Chu H-Y, Sprouffske K, Wagner A
Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
The Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Genopode, Lausanne, Switzerland.
J Evol Biol. 2017 Sep;30(9):1692-1711. doi: 10.1111/jeb.13132. Epub 2017 Jul 13.
The benefits and detriments of recombination for adaptive evolution have been studied both theoretically and experimentally, with conflicting predictions and observations. Most pertinent experiments examine recombination's effects in an unchanging environment and do not study its genomewide effects. Here, we evolved six replicate populations of either highly recombining R or lowly recombining R E. coli strains in a changing environment, by introducing the novel nutrients L-arabinose or indole into the environment. The experiment's ancestral strains are not viable on these nutrients, but 130 generations of adaptive evolution were sufficient to render them viable. Recombination conferred a more pronounced advantage to populations adapting to indole. To study the genomic changes associated with this advantage, we sequenced the genomes of 384 clones isolated from selected replicates at the end of the experiment. These genomes harbour complex changes that range from point mutations to large-scale DNA amplifications. Among several candidate adaptive mutations, those in the tryptophanase regulator tnaC stand out, because the tna operon in which it resides has a known role in indole metabolism. One of the highly recombining populations also shows a significant excess of large-scale segmental DNA amplifications that include the tna operon. This lineage also shows a unique and potentially adaptive combination of point mutations and DNA amplifications that may have originated independently from one another, to be joined later by recombination. Our data illustrate that the advantages of recombination for adaptive evolution strongly depend on the environment and that they can be associated with complex genomic changes.
关于重组对适应性进化的利弊，已从理论和实验两方面进行了研究，但预测结果和观察结果存在冲突。大多数相关实验考察的是重组在不变环境中的作用，并未研究其全基因组效应。在此，我们通过在环境中引入新的营养物质L-阿拉伯糖或吲哚，使六个高度重组的R或低度重组的R大肠杆菌菌株的重复群体在变化的环境中进化。实验的祖先菌株在这些营养物质上无法存活，但经过130代的适应性进化足以使其存活。重组对适应吲哚的群体赋予了更显著的优势。为了研究与这种优势相关的基因组变化，我们对实验结束时从选定重复群体中分离出的384个克隆的基因组进行了测序。这些基因组包含从点突变到大规模DNA扩增的复杂变化。在几个候选适应性突变中，色氨酸酶调节因子tnaC中的突变尤为突出，因为它所在的tna操纵子在吲哚代谢中具有已知作用。其中一个高度重组的群体还显示出大量包括tna操纵子在内的大规模节段性DNA扩增。这个谱系还显示出一种独特的、可能具有适应性的点突变和DNA扩增组合，它们可能彼此独立起源，随后通过重组结合在一起。我们的数据表明，重组对适应性进化的优势在很大程度上取决于环境，并且可能与复杂的基因组变化相关。
