The ω subunit stabilizes transcribing RNA polymerase to balance processivity and DNA repair

ABSTRACT: Escherichia coli RNAP holoenzyme consists of five core subunits – αI/αII, β, β’, ω, and one of the seven σ factors. The roles of the α, β, and β’ subunits are well-studied, but the function of the ω subunit remains unknown, despite it being universally conserved across all domains of life. One of the first studies regarding the ω subunit proposed that it serves as a chaperone for the RNA polymerase. The ω deletion has been linked to altered σ factor recruitment to the core enzyme, increasing expression from stationary/stress response genes. Lastly, the ω subunit has been linked to altered RNAP distribution across xenogenes and horizontally acquired operons and has been shown to decrease Rho-dependent polarity. In this study, we investigated ω effects on RNAP activities using a variety of in vivo and in vitro approaches. Our biochemical data showed no differences in initiation, elongation, pausing, or two model phage terminators (T7 and P14), in the presence or absence of ω. But ω deletion increased termination at NusA-dependent (rscX), or ribosomal (rrnB T1) terminators. RNA-seq profiling of the E. coli ΔrpoZ clean deletion strain did not show significant changes in gene expression for genes showing altered Δω RNAP-distribution, or genes controlled by σS. Finally, CRISPRi screening for WT and ΔrpoZ strains suggested that Rho and DksA could potentially influence ω function. Subsequent analysis of strains lacking DksA and having reduced expression of Rho showed that the rpoZ deletion increases survival in the presence of genotoxic agents and suggested that ω may stabilize the EC in vivo to modulate the resolution of collisions between RNA polymerase and replisome.

ORGANISM(S): Escherichia coli K-12

PROVIDER: GSE328708 | GEO | 2026/04/30

REPOSITORIES: GEO