Molecular Cell
Volume 20, Issue 3, 11 November 2005, Pages 357-366
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Article
Holoenzyme Switching and Stochastic Release of Sigma Factors from RNA Polymerase In Vivo

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Summary

We investigated the binding of E. coli RNA polymerase holoenzymes bearing σ70, σS, σ32, or σ54 to the ribosomal RNA operons (rrn) in vivo. At the rrn promoter, we observed “holoenzyme switching” from Eσ70 to EσS or Eσ32 in response to environmental cues. We also examined if sigma factors are retained by core polymerase during transcript elongation. At the rrn operons, σ70 translocates briefly with the elongating polymerase and is released stochastically from the core polymerase with an estimated half-life of ∼4–7 s. Similarly, at gadA and htpG, operons that are targeted by EσS and Eσ32, respectively, we find that σS and σ32 also dissociate stochastically, albeit more rapidly than σ70, from the elongating core polymerase. Up to ∼70% of Eσ70 (the major vegetative holoenzyme) in rapidly growing cells is engaged in transcribing the rrn operons. Thus, our results suggest that at least ∼70% of cellular holoenzymes release σ70 during transcript elongation. Release of sigma factors during each round of transcription provides a simple mechanism for rapidly reprogramming polymerase with the relevant sigma factor and is consistent with the occurrence of a “sigma cycle” in vivo.

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