Codon usage in the G+C-rich Streptomyces genome.
Codon usage in the G+C-rich Streptomyces genome.
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DOI：
10.1016/0378-1119(92)90669-g
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发表时间：
1992-04
期刊：
影响因子：
3.5
通讯作者：
Frank Wright;M. Bibb
中科院分区：
文献类型：
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作者：
Frank Wright;M. Bibb
分析了来自革兰氏阳性原核链霉菌属的64个基因的密码子使用（CU）模式。尽管链霉菌基因组的总体G+ C含量极高（估计为0.74），但单个基因的G+ C含量在0.610至0.797之间变化，并且具有在0.764至0.983之间变化的第三密码子位置G+ C含量（GC 3s）。GC 3的变化解释了CU模式变化的一个重要部分。这与链霉菌基因组的进化模型一致，其中偏置突变压力导致高平均G+ C含量与平均值的随机变化，尽管观察到的变化大于从简单的二项式模型预期的变化。样品中唯一可以确信地预测为高表达的基因，天蓝色链霉菌A3的EF-Tu（2）（GC 3s = 0.927），在四个密码子家族中的几个中显示第三位C的偏好性，并且Arg和Gly密码子分别为CGY和GGY（Y=嘧啶）;在富含G+ C的浅黄色微球菌基因组的高表达基因中发现了类似的CU模式。因此，链霉菌中的密码子使用似乎主要由突变偏好决定，弱翻译选择仅在高表达基因中起作用。我们讨论了链霉菌极端密码子偏好可能产生的后果，并考虑了它可能是如何进化的。提供了一组CU表，用于定位蛋白质编码区的计算机程序。
The codon usage (CU) patterns of 64 genes from the Gram+ prokaryotic genus Streptomyces were analysed. Despite the extremely high overall G+ C content of the Streptomyces genome (estimated at 0.74), individual genes varied in G+ C content from 0.610 to 0.797, and had third codon position G+ C contents (GC3s) that varied from 0.764 to 0.983. The variation in GC3s explains a significant proportion of the variation in CU patterns. This is consistent with an evolutionary model of the Streptomyces genome where biased mutation pressure has led to a high average G+ C content with random variation about the mean, although the variation observed is greater than that expected from a simple binomial model. The only gene in the sample that can be confidently predicted to be highly expressed, EF-Tu of Streptomyces coelicolor A3 (2)(GC 3 s= 0.927), shows a preference for a third position C in several of the four codon families, and for CGY and GGY for Arg and Gly codons, respectively (Y= pyrimidine); similar CU patterns are found in highly expressed genes of the G+ C-rich Micrococcus luteus genome. It thus appears that codon usage in Streptomyces is determined predominantly by mutation bias, with weak translational selection operating only in highly expressed genes. We discuss the possible consequences of the extreme codon bias of Streptomyces and consider how it may have evolved. A set of CU tables is provided for use with computer programs that locate protein-coding regions.