Basak S, Banerjee T, Gupta S K, Ghosh T C
Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India.
J Biomol Struct Dyn. 2004 Oct;22(2):205-14. doi: 10.1080/07391102.2004.10506996.
Base composition, codon usages and amino acid usages have been analyzed by taking 529 orthologous sequences of Aquifex aeolicus and Bacillus subtilis, having different optimal growth temperatures. These two bacteria do not have significant difference in overall GC composition, but GC(1+2) and GC3 levels were found to vary significantly. Significant increments in purine content and GC3 composition have been observed in the coding sequences of Aquifex aeolicus than its Bacillus subtilis counterparts. Correspondence analyses on codon and amino acid usages reveal that variation in base composition actually influences their codon and amino acid usages. Two selection pressures acting on the nucleotide level (GC3 and purine enrichment), causes variation in the amino acid usage differently in different protein secondary structures. Our results suggest that adaptation of amino acid usages in coil structure of Aquifex aeolicus proteins is under the control of both purine increment and GC3 composition, whereas the adaptation of the amino acids in the helical region of thermophilic bacteria is strongly influenced by the purine content. Evolutionary perspectives concerning the temperature adaptation of DNA and protein molecules of these two bacteria have been discussed on the basis of these results.
通过选取嗜热栖热菌和枯草芽孢杆菌的529个直系同源序列，分析了碱基组成、密码子使用情况和氨基酸使用情况，这两种细菌具有不同的最适生长温度。这两种细菌的总体GC组成没有显著差异，但发现GC(1+2)和GC3水平有显著变化。与枯草芽孢杆菌的对应序列相比，嗜热栖热菌的编码序列中嘌呤含量和GC3组成有显著增加。对密码子和氨基酸使用情况的对应分析表明，碱基组成的变化实际上会影响它们的密码子和氨基酸使用情况。作用于核苷酸水平的两种选择压力（GC3和嘌呤富集），在不同的蛋白质二级结构中对氨基酸使用情况产生不同的影响。我们的结果表明，嗜热栖热菌蛋白质卷曲结构中氨基酸使用情况的适应性受嘌呤增加和GC3组成的共同控制，而嗜热菌螺旋区域中氨基酸的适应性受嘌呤含量的强烈影响。基于这些结果，讨论了这两种细菌DNA和蛋白质分子温度适应性的进化观点。
