The ω subunit stabilizes transcribing RNA polymerase to balance processivity and collision resolution

Abstract The ubiquitous subunit of RNA polymerase (RNAP), ω/RPB6, is traditionally viewed as an assembly chaperone or bacterial σ-factor competition modulator. This study redefines the role of Escherichia coli ω, encoded by the rpoZ gene. Unexpectedly, ΔrpoZ strain does not exhibit major defects in σS-dependent stress responses, indicating its primary function lies elsewhere. Our CRISPRi screen suggested that losing ω may promote survival during transcription-replication conflicts. Consistently, we show that loss of ω sensitizes RNAP to termination, reduces RNAP processivity, and suppresses toxic effects of DNA-damaging agents in strains lacking functional DksA, Rho, or SeqA; DksA and Rho promote the release of stalled RNAP from nucleic acids, while SeqA prevents aberrant replication initiation. These findings suggest that loss of ω facilitates the removal of stalled RNAP, preventing catastrophic replisome collisions. We propose that ω/RPB6 homologs may balance RNAP processivity with controlled release to preserve genome integrity across all domains of life. Competing Interest Statement The authors have declared no competing interest.