Lrp (leucine-responsive regulatory protein) is a major regulatory prot
ein involved in the expression of numerous operons in Escherichia coli
. For ilvIH, one of the operons positively regulated by Lrp, Lrp binds
to multiple sites upstream of the transcriptional start site and acti
vates transcription. An alignment of 12 Lrp binding sites within ilvIH
DNA from two different organisms revealed a tentative consensus seque
nce AGAAT TTTATTCT (Q. Wang, M. Sacco, E. Ricca, C. T. Lago, M. DeFeli
ce, and J. M. Calvo, Mol. Microbiol. 7:883-891, 1993). To further char
acterize the binding specificity of Lrp, we used a variation of the Se
lex procedure of C. Tuerk and L. Gold (Science 249:505-510, 1990) to i
dentify sequences that bound Lrp out of a pool of 10(12) different DNA
molecules. We identified 63 related DNA sequences that bound Lrp and
estimated their relative binding affinities for Lrp. A consensus seque
nce derived from analysis of these sequences, YAGHAWATTWT DCTR, where
Y = C or T, H = not G, W = A or T, D = not C, and R = A or G, contains
clear dyad symmetry and is very similar to the one defined earlier. T
o test the idea that Lrp in the presence of leucine might bind to a di
fferent subset of DNA sequences, we carried out a second selection exp
eriment,vith leucine present during the binding reactions. DNA sequenc
es selected in the presence or absence of leucine were similar, and le
ucine did not stimulate binding to any of the sequences that were sele
cted in the presence of leucine. Therefore, it is unlikely that leucin
e changes the specificity of Lrp binding.