【作者】 李娟；

【导师】 薛庆中；

【作者基本信息】 浙江大学 ， 生物信息学， 2005， 硕士

【摘要】 该论文比较了水稻和拟南芥全基因组MYB和MADS两转录因子的密码子用法偏性,阐述了他们的结构特点、并作了系统进化分析;所得结果将有助于对植物转录因子的相互作用及基因表达和调控方式的深入探讨,在作物育种上也有潜在价值。1、植物转录因子的研究进展 植物各种诱导型基因的表达主要受特定转录因子在转录水平上的调控。典型的转录因子含有DNA结合区、转录调控区、寡聚化位点及核定位信号专区等功能区域。本文简要介绍转录因子的概念、结构及分类。同时分别介绍了MYB和MADS两转录因子的研究概况。2、拟南芥及水稻转录因子MADS密码子的偏好性比较 大多数与花发育相关的功能基因属于MADS基因家族。应用CodonW的因子分析表明,拟南芥MADS转录因子家族偏好使用A、U结尾的密码子,而水稻MADS转录因子家族偏好使用G、C结尾的密码子。同时通过氨基酸序列的多重比对表明密码子偏好性与氨基酸序列及二级结构之间存在关联,证实了不同的密码子编码的氨基酸位于蛋白质二级结构的特定位置。3、水稻和拟南芥MADS转录因子家族结构及系统进化分析 从水稻和拟南芥全基因组中分别得到了42条和25条水稻MADS盒蛋白,其中拟南芥MADS盒ORF的平均长度为247aa,GC含量较低(42.59%),而水稻平均长度为222aa,GC含量较高(56.91%)。拟南芥极性氨基酸含量最高(30%),而水稻中疏水性氨基酸含量最高(33%)。通过多序列比对,进一步确定了MADS盒基因的4个区域,及MADS区域的氨基酸保守基序:M-R(-)7I(-)5R(-)2T(-)2KRR-GL--KA(-)5LC。将已知的17条氨基酸序列,42条拟南芥和25条水稻MADS序列进行系统进化分析,发现这些序列分别归属在AGL2、AGL6、SQUA、AG、GLO、AP3和未知的新亚家族,每个亚家族可能在花发育中扮演重要的的调节作用。更多还原

【Abstract】 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.更多还原