  We have developed a mathematical model of transcriptional activation by MarA
in Escherichia coli, and used the model to analyze measurements of
MarA-dependent activity of the marRAB, sodA, and micF promoters in mar-rob-
cells. The model rationalizes an unexpected poor correlation between the
mid-point of in vivo promoter activity profiles and in vitro equilibrium
constants for MarA binding to promoter sequences. Analysis of the promoter
activity data using the model yielded the following predictions regarding
activation mechanisms: (1) MarA activation of the marRAB, sodA, and micF
promoters involves a net acceleration of the kinetics of transitions after RNA
polymerase binding, up to and including promoter escape and message elongation;
(2) RNA polymerase binds to these promoters with nearly unit occupancy in the
absence of MarA, making recruitment of polymerase an insignificant factor in
activation of these promoters; and (3) instead of recruitment, activation of
the micF promoter might involve a repulsion of polymerase combined with a large
acceleration of the kinetics of polymerase activity. These predictions are
consistent with published chromatin immunoprecipitation assays of interactions
between polymerase and the E. coli chromosome. A lack of recruitment in
transcriptional activation represents an exception to the textbook description
of activation of bacterial sigma-70 promoters. However, use of accelerated
polymerase kinetics instead of recruitment might confer a competitive advantage
to E. coli by decreasing latency in gene regulation.
