Relationships among stop codon usage bias, its context, isochores, and gene expression level in various eukaryotes
Relationships among stop codon usage bias, its context, isochores, and gene expression level in various eukaryotes
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DOI：
10.1007/s00239-004-0277-3
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发表时间：
2005-10-01
影响因子：
3.9
通讯作者：
Luo, JH
中科院分区：
文献类型：
--
作者：
Sun, JC;Chen, M;Luo, JH
众所周知，终止密码子在蛋白质合成过程中起着至关重要的作用。然而，很少有人努力调查终止密码子的使用是否表现出偏差，例如广泛观察到的同义密码子的使用。在这里，我们系统地研究了各种真核生物中的终止密码子使用偏差及其与其背景、GC3 含量、基因表达水平和二级结构的关系。结果表明，不同真核生物中终止密码子的使用存在很强的偏差，即UAA在低等真核生物中过多，UGA在高等真核生物中过多，而UAG在所有真核生物中最少使用。基于信息内容和标识分析，发现不同真核生物类别中每个终止密码子的不同保守模式。 GC3含量随着生物体复杂性的增加而增加。二级结构预测表明，UAA 通常与环结构相关，而 UGA 更均匀地存在于环和茎结构中，即 UGA 较少偏向于具有特定结构。然而，终止密码子使用偏差与个体真核生物中的 GC3 含量和基因表达水平没有显着关系。结果表明，基因组复杂性和 GC3 含量可能导致不同真核生物的终止密码子使用偏差。我们的结果表明，终止密码子与同义密码子一样，在使用中表现出偏差。需要进行更多的工作来了解这些偏差的原因及其与蛋白质终止机制的关系。
It is well known that stop codons play a critical role in the process of protein synthesis. However, little effort has been made to investigate whether stop codon usage exhibits biases, such as widely seen for synonymous codon usage. Here we systematically investigate stop codon usage bias in various eukaryotes as well as its relationships with its context, GC3 content, gene expression level, and secondary structure. The results show that there is a strong bias for stop codon usage in different eukaryotes, i.e., UAA is overrepresented in the lower eukaryotes, UGA is overrepresented in the higher eukaryotes, and UAG is least used in all eukaryotes. Different conserved patterns for each stop codon in different eukaryotic classes are found based on information content and logo analysis. GC3 contents increase with increasing complexity of organisms. Secondary structure prediction revealed that UAA is generally associated with loop structures, whereas UGA is more uniformly present in loop and stem structures, i.e., UGA is less biased toward having a particular structure. The stop codon usage bias, however, shows no significant relationship with GC3 content and gene expression level in individual eukaryotes. The results indicate that genomic complexity and GC3 content might contribute to stop codon usage bias in different eukaryotes. Our results indicate that stop codons, like synonymous codons, exhibit biases in usage. Additional work will be needed to understand the causes of these biases and their relationship to the mechanism of protein termination.