(410h) Convergent Transcription and Transcriptional Interference as a Regulatory Element in the Rhamnose Regulon of Escherichia Coli

The behavior of a circuit may also be determined by how it is physically encoded within the genome. By physical encoding, we mean the orientation and relative proximity of a transcription factor to its target structural genes. In particular, a given regulatory mechanism involving multiple genes can be physically arranged in any number of ways. The specific location of the genes may, therefore, represent an additional factor determining circuit behavior. In other words, two circuits involving the same genes and regulatory mechanism can potentially behave differently if they are physically encoded in alternate configurations.

In this work, we investigated the role of transcriptional interference due to convergent promoters using the rhamnose (rha) system from Escherichia coli as our model. RhaR and RhaS are transcriptional activators that respond to availability of L-rhamnose in the surrounding media. RhaR activates rhaSR operon and RhaS activates transcription of operon that encodes enzymes essential for L-rhamnose catabolic enzymes, rhaBAD, and the operon that encodes the L-rhamnose transporter, rhaT. The genes in this system are arranged in such a way that rhaSR and rhaT are expressed from convergent promoters with the C-terminals of rhaR and rhaT overlapping.

We report the effect of transcriptional interference between rhaR and rhaT on the dynamics of gene expression in the rhamnose utilization network in E. coli. Using a number of genetic constructs, we eliminated transcriptional interference between rhaR and rhaT and demonstrate that this leads to a faster and greater induction of the rhaBAD operon. Based on our results, we conclude that the physical arrangement of the genes on the chromosome plays an important role in governing gene expression dynamics.