$E.coli$相互作用蛋白的密码子偏好模式
Codon Bias Patterns of $E.coli$'s Interacting Proteins
摘要：
同义密码子，即，编码相同氨基酸的DNA核苷酸三联体在各种生物体中的使用不同。这种现象的生物学意义，称为密码子使用偏好，仍然存在争议。为了阐明这一点，我们提出了一个新的密码子偏好指数，$CompAI$，这是基于翻译过程中同源和近同源tRNA之间的竞争，而不被调整到高表达基因的使用偏好。我们对$E.coli$的密码子偏好进行了全基因组评估，将$CompAI$与其他广泛使用的指数：$tAI$、$CAI$和$Nc$进行了比较。我们发现，$CompAI$和$tAI$捕获类似的信息，正相关的基因保守性，测量ERI，和必要性，而$CAI$和$Nc$似乎是不太敏感的进化功能参数。值得注意的是，$tAI$和$CompAI$与ERI的变异率允许获得一致地属于特定的直链淀粉基因簇（COG）的基因组。我们还研究了基因组水平上密码子偏好性与$E.coli$中蛋白质-蛋白质相互作用网络特征的相关性。我们发现，网络中连接最紧密的社区具有相似的密码子偏好水平（通过$CompAI$和$tAI$测量）。相反，两个基因之间密码子偏好的微小差异在统计学上是相应蛋白质相互作用的先决条件。重要的是，在所有密码子偏好指数中，$CompAI$在相互作用组的群落中具有最一致的分布，这表明同源和近同源tRNA之间的竞争对于解释密码子使用适应的重要性。
英文摘要：
Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In order to shed light on this point, we propose a new codon bias index, $CompAI$, that is based on the competition between cognate and near-cognate tRNAs during translation, without being tuned to the usage bias of highly expressed genes. We perform a genome-wide evaluation of codon bias for $E.coli$, comparing $CompAI$ with other widely used indices: $tAI$, $CAI$, and $Nc$. We show that $CompAI$ and $tAI$ capture similar information by being positively correlated with gene conservation, measured by ERI, and essentiality, whereas, $CAI$ and $Nc$ appear to be less sensitive to evolutionary-functional parameters. Notably, the rate of variation of $tAI$ and $CompAI$ with ERI allows to obtain sets of genes that consistently belong to specific clusters of orthologous genes (COGs). We also investigate the correlation of codon bias at the genomic level with the network features of protein-protein interactions in $E.coli$. We find that the most densely connected communities of the network share a similar level of codon bias (as measured by $CompAI$ and $tAI$). Conversely, a small difference in codon bias between two genes is, statistically, a prerequisite for the corresponding proteins to interact. Importantly, among all codon bias indices, $CompAI$ turns out to have the most coherent distribution over the communities of the interactome, pointing to the significance of competition among cognate and near-cognate tRNAs for explaining codon usage adaptation.
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