密码子位点特征初步研究和组蛋白基因进化动力学比较

【作者】 赵国焓；

【导师】 许晓风；

【作者基本信息】 南京师范大学 ， 遗传学， 2007， 硕士

【摘要】 采用生物信息学的方法，对GenBank和KEGG和DW等数据库中记录的20个物种187511个CDS的密码子碱基分布和各类真核生物H2A和H2B基因的分子数据进行了较为系统的分析，取得了以下主要研究结果：1．某种碱基在各位点上的含量与该碱基的总含量都存在正相关。碱基含量对该碱基在第三密码位的分布的影响要远大于其他的两个密码位。这一现象起到对蛋白质进化稳定性的调节作用。2．密码子的使用过程中T在第二位使用的频率远大于第一位，G在第一位的使用频率则比第二位高的多。这一现象同密码表中该位点的碱基所编码的氨基酸特征有极大的关系。3．同一基因在不同物种中T在第二密码位和第一密码位的比值与基因组比值的差距各不相同，这可能是在生物由低级向高级进化过程中，非保守基因含量的增加有关。4．在动物中组蛋白H2A、H2B的表达效率与GC含量和GC3含量呈显著的正相关，真菌恰好相反，两者呈负相关，而植物却表现出不相关。表明三类生物H2A、H2B密码子偏爱使用所承受的选择压力明显不同，其中，动物的正选择压是密码子与反密码子作用的稳定性，真菌的正选择压则是密码子与反密码子作用的效率性，植物则选择了稳定和效率的平衡。5．H2A、H2B基因的ps和pN在三类生物的种间和种内的表现为：动物和植物PS>>PN，真菌PS~PN，单细胞酵母PS<<PN。动物和植物H2A、H2B遵从净化选择下的birth-and-death模式，真菌遵从介于净化选择下的birth-and-death和协同进化之间的模式，单细胞酵母则遵从协同进化模式。更多还原

【Abstract】 By using the method of bioinformatics, we analyzed the distributing of 187511 CDS’ codon bases from 20 species and different organisms’ histone genes H2A and H2B. These data are all from GenBank, KEGG and DW DateBase.The results are as follows:1. Within the 20 species, one codon content in each codon position has the obvious positive correlation with the codon’s whole content. The effect of codon content in 3rd codon position shows much grater than the other positions. This phenomenon plays a part in the stabilization of protein evolution.2. In usage of codons, the frequency of T in 2nd codon position is much higher than in 1st codon position; on the contrary, the frequency of C in 2nd codon position is much lower than in 1st codon position. The character of amino acid coding by the base in this position plays an important part in this conclusion.3. The discrepancy between T2/T1 values of the same gene and those of the genomes are different in different species. The reason maybe is that: with the evolution of the organism from the lower species to the higher species, the content of non-keeping genes is much more than before.4. Within the animals’ H2A and H2B, the GC% and GC3% has the obvious positive correlation with thire expression efficiency. On the contrary, fungi show the negative correlation and plants show no correlation. Fungi, plants and animals’ H2A, H2B genes have gone through different selection pression in of synonymous codons’ usage; fungi H2A, H2B genes’ positive selection is translation efficiency while animals’ positive selection is translation stability. Otherwise plants choose the balance between translation efficiency and translation stability.5. Fungi, plants and animals H2A, H2B genes’ p_S and p_N behaviors both within and between species are quite different, with plants and animals H2A, H2B genes’ showing p_S>>p_N, fungi H2A and H2B genes’ showing p_S≈p_N, yeasts H2A and H2B showing p_N>>p_S. So they may follow different evolution models, with plants and animals’ H2A, H2B genes following the birth-and-death model, fungi’s H2A, H2B genes following the between birth-and-death model and concerted evolution model, and yeasts’ H2A and H2B genes following the concerted evolution model.更多还原