:10.1104/pp.108.135053

[33]   Rohde, A., Morreel, K., Ralph, J., Goeminne, G., Hostyn, V., Rycke, R.D., Kushnir, S., Doorsselaere, J.V., Joseleau, J., Vuylsteke, M., Van Driessche, G., Van Beeumen, J., Messens, E. and Boerjan, W. (2004) Molecular phenotyping of the pal1 and pal2 mutants of Arabidopsis thaliana reveals far-reaching consequences on phenylpropanoid, amino acid, and carbohydrate metabolism. Plant Cell, 16, 2749-2771. doi:10.1105/tpc.104.023705

[34]   Khanna, R., Shen, Y., Toledo-Ortiz, G., Kikis, E.A., Johannesson, H., Hwang, Y. and Quail, P.H. (2006) Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in arabidopsis are necessary for optimal deetiolation. Plant Cell, 18, 2157- 2171. doi:10.1105/tpc.106.042200

[35]   Cheong, Y.H., Chang, H., Gupta, R., Wang, X., Zhu, T., Luan, S. (2002) Transcriptional profiling reveals novel interactions between wounding, pathogen, abiotic stress, and hormonal responses in arabidopsis. Plant Physiology, 129, 661-677. doi:10.1104/pp.002857

[36]   Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402. doi:10.1093/nar/25.17.3389

[37]   Stanke, M., Diekhans, M., Baertsch, R. and Haussler, D. (2008)Using native and syntenically mapped cDNA alignments to improve de novo gene finding, Bioinformatics, 24, 637-644. doi:10.1093/bioinformatics/btn013

[38]   Yan, H., Ding, Y. and Wu, Y. (2009) Genetic engineering and molecular biology lab tutorial. Wuhan University Publisher, Wuhan, 3-9.

[39]   Skirycz, A., Radziejwoski, A., Busch, W., Hannah, M.A., Czeszejko, J., Kwa?niewski, M., Zanor, M., Lohmann, J.U., De Veylder, L., Witt, I. and Mueller-Roeber, B. (2008) The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana. Plant Journal, 56, 779-792. doi:10.1111/j.1365-313X.2008.03641.x

[40]   Hoffmann, R. and Valencia, A. (2004) A gene network for navigating the literature. Nature Genetics, 36, 664. doi:10.1038/ng0704-664

[41]   Hoffmann, R. and Valencia, A. (2004) iHOP-Information Hyperlinked over Proteins.

[42]   Varagona, M.J., Schmidt, R.J. and Raikhel, N.V. (1992) Nuclear localization signals required for nuclear targeting of the maize regulatory protein Opaque-2. Plant Cell, 4, 1213-1227.

[43]   Hicks, C.R., Smith, H.M.S., Shieh, M. and Raikhel, N.V. (1995) Three classes of nuclear import signals bind to plant nuclei. Plant Physiology, 107, 1055-1058. doi:10.1104/pp.107.4.1055

[44]   Jung, S., Tate, P.L., Horn, R., Kochert, G., Moore, K. and Abbott, A.G. (2003) The phylogenetic relationship of possible progenitors of the cultivated peanut, Journal of Heredity, 94, 334-340. doi:10.1093/jhered/esg061

[45]   Imaizumi, T., Schultz, T.F., Harmon, F.G., Ho, L.A. and Kay, S.A. (2005) FKF1 F-Box protein mediates cyclic degradation of a repressor of CONSTANS in arabidopsis. Science, 309, 293-297. doi:10.1126/science.1110586

[46]   Sawa, M., Nusinow, D.A., Kay, S.A. and Imaizum, T. (2007) FKF1 and GIGANTEA complex formation is required for day-length measurement in arabidopsis. Science, 318, 261-265. doi:10.1126/science.1146994

[47]   Fornara, F., Panigrahi, K.C.S., Gissot, L., Sauerbrunn, N., Rühl, M., Jarillo, J.A. and Coupland, G. (2009) Arabidopsis DOF transcription factors act redundantly to reduce CONSTANS expression and are essential for a photoperiodic flowering response. Development Cell, 17, 75-86. doi:10.1016/j.devcel.2009.06.015