Banerjee T, Basak S, 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 Aug;22(1):13-23. doi: 10.1080/07391102.2004.10506976.
Endosymbiotic relationship has great effect on ecological system. Codon and amino acid usages bias of endosymbiotic bacteria Blochmannia floridanus (whose host is an ant Camponotus floridanus) was investigated using experimentally known genes of this organism. Correspondence Analysis on RSCU values show that there exists only one single explanatory major axis that is linked to the strand specific mutational biases. Majority of the genes have a tendency to concentrate on the leading strand, which may be related to the adaptive property related to the replication mechanisms. Amino acid usages were markedly different between the highly and lowly expressed genes in this organism and in particular, GC rich amino acids were found to occur significantly higher in highly expressed genes than the lowly expressed genes. Comparative analyses of the orthologous genes of Escherichia coli and Blochmannia floridanus show that highly expressed genes are significantly more conserved than lowly expressed genes. Based on our results we concluded that strand specific mutational bias is strongly operational in selecting the codon usage in this organism. Replicational-transcriptional selection can be invoked from the presence of majority of highly expressed genes in the leading strand. Conservation of GC rich amino acids in the highly expressed genes to its ancestor is the major source of variation in amino acid usages in the organism. Hydrophobicity of the genes is the second major source in differentiating the genes according to their amino acid usages in this organism.
内共生关系对生态系统有很大影响。利用已知的佛罗里达布氏菌（其宿主为佛罗里达弓背蚁）的实验基因，研究了该内共生细菌的密码子和氨基酸使用偏好。对相对同义密码子使用值（RSCU）的对应分析表明，仅存在一个与链特异性突变偏好相关的单一解释性主轴。大多数基因倾向于集中在前导链上，这可能与复制机制的适应性有关。在该生物体中，高表达基因和低表达基因的氨基酸使用情况明显不同，特别是富含GC的氨基酸在高表达基因中的出现频率显著高于低表达基因。对大肠杆菌和佛罗里达布氏菌直系同源基因的比较分析表明，高表达基因比低表达基因显著更保守。基于我们的研究结果，我们得出结论，链特异性突变偏好在该生物体密码子使用的选择中起着重要作用。前导链中大多数高表达基因的存在可归因于复制-转录选择。高表达基因中富含GC的氨基酸与其祖先的保守性是该生物体氨基酸使用差异的主要来源。在该生物体中，根据氨基酸使用情况区分基因的第二个主要来源是基因的疏水性。
