We used the model to analyze the intergenic regions of the Escherichia coli ( 40 ) and S. enterica ( 41 ) genomes by using relaxed thresholds ( 25 ) , which allowed the recovery of PhoP-regulated promoters with weak matching to the PhoP box consensus , such as the Salmonella pmrD promoter , that could not be detected by using consensus cutoffs ( 2 , 25 ) despite being regulated and footprinted by the PhoP protein ( 18 , 26 ) .
the Salmonella pmrD promoter could not be detected by using consensus cutoffs despite being regulated by the PhoP protein
the Salmonella pmrD promoter could not be detected by using consensus cutoffs despite being regulated by the PhoP protein
the pmrD promoter harbors binding sites for both the PhoP
When the strain was shifted from repressing to inducing concentrations , binding of PhoP to the pmrD promoters increased during the first 10 min .
When the strain was shifted from repressing to inducing Mg2 , binding of PhoP to the pmrD promoters increased during the first 10 min .
When the strain was shifted from repressing to inducing concentrations , binding of PhoP to the pmrD promoters then asymptotically reached the steady-state levels .
When the strain was shifted from repressing to inducing Mg2 , binding of PhoP to the pmrD promoters then asymptotically reached the steady-state levels .
To identify the PhoP-regulated gene ( s ) responsible for motility on 0.3 % agarose low Mg2 + media , we tested the behavior of strains mutated in each of 19 different PhoP-activated genes ( mgtA , mgtB , mgtC , mig-14 , pagC , pagK , pagM , pagN , pagO , pagP , pcgL , pgtE , phoN , pmrD , rstA , slyA , ugtL , virK , and yobG ) .