Bidirectional promoters in Escherichia coli: regulatory rules and implications for gene expression noise

In prokaryotes, bidirectional promoters are pseudo-symmetrical DNA sequences that stimulate divergent transcription. Ubiquitous, and far more likely to drive messenger RNA production than directional promoters, nothing is known about their control. For example, symmetry allows bidirectional promoters to engage RNA polymerase in two possible orientations. As one binding event prevents the other, there is potential for regulation at this step. Here, we show that basal transcription, from all five tested bidirectional promoters, is too low for RNA polymerase competition. Hence, synthesis of one RNA does not impact the divergent pair. Conversely, if transcription in one direction is substantially activated, divergent RNA production can be repressed. Often, this results from RNA polymerase competition alone. Unexpectedly, this also impacts population-level gene expression noise. Specifically, if transcription is constrained, by RNA polymerase interference, cell-to-cell variation is reduced. We anticipate that our findings will help to establish rules for understanding bidirectional promoters, which have hardly been studied, in many bacteria.