Parallel changes in qene expression after 20,000 generations of evolution in Escherichia coli
Parallel changes in qene expression after 20,000 generations of evolution in Escherichia coli
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DOI：
10.1073/pnas.0334340100
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发表时间：
2003-02-04
影响因子：
11.1
通讯作者：
Lenski, RE
中科院分区：
文献类型：
--
作者：
Cooper, TF;Rozen, DE;Lenski, RE
来自共同祖先的12个大肠杆菌种群在葡萄糖限制的培养基中进化了2万代。在这里，我们使用DNA表达阵列来检查两个种群的基因表达谱是否平行进化，这将表明适应，并深入了解其适应的机制。我们比较了祖先的表达谱和2万代后从两个种群中取样的克隆。两个群体中有59个基因的表达发生了显著变化。值得注意的是，所有59个基因都相对于祖先发生了相同的变化。这些基因中有许多是cAMP-cAMP受体蛋白（CRP）和四磷酸鸟苷（ppGpp）调控的成员。对控制这些调控效应的几个基因进行测序，在一个种群中发现了一个非同义突变。将这种突变移到祖先背景中表明，它增加了适应性，并产生了许多在2万代之后才显现出来的表达变化。同样的突变在引入其他进化种群时对适应性没有影响，这表明已经存在类似效果的突变。我们的研究证明了表达阵列在解决进化问题方面的效用，包括在独立谱系中平行进化的定量测量和有益突变的鉴定。
Twelve populations of Escherichia coli, derived from a common ancestor, evolved in a glucose-limited medium for 20,000 generations. Here we use DNA expression arrays to examine whether gene-expression profiles in two populations evolved in parallel, which would indicate adaptation, and to gain insight into the mechanisms underlying their adaptation. We compared the expression profile of the ancestor to that of clones sampled from both populations after 20,000 generations. The expression of 59 genes had changed significantly in both populations. Remarkably, all 59 were changed in the same direction relative to the ancestor. Many of these genes were members of the cAMP-cAMP receptor protein (CRP) and guanosine tetraphosphate (ppGpp) regulons. Sequencing of several genes controlling the effectors of these regulons found a nonsynonymous mutation in spoT in one population. Moving this mutation into the ancestral background showed that it increased fitness and produced many of the expression changes manifest after 20,000 generations. The same mutation had no effect on fitness when introduced into the other evolved population, indicating that a mutation of similar effect was present already. Our study demonstrates the utility of expression arrays for addressing evolutionary issues including the quantitative measurement of parallel evolution in independent lineages and the identification of beneficial mutations.