Wang J, Zhang C T
Department of Physics, Tianjin University, China.
J Biomol Struct Dyn. 2001 Jun;18(6):872-80. doi: 10.1080/07391102.2001.10506714.
The codon usage in the Vibrio cholerae genome is analyzed in this paper. Although there are much more genes on the chromosome 1 than on chromosome 2, the codon usage patterns of genes on the two chromosomes are quite similar, indicating that the two chromosomes may have coexisted in the same cell for a very long history. Unlike the base frequency pattern observed in other genomes, the G+C content at the third codon position of the V. cholerae genome varies in a rather small interval. The most notable feature of codon usage of V. cholerae genome is that there is a fraction of genes show significant bias in base choice at the second codon position. The 2,006 known genes can be classified into two clusters according to the base frequencies at this position. The smaller cluster contains 227 genes, most of which code for proteins involved in transport and binding functions. The encoding products of these genes have significant bias in amino acids composition as compared with other genes. The codon usage patterns for the 1,836 function unknown ORFs are also analyzed, which is useful to study their functions.
本文分析了霍乱弧菌基因组中的密码子使用情况。虽然1号染色体上的基因比2号染色体上的多得多，但两条染色体上基因的密码子使用模式非常相似，这表明两条染色体可能在同一细胞中共存了很长时间。与其他基因组中观察到的碱基频率模式不同，霍乱弧菌基因组第三密码子位置的G+C含量在相当小的区间内变化。霍乱弧菌基因组密码子使用的最显著特征是有一部分基因在第二密码子位置的碱基选择上表现出显著偏差。根据该位置的碱基频率，2006个已知基因可分为两个簇。较小的簇包含227个基因，其中大多数编码参与转运和结合功能的蛋白质。与其他基因相比，这些基因的编码产物在氨基酸组成上有显著偏差。还分析了1836个功能未知的开放阅读框的密码子使用模式，这有助于研究它们的功能。
