Escherichia coli promoter -10 and -35 region homologies correlate with binding and isomerization kinetics.

The DNA promoter sequence at which gene transcription is initiated in Escherichia coli contains two distinct regions of conserved nucleotides. Coefficients of homology to the -10 region and the -35 region were computed for many different prokaryotic promoters. Linear equations were derived that relate the degree of homology for each promoter region to the two kinetic constants that describe the interaction of RNA polymerase with the promoter site on DNA: the strength KB of binding to form closed complex, and the rate kf of isomerization to form open complex. A graphical plot of -35 versus -10 promoter region homologies for many promoters suggest that certain classes of prokaryotic operons might utilize differential degrees of consensus homology in these two regions to achieve specific control over kf and KB, in addition to modulating overall promoter strength.