Selective repression by Fis and H-NS at the Escherichia coli dps promoter

Dps is a nucleoid-associated protein that plays a major role in condensation of the Escherichia coli chromosome in stationary phase. Here we show that two other nucleoid-associated proteins, Fis and H-NS, can bind at the dps gene promoter and downregulate its activity. Both Fis and H-NS selectively repress the dps promoter, preventing transcription initiation by RNA polymerase containing σ⁷⁰, the housekeeping σ factor, but not by RNA polymerase containing σ³⁸, the stationary-phase σ factor. Fis represses by trapping RNA polymerase containing σ⁷⁰ at the promoter. In contrast, H-NS functions by displacing RNA polymerase containing σ⁷⁰, but not RNA polymerase containing σ³⁸. Dps levels are known to be very low in exponentially growing cells and rise sharply as cells enter stationary phase. Conversely, Fis levels are high in growing cells but fall to nearly zero in stationary-phase cells. Our data suggest a simple model to explain how the Dps-dependent super-compaction of the folded chromosome is triggered as cell growth ceases.