A role for a small stable RNA in modulating the activity of DNA-binding proteins

The 10Sa RNA, encoded by the E. coli ssrA gene, appears to modulate action of some DNA-binding proteins. When ssrA is inactivated, lacZ expression from the lac operon, as well as galK from a gal operon fused to a phage lambda promoter, is reduced from that observed in bacteria wild-type for ssrA. These differences are not observed if the relevant repressor is inactive, suggesting that in the absence of 10Sa RNA binding of LacI and lambda cI repressors is enhanced. Gel mobility shifts show that 10Sa RNA binds these repressors and that an excess of 10Sa RNA competes for binding of lambda cI with a DNA fragment containing the OR2 repressor-binding sequence. Similar observations were made in studies of the E. coli LexA repressor and phage P22 C1 transcription activator proteins. These results suggest that direct interaction with 10Sa RNA may explain this modulation of protein-DNA interactions.