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A general mechanism for transcription bubble nucleation in bacteria.

Andreas U MuellerJames ChenMengyu WuCourtney ChiuB Tracy NixonElizabeth A CampbellSeth A Darst
Published in: Proceedings of the National Academy of Sciences of the United States of America (2023)
Bacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ 70 , nucleates DNA melting via recognition of conserved bases of the promoter -10 motif, which are unstacked and captured in pockets of σ 70 . By contrast, the mechanism of transcription bubble nucleation and formation during the unrelated σ N -mediated transcription initiation is poorly understood. Herein, we combine structural and biochemical approaches to establish that σ N , like σ 70 , 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.
Keyphrases
  • transcription factor
  • gene expression
  • high resolution
  • dna methylation
  • dna binding
  • magnetic resonance imaging
  • machine learning
  • mass spectrometry
  • cell free
  • immune response
  • nuclear factor
  • toll like receptor