Sau K, Gupta S K, Sau S, Ghosh T C
Bioinformatics Centre, Bose Institute, P1/12, CIT Scheme VII M, Calcutta 700 054, India.
Virus Res. 2005 Nov;113(2):123-31. doi: 10.1016/j.virusres.2005.05.001.
To reveal the factors influencing architecture of protein-coding genes in staphylococcal phages, relative synonymous codon usage variation has been investigated in 920 protein-coding genes of 16 staphylococcal phages. As expected for AT rich genomes, there are predominantly A and T ending codons in all 16 phages. Both Nc plot and correspondence analysis on relative synonymous codon usage indicates that mutation bias influences codon usage variation in the 16 phages. Correspondence analysis also suggests that translational selection and gene length also influence the codon usage variation in the phages to some extent and codon usage in staphylococcal phages is phage-specific but not S. aureus-specific. Further analysis indicates that among 16 staphylococcal phages, 44AHJD, P68 and K may be extremely virulent in nature as most of their genes have high translation efficiency. If this is true, then above three phages may be useful for curing staphylococcal infections.
为揭示影响葡萄球菌噬菌体中蛋白质编码基因结构的因素，对16种葡萄球菌噬菌体的920个蛋白质编码基因中的相对同义密码子使用变异进行了研究。正如富含AT的基因组所预期的那样，所有16种噬菌体中主要是A和T结尾的密码子。关于相对同义密码子使用的Nc图和对应分析表明，突变偏好影响16种噬菌体中的密码子使用变异。对应分析还表明，翻译选择和基因长度也在一定程度上影响噬菌体中的密码子使用变异，并且葡萄球菌噬菌体中的密码子使用是噬菌体特异性的，而不是金黄色葡萄球菌特异性的。进一步分析表明，在16种葡萄球菌噬菌体中，44AHJD、P68和K在本质上可能具有极强的毒性，因为它们的大多数基因具有较高的翻译效率。如果这是真的，那么上述三种噬菌体可能对治疗葡萄球菌感染有用。
