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

Abstract

The ubiquitous subunit of RNA polymerase (RNAP), {omega}/RPB6, is traditionally viewed as an assembly chaperone or bacterial {sigma}-factor competition modulator. This study redefines the role of Escherichia coli {omega}, encoded by the rpoZ gene. Unexpectedly,{Delta} rpoZ strain does not exhibit major defects in {sigma}S-dependent stress responses, indicating its primary function lies elsewhere. Our CRISPRi screen suggested that losing {omega} may promote survival during transcription-replication conflicts. Consistently, we show that loss of {omega} 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 {omega} facilitates the removal of stalled RNAP, preventing catastrophic replisome collisions. We propose that {omega}/RPB6 homologs may balance RNAP processivity with controlled release to preserve genome integrity across all domains of life.