Maximum rrn promoter activity in Escherichia coli at saturating concentrations of free RNA polymerase

During fast growth, the rrn P1 promoters of Escherichia coli operate at their maximum strength, but below their maximum activity (Vmax), since they are not saturated with RNA polymerase. Since higher concentrations of free RNA polymerase are expected to be found in strains carrying rrn deletions, we have analyzed reported electron micrographs of rrn operons from rrn deletion strains growing at maximal rates (at 37 °C) in LB medium [1]. We conclude that, in a strain with four of the seven rrn operons inactivated by partial deletions, transcripts are initiated at rrn P1 promoters 1.6-fold more rapidly than in the wild-type strain and the entirety of the rrn operon is transcribed at a 1.5-fold higher average elongation rate due to shortened pauses in the 16S and 23S regions. Under this condition, traffic congestion occurs in front of a pause site in the 5′ leader region of the rrn operon near the beginning of the 16S gene; the congestion extends all the way back to the promoter, impedes promoter clearance and limits the promoter activity to one initiation per 0.56 s. This corresponds to a promoter activity of 107 transcripts/min and is assumed to be close to the Vmax of rrn P1 promoters.