Regulator Trafficking on Bacterial Transcription Units In Vivo

Abstract

Summary The in vivo trafficking patterns on DNA by the bacterial regulators of transcript elongation σ70, ρ, NusA, and NusG and the explanation for high promoter-proximal levels or peaks of RNA polymerase (RNAP) are unknown. Genome-wide ChIP-chip on E. coli revealed distinct association patterns of regulators as RNAP transcribes away from promoters (ρ first, then NusA, and then NusG). However, the interactions of elongating complexes with these regulators, including a weak interaction with σ70, did not differ significantly among most transcription units. A modest variation of NusG signal among genes reflected increased NusG interaction as transcription progresses, rather than functional specialization of elongating complexes. Promoter-proximal RNAP peaks were offset from σ70 peaks in the direction of transcription and co-occurred with NusA and ρ peaks, suggesting that the RNAP peaks reflected elongating, rather than initiating, complexes. However, inhibition of ρ did not increase RNAP levels within genes downstream of the RNAP peaks, suggesting the peaks are caused by a mechanism other than simple ρ-dependent attenuation.