论文标题

基因环境相互作用引起的极端拮抗作用

Extreme antagonism arising from gene-environment interactions

论文作者

Wytock, Thomas P., Zhan, Manjing, Jinich, Adrian, Fiebig, Aretha, Crosson, Sean, Motter, Adilson E.

论文摘要

生物系统中发生的拮抗相互作用,当一种扰动钝化另一种效果时发生,通常被解释为证据表明两种扰动会影响相同的细胞途径或功能。然而,这种解释忽略了极端的拮抗相互作用,其中原本有害的扰动弥补了由于先前的扰动而丢失的功能。在这里,我们报告了基因环境相互作用,这些相互作用涉及在宽松环境中有害但在限制生长的特定环境中有益的基因突变。这些极端的拮抗相互作用构成了先前观察到的基因相互作用的合成救援的基因 - 环境类似物。我们的方法使用两个独立的自适应进化步骤来解决缺乏实验方法来系统地识别这种极端相互作用的方法。我们通过将其依次将其转化为没有抗生素利福平的葡萄糖培养基来应用大肠杆菌的方法。该方法确定了多种突变,这些突变在利福平存在和有害的情况下是有益的。转录的分析表明,拮抗自适应突变抑制了严格的响应样转录程序,而非抗抗逆性突变具有相反的转录曲线。我们的方法代表了极端拮抗基因相互作用的系统表征的一步,该相互作用可用于识别靶标以选择抗生素耐药性。

Antagonistic interactions in biological systems, which occur when one perturbation blunts the effect of another, are typically interpreted as evidence that the two perturbations impact the same cellular pathway or function. Yet, this interpretation ignores extreme antagonistic interactions wherein an otherwise deleterious perturbation compensates for the function lost due to a prior perturbation. Here, we report on gene-environment interactions involving genetic mutations that are deleterious in a permissive environment but beneficial in a specific environment that restricts growth. These extreme antagonistic interactions constitute gene-environment analogs of synthetic rescues previously observed for gene-gene interactions. Our approach uses two independent adaptive evolution steps to address the lack of experimental methods to systematically identify such extreme interactions. We apply the approach to Escherichia coli by successively adapting it to defined glucose media without and with the antibiotic rifampicin. The approach identified multiple mutations that are beneficial in the presence of rifampicin and deleterious in its absence. The analysis of transcription shows that the antagonistic adaptive mutations repress a stringent response-like transcriptional program, while non-antagonistic mutations have an opposite transcriptional profile. Our approach represents a step toward the systematic characterization of extreme antagonistic gene-drug interactions, which can be used to identify targets to select against antibiotic resistance.

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