Transcription Past Loop Forming Repressor Proteins

Abstract

Topology plays a major role in the transcriptional regulation of genetic information. Among the most ubiquitous topological elements are loops that form when proteins simultaneously bind to two non-contiguous sites along the DNA. This topology increases the local concentration of the protein around each of the sites and effectively stabilizes the bound protein. Thus looping is expected to increase the inhibition of transcription through repressor binding sites. This is likely to be important for the inhibition of the genes responsible for lactose metabolism in E. coli. Indeed the lac repressor can form loops between a site near the promoter (O1) and another either −92 (O3) or +401 (O2) base pairs away along the DNA. Although LacI bound to a single site is an effective impediment to transcription in vitro, experiments in bacteria have shown that an auxiliary site greatly enhances repression. To directly test this idea, a strong promoter was placed 200 base pairs ahead of lac repressor (LacI) binding sites separated by 400 bp. The outcome of in vitro transcription along such templates in the presence of high LacI concentrations that produced loops in 50% of molecules was visualized with atomic force microscopy.