General rules for optimal codon choice.
General rules for optimal codon choice.
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DOI：
10.1371/journal.pgen.1000556
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发表时间：
2009-07
期刊：
影响因子：
4.5
通讯作者：
Petrov DA
中科院分区：
文献类型：
--
作者：
Hershberg R;Petrov DA
不同的同义密码子在不同的生物体中由于翻译效率和准确性而受到自然选择的青睐。管理不同生物体中有利密码子身份的规则仍然不清楚。事实上，我们不知道是否存在这样的规则，或者是否在进化过程中，在类似于一系列冻结事故的过程中，偏好的密码子是随机选择的。在这里，我们通过首次识别675种细菌，52种古细菌和10种真菌中的有利密码子来研究这个问题。我们使用了大量的测试来表明，所确定的密码子确实可能是有利的，并发现在所有研究的生物体中，有利密码子的身份跟踪基因组的GC含量。一旦考虑到基因组GC含量对选择性偏好密码子选择的影响，控制偏好密码子身份的其他通用氨基酸特异性规则就变得明显。我们的研究结果第一次提供了一套明确的规则，管理选择性偏好密码子使用的演变。基于这些结果，我们描述了一个假设的场景，即选择性偏好密码子身份的进化转变如何发生，而不会因密码子偏好而暂时削弱自然选择。密码子偏好性是一种长期被认识和研究的生物学现象。然而，关于密码子使用的几个基本问题仍然没有得到解决。在这里，我们解决这样一个基本的悬而未决的问题：选择有利于翻译的准确性和效率的密码子的身份差异很大，乍一看，基因组之间的特异性。在不同的基因组中，有哪些规则决定了偏爱的密码子的身份？我们系统地鉴定了675种细菌、52种古细菌和10种真菌的最佳密码子。使用这些数据，我们表明，普遍在所有细菌，古细菌和真菌的青睐密码子的身份跟踪作为一个整体的基因组的核苷酸含量。一旦考虑到核苷酸含量对选择性偏好密码子选择的影响，另外，直到现在还未知的，支配选择性偏好密码子的身份的通用氨基酸特异性规则变得明显。最后，我们使用我们的研究结果提供了一个合理的方案，最佳密码子的身份如何可以通过跟踪基因组的核苷酸模式，而不需要减少选择基因组之间的转移。
Different synonymous codons are favored by natural selection for translation efficiency and accuracy in different organisms. The rules governing the identities of favored codons in different organisms remain obscure. In fact, it is not known whether such rules exist or whether favored codons are chosen randomly in evolution in a process akin to a series of frozen accidents. Here, we study this question by identifying for the first time the favored codons in 675 bacteria, 52 archea, and 10 fungi. We use a number of tests to show that the identified codons are indeed likely to be favored and find that across all studied organisms the identity of favored codons tracks the GC content of the genomes. Once the effect of the genomic GC content on selectively favored codon choice is taken into account, additional universal amino acid specific rules governing the identity of favored codons become apparent. Our results provide for the first time a clear set of rules governing the evolution of selectively favored codon usage. Based on these results, we describe a putative scenario for how evolutionary shifts in the identity of selectively favored codons can occur without even temporary weakening of natural selection for codon bias. Codon bias is a long recognized and long studied biological phenomenon. Yet several basic questions regarding codon usage remain unresolved. Here, we address one such basic open question: the identity of the codons that are favoured by selection for translation accuracy and efficiency varies greatly and, at first glance, idiosyncratically among genomes. What are the rules governing the identity of favoured codons in the different genomes? We systematically identified the optimal codons of 675 bacteria, 52 archea, and 10 fungi. Using these data, we show that universally across all bacteria, archea, and fungi the identity of the favoured codons tracks the nucleotide content of the genome as a whole. Once the effect of nucleotide content on selectively favored codon choice is taken into account, additional, until now unknown, universal amino acid specific rules governing the identity of selectively favored codons become apparent. Finally, we use our findings to offer a plausible scenario as to how the identity of optimal codons can shift between genomes by tracking the nucleotide patterns of the genome and without necessitating a reduction in selection.
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DOI：
10.1073/pnas.96.8.4482
发表时间：
1999-04-13
影响因子：
11.1
作者：
Duret, L;Mouchiroud, D
通讯作者：
Mouchiroud, D
影响因子：
3.4
作者：
Vicario S;Moriyama EN;Powell JR
通讯作者：
Powell JR
影响因子：
5.6
作者：
CRICK, FHC
通讯作者：
CRICK, FHC
影响因子：
3.9
作者：
Kanaya, S;Yamada, Y;Ikemura, T
通讯作者：
Ikemura, T
影响因子：
3.5
作者：
Kanaya, S;Yamada, Y;Ikemura, T
通讯作者：
Ikemura, T