Salim Hannah M W, Ring Karen L, Cavalcanti Andre R O
Biology Department, Pomona College, 175 w 6th street, Claremont, CA 91711, USA.
Protist. 2008 Apr;159(2):283-98. doi: 10.1016/j.protis.2007.11.003. Epub 2008 Jan 22.
We used the recently sequenced genomes of the ciliates Tetrahymena thermophila and Paramecium tetraurelia to analyze the codon usage patterns in both organisms; we have analyzed codon usage bias, Gln codon usage, GC content and the nucleotide contexts of initiation and termination codons in Tetrahymena and Paramecium. We also studied how these trends change along the length of the genes and in a subset of highly expressed genes. Our results corroborate some of the trends previously described in Tetrahymena, but also negate some specific observations. In both genomes we found a strong bias toward codons with low GC content; however, in highly expressed genes this bias is smaller and codons ending in GC tend to be more frequent. We also found that codon bias increases along gene segments and in highly expressed genes and that the context surrounding initiation and termination codons are always AT rich. Our results also suggest differences in the efficiency of translation of the reassigned stop codons between the two species and between the reassigned codons. Finally, we discuss some of the possible causes for such translational efficiency differences.
我们利用最近测序的嗜热四膜虫和四尾草履虫的基因组来分析这两种生物的密码子使用模式；我们分析了四膜虫和草履虫的密码子使用偏好、谷氨酰胺密码子使用情况、GC含量以及起始和终止密码子的核苷酸上下文。我们还研究了这些趋势如何沿基因长度以及在一组高表达基因中发生变化。我们的结果证实了先前在四膜虫中描述的一些趋势，但也否定了一些具体观察结果。在这两个基因组中，我们都发现了对低GC含量密码子的强烈偏好；然而，在高表达基因中，这种偏好较小，以GC结尾的密码子往往更频繁。我们还发现密码子偏好沿着基因片段和在高表达基因中增加，并且起始和终止密码子周围的上下文总是富含AT。我们的结果还表明，在这两个物种之间以及重新分配后的密码子之间，重新分配的终止密码子的翻译效率存在差异。最后，我们讨论了这种翻译效率差异的一些可能原因。
