Figure 9. Models for H-NS effects on pausing, Rho termination, and DNA bridging.
(A) As RNAP elongates through bridged filaments, pause durations increase for one or both of two reasons: (i) the off-rate of bridged H-NS is slower than the elongation rate of RNAP, leading to a roadblock (physical barrier; black bar); or (ii) H-NS bridging creates a closed topological domain that accumulates positive and negative supercoiling (torsional stress) in front and behind the EC, respectively, because free rotation of the DNA is blocked by bridged H-NS contacts and free rotation of the EC is blocked by steric clash between the bridged H-NS–DNA filament and the nascent RNA, including macromolecules like Rho or ribosomes bound to the nascent RNA (Liu and Wang, 1987). Blue arrows depict the rotation of DNA required to avoid torsional strain when the DNA is unconstrained. Both the under-winding (behind EC) and over-winding (in front of EC) torsional stresses will increase the propensity for RNAP to backtrack, thus increasing the duration of pauses that involve backtracking and increasing the kinetic window for Rho-dependent termination at backtrack pauses. (B) At 66 H-NS/kb, H-NS-free DNA segments allow DNA-binding domains from initially formed linear filaments to interact and form bridged filaments (top). At 200 H-NS/kb, all DNA segments become occupied by H-NS, leaving no available unbound DNA for formation of bridged filaments (bottom).