Differential stringent control of Escherichia coli rRNA promoters: effects of ppGpp, DksA and the initiating nucleotides

Abstract

Transcription of rRNAs inEscherichia coliis directed from seven redundant rRNA operons, which are mainly regulated by their P1 promoters. Here we demonstrate byin vivomeasurements that the amounts of individual rRNAs transcribed from the different operons under normal growth vary noticeably although the structures of all the P1 promoters are very similar. Moreover, we show that starvation for amino acids does not affect the seven P1 promoters in the same way. Notably, reduction of transcription fromrrnDP1 was significantly lower compared to the other P1 promoters. The presence of DksA was shown to be crucial for the ppGpp-dependent downregulation of all P1 promoters. BecauserrnDP1 is the onlyrrnpromoter starting with GTP instead of ATP, we performed studies with a mutantrrnDpromoter, where the initiating G+1 is replaced by A+1. These analyses demonstrated that the ppGpp sensitivity ofrrnP1 promoters depends on the nature and concentration of initiating nucleoside triphosphates (iNTPs). Our results support the notion that the seven rRNA operons are differentially regulated and underline the importance of a concerted activity between ppGpp, DksA and an adequate concentration of the respective iNTP.