FIGURE 5.
A model summarizing the two modes of 6S RNA-dependent regulation: 6S RNA binding affinity to Eσ70 and pRNA-induced release rate. Levels of free core enzyme (E, large circle) and free sigma factors (σ70 and σS shown) determine the formation rate of Eσ70 complex (superimposed circles). This complex is depleted by the formation of either a bound 6S RNA:Eσ70 complex (top path) or DNA:Eσ70 complex (bottom path). This competitive binding provides a 6S RNA-dependent mechanism to distinguish between strong and weak DNA promoters that depend on 6S RNA intrinsic binding affinity and cellular concentration. The characteristic time for pRNA-induced 6S RNA release (t1/2), which is sensitive to free magnesium and weakly to NTP levels, provides a mechanism to sequester core polymerase from use, effectively lowering the concentration of free polymerase (E) in the cell.