Ongoing evolution of strand composition in bacterial genomes
Ongoing evolution of strand composition in bacterial genomes
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DOI：
10.1093/oxfordjournals.molbev.a003966
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发表时间：
2001-09-01
影响因子：
10.7
通讯作者：
Danchin, A
中科院分区：
文献类型：
--
作者：
Rocha, EPC;Danchin, A
我们试图确定复制链偏向的建立所涉及的替换，它已被认为是细菌基因组进化中的一个重要进化因素。首先，我们分析了28个完整的细菌基因组的组成不对称性，并用它来测试胞嘧啶的不对称脱氨基可能是这种偏见的根源。该模型显示了与数据的显著相关性，但没有解释很大一部分差异，并表明与TA偏差相比，GC偏差被系统性地低估了。其次，我们分析了五个自物种形成以来没有发生过链转换的衣原体全序列基因组中作用于基因的替换。这一分析表明，在沙眼衣原体和沙眼衣原体中，替换是不平衡的，链偏向仍然是这些基因中正在进行的过程。第三，我们确定了在物种形成后改变了链的基因适应过程中涉及的替换。这些基因很快适应了新链的倾斜组成，主要是由于C-->；T、A-->；G和C-->；G的不对称替换。对枯草芽孢杆菌和嗜盐芽孢杆菌分化后交换链的基因的分析加强了这一观察结果。最后，在分析衣原体替代不对称性的基础上，提出了一个更具推广意义的模型。这个模型很好地符合细菌基因组提供的数据，这些数据表现出强烈的链偏向。
We tried to identify the substitutions involved in the establishment of replication strand bias, which has been recognized as an important evolutionary factor in the evolution of bacterial genomes. First, we analyzed the composition asymmetry of 28 complete bacterial genomes and used it to test the possibility that asymmetric deamination of cytosine might be at the origin of the bias. The model showed significant correlation to the data but left unexplained a significant portion of the variance and indicated a systematic underestimation of GC skews in comparison with TA skews. Second, we analyzed the substitutions acting on the genes from five fully sequenced Chlamydia genomes that had not suffered strand switch since speciation. This analysis showed that substitutions were not at equilibrium in Chlamydia trachomatis or in C. muridarum and that strand bias is still an on-going process in these genes. Third, we identified substitutions involved in the adaptation of genes that had switched strands after speciation. These genes adapted quickly to the skewed composition of the new strand, mostly due to C-->T, A-->G, and C-->G asymmetric substitutions. This observation was reinforced by the analysis of genes that switched strands after divergence between Bacillus subtilis and B. halodurans. Finally, we propose a more extended model based on the analysis of the substitution asymmetries of Chlamydia. This model fits well with the data provided by bacterial genomes presenting strong strand bias.