Large Scale Comparative Codon-Pair Context Analysis Unveils General Rules that Fine-Tune Evolution of mRNA Primary Structure
Large Scale Comparative Codon-Pair Context Analysis Unveils General Rules that Fine-Tune Evolution of mRNA Primary Structure
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DOI：
10.1371/journal.pone.0000847
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发表时间：
2007-09-05
期刊：
影响因子：
3.7
通讯作者：
Santos, Manuel A. S.
中科院分区：
文献类型：
--
作者：
Moura, Gabriela;Pinheiro, Miguel;Santos, Manuel A. S.
背景密码子使用和密码子对上下文是影响mRNA解码保真度的重要基因一级结构特征。为了确定塑造密码子对上下文和最小化mRNA解码错误的一般规则，我们对119个完全测序的基因组进行了大规模比较密码子对上下文分析。方法/主要发现。我们已经开发了用于大规模比较密码子对上下文分析的数学和软件工具。这些方法揭示了在生命的3个领域中控制mRNA进化的一般和物种特异性密码子对上下文规则。我们发现，细菌和古细菌mRNA一级结构的进化主要取决于翻译机制的限制，而在真核生物中，DNA甲基化和三核苷酸重复序列对密码子对上下文施加了强烈的偏见。结论.这些数据突出了原核和真核mRNA解码规则之间的根本差异，这些差异部分独立于密码子的使用。
Background. Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. Methodologies/Principal Findings. We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. Conclusions. The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage.