Codon Bias And Phylogenetics Analysis Of MADS And MYB Transcription Factors In Rice And Arabidopsis

Genome -wide comparisons of MYB and MADS transcriptional factor on codon bias are made in Arabidopsis and Rice. The results obtained by using the structure and phylogenetics analysis of both the transcription factors will be helpful to investigate their interaction between different genes and gene expression and regulation, and also will be potential in the crop breeding.1. The reaching developmant of transcription factors in plantThe inducing genes are controlled mainly by transcription factors at the transcription levels in plant. The typical transcription factors have the function domains such as DNA-binding domain, transcription regulation domain, oligomerization site, nuclear localization signal site and so on. This article introduced the concept, structure and classification of the transcription factors in brief. We also introduced general situation of MYB and MADS transcription factors.2. Comparison of MADS transcriptional factor on codon bias in Arabidopsis and RiceMost of the flower development-related functional genes are belong to MADS transcription factors families. Through the factorial correspondence analysis(FCA) of CodonW, we can find out that MADS transcriptional factors in Arabidopsis prefer to A-ending and U-ending codons, while that in rice prefer to G-ending and C-ending codons. By using the ClustalX for searching the relation between the bias of the codons and second structure of the MADS, we confirm that the amino acids coding by different codons are on the special position of the second structure of the proteins.3. The structure and phylogenetics analysis of MADS transcription factors in plants42 Arabidopsis and 25 Rice MADS-box proteins have been obtained in this article. The average length of MADS-box proteins in Arabidopsis (247aa) is some longer than it in Rice (222aa). The GC content in Arabidopsis (42.59%) is lower than it in Rice (56.91%). In Arabidopsis the polar amino acids is highest and in Rice the hydrophobic amino acids is the highest. Meanwhile, multisequences alignments have been done to confirm the 4 domains and the amino acids motifs (M-R(-)7I(-)5R(-)2T(-)2KRR-GL- -KA(-)5LC). Through phylogenetics analysis with 17 known sequences, 42 Arabidopsis sequences and 25 Rice sequences have been divided into AGL2, AGL6, SQUA, AG, GLO, AP3 and a new sub-family that have the different function in the floral development.4. Comparison of MYB transcriptional factor on codon bias in Arabidopsis and RiceThe GC contents of MYB transcription factors in Arabidopsis and Rice have significant difference, Rice with high GC content prefer to the C-ending and G-ending codons which are of 68.8% and 46.2% separated. However Arabidopsis with low GC content doesn't prefer to C-ending and G-ending codons which only are of 21.6% and 6.3%. Confered that GC content of MYB transcription factors in Arabidopsis and Rice have crucial effect on codon bias. Factorial correspondence analysis(FCA) of CodonW indicated that MYB transcription factors in Arabidopsis prefer to A-ending and U-ending codons. A-ending and U-ending codons grouped together and could be distinguished from two other groups the C-ending and G-ending codons on the picture of the FCA. Meanwhile we find that the usage bias of codons have made some influences on second structure.Plant MYB transcription factors are characterized by containing a structurally conserved MYB domain and play ubiquitous roles in the regulation of plant development and metabolism. Studying the codon bias of MYB is very significance to the plant. We have compared the codon usage of transcriptional factors in Arabidopsis and Rice. Through the factorial correspondence analysis(FCA) of CodonW, We can find out thatMYB transcriptional factors all prefer to A-ending and U-ending codons.,A-ending and U-ending codons grouped together and could be distinguished from two other groups the C-ending and G-ending codons on the picture of the FCA. Meanwhile we analysis the second structure of MYB and find that the usage bias of codons have made some influences on it.5. The analysis of MYB transcription factors in Arabidopsis and Rice96 and 116 transcription factors have been found in the Rice and Arabidopsis through the genome researching. R1R2 subfamilies is the largest which are 62.2% and 71.6%. Then the larger is the Rl subfamilies and the less subfamilies is the R1R2R3. 11 Arabidopsis and 13 Rice R1R2R3 MYB proteins have been compared in this article. The average length of R1R2R3 MYB proteins in Arabidopsis (381aa) is longer than it in Rice (283aa). The GC content in Arabidopsis (42.6%) is lower than it in Rice (67%). In the both plants, the contents of all kinds of amino acids are similar to each other. Meanwhile, the domains have been conformed through the multisequences alignment, and these proteins have been set off as 6 groups in order to analysis their functions. The R1R2R3 subfamilies have high homologous to that in animal and epiphyte.