PDF(Pubmed)
Abstract：
In bacteria stop codons are recognized by one of two class I release factors (RF1) recognizing TAG, RF2 recognizing TGA, and TAA being recognized by both. Variation across bacteria in the relative abundance of RF1 and RF2 is thus hypothesized to select for different TGA/TAG usage. This has been supported by correlations between TAG:TGA ratios and RF1:RF2 ratios across multiple bacterial species, potentially also explaining why TAG usage is approximately constant despite extensive variation in GC content. It is, however, possible that stop codon trends are determined by other forces and that RF ratios adapt to stop codon usage, rather than vice versa. Here, we determine which direction of the causal arrow is the more parsimonious. Our results support the notion that RF1/RF2 ratios become adapted to stop codon usage as the same trends, notably the anomalous TAG behavior, are seen in contexts where RF1:RF2 ratios cannot be, or are unlikely to be, causative, that is, at 3\'untranslated sites never used for translation termination, in intragenomic analyses, and across archaeal species (that possess only one RF1). We conclude that specifics of RF biology are unlikely to fully explain TGA/TAG relative usage. We discuss why the causal relationships for the evolution of synonymous stop codon usage might be different from those affecting synonymous sense codon usage, noting that transitions between TGA and TAG require two-point mutations one of which is likely to be deleterious.
摘要：
在细菌中，终止密码子被识别TAG的两种I类释放因子（RF1）之一识别，RF2识别TGA，和TAA被两者认可。因此假设在RF1和RF2的相对丰度中的跨细菌的变化,以选择不同的TGA/TAG使用。TAG：TGA比率和RF1：RF2比率在多种细菌物种之间的相关性支持了这一点。这也可能解释了为什么尽管GC含量变化很大，但TAG的使用却大致恒定。是的,然而,可能终止密码子的趋势是由其他力量决定的，并且RF比率适应终止密码子的使用，而不是反之亦然。这里,我们确定因果箭头的哪个方向更简约。我们的结果支持RF1/RF2比率适应终止密码子使用的观点，特别是异常的TAG行为，在RF1:RF2比率无法达到的情况下，或者不太可能，因果关系,也就是说,在3个未翻译的网站上，从未用于翻译终止，在基因组内分析中，跨古细菌物种（仅拥有一个RF1）。我们得出结论，RF生物学的细节不太可能完全解释TGA/TAG的相对用法。我们讨论了为什么同义终止密码子使用进化的因果关系可能与影响同义密码子使用的因果关系不同，注意到TGA和TAG之间的转换需要两点突变,其中一个可能是有害的.
