Data and code from: "Multidimensional plasticity of gene expression underlying higher macrolide tolerance in saline and warm environments"

Organisms are routinely exposed to multiple environmental stresses, increasingly intensified by human activities. While adaptation occurs over the scale of at least a few generations, phenotypic plasticity enables rapid adjustment to environmental changes. Gene expression is a central plastic trait that mediates phenotypic change, yet how synergistic or antagonistic fitness effects arise from interactions among transcriptional responses remains poorly understood. Here, we introduce a general framework to classify interactions at the gene-expression level, and discuss their evolutionary consequences in the pressing context of antibiotic resistance. We analyzed the transcriptional response of Escherichia coli to azithromycin (AZI) across two salinity and temperature conditions. De novo and antagonistic interactions were prevalent, with evidence of cross-regulation between salt and AZI. High salinity increased tolerance by two orders of magnitude and, similarly to AZI, promoted a metabolic shift from carbon to nitrogen, potentially facilitating the clearance of macrolide-induced misfolded proteins. Reduced temperature, which cancelled the salinity protective effect, enhanced carbon metabolism and counteracted this shift. Salinity additionally restored stress-response pathways, largely repressed by AZI. Third-order interactions attenuated the contribution of salinity relative to AZI, but the number of affected genes declined exponentially with interaction order, suggesting that higher-order interactions at the gene-expression level should play a minor role in the responses to multiple stressors. By modulating transcriptional responses to AZI, simple environmental parameters ultimately reshaped the adaptive landscape of antibiotic resistance, altering the spectrum of resistance mutations likely be fixed.生物体日常会暴露于多种环境胁迫之中，而这类胁迫正因人类活动而日益加剧。尽管适应性演化通常需要至少数代的时间尺度，但表型可塑性（phenotypic plasticity）可使生物快速响应环境变化完成调整。基因表达是介导表型变化的核心可塑性性状，然而转录反应之间的相互作用如何产生协同或拮抗的适合度效应，目前仍未得到充分解析。本研究提出了一个用于分类基因表达层面相互作用的通用框架，并结合抗生素耐药性这一紧迫的研究背景，探讨了这类相互作用的演化效应。我们分析了大肠杆菌（Escherichia coli）在两种盐度与温度条件下，针对阿奇霉素（azithromycin，AZI）的转录反应。研究发现，从头型（de novo）相互作用与拮抗相互作用十分普遍，且存在盐度与AZI之间的交叉调控证据。高盐度可使耐受性提升两个数量级，且与AZI类似，会推动代谢模式从碳代谢转向氮代谢，这可能有助于清除大环内酯类药物诱导的错误折叠蛋白。温度降低会抵消盐度的保护效应，同时增强碳代谢过程，并逆转上述代谢转向。此外，盐度还可恢复被AZI大幅抑制的应激反应通路。三阶相互作用会削弱盐度相较于AZI的贡献效应，但受影响的基因数量会随相互作用阶数呈指数级下降，这表明基因表达层面的高阶相互作用，在生物应对多重胁迫的反应中仅发挥次要作用。通过调控针对AZI的转录反应，简单的环境参数最终会重塑抗生素耐药性的适应性景观，并改变大概率会被固定的耐药突变的谱型。