A non‐native C‐terminal extension of the β’ subunit compromises RNA polymerase and Rho functions

Escherichia coli RfaH abrogates Rho‐mediated polarity in
lipopolysaccharide core biosynthesis operons, and ΔrfaH cells are
hypersensitive to antibiotics, bile salts, and detergents. Selection for
rfaH suppressors that restore growth on SDS identified a
temperature‐sensitive mutant in which 46 C‐terminal residues of the RNA
polymerase (RNAP) β’ subunit are replaced with 23 residues carrying a net
positive charge. Based on similarity to rpoC397, which confers a
temperature‐sensitive phenotype and resistance to bacteriophages, we named
this mutant rpoC397*. We show that SDS resistance depends on a single
nonpolar residue within the C397* tail, whereas basic residues are
dispensable. In line with its mimicry of RfaH, C397* RNAP is resistant to
Rho but responds to pause signals, NusA, and NusG in vitro similarly to
the wild‐type enzyme and binds to Rho and Nus factors in vivo. Strikingly,
the deletion of rpoZ, which encodes the ω “chaperone” subunit, restores
rpoC397* growth at 42°C but has no effect on SDS sensitivity. Our results
suggest that the C397* tail traps the ω subunit in an inhibitory state
through direct contacts and hinders Rho‐dependent termination through
long‐range interactions. We propose that the dynamic and hypervariable
β’•ω module controls RNA synthesis in response to niche‐specific signals.