The transcriptional response of genes to RpoS concentration in Escherichia coli is not determined by core promoter sequences

The alternative sigma factor RpoS is an important regulatory protein in Escherichia coli, responsible for mediating the general stress response. RpoS levels vary continuously in response to different stresses. Previous work has shown that genes vary in their responsiveness to increasing RpoS concentrations, with some genes being \"sensitive,\" requiring only a low level of RpoS to be relatively highly expressed, while other genes are \"insensitive,\" only being highly expressed in the presence of high levels of RpoS. In other systems, this type of variation is caused by interactions between the regulatory protein and the DNA it binds. To see if this is the case for RpoS, we measured twelve RpoS binding site mutants for their effects on maximal expression and responsiveness to increasing RpoS concentration. While maximal expression varied over an order of magnitude across these twelve constructs, the responsiveness to increasing RpoS concentration was largely unaffected, suggesting that the RpoS binding site alone is not responsible for a genes sensitivity or insensitivity to RpoS. In addition, we swapped the RpoS binding region between sensitive and insensitive promoters and found no change in the behavior of the promoter. Taken together, these results argue that differences in sensitivity of the RpoS-dependent promoters are not due to interactions between RpoS and the various DNA sites it binds.