eLife (Feb 2019)

Delayed inhibition mechanism for secondary channel factor regulation of ribosomal RNA transcription

  • Sarah K Stumper,
  • Harini Ravi,
  • Larry J Friedman,
  • Rachel Anne Mooney,
  • Ivan R Corrêa Jnr,
  • Anne Gershenson,
  • Robert Landick,
  • Jeff Gelles

DOI
https://doi.org/10.7554/eLife.40576
Journal volume & issue
Vol. 8

Abstract

Read online

RNA polymerases (RNAPs) contain a conserved ‘secondary channel’ which binds regulatory factors that modulate transcription initiation. In Escherichia coli, the secondary channel factors (SCFs) GreB and DksA both repress ribosomal RNA (rRNA) transcription, but SCF loading and repression mechanisms are unclear. We observed in vitro fluorescently labeled GreB molecules binding to single RNAPs and initiation of individual transcripts from an rRNA promoter. GreB arrived and departed from promoters only in complex with RNAP. GreB did not alter initial RNAP-promoter binding but instead blocked a step after conformational rearrangement of the initial RNAP-promoter complex. Strikingly, GreB-RNAP complexes never initiated at an rRNA promoter; only RNAP molecules arriving at the promoter without bound GreB produced transcript. The data reveal that a model SCF functions by a ‘delayed inhibition’ mechanism and suggest that rRNA promoters are inhibited by GreB/DksA because their short-lived RNAP complexes do not allow sufficient time for SCFs to dissociate.

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