Stationary phase reorganisation of the Escherichia coli transcription machinery by Crl protein, a fine-tuner of σs activity and levels

Abstract

Upon environmental changes, bacteria reschedule gene expression by directing alternative sigma factors to core RNA polymerase (RNAP). This sigma factor switch is achieved by regulating relative amounts of alternative sigmas and by decreasing the competitiveness of the dominant housekeeping σ70. Here we report that during stationary phase, the unorthodox Crl regulator supports a specific sigma factor, σS (RpoS), in its competition with σ70 for core RNAP by increasing the formation of σS‐containing RNAP holoenzyme, EσS. Consistently, Crl has a global regulatory effect in stationary phase gene expression exclusively through σS, that is, on σS‐dependent genes only. Not a specific promoter motif, but σS availability determines the ability of Crl to exert its function, rendering it of major importance at low σS levels. By promoting the formation of EσS, Crl also affects partitioning of σS between RNAP core and the proteolytic σS‐targeting factor RssB, thereby playing a dual role in fine‐tuning σS proteolysis. In conclusion, Crl has a key role in reorganising the Escherichia coli transcriptional machinery and global gene expression during entry into stationary phase.