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A Novel Initiation Pathway in Escherichia Coli Transcription

By Eitan Lerner, SangYoon Chung, Benjamin L Allen, Shuang Wang, Jookyung J. Lee, Winson S. Lu, Wilson L. Grimaud, Antonino Ingargiola, Xavier Michalet, Yazan Alhadid, Sergei Borukhov, Terence Strick, Dylan J. Taatjes, Shimon Weiss

Posted 04 Mar 2016
bioRxiv DOI: 10.1101/042432 (published DOI: 10.1073/pnas.1605038113)

Initiation is a highly regulated, rate-limiting step in transcription. We employed a series of approaches to examine the kinetics of RNA polymerase (RNAP) transcription initiation in greater detail. Quenched kinetics assays, in combination with magnetic tweezer experiments and other methods, showed that, contrary to expectations, RNAP exit kinetics from later stages of initiation (e.g. from a 7-base transcript) was markedly slower than from earlier stages. Further examination implicated a previously unidentified intermediate in which RNAP adopted a long-lived backtracked state during initiation. In agreement, the RNAP-GreA endonuclease accelerated transcription kinetics from otherwise delayed initiation states and prevented RNAP backtracking. Our results indicate a previously uncharacterized RNAP initiation state that could be exploited for therapeutic purposes and may reflect a conserved intermediate among paused, initiating eukaryotic enzymes.

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