Sequence-dependent model of genes with dual σ factor preference

Inference of transcriptome signatures of Escherichia coli in long-term stationary phase

“…However, we also found that some of the highly expressed carbohydrate transport genes in STS showed lower expression levels in short-term stationary phase than exponential phase in the previous study (Fig. S4) 18 .…”

“…When we compared the expression profiles between the previous and our studies, there were mainly three types of transcriptional changes in this category: down-regulated in short-term stationary phase commonly in both studies; up-regulated in short-term stationary phase commonly in both studies; up-regulated only in our study. The genes encoding the glucose phosphotransferase system (e.g., ptsG and ptsH) exhibited lower expression levels both in STS (our study) or short-term stationary phase (the previous study) 18 , which would correspond to the depletion of glucose (a major carbon source) from the exponentially growing phase. Transport genes responsible for the uptake of rhamnose, melibiose, and mannitol (i.e., rhaT, melB, and mtlA) showed higher expressions in short-term stationary phase in both studies, and utilization of those carbohydrates would be up-regulated in both experimental conditions.…”

“…Especially, the gene sets involved in protein biosynthesis (i.e., translation) screened as a lower expressed functional category in short-term stationary phase compared to exponential phase in the other E. coli strain 18 , and down-regulation of this gene set is not specific to our experimental setup. As these biosynthetic gene sets are involved in the synthesis of major cellular components and essential for cellular growth in E. coli 35,36 , their low expression levels would be one of the possible mechanisms to explain the non-growing state of cells in both short-and long-term stationary phase, which is a common tendency of bacterial transcriptional response after halting growth [37][38][39][40][41] .…”

A library of reporters of the global regulators of gene expression ofEscherichia coli

“…These sources include variability in RNAP and ribosome numbers. For example, recent studies reported that single-cell RNAP numbers can differ by ∼45% in cells growing in the same conditions, specifically in the exponential and stationary growth phases (Baptista et al , 2022). We thus corrected the model by adding a constant α (representing a lower noise limit).…”

“…Specifically, since GRs compose a large fraction of the TFN, tracking their levels over time is necessary to identify the triggers of phenotypic modifications that cells undergo during stress adaptation. For example, in (Baptista et al , 2022), tracking σ 38 levels overtime using a fast-maturing fluorescent protein, allowed establishing that they only change after the beginning of the transition to stationary growth. Tracking more GRs would have allowed determining, e.g., if some of them changed prior to this transition (and, thus, potentially, acted as triggers).…”