CRP: The cyclic AMP receptor protein, CRP, undergoes an allosteric change by binding to cAMP. Only the cAMP.CRP complex can bind to specific DNA sequences near many promoters and activate transcription. Isolation and genetic characterization of crp mutants that make either allosterically defective or cAMP-independent CRPs and biochemical studies of the purified proteins have established that: (1) cAMP binding induces amino acid 138 at the hinge region to interact with amino acid 141 for hinge reorientation. A polar-polar interaction between the two sites makes the protein cAMP independent, whereas a hydrophobic amino acid at 138, e.g., 138A or 138V makes the protein allosteric defective. An intragenic suppressor can restore the normal activity of 138A or 138V mutation. The results are consistent with the model that protrusion of the DNA- recognizing F-helix is needed for its DNA major groove interaction. We have crystallized some of these mutants for X-ray diffraction. (2) In vitro transcriptions with purified proteins and supercoiled mini DNA circles as template for cAMP dependent transcription of lac promoter have shown that one can introduce discontinuity in one of the two strands between CRP and RNA polymerase binding sites and still retain CRP-mediated transcription, suggesting that CRP is unlikely to act by supercoiling DNA locally. (3) In order to test that CRP contacts RNA polymerase for transcription, the CRP binding site was put in trans to the promoter by concatenation of two DNA circles; under these conditions CRP did not activate transcription, but did inhibit the basal level of CRP independent transcription, suggesting an interaction, albeit improper, could occur in trans. OxyR: The gene regulatory protein, OxyR, binds to DNA and represses transcription, whereas an oxidized form of OxyR, induced by reactive oxygen species, binds to DNA to activate gene transcription. Whether recognized by reduced or oxidized form of OxyR, the interacting DNA sites unexpectedly show very little sequence similarity. Oxidation of OxyR brings about a conformational change in the protein, which can be reversed by reducing agents. The reversibility is now being studied by mutational changes. The basis of specific DNA recognition is being studied by isolating and characterizing mutant DNA sites.
