The timing of transcription of RpoS-dependent genes varies across multiple stresses inEscherichia coliK-12

Abstract

The alternative sigma factor RpoS regulates transcription of over 1000 genes in Escherichia coli in response to many different stresses. RpoS levels rise continuously after exposure to stress, and the consequences of changing levels of RpoS for the temporal patterns of expression of RpoS-regulated genes has not been described. We measured RpoS levels at various times during the entry to stationary phase, or in response to high osmolarity or low temperature, and found that the time required to reach maximum levels varied by several hours. We quantified the transcriptome across these stresses using RNA-seq. The number of differentially expressed genes differed among stresses, with 1379 DE genes were identified in in stationary phase, 633 in high osmolarity, and 302 in cold shock. To quantify the timing of gene expression, we fit sigmoid or double sigmoid models to differentially expressed genes in each stress. During the entry into stationary phase, genes whose expression rose earlier tended to be those that had been found to respond most strongly to low levels of RpoS. The timing of individual genes' expression was not correlated across stresses. Taken together, our results demonstrate E. coli activates RpoS with different timing in response to different stresses, which in turn generates a unique pattern of timing of the transcription response to each stress.

The transcriptional response to low temperature is weakly conserved across theEnterobacteriaceae

“…This implies that while RpoS regulates many genes in the cold, it is only a fraction of the genes that are cold- regulated overall. Reassuringly, of the 232 DE genes in E. coli in this study, 189 (81%) were previously identified as RpoS-regulated at 15°C by Adams et al (39). In S. enterica, 189 genes are DE between wt and Δ rpoS strain, 80% of the number of genes that are RpoS-regulated in E. coli.…”

“…The alternative sigma factor RpoS is known to be activated at low temperature in E. coli where it regulates the expression of several hundred genes (39). We compared the role of RpoS in E. coli and its close relative S. enterica during growth at 15°C.…”

Enhancing the Activity of a Self-Inducible Promoter in Escherichia coli through Saturation Mutation and High-Throughput Screening

“…Different stressed environments activate σ S in various ways, thereby influencing the levels of σ S and affecting certain promoters [29,31,54]. For instance, only 156 of the 1663 genes tested and their promoters can be activated in all of the stressed conditions tested (stationary phase, high osmolarity, and low temperature) were reported in a previous study [29].…”

“…Different stressed environments activate σ S in various ways, thereby influencing the levels of σ S and affecting certain promoters [29,31,54]. For instance, only 156 of the 1663 genes tested and their promoters can be activated in all of the stressed conditions tested (stationary phase, high osmolarity, and low temperature) were reported in a previous study [29]. In the ideal fermentation model, the logarithmic phase is typically characterized by an abundance of nutrients, while the stationary phase is marked by high osmotic pressure and starvation.…”

“…Once E. coli strains enter the stationary phase, the transcription factor associated with the RNA polymerase core enzyme is replaced with sigma s (σ S , alternative transcription factor) from sigma 70 (σ 70 , housekeeping transcription factor) [18,19] due to the active expression of the rpoS gene, the reduction in σ S proteolysis, and the accumulation of factors that support Eσ S formation [20][21][22][23][24][25][26] caused by multiple survival stresses [27,28]. Selfinducible promoters recognized and combined by σ S initiate over one thousand stationary phase genes [29][30][31], including stress genes, membrane protein genes, and metabolic enzyme genes [32][33][34][35][36][37], which can protect stationary-phase E. coli against environmental stress. This relationship between environmental stress and the σ S factor determines the bacterium's greater capacity to adapt to adversity during the stationary phase rather than the logarithmic phase.…”