We focus on unusual aspects of transcription regulation mediated by (p)ppGpp. These phenomena are unusual in bacteria by not involving sequence-specific DNA binding protein repressors or inducers. Instead, (p)ppGpp seems to somehow modify the kinetic properties of RNA polymerase recognition of promoters through synergistic interactions with individual members of a new class of structurally similarly secondary channel proteins. The growing list of proteins with these new functions includes DksA and the GreA/B elongation factors. The list is extended now through a collaboration to include a protein (TraR) encoded on the E. coli F conjugation episome. This year we have also characterized a small RNA (GraL) that is transcribed within the GreA leader from tandem housekeeping (Sigma-D) and stress (Sigma-E) promoters. Although GraL enhances bacterial fitness during growth, its regulatory target remains curiously elusive. Other genetic approaches have led us to define new regulatory roles for (p)ppGpp activation of tktB in intermediary metabolism as well as the suggestion that AppppA might substitute for some (p)ppGpp regulatory attributes. Finally, again in collaboration, a sensitive and specific fluorescent probe for (p)ppGpp abundance has been developed that will allow isotope-free (p)ppGpp assays.
