G+C3 structuring along the genome:: A common feature in prokaryotes
G+C3 structuring along the genome:: A common feature in prokaryotes
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DOI：
10.1093/molbev/msg022
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发表时间：
2003-04-01
影响因子：
10.7
通讯作者：
Perrière, G
中科院分区：
文献类型：
--
作者：
Daubin, V;Perrière, G
原核基因组中基因核苷酸含量的异质性通常被解释为三个主要现象的结果：（1）基因在翻译过程中和翻译后都经历不同的选择压力（影响密码子和氨基酸选择）;（2）基因无论是在前导链还是在滞后链上都经历不同的突变压力;以及（3）由于横向转移，基因可能具有不同的系统发育起源。然而，这种观点忽略了在染色体上组织遗传信息的必要性，这些信息需要复制和折叠，这可能会对单个基因进化增加限制。因此，基因可能会受到不同的突变和选择压力，这取决于它们在基因组中的位置。在本文中，我们分析了结构不同的密码子使用措施沿着完全测序的细菌基因组。我们发现，它们中的大多数是高度结构化的，这表明基因具有不同的碱基含量，这取决于它们在染色体上的位置。在大多数细菌门中发现了一种特殊的基因组结构模式，在复制末端附近有A+ T富集的趋势，这可能反映了常见的染色体限制。一些物种可能已经失去了这种模式，可能是因为基因组重排或外来DNA的整合。我们发现，在几个物种中，这种富集与进化速率的增加，我们讨论了这些结果的进化意义。我们认为，作用于环状染色体的结构约束是不可忽视的，这种自然结构的细菌基因组可能是高估的横向基因转移预测使用密码子组成指数的原因。
The heterogeneity of gene nucleotide content in prokaryotic genomes is commonly interpreted as the result of three main phenomena: (1) genes undergo different selection pressures both during and after translation (affecting codon and amino acid choice); (2) genes undergo different mutational pressure whether they are on the leading or lagging strand; and (3) genes may have different phylogenetic origins as a result of lateral transfers. However, this view neglects the necessity of organizing genetic information on a chromosome that needs to be replicated and folded, which may add constraints to single gene evolution. As a consequence, genes are potentially subjected to different mutation and selection pressures, depending on their position in the genome. In this paper, we analyze the structuring of different codon usage measures along completely sequenced bacterial genomes. We show that most of them are highly structured, suggesting that genes have different base content, depending on their location on the chromosome. A peculiar pattern of genome structure, with a tendency toward an A+T-enrichment near the replication terminus, is found in most bacterial phyla and may reflect common chromosome constraints. Several species may have lost this pattern, probably because of genome rearrangements or integration of foreign DNA. We show that in several species, this enrichment is associated with an increase of evolutionary rate and we discuss the evolutionary implications of these results. We argue that structural constraints acting on the circular chromosome are not negligible and that this natural structuring of bacterial genomes may be a cause of overestimation in lateral gene transfer predictions using codon composition indices.