Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes
Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes
复制标题
突变率增加与原核生物基因组减少有关
DOI：
10.1016/j.cub.2020.07.034
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发表时间：
2020-10-05
期刊：
影响因子：
9.2
通讯作者：
Lo, Nathan
中科院分区：
文献类型：
--
作者：
Bourguignon, Thomas;Kinjo, Yukihiro;Lo, Nathan
驱动整个生命之树的基因组大小变化的进化过程仍然没有得到解决。有效种群大小（N-e）被认为在形成基因组大小方面发挥重要作用[1-3]-一个关键的例子是昆虫内共生体的基因组减少，其在传播过程中经历种群瓶颈[4]。然而，在具有大N-e的海洋和陆地原核生物物种中存在减少的基因组，表明基因组减少受到多种过程的影响[3]。一个候选过程是增强突变率，这可以增加适应能力，但也可以促进基因丢失。为了研究与原核生物基因组减少相关的进化力量，我们对来自5个细菌和古细菌门的9个谱系进行了分子进化和基因组分析。我们发现，在9个谱系中的7个中，基因丢失率与同义替换率（突变率的代理）密切相关。而基因丢失率与非同义/同义替换率（d（N）/d（S））的比值相关性较弱或不相关。这些结果表明，基因组减少在很大程度上与突变率增加有关，而基因丢失和N-e变化之间的关联则不太明确。具有相对较高d（S）和d（N）以及较小基因组的谱系缺乏多个DNA修复基因，这为突变率增加提供了近因。我们的研究结果表明，类似的机制驱动基因组减少细胞内和自由生活的原核生物，与发展一个全面的原核生物基因组大小进化理论的影响。
The evolutionary processes that drive variation in genome size across the tree of life remain unresolved. Effective population size (N-e) is thought to play an important role in shaping genome size [1-3]-a key example being the reduced genomes of insect endosymbionts, which undergo population bottlenecks during transmission [4]. However, the existence of reduced genomes in marine and terrestrial prokaryote species with large N-e indicate that genome reduction is influenced by multiple processes [3]. One candidate process is enhanced mutation rate, which can increase adaptive capacity but can also promote gene loss. To investigate evolutionary forces associated with prokaryotic genome reduction, we performed molecular evolutionary and phylogenomic analyses of nine lineages from five bacterial and archaeal phyla. We found that gene-loss rate strongly correlated with synonymous substitution rate (a proxy for mutation rate) in seven of the nine lineages. However, gene-loss rate showed weak or no correlation with the ratio of nonsynonymous/synonymous substitution rate (d(N)/d(S)). These results indicate that genome reduction is largely associated with increased mutation rate, while the association between gene loss and changes in N-e is less well defined. Lineages with relatively high d(S) and d(N), as well as smaller genomes, lacked multiple DNA repair genes, providing a proximate cause for increased mutation rates. Our findings suggest that similar mechanisms drive genome reduction in both intracellular and free-living prokaryotes, with implications for developing a comprehensive theory of prokaryote genome size evolution.