Khitiri, B. | bioRxiv Science

bioRxiv2026

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

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.

genetics↗

bioRxiv2026

Selective targeting of a histone-like silencer Sfx to the R6K conjugal transfer operon

Conjugative plasmids drive bacterial evolution and antibiotic resistance spread, yet their gene expression must be silenced to protect the host. A histone-like protein H-NS represses many mobile and sedentary xenogenes but fails to silence the conjugal transfer vir operon of R6K, a prototype IncX plasmid. Instead, R6K encodes its own H-NS homolog, Sfx, to repress the vir operon. Here, we show that, unlike other plasmid silencers that target promoters, Sfx cooperates with Rho factor to arrest transcription elongation. ChIP-seq reveals that despite sharing similar DNA motifs and a preference for negative supercoiling, Sfx and H-NS occupy distinct niches: Sfx binds weakly to the chromosome but is enriched on the R6K vir operon, from which H-NS is excluded. We hypothesize that this selective targeting is mediated by Sfx-vir interactions and phase separation. We show that Sfx binding to vir DNA critically depends on DNA topology but not on the target location. Our results suggest that Sfx phase separates with R6K to ensure its preferential recruitment to the plasmid DNA and forms stable nucleoprotein filaments that are impermeable to competitors. These findings reveal how histone-like proteins can partition the genome into distinct regulatory niches, a strategy likely mirrored across all life. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/707533v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1ee08a9org.highwire.dtl.DTLVardef@7ab423org.highwire.dtl.DTLVardef@1c89543org.highwire.dtl.DTLVardef@1bfa132_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗