Recognition of nonconserved bases in the P22 operator by P22 repressor requires specific interactions between repressor and conserved bases

The ability of P22 repressor protein to distinguish between the six naturally occurring operator binding sites is critically important in determining whether the bacteriophage chooses to grow lytically or lysogenically. We have shown that changes in the highly conserved bases at P22 operator positions 3, 5, 6, and 7 prevent specific binding of P22 repressor. Moreover, studies of mutant proteins identified the three repressor amino acids that directly contact these conserved bases. The pattern of operator sequence conservation permits these direct amino acid- base pair interactions to occur in all except one of the 12 operator half- sites in the phage chromosome. Therefore, repressor differential affinity for these sites cannot be due to these highly conserved base pair-amino acid interactions. Our binding studies show that the nonconserved bases at positions 2 and 4 also play an important role in determining the relative affinity of the naturally occurring P22 operators for P22 repressor. Our data indicate that the direct contacts between the three solvent-exposed amino acids and the conserved bases in the binding site lock these amino acids in place, forming a scaffold allowing the rest of the amino acids side chains to form weaker interactions with the nonconserved bases in the binding site.