Evidence that mutation is universally biased towards AT in bacteria.
Evidence that mutation is universally biased towards AT in bacteria.
复制标题
DOI：
10.1371/journal.pgen.1001115
复制
发表时间：
2010-09-09
期刊：
影响因子：
4.5
通讯作者：
Petrov DA
中科院分区：
文献类型：
--
作者：
Hershberg R;Petrov DA
突变是推动进化和适应的引擎，因为它产生了自然选择作用的变异。突变是一个随机的过程，但会根据某些偏好发生。阐明突变偏差及其在物种间和基因组内的变化方式对于理解进化和适应至关重要。在这里，我们证明了克隆病原体的进化下，严重放松选择是唯一适合研究细菌的突变偏差。我们估计突变模式使用序列数据集从五个这样的克隆病原体属于四个不同的细菌分支，跨越大部分的基因组核苷酸含量的范围。我们证明，在不同类型的网站和所有四个分支突变是一贯偏向AT。即使在具有高基因组GC含量的进化枝中也是如此。在所有研究的情况下，对AT的突变偏好主要是由于C/G到T/A转换的高速率。这些结果表明，细菌突变偏好的可变性远远低于以前的想法。他们进一步证明，核苷酸含量的变化不能完全源于突变偏好的变化，并且自然选择和/或类似自然选择的过程（例如有偏好的基因转换）强烈影响核苷酸含量。自然选择通过突变产生的变异性进行分类，并使进化偏向更适合的结果。然而，由于突变本身并不完全是随机的，它也可以独立于选择而偏向进化的方向。例如，通常认为细菌中核苷酸含量的极端变化（从20%到80% GC）主要是由朝向或远离GC的突变偏差的极端差异驱动的。在这里，我们表明，最近开发的克隆，致病的生活方式的细菌谱系弱选择下的演变，这些细菌的多态性可以作为一个公平的代理突变谱。我们分析了大的序列数据集，从五个克隆病原体在四个不同的细菌分支跨越大部分的基因组核苷酸含量的范围。我们发现，令人惊讶的是，在每种情况下，突变都是AT偏向的，程度非常相似，并且在每种情况下，它都是由C/G到T/A的转变主导的。这表明，突变的偏见是远远小于变量比以前假设的细菌核苷酸含量的变化是不完全是由于突变的偏见。相反，自然选择或类似选择的过程，如偏向基因转换，强烈影响细菌中的核苷酸含量。
Mutation is the engine that drives evolution and adaptation forward in that it generates the variation on which natural selection acts. Mutation is a random process that nevertheless occurs according to certain biases. Elucidating mutational biases and the way they vary across species and within genomes is crucial to understanding evolution and adaptation. Here we demonstrate that clonal pathogens that evolve under severely relaxed selection are uniquely suitable for studying mutational biases in bacteria. We estimate mutational patterns using sequence datasets from five such clonal pathogens belonging to four diverse bacterial clades that span most of the range of genomic nucleotide content. We demonstrate that across different types of sites and in all four clades mutation is consistently biased towards AT. This is true even in clades that have high genomic GC content. In all studied cases the mutational bias towards AT is primarily due to the high rate of C/G to T/A transitions. These results suggest that bacterial mutational biases are far less variable than previously thought. They further demonstrate that variation in nucleotide content cannot stem entirely from variation in mutational biases and that natural selection and/or a natural selection-like process such as biased gene conversion strongly affect nucleotide content. Natural selection sorts through the variability generated by mutation and biases evolution toward fitter outcomes. However, because mutation is itself not entirely random it can also bias the direction of evolution independently of selection. For instance, it is often assumed that the extreme variation observed in nucleotide content among bacteria (from ∼20% to ∼80% GC) is predominantly driven by extreme differences in mutational biases towards or away from GC. Here, we show that bacterial lineages that recently developed clonal, pathogenic lifestyles evolve under weak selection and that polymorphisms in these bacteria can be used as a fair proxy for mutational spectra. We analyze large sequence datasets from five clonal pathogens in four diverse bacterial clades spanning most of the range of genomic nucleotide content. We find that, surprisingly, mutation is AT-biased in every case to a very similar degree and in each case it is dominated by transitions from C/G to T/A. This demonstrates that mutational biases are far les variable than previously assumed and that variation in bacterial nucleotide content is not due entirely to mutational biases. Rather natural selection or a selection like process such as biased gene conversion strongly affect nucleotide content in bacteria.
登录
查看更多内容
影响因子：
30.8
作者：
Holt, Kathryn E.;Parkhill, Julian;Mazzoni, Camila J.;Roumagnac, Philippe;Weill, Francois-Xavier;Goodhead, Ian;Rance, Richard;Baker, Stephen;Maskell, Duncan J.;Wain, John;Dolecek, Christiane;Achtman, Mark;Dougan, Gordon
通讯作者：
Dougan, Gordon
影响因子：
3.3
作者：
Haddrill, Penelope R.;Charlesworth, Brian
通讯作者：
Charlesworth, Brian
影响因子：
4.5
作者：
Hershberg R;Petrov DA
通讯作者：
Petrov DA
影响因子：
3.9
作者：
Andersson, SGE;Sharp, PM
通讯作者：
Sharp, PM
影响因子：
10.7
作者：
Balbi, Kevin J.;Rocha, Eduardo P. C.;Feil, Edward J.
通讯作者：
Feil, Edward J.