A general mechanism for transcription bubble nucleation in bacteria

Andreas U. Mueller, James Chen, Mengyu Wu, Courtney Chiu, B. Tracy Nixon, Elizabeth A. Campbell, Seth A. Darst

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Bacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ70, nucleates DNA melting via recognition of conserved bases of the promoter −10 motif, which are unstacked and captured in pockets of σ70. By contrast, the mechanism of transcription bubble nucleation and formation during the unrelated σN-mediated transcription initiation is poorly understood. Herein, we combine structural and biochemical approaches to establish that σN, like σ70, captures a flipped, unstacked base in a pocket formed between its N-terminal region I (RI) and extra-long helix features. Strikingly, RI inserts into the nascent bubble to stabilize the nucleated bubble prior to engagement of the obligate ATPase activator. Our data suggest a general paradigm of transcription initiation that requires σ factors to nucleate an early melted intermediate prior to productive RNA synthesis.

Original languageEnglish (US)
Article numbere2220874120
JournalProceedings of the National Academy of Sciences of the United States of America
Volume120
Issue number14
DOIs
StatePublished - Apr 4 2023

All Science Journal Classification (ASJC) codes

  • General

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