Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here we use the E. coli long-term evolution experiment (LTEE) as a model to address this challenge. To bridge the gap between disparate genomic changes and parallel fitness gains, we characterize the landscape of transcriptional and translational changes across 11 replicate populations evolving in parallel for 50,000 generations. By quantifying absolute changes in mRNA abundances, we show that not only do all evolved lines have more mRNAs but that this increase in mRNA abundance scales with cell size. We also find that despite few shared mutations at the genetic level, clones from replicate populations in the LTEE are remarkably similar to each other in their gene expression patterns at both the transcriptional and translational levels. Furthermore, we show that the bulk of the expression changes are due to changes at the transcriptional level with very few translational changes. Finally, we show how mutations in transcriptional regulators lead to consistent and parallel changes in the expression levels of downstream genes, thereby linking genomic changes to parallel fitness gains in the LTEE. These results deepen our understanding of the molecular mechanisms underlying complex adaptations and provide insights into the repeatability of evolution.

中文翻译：

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细菌适应22年以来的转录和翻译变化情况

生物可以通过多种变异途径适应环境。在许多突变具有相似的表型和适应性效应的基因水平上，这种冗余可能使弄清复杂适应的分子机制变得困难。在这里，我们使用大肠杆菌长期进化实验（LTEE）作为模型来应对这一挑战。为了弥合不同基因组变化和平行适应性增益之间的差距，我们表征了平行进化50,000代的11个重复种群的转录和翻译变化情况。通过定量mRNA丰度的绝对变化，我们表明不仅所有进化的品系都具有更多的mRNA，而且随着细胞大小mRNA丰度规模的增加。我们还发现，尽管在遗传水平上几乎没有共同的突变，LTEE中复制种群的克隆在转录和翻译水平上的基因表达方式都非常相似。此外，我们显示出大部分表达变化是由于转录水平的变化而很少有翻译变化。最后，我们展示了转录调节因子的突变如何导致下游基因表达水平的一致和平行变化，从而将基因组变化与LTEE中的平行适应性增益联系起来。这些结果加深了我们对潜在的复杂适应分子机制的理解，并提供了对进化的可重复性的见解。我们表明，大部分表达变化是由于转录水平的变化而很少有翻译变化。最后，我们展示了转录调节因子的突变如何导致下游基因表达水平的一致和平行变化，从而将基因组变化与LTEE中的平行适应性增益联系起来。这些结果加深了我们对潜在的复杂适应分子机制的理解，并提供了对进化的可重复性的见解。我们表明，大部分表达变化是由于转录水平的变化而很少有翻译变化。最后，我们展示了转录调节因子的突变如何导致下游基因表达水平的一致和平行变化，从而将基因组变化与LTEE中的平行适应性增益联系起来。这些结果加深了我们对潜在的复杂适应分子机制的理解，并提供了对进化的可重复性的见解。