Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival

Upon sensing an impending saturation level of their population density, Escherichia coli cells enter into the stationary phase. We have identified structural and functional modulations of the nucleoid, the transcription apparatus and the translation machinery occurring during the transition from exponential growth to stationary phase. The major DNA-binding proteins, Fis, HU and Hfq, in the exponential-phase nucleoid are replaced by a single stationary-phase protein Dps, thereby compacting the nucleoid and ultimately leading to silencing of the DNA functions. The transcription apparatus is modified by replacing the major promoter recognition subunit, sigma(70), with sigma(S). A stationary-phase protein, Rsd (Regulator of sigma D), with the binding activity of sigma(70) is involved in the efficient replacement of sigma and/or the storage of unused sigma(70). Changes in cytoplasmic composition also differentially influence the activity of E sigma(70) and E sigma(S) holoenzymes. Together, these effects may result in the preferential transcription of stationary-phase specific genes. The translation machinery is also modulated in stationary phase, by the formation of translationally incompetent 100S ribosomes. A small stationary-phase protein, RMF (Ribosome Modulation Factor), is involved in the dimerization of 70S ribosome monomers.