POISED σ54 RNAP CAN BLOCK TRANSCRIPION OF AN UPSTREAM APPROACHING RNAP FROM A NEARBY PROMOTER

Bacterial enhancers are non-translated DNA sequences which play an indispensable roll in gene regulation. In bacteria, enhancers function as molecular integrators that are responsible for turning on gene only in response to particular stresses (e.g. Nitrogen deprivation). The architecture of bacterial enhancers typically consists of a tandem of activator binding sites (e.g. NtrC), which are located several tens to hundreds of base-pairs upstream of a poised σ54-dependent promoter. The intervening region usually also harbors additional binding sites for transcription factors, most often IHF. Bacterial enhancers are able to initiate transcription via DNA looping, which allows the upstream activator to interact with the poised holoenzyme complex, facilitating its release.

We have discovered a new transcription regulation mechanism in which a poised σ54 RNAP can also block the transcription of an upstream approaching RNAP from a nearby promoter. This blocking mechanism only works in the 5’-3’ directions, as RNAPs approaching from the 3’-5’ direction are unhindered by the presence of the promoter. In order to test for the prevalence of this mechanism, we are in the process of analyzing data from a high-throughput experiment, which was design to screen for additional “silencing” σ54-dependent promoters. Our screen consisted of 10,000 putative σ54 RNAP binding sites that were taken predominantly from two genomes (E.coli, V. cholerae). This new mechanism can shed light on many promoter architectures found in the genome, and become a new tool for gene regulation in synthetic biology.