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bioRxiv · 10.1101/422220

The elemental mechanism of transcriptional pausing

Saba, J.·Chua, X.·Mishanina, T. V.·Nayak, D.·Windgassen, T. A.·Mooney, R. A.·Landick, R.
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Abstract

Transcriptional pausing underpins regulation of cellular RNA biogenesis. A consensus pause sequence that acts on RNA polymerases (RNAPs) from bacteria to mammals halts RNAP in an elemental paused state from which longer-lived pauses can arise. Although the structural foundations of pauses prolonged by backtracking or nascent RNA hairpins are recognized, the fundamental mechanism of the elemental pause is less well-defined. Here we report a mechanistic dissection that establishes the elemental pause signal (i) is multipartite; (ii) causes a modest conformational shift that puts RNAP in an off-pathway state in which template base loading but not RNA translocation is inhibited; and (iii) can easily enter pretranslocated and one-base-pair backtracked states despite principally occupying the half-translocated state observed in cryo-EM structures of paused RNAPs. Our findings provide a mechanistic basis for the elemental pause and a framework to understand how pausing is modulated by sequence, cellular conditions, and regulators.

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Saba, J., Chua, X., Mishanina, T. V., Nayak, D., Windgassen, T. A., Mooney, R. A., Landick, R.. 2018-09-19. The elemental mechanism of transcriptional pausing. https://doi.org/10.1101/422220

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