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首页> 外文期刊>Computational Biology and Bioinformatics, IEEE/ACM Transactions on >Evolutionary Pressures on the Yeast Transcriptome
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Evolutionary Pressures on the Yeast Transcriptome

机译：酵母转录组的进化压力

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摘要

Codon usage bias (CUB) is the well known phenomenon that the frequency of synonymous codons is unequal. This is presumably the result of adaptive pressures favouring some codons over others. The underlying reason for this pressure is unknown, although a large number of possible driver mechanisms have been proposed; one of them is the decoding time. The standard model to calculate decoding time is the Gromadski-Rodnina model. Yet, recently, there have been a number of studies arguing to the effect that this conventional speed-model is not relevant to understand the dynamics of translation. However, results remain inconclusive so far. This contribution takes a novel approach to address this issue based on comparing mRNA with random synonymous variants to estimate the evolutionary pressures that have acted on the transcriptome. It emerges that over 70 percent of ORFs have been subject to a strong selection pressure for translation speed and that there is also a strong selection pressure for the avoidance of traffic jams. Finally, it is also shown that both homogeneous and very heterogeneous transcripts are over-represented. These results corroborate the validity of the Gromadski-Rodnina model.
机译：密码子使用偏倚（CUB）是众所周知的现象，即同义密码子的频率不相等。据推测，这是自适应压力导致某些密码子胜于其他密码子的结果。尽管提出了许多可能的驱动器机制，但造成这种压力的根本原因尚不清楚。其中之一是解码时间。计算解码时间的标准模型是Gromadski-Rodnina模型。然而，最近，有许多研究争论这种传统速度模型与理解翻译动力学无关。但是，到目前为止，结果仍然不确定。这种贡献采用了一种新颖的方法来解决这个问题，其基础是将mRNA与随机同义变体进行比较，以估算作用于转录组的进化压力。结果表明，超过70％的ORF承受着很大的翻译速度选择压力，并且还存在着避免交通堵塞的强大选择压力。最后，还表明同质和非常异质的转录本都被过度代表。这些结果证实了Gromadski-Rodnina模型的有效性。

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