In vivo transcription of rRNA operons in Escherichia coli initiates with purine nucleoside triphosphates at the first promoter and with CTP at the second promoter.

32P-labeled RNA was isolated from growing Escherichia coli and the 5' end nucleoside triphosphates of rRNA were analyzed after hybridization to various DNA fragments derived from one of the rRNA operons, rrnE. The results show that there are two transcription start sites for each rRNA operon in vivo, one initiating with ATP (or GTP), and the second initiating with CTP. Transcription from the first site was observed to be stronger than that from the second site. These two sites correspond to the two promoters identified in the previous in vitro studies, indicating that the two promoters are used in vivo. These results also demonstrate previously unrecognized transcription initiation with CTP in growing E. coli cells.