Mutations affecting cooperative DNA binding of phage HK022 CI repressor

Cooperative protein-DNA interactions play critical roles in gene regulation in all organisms. Among the best-studied cooperative interactions is that of phage lambda repressor, which binds cooperatively to two adjacent operators. Similar cooperative interactions are also shown by several other lambdoid phage repressors, including HK022 CI repressor, which we study here. This protein has a much higher degree of cooperativity than seen with lambda repressor, and previous evidence has suggested that cooperativity may play roles in HK022 gene regulation that have no parallel in lambda. We have isolated several cooperativity or Coop- mutations in HK022 cI. These mutant proteins were partially defective in vivo for binding to two adjacent operators, but normal or nearly so for binding to a single operator. Two mutations showed mutual suppression, in that the double mutation had wild-type behavior. Analysis of several purified mutant proteins showed that they were also defective for cooperative binding in vitro. Unexpectedly, the mutant proteins showed an altered pattern of in vitro binding to DNA at non-operator sites. Several of them also increased the rate of specific repressor cleavage. We propose a conformational model in which the various functions of the wild-type protein are carried out by differing conformations; these conformations are normally in balance, and the mutations perturb this balance.