Separate base usages of genes located on the leading and lagging strands in Chlamydia muridarum revealed by the Z curve method.
Separate base usages of genes located on the leading and lagging strands in Chlamydia muridarum revealed by the Z curve method.
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DOI：
10.1186/1471-2164-8-366
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发表时间：
2007-10-10
期刊：
影响因子：
4.4
通讯作者：
Yu XJ
中科院分区：
文献类型：
--
作者：
Guo FB;Yu XJ
在过去的几年中，细菌基因组中前导链和后导链之间的核苷酸组成不对称已成为深入研究的主题。有趣的是，几乎所有的细菌基因组都表现出相同的碱基不对称。本研究旨在探讨muridarum衣原体基因组的链偏性，并展示Z曲线方法在定量区分前导链和滞后链上基因的潜力。用Z曲线法分析了黄颡鱼基因组中蛋白质编码基因碱基的出现频率。结果表明，位于两条复制链上的基因具有不同的碱基用法。K-means聚类算法根据Z曲线方法的变量u1 - u9在9-D空间中的位置，可以将大约94%的基因分配到正确的链上，这比基于RSCU的K-means正确分类的结果高出几个百分点。碱基用法和密码子用法分析表明，前导链上的基因G多于C， T多于A，特别是在第3个密码子位置。在后链上的基因则相反。完整染色体序列的Z曲线的y分量表明，在没有分离碱基和/或密码子用法的情况下，C. muridarum基因组中G超过C和T超过A比其他细菌基因组中更为显著。此外，对于伯氏疏螺旋体、梅毒螺旋体、墨氏衣原体和沙眼衣原体的基因组，虽然观察到不同的碱基和/或密码子使用，但与其他细菌基因组相比，发现了更近的系统发育距离。C. muridarum碱基组成的链偏置性质与大多数其他细菌基因组相似。然而，C. muridarum的前导链和滞后链之间的碱基组成不对称比其他细菌更为明显。推测G/C和T/A显著的链偏性是导致紫锥虫出现碱基或密码子分离用法的原因。另一方面，具有不同碱基和/或密码子用法的四种细菌基因组之间更近的系统发育距离是必要的，而不是偶然的。Z曲线法在定量分析DNA序列时可能比RSCU法更灵敏。
The nucleotide compositional asymmetry between the leading and lagging strands in bacterial genomes has been the subject of intensive study in the past few years. It is interesting to mention that almost all bacterial genomes exhibit the same kind of base asymmetry. This work aims to investigate the strand biases in Chlamydia muridarum genome and show the potential of the Z curve method for quantitatively differentiating genes on the leading and lagging strands. The occurrence frequencies of bases of protein-coding genes in C. muridarum genome were analyzed by the Z curve method. It was found that genes located on the two strands of replication have distinct base usages in C. muridarum genome. According to their positions in the 9-D space spanned by the variables u1 – u9 of the Z curve method, K-means clustering algorithm can assign about 94% of genes to the correct strands, which is a few percent higher than those correctly classified by K-means based on the RSCU. The base usage and codon usage analyses show that genes on the leading strand have more G than C and more T than A, particularly at the third codon position. For genes on the lagging strand the biases is reverse. The y component of the Z curves for the complete chromosome sequences show that the excess of G over C and T over A are more remarkable in C. muridarum genome than in other bacterial genomes without separating base and/or codon usages. Furthermore, for the genomes of Borrelia burgdorferi, Treponema pallidum, Chlamydia muridarum and Chlamydia trachomatis, in which distinct base and/or codon usages have been observed, closer phylogenetic distance is found compared with other bacterial genomes. The nature of the strand biases of base composition in C. muridarum is similar to that in most other bacterial genomes. However, the base composition asymmetry between the leading and lagging strands in C. muridarum is more significant than that in other bacteria. It's supposed that the remarkable strand biases of G/C and T/A are responsible for the appearance of separate base or codon usages in C. muridarum. On the other hand, the closer phylogenetic distance among the four bacterial genomes with separate base and/or codon usages is necessary rather than occasional. It's also shown that the Z curve method may be more sensitive than RSCU when being used to quantitatively analyze DNA sequences.
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