School of Natural Sciences, Massey University, Auckland, New Zealand.
Max Planck Institute for Biology, Tübingen, Germany.
Nat Ecol Evol. 2022 Aug;6(8):1165-1179. doi: 10.1038/s41559-022-01783-2. Epub 2022 Jun 20.
Bacteria often respond to dynamically changing environments by regulating gene expression. Despite this regulation being critically important for growth and survival, little is known about how selection shapes gene regulation in natural populations. To better understand the role natural selection plays in shaping bacterial gene regulation, here we compare differences in the regulatory behaviour of naturally segregating promoter variants from Escherichia coli (which have been subject to natural selection) to randomly mutated promoter variants (which have never been exposed to natural selection). We quantify gene expression phenotypes (expression level, plasticity and noise) for hundreds of promoter variants across multiple environments and show that segregating promoter variants are enriched for mutations with minimal effects on expression level. In many promoters, we infer that there is strong selection to maintain high levels of plasticity, and direct selection to decrease or increase cell-to-cell variability in expression. Taken together, these results expand our knowledge of how gene regulation is affected by natural selection and highlight the power of comparing naturally segregating polymorphisms to de novo random mutations to quantify the action of selection.
细菌通常通过调节基因表达来应对动态变化的环境。尽管这种调控对于生长和生存至关重要，但对于自然种群中基因调控是如何受到选择影响的，我们知之甚少。为了更好地理解自然选择在塑造细菌基因调控方面所起的作用，我们比较了来自大肠杆菌的自然分离的启动子变异体（已受到自然选择）和随机突变的启动子变异体（从未经历过自然选择）之间的调控行为差异。我们在多个环境中对数百个启动子变异体的基因表达表型（表达水平、可塑性和噪声）进行了量化，并表明分离的启动子变异体富集了对表达水平影响最小的突变。在许多启动子中，我们推断出存在强烈的选择来维持高水平的可塑性，并直接选择降低或增加细胞间表达的变异性。总的来说，这些结果扩展了我们对基因调控如何受到自然选择影响的认识，并强调了比较自然分离的多态性与从头随机突变来量化选择作用的力量。
