RNA-DNA and DNA-DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate

Nucleic Acids Research
Maria L KireevaMikhail Kashlev

Abstract

Translocation of RNA polymerase (RNAP) along DNA may be rate-limiting for transcription elongation. The Brownian ratchet model posits that RNAP rapidly translocates back and forth until the post-translocated state is stabilized by NTP binding. An alternative model suggests that RNAP translocation is slow and poorly reversible. To distinguish between these two models, we take advantage of an observation that pyrophosphorolysis rates directly correlate with the abundance of the pre-translocated fraction. Pyrophosphorolysis by RNAP stabilized in the pre-translocated state by bacteriophage HK022 protein Nun was used as a reference point to determine the pre-translocated fraction in the absence of Nun. The stalled RNAP preferentially occupies the post-translocated state. The forward translocation rate depends, among other factors, on melting of the RNA-DNA base pair at the upstream edge of the transcription bubble. DNA-DNA base pairing immediately upstream from the RNA-DNA hybrid stabilizes the post-translocated state. This mechanism is conserved between E. coli RNAP and S. cerevisiae RNA polymerase II and is partially dependent on the lid domain of the catalytic subunit. Thus, the RNA-DNA hybrid and DNA reannealing at the upstream ...Continue Reading

Citations

Sep 10, 2019·Nucleic Acids Research·Ranjit K PrajapatiGeorgiy A Belogurov
Feb 15, 2020·PLoS Computational Biology·Jordan DouglasAlexei J Drummond
Aug 24, 2018·Nature·Seychelle M VosPatrick Cramer
Dec 18, 2020·Nucleic Acids Research·Jin QianLaura Finzi
Apr 25, 2021·Biophysical Journal·D W Bo BroadwaterHarold D Kim

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Methods Mentioned

BETA
footprinting

Software Mentioned

Nun

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