Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo

We investigated the binding of E. coli RNA polymerase holoenzymes bearing sigma(70), sigma(S), sigma(32), or sigma(54) to the ribosomal RNA operons (rrn) in vivo. At the rrn promoter, we observed holoenzyme switching from E sigma(70) to E sigma(s) or E sigma(32) in response to environmental cues. We also examined if sigma factors are retained by core polymerase during transcript elongation. At the rrn operons, sigma(70) translocates briefly with the elongating polymerase and is released stochastically from the core polymerase with an estimated half-life of similar to 4-7 s. Similarly, at gadA and htpG, operons that are targeted by E sigma(S) and E sigma(32), respectively, we find that sigma(S) and sigma(32) also dissociate stochastically, albeit more rapidly than sigma(70), from the elongating core polymerase. Up to similar to 70% of E sigma(70) (the major vegetative holoenzyme) in rapidly growing cells is engaged in transcribing the rrn operons. Thus, our results suggest that at least similar to 70% of cellular holoenzymes release sigma(70) 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.