The Trihelix transcription factor family plays an essential role in plant growth, development and stress response. However, the studies about identification and analysis of this gene family in rice on the genome-wide level have not been reported. In this study, 31 members of the Trihelix family, which contain highly conserved and characteristic trihelix domain through sequence clustering and functional domains analysis, were identified in rice genome database using bioinformatic tools. These members could be classified into 5 subfamilies (I~V) based on the evolutionary relationship and domain characteristics. Clustering analyses of the Trihelix family in rice, Arabidopsis, Brachypodium distachyom and Sorghum bicolor showed that each species contained different members of subfamily although the classification of the Trihelix family were consistent in these four species, which indicated that the differentiation of the Trihelix gene family occur earlier than that of these species. The conserved motifs in the Trihelix family of rice analyzed using the MEME program were highly consistent with the results of clustering analyses. Intraspecific and interspecific chromosomal replication in partial Trihelix family members were found to exist in rice and between rice and other species through chromosome replication analysis. Microarray data analysis revealed diverse expression patterns of Trihelix family genes in different tissues of rice or in response to six different phytohormones. Moreover, 20 members of the Trihelix transcription factor family were found to interact with other proteins in rice using RiceFRIEND online database analysis. Therefore, our results preliminarily identified the evolution, chromosome distribution and replication, expression patterns, phytohormones response of the Trihelix transcription factor family and the interaction between trihelix family proteins and other proteins in rice, which will provide a basis to further reveal the molecular evolution and biological function of the Trihelix transcription factor family.
[1] 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(5499): 2105-2110.
[2] 罗军玲, 赵娜, 卢长明. 植物Trihelix转录因子家族研究进展. 遗传, 2012, 34(12): 1551-1560.
[3] Kaplan-Levy RN, Brewer PB, Quon T, Smyth DR. The Trihelix family of transcription factors-light, stress and development. Trends Plant Sci , 2012, 17(3): 163-171.
[4] Green PJ, Kay SA, Chua NH. Sequence-specific interactions of a pea nuclear factor with light-responsive elements upstream of the rbcS-3A gene. EMBO J , 1987, 6(9): 2543-2549.
[5] Perisic O, Lam E. A tobacco DNA binding protein that interacts with a light-responsive box II element. Plant Cell , 1992, 4(7): 831-838.
[6] Le Gourrierec J, Li YF, Zhou DX. Transcriptional activation by Arabidopsis GT-1 may be through interaction with TFIIA-TBP-TATA complex. Plant J , 1999, 18(6): 663-668.
[7] Kay SA, Keith B, Shinozaki K, Chye ML, Chua NH. The rice phytochrome gene: structure, autoregulated expression, and binding of GT-1 to a conserved site in the 5' upstream region. Plant Cell , 1989, 1(3): 351-360.
[8] Dehesh K, Bruce WB, Quail PH. A trans-acting factor that binds to a GT-motif in a phytochrome gene promoter. Science , 1990, 250(4986): 1397-1399.
[9] Dehesh K, Hung H, Tepperman JM, Quail PH. GT-2: a transcription factor with twin autonomous DNA-binding domains of closely related but different target sequence specificity. EMBO J , 1992, 11(11): 4131-4144.
[10] Brewer PB, Howles PA, Dorian K, Griffith ME, Ishida T, Kaplan-Levy RN, Kilinc A, Smyth DR. PETAL LOSS , a trihelix transcription factor gene, regulates perianth architecture in the Arabidopsis flower. Development , 2004, 131(16): 4035-4045.
[11] Lampugnani ER, Kilinc A, Smyth DR. PETAL LOSS is a boundary gene that inhibits growth between developing sepals in Arabidopsis thaliana . Plant J , 2012, 71(5): 724-735.
[12] Griffith ME, da Silva Conceicão A, Smyth DR. PETAL LOSS gene regulates initiation and orientation of second whorl organs in the Arabidopsis flower. Development , 1999, 126(24): 5635-5644.
[13] Lin ZW, Griffith ME, Li XR, Zhu ZF, Tan LB, Fu YC, Zhang WX, Wang XK, Xie DX, Sun CQ. Origin of seed shattering in rice ( Oryza sativa L.). Planta , 2007, 226(1): 11-20.
[14] Fang YJ, Xie KB, Hou X, Hu HH, Xiong LZ. Systematic analysis of GT factor family of rice reveals a novel subfamily involved in stress responses. Mol Genet Genomics , 2010, 283(2): 157-169.
[15] Barr MS, Willmann MR, Jenik PD. Is there a role for trihelix transcription factors in embryo maturation? Plant Signal Behav , 2012, 7(2): 205-209.
[16] Kuromori T, Wada T, Kamiya A, Yuguchi M, Yokouchi T, Imura Y, Takabe H, Sakurai T, Akiyama K, Hirayama T, Okada K, Shinozaki K. A trial of phenome analysis using 4000 Ds -insertional mutants in gene-coding regions of Arabidopsis . Plant J , 2006, 47(4): 640-651.
[17] Kitakura S, Fujita T, Ueno Y, Terakura S, Wabiko H, Machida Y. The protein encoded by oncogene 6b from Agrobacterium tumefaciens interacts with a nuclear protein of tobacco. Plant Cell , 2002, 14(2): 451-463.
[18] Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer ELL, Tate J, Punta M. Pfam: the protein families database. Nucleic Acids Res , 2014, 42(D1): D222-D230.
[19] Letunic I, Doerks T, Bork P. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res , 2012, 40(D1): D302-D305.
[20] Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios I, Stockinger H. ExPASy: SIB bioinformatics resource portal. Nuclei
