Underproduction of σ70 mimics a stringent response: A proteome approach

Abstract

When Escherichia coli cells enter stationary phase due to carbon starvation the synthesis of ribosomal proteins is rapidly repressed. In a ΔrelA ΔspoT mutant, defective in the production of the alarmone guanosine tetraphosphate (ppGpp), this regulation of the levels of the protein synthesizing system is abolished. Using a proteomic approach we demonstrate that the production of the vast majority of detected E. coli proteins are decontrolled during carbon starvation in the ΔrelA ΔspoT strain and that the starved cells behave as if they were growing exponentially. In addition we show that the inhibition of ribosome synthesis by the stringent response can be qualitatively mimicked by artificially lowering the levels of the housekeeping σ factor, σ70. In other words, genes encoding the protein-synthesizing system are especially sensitive to reduced availability of Δ70 programmed RNA polymerase. This effect is not dependent on ppGpp since lowering the levels of Δ70 gives a similar but less pronounced effect in a ppGpp0 strain. The data is discussed in view of the models advocating for a passive control of gene expression during stringency based on alterations in RNA polymerase availability.