From the Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093.
J Biol Chem. 2013 Nov 15;288(46):33096-106. doi: 10.1074/jbc.M113.511469. Epub 2013 Oct 2.
Understanding the evolution of functional RNA molecules is important for our molecular understanding of biology. Here we tested experimentally how two evolutionary parameters, selection pressure and recombination, influenced the evolution of an evolving RNA population. This was done using four parallel evolution experiments that employed low or gradually increasing selection pressure, and recombination events either at the end or dispersed throughout the evolution. As model system, a trans-splicing group I intron ribozyme was evolved in Escherichia coli cells over 12 rounds of selection and amplification, including mutagenesis and recombination. The low selection pressure resulted in higher efficiency of the evolved ribozyme populations, whereas differences in recombination did not have a strong effect. Five mutations were responsible for the highest efficiency. The first mutation swept quickly through all four evolving populations, whereas the remaining four mutations accumulated later and more efficiently under low selection pressure. To determine why low selection pressure aided this evolution, all evolutionary intermediates between the wild type and the 5-mutation variant were constructed, and their activities at three different selection pressures were determined. The resulting fitness profiles showed a high cooperativity among the four late mutations, which can explain why high selection pressure led to inefficient evolution. These results show experimentally how low selection pressure can benefit the evolution of cooperative mutations in functional RNAs.
理解功能 RNA 分子的进化对于我们从分子水平理解生物学是很重要的。在这里，我们通过四个平行的进化实验来测试两个进化参数（选择压力和重组）如何影响一个不断进化的 RNA 群体的进化。这四个实验分别采用了低选择压力或逐渐增加的选择压力，以及在进化结束时或分散在整个进化过程中发生重组事件。作为模型系统，在大肠杆菌细胞中经过 12 轮选择和扩增，包括诱变和重组，对一个转剪接的 I 型内含子核酶进行了进化。低选择压力导致进化的核酶群体效率更高，而重组的差异没有产生强烈的影响。有五个突变负责最高的效率。第一个突变迅速在所有四个进化群体中传播，而其余四个突变在低选择压力下积累得更晚，效率更高。为了确定为什么低选择压力有助于这种进化，我们构建了从野生型到 5 个突变体之间的所有进化中间产物，并在三种不同的选择压力下测定了它们的活性。得到的适应度曲线显示，四个晚期突变之间具有很高的协同性，这可以解释为什么高选择压力导致进化效率低下。这些结果从实验上表明了低选择压力如何有利于功能性 RNA 中合作性突变的进化。
