A stationary phase protein in Escherichia coli with binding activity to the major σ subunit of RNA polymerase

Switching of the transcription pattern in Escherichia coli during the growth transition from exponential to stationary phase is accompanied by the replacement of the RNA polymerase-associated σ(70) subunit (σ(D)) with σ(38) (σ(S)). A fraction of the σ(70) subunit in stationary phase cell extracts was found to exist as a complex with a novel protein, designated Rsd (Regulator of sigma D). The intracellular level of Rsd starts to increase during the transition from growing to stationary phase. The rsd gene was identified at 90 min on the E. coli chromosome. Overexpressed and purified Rsd protein formed complexes in vitro with σ(70) but not with other σ subunits, σ(N), σ(S), σ(H), σ(F), and σ(E). Analysis of proteolytic fragments of σ(70) indicated that Rsd binds at or downstream of region 4, the promoter −35 recognition domain. The isolated Rsd inhibited transcription in vitro to various extents depending on the promoters used. We propose that Rsd is a stationary phase E. coli protein with regulatory activity of the σ(70) function.