PT  - JOURNAL ARTICLE
AU  - Jason Saba
AU  - Xien Chua
AU  - Tatiana V. Mishanina
AU  - Dhananjaya Nayak
AU  - Tricia A. Windgassen
AU  - Rachel A. Mooney
AU  - Robert Landick
TI  - The elemental mechanism of transcriptional pausing
AID  - 10.1101/422220
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 422220
4099  - http://biorxiv.org/content/early/2018/09/19/422220.short
4100  - http://biorxiv.org/content/early/2018/09/19/422220.full
AB  - 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.