The interaction of ω2 with the RNA polymerase β' subunit functions as an activation to repression switch

Abstract

The ω gene is encoded in broad-host range and low-copy plasmids. It is genetically linked to antibiotic resistance genes of the major human pathogens of phylum Firmicutes. The homodimeric forms of ω (ω2) coordinate the plasmid copy number control, faithful partition (ω2 and δ2) and better-than-random segregation (ζϵ2ζ) systems. The promoter (P) of the ωϵζ operon (Pω) transiently interacts with ω2. Adding δ2 facilitates the formation of stable ω2·Pω complexes. Here we show that limiting ω2 interacts with the N-terminal domain of the β' subunit of the Bacillus subtilis RNA polymerase (RNAP-σ(A)) vegetative holoenzyme. In this way ω2 recruits RNAP-σ(A) onto Pω DNA. Partial Pω occupancy by ω2 increases the rate at which RNAP-σ(A) complex shifts from its closed (RPC) to open (RPO) form. This shift increases transcription activation. Adding δ2 further increases the rate of Pω transcription initiation, perhaps by stabilizing the ω2·Pω complex. In contrast, full operator occupancy by ω2 facilitates RPC formation, but it blocks RPO isomerization and represses Pω utilization. The stimulation and inhibition of RPO formation is the mechanism whereby ω2 mediates copy number fluctuation and stable plasmid segregation. By this mechanism, ω2 also indirectly influences the acquisition of antibiotic resistance genes.