E. Coli RNA Polymerase Searches for Promoters through 3D Diffusion

Abstract

Gene expression, DNA replication, and genome maintenance all start with site-specific DNA binding proteins, which must recognize specific targets from among a vast excess of nonspecific DNA. For example, to initiate transcription, E. coli RNA polymerase (RNAP) must locate promoter sequences, which comprise <2% of the bacterial genome. This promoter search problem remains one of the least understood aspects of gene expression, largely due to the transient nature of intermediates involved in the search process. Here we use single-molecule microscopy to visualize RNAP in real time as it searches for promoters, and we develop a theoretical framework that allows us to analyze target searches at the submicroscopic scale based on single-molecule promoter association rates. Contrary to long-held assumptions, we demonstrate that the promoter search by E. coli RNAP is dominated entirely by 3D diffusion, which has direct implications for understanding how E. coli RNAP and other proteins locate their targets within physiological settings.