Regulator Trafficking on Bacterial Transcription Units In Vivo

SummaryThe trafficking patterns of the bacterial regulators of transcript elongation σ70, ρ, NusA, and NusG on genes in vivo and the explanation for promoter-proximal peaks of RNA polymerase (RNAP) are unknown. Genome-wide, E. coli ChIP-chip revealed distinct association patterns of regulators as RNAP transcribes away from promoters (ρ first, then NusA, then NusG). However, the interactions of elongating complexes with these regulators 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 from the RNAP peaks, suggesting the peaks are caused by a mechanism other than ρ-dependent attenuation.