Comparison of synonymous codon distribution patterns of bacteriophage and host genomes.
Comparison of synonymous codon distribution patterns of bacteriophage and host genomes.
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DOI：
10.1093/dnares/5.6.319
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发表时间：
1998-12-31
期刊：
影响因子：
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通讯作者：
Kutter, E
中科院分区：
文献类型：
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作者：
Kunisawa, T;Kanaya, S;Kutter, E
比较了噬菌体和宿主基因组的同义密码子使用模式。用基因的G + C碱基组成（fgc）和最佳密码子比例（fop）两个指标进行比较。基因组上所有编码序列的同义密码子使用数据表示为fop与fgc平面中的点云。大肠杆菌编码序列似乎表现出两个阶段，“上升”和“平坦”阶段。在fgc vs.fop图中，生存所必需的基因和被认为是天然的基因位于平坦阶段，而来自原噬菌体和转座子的外源型基因位于上升阶段，斜率几乎为1。温带植物P4、P2、N15和λ基因的同义密码子分布模式与E.大肠杆菌上升期基因。相比之下，来自毒性噬菌体T7或T4的基因（鉴定了噬菌体编码的DNA聚合酶）在fop与fgc平面中落入斜率接近零的线性曲线中。这些结果可能提示T_7、T_4和E.大肠杆菌平相基因受到定向突变压力，并由复制中使用的DNA聚合酶决定。噬菌体基因的fop值存在显著变化，表明对基因表达水平的调整。对流感嗜血杆菌、枯草芽孢杆菌、结核分枝杆菌及其具有完整基因组序列的菌株进行了类似的密码子分布模式分析。
Synonymous codon usage patterns of bacteriophage and host genomes were compared. Two indexes, G + C base composition of a gene (fgc) and fraction of translationally optimal codons of the gene (fop), were used in the comparison. Synonymous codon usage data of all the coding sequences on a genome are represented as a cloud of points in the plane of fop vs. fgc. The Escherichia coli coding sequences appear to exhibit two phases, "rising" and "flat" phases. Genes that are essential for survival and are thought to be native are located in the flat phase, while foreign-type genes from prophages and transposons are found in the rising phase with a slope of nearly unity in the fgc vs. fop plot. Synonymous codon distribution patterns of genes from temperate phages P4, P2, N15 and lambda are similar to the pattern of E. coli rising phase genes. In contrast, genes from the virulent phage T7 or T4, for which a phage-encoded DNA polymerase is identified, fall in a linear curve with a slope of nearly zero in the fop vs. fgc plane. These results may suggest that the G + C contents for T7, T4 and E. coli flat phase genes are subject to the directional mutation pressure and are determined by the DNA polymerase used in the replication. There is significant variation in the fop values of the phage genes, suggesting an adjustment to gene expression level. Similar analyses of codon distribution patterns were carried out for Haemophilus influenzae, Bacillus subtilis, Mycobacterium tuberculosis and their phages with complete genomic sequences available.