Transcription Through Roadblock Systems Reveals A Hybrid Transit Mechanism.

During transcription, RNA polymerases (RNAPs) must transit through roadblocks of various strengths to produce biologically meaningful transcripts. The roadblocking strength of DNA binding proteins varies significantly according to their affinity for DNA. Here we demonstrate that Escherichia coli RNAP can adopt a hybrid mechanism consisting of a passive and an active pathway to effectively transit through two roadblocks of different strengths, the lac repressor protein and EcoRI Q111. The passive pathway, where RNAP waits for the dissociation of the roadblock, is efficient against relatively weak roadblocks. The active mechanism, where RNAP dislodges the roadblock by repetitive cycles of backtracking and recovery, is essential for transit through strong roadblocks. Force direction and transcription factor GreA can bias the choice between the two pathways and modulate the rate of passage through roadblocks. These results further our understanding of how RNAPs transit through roadblocks.