Promoter selectivity of Escherichia coli RNA polymerase. Differential stringent control of the multiple promoters from ribosomal RNA and protein operons.

Using the in vitro mixed transcription system (Kajitani, M., and Ishihama, A. (1983) Nucleic Acids Res. 11, 671-686; Kajitani, M., and Ishihama, A. (1983) Nucleic Acids Res., 11, 3873-3889) we examined the effect of guanosine 3'-diphosphate, 5'-diphosphate (ppGpp), the chemical mediator of stringent control, on transcription of various Escherichia coli DNA fragments, each carrying a single specific promoter. We found that ppGpp inhibits transcription of stringently controlled genes, rrnE, rpsA, and rplJ, coding for ribosomal RNA, ribosomal protein S1 and L10, respectively, but not that of trp (tryptophan) and lacUV5 (lactose) genes. Among the multiple promoters of the rrnE and rpsA operons, the upstream promoters, rrnEp1 and rpsAp1, are subject to repression by ppGpp but the downstream promoters, rrnEp2 and rpsAp3, are insensitive. Taking these facts and the intrinsic strength of the respective promoters together, we suggest that the multiple promoters within the single and same operons play different physiological roles and are regulated by independent mechanisms. The inhibition by ppGpp takes place even after formation of open complexes, suggesting that the RNA polymerase bound to the sensitive promoters is accessible for interaction with ppGpp leading to rapid decay of the open complexes. During this study, we noticed that some promoters including recAp are activated in the presence of ppGpp, raising a possibility that ppGpp has dual effects on the promoter function.