Codon usage domains over bacterial chromosomes
Codon usage domains over bacterial chromosomes
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DOI：
10.1371/journal.pcbi.0020037
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发表时间：
2006-04-01
影响因子：
4.3
通讯作者：
Vergassola, Massimo
中科院分区：
文献类型：
--
作者：
Bailly-Bechet, Marc;Danchin, Antoine;Vergassola, Massimo
分析了原核生物基因组密码子偏好性分布的地理学特征及其对染色体结构的影响。为此，我们介绍了一种基于信息论的聚类方法，专门设计的聚类基因根据其密码子的使用，并将其应用到大肠杆菌和枯草芽孢杆菌的编码序列。在每个生物体中鉴定的簇之一被发现与表达水平相关，正如预期的那样，但其他组的特征是属于不同功能组的基因的过度表达，即水平转移的基因、运动性和中间代谢。此外，我们发现，具有类似的偏见的基因往往是接近彼此的染色体上，并组织在连贯的域，比操纵子更广泛，展示了翻译的作用，在构建细菌染色体。有人认为，这种效应的相当大的贡献来自于由tRNA的回收诱导的动态比较，导致基因表达率依赖于其基因组和表达背景。
The geography of codon bias distributions over prokaryotic genomes and its impact upon chromosomal organization are analyzed. To this aim, we introduce a clustering method based on information theory, specifically designed to cluster genes according to their codon usage and apply it to the coding sequences of Escherichia coli and Bacillus subtilis. One of the clusters identified in each of the organisms is found to be related to expression levels, as expected, but other groups feature an over-representation of genes belonging to different functional groups, namely horizontally transferred genes, motility, and intermediary metabolism. Furthermore, we show that genes with a similar bias tend to be close to each other on the chromosome and organized in coherent domains, more extended than operons, demonstrating a role of translation in structuring bacterial chromosomes. It is argued that a sizeable contribution to this effect comes from the dynamical compartimentalization induced by the recycling of tRNAs, leading to gene expression rates dependent on their genomic and expression context.