The RpoS subunit of RNA polymerase controls the expression of numerous genes involved in stationary phase and in response to different stress conditions. The regulatory protein Crl increases the activity of RpoS by direct interaction with the RpoS-holoenzyme. In order to define the extent of the Crl regulon, we have used two-dimensional SDS-PAGE electrophoresis to measure the role of Crl in regulating the expression of the E. coli proteome in stationary phase at 30°C. By comparing the proteome of four strains (WT, crl-, rpoS- and crl-rpoS-), we have observed that the intensity of 74 spots was modified in at least one mutant context. 62 spots were identified by mass spectrometry and correspond to 40 distinct proteins. They were classified in four main categories: DNA metabolism, central metabolism, response to environmental modifications, and miscellaneous. Three proteins were specifically involved in quorum sensing: TnaA (the tryptophanase that converts tryptophane to indole), WrbA (Trp Repressor-binding protein) and YgaG (homologous to LuxS, autoinducer-2 synthase). Since little is known about the regulation of Crl expression, we have investigated the influence of diffusible molecules on the expression of Crl. Using western blotting experiments, we shown that, at 30°C, diffusible molecule(s) produced during the transition phase between exponential and stationary phase induce a premature expression of Crl. Indole was tested as one of the potential candidates: at 37°C, it is present in the extracellular medium at a constant concentration, but at 30°C, its concentration peaks during the transition phase. When indole was added to the culture medium, it also induced prematurely the expression of Crl at both the trancriptional and translational levels in a Crl dependent manner. Crl may thus be considered a new environmental sensor via the indole concentration.