Romero Héctor, Zavala Alejandro, Musto Héctor, Bernardi Giorgio
Laboratorio di Evoluzione Molecolare, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples 80121, Italy.
Gene. 2003 Oct 23;317(1-2):141-7. doi: 10.1016/s0378-1119(03)00701-7.
In this paper, the main factors shaping codon usage in three species of fishes that belong to the family Cyprinidae (namely Brachidanio rerio, Cyprinus carpio, and Carassius auratus) are reported. Correspondence analysis (COA), a commonly used multivariate statistical approach, was used to analyze codon usage bias. Our results show that the main trend is strongly correlated with the GC(3) content at silent sites of each sequence. On the other hand, the second axis discriminates between presumed highly and lowly expressed genes, a result that is confirmed by the distribution of matching expressed sequence tags (ESTs) along that axis. Translational selection appears, therefore, to influence synonymous codon usage in these fishes. The comparison of codon usages of the sequences displaying the extreme values on the second axis indicates that several codons are significantly incremented among the heavily expressed sequences. Interestingly, several of these triplets are not only shared by the three fishes but also by Xenopus laevis, another cold-blooded vertebrate in which translational selection influences codon choices. We postulate that natural selection was operative for codon usage in the last common ancestor of these fishes and Xenopus, and will probably be detected in cold-blooded vertebrates in general. Finally, we raise the possibility that the same phenomena will be found among warm-blooded vertebrates.
本文报道了鲤科三种鱼类（即斑马鱼、鲤鱼和鲫鱼）中影响密码子使用的主要因素。对应分析（COA）是一种常用的多元统计方法，用于分析密码子使用偏好。我们的结果表明，主要趋势与每个序列沉默位点的GC(3)含量密切相关。另一方面，第二轴区分了假定的高表达基因和低表达基因，这一结果通过匹配的表达序列标签（EST）沿该轴的分布得到了证实。因此，翻译选择似乎影响了这些鱼类的同义密码子使用。对在第二轴上显示极值的序列的密码子使用情况进行比较表明，在高表达序列中，有几个密码子显著增加。有趣的是，这些三联体中的几个不仅在这三种鱼类中共享，而且在非洲爪蟾（另一种翻译选择影响密码子选择的冷血脊椎动物）中也存在。我们推测，自然选择在这些鱼类和非洲爪蟾的最后一个共同祖先中对密码子使用起作用，并且可能在一般冷血脊椎动物中也能检测到。最后，我们提出在温血脊椎动物中也可能发现相同现象的可能性。
