Sequence-dependent model of genes with dual σ factor preference

Escherichia coli uses s factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single s factor, approximately 5% of them have dual s factor preference. The most common are those responsive to both s70, which controls housekeeping genes, and s38, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that ‘σ70+38 genes’ are nearly as upregulated in stationary growth as ‘σ38 genes’. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in σ38 levels. We then propose and validate a sequence dependent model of σ70+38 genes, with dual sensitivity to s38 and s70, that is applicable in the exponential and stationary growth phases, as well in the transient period in between. We further propose a general model, applicable to other stresses and σ factor combinations. Given this, promoters controlling σ70+38 genes (a...

大肠杆菌（Escherichia coli）利用σ因子在应激条件下快速调控大量基因群。尽管其大多数基因仅响应单一σ因子，但约5%的基因具有双σ因子偏好性。最常见的是同时响应σ70和σ38的基因——σ70调控管家基因，而σ38在稳定期生长及应激状态下激活基因。通过RNA测序（RNA-seq）和流式细胞术（flow-cytometry）测量，我们发现“σ70+38基因”在稳定期生长中的上调程度几乎与“σ38基因”相当。此外，我们发现其启动子序列与对σ38水平变化的响应强度之间存在明确的定量关系。随后，我们提出并验证了σ70+38基因的序列依赖模型，该模型对σ38和σ70具有双重敏感性，适用于指数生长期、稳定期生长阶段以及两者之间的过渡期。我们进一步提出了一个通用模型，适用于其他应激条件及σ因子组合。基于此，调控σ70+38基因的启动子（a...