Sahu K, Gupta S K, Sau S, Ghosh T C
Bioinformatics Centre, Bose Institute, P1/12 - CIT Scheme VII M, Calcutta 700 054, India.
J Biomol Struct Dyn. 2005 Aug;23(1):63-71. doi: 10.1080/07391102.2005.10507047.
To study the possible codon usage and base composition variation in the bacteriophages, fourteen mycobacteriophages were used as a model system here and both the parameters in all these phages and their plating bacteria, M. smegmatis had been determined and compared. As all the organisms are GC-rich, the GC contents at third codon positions were found in fact higher than the second codon positions as well as the first + second codon positions in all the organisms indicating that directional mutational pressure is strongly operative at the synonymous third codon positions. Nc plot indicates that codon usage variation in all these organisms are governed by the forces other than compositional constraints. Correspondence analysis suggests that: (i) there are codon usage variation among the genes and genomes of the fourteen mycobacteriophages and M. smegmatis, i.e., codon usage patterns in the mycobacteriophages is phage-specific but not the M. smegmatis-specific; (ii) synonymous codon usage patterns of Barnyard, Che8, Che9d, and Omega are more similar than the rest mycobacteriophages and M. smegmatis; (iii) codon usage bias in the mycobacteriophages are mainly determined by mutational pressure; and (iv) the genes of comparatively GC rich genomes are more biased than the GC poor genomes. Translational selection in determining the codon usage variation in highly expressed genes can be invoked from the predominant occurrences of C ending codons in the highly expressed genes. Cluster analysis based on codon usage data also shows that there are two distinct branches for the fourteen mycobacteriophages and there is codon usage variation even among the phages of each branch.
为了研究噬菌体中可能的密码子使用情况和碱基组成变化，本文以14种分枝杆菌噬菌体作为模型系统，测定并比较了所有这些噬菌体及其宿主菌耻垢分枝杆菌的相关参数。由于所有生物都富含GC，实际上发现所有生物中第三个密码子位置的GC含量高于第二个密码子位置以及第一个 + 第二个密码子位置，这表明定向突变压力在同义第三个密码子位置强烈起作用。Nc图表明，所有这些生物中的密码子使用变化受组成限制以外的其他因素控制。对应分析表明：（i）14种分枝杆菌噬菌体和耻垢分枝杆菌的基因和基因组之间存在密码子使用变化，即分枝杆菌噬菌体中的密码子使用模式是噬菌体特异性的，而不是耻垢分枝杆菌特异性的；（ii）Barnyard、Che8、Che9d和Omega的同义密码子使用模式比其他分枝杆菌噬菌体和耻垢分枝杆菌更相似；（iii）分枝杆菌噬菌体中的密码子使用偏好主要由突变压力决定；（iv）GC含量相对较高的基因组的基因比GC含量低的基因组更具偏好性。从高表达基因中以C结尾的密码子占主导地位，可以推断翻译选择在决定高表达基因的密码子使用变化中起作用。基于密码子使用数据的聚类分析还表明，14种分枝杆菌噬菌体有两个不同的分支，并且每个分支的噬菌体之间也存在密码子使用变化。
