Causes of insertion sequences abundance in prokaryotic genomes
Causes of insertion sequences abundance in prokaryotic genomes
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DOI：
10.1093/molbev/msm014
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发表时间：
2007-04-01
影响因子：
10.7
通讯作者：
Rocha, Eduardo P. C.
中科院分区：
文献类型：
--
作者：
Touchon, Marie;Rocha, Eduardo P. C.
插入序列（IS）是原核生物中最小且最常见的转座元件，它们通过促进基因失活和基因组可塑性而发挥重要的进化作用。它们的基因组丰度变化了几个数量级，原因基本上是未知的，并被广泛推测。目前的数百个基因组的可用性，使许多这些假设，值得注意的是，IS丰度与水平基因转移（HGT），基因组大小，致病性，非强制性生态协会，人类协会的频率呈正相关。因此，我们在262个原核基因组中重新注释了IS，并测试了这些假设，表明当使用适当的对照时，IS家族特异性，致病性或人类关联影响IS丰度或密度没有经验基础。HGT似乎是IS存在的必要条件，但不能单独解释超过20%的生物体中IS的缺失，其中一些生物体显示出高HGT率。基因转移也不是基因组中IS元件丰度的重要决定因素，这表明IS丰度在转座水平和随后的自然选择而不是感染水平上受到控制。当控制基因组大小时，参与强制性关联的原核生物具有较少的IS，但这可能是由一些性隔离引起的。令人惊讶的是，基因组大小是IS数量和密度的唯一重要预测因素。单独，它解释了超过40%的变异的IS丰度。因为我们发现基因组大小和IS丰度与最小倍增时间呈负相关，所以我们得出结论，快速复制的选择不能解释小基因组中发现的少数IS。相反，我们的证据表明，IS的数量是由频率控制的高度有害的插入目标。事实上，IS丰度随着基因组大小而迅速增加，这是在强选择下发现的基因密度（如必需基因）的确切相反趋势。因此，对于IS来说，基因组越大越好。
Insertion sequences (ISs) are the smallest and most frequent transposable elements in prokaryotes where they play an important evolutionary role by promoting gene inactivation and genome plasticity. Their genomic abundance varies by several orders of magnitude for reasons largely unknown and widely speculated. The current availability of hundreds of genomes renders testable many of these hypotheses, notably that IS abundance correlates positively with the frequency of horizontal gene transfer (HGT), genome size, pathogenicity, nonobligatory ecological associations, and human association. We thus reannotated ISs in 262 prokaryotic genomes and tested these hypotheses showing that when using appropriate controls, there is no empirical basis for IS family specificity, pathogenicity, or human association to influence IS abundance or density. HGT seems necessary for the presence of ISs, but cannot alone explain the absence of ISs in more than 20% of the organisms, some of which showing high rates of HGT. Gene transfer is also not a significant determinant of the abundance of IS elements in genomes, suggesting that IS abundance is controlled at the level of transposition and ensuing natural selection and not at the level of infection. Prokaryotes engaging in obligatory associations have fewer ISs when controlled for genome size, but this may be caused by some being sexually isolated. Surprisingly, genome size is the only significant predictor of IS numbers and density. Alone, it explains over 40% of the variance of IS abundance. Because we find that genome size and IS abundance correlate negatively with minimal doubling times, we conclude that selection for rapid replication cannot account for the few ISs found in small genomes. Instead, we show evidence that IS numbers are controlled by the frequency of highly deleterious insertion targets. Indeed, IS abundance increases quickly with genome size, which is the exact inverse trend found for the density of genes under strong selection such as essential genes. Hence, for ISs, the bigger the genome the better.