DNA-STRUCTURE AND FLEXIBILITY IN THE SEQUENCE-SPECIFIC BINDING OF PAPILLOMAVIRUS E2 PROTEINS

The papillomavirus E2 proteins are transcriptional regulators that bin d to a consensus DNA sequence ACCG NNNN CGGT. Multiple copies of this binding site are found in the viral genomes. The affinities of the nat urally occurring binding sites for the E2 proteins are predominantly d ependent upon the sequence of the NNNN spacer. The hierarchies of bind ing site affinities among the sites present in the viral genomes resul t in differential occupancy during the viral life-cycle. Ln turn, this differential binding regulates transcription from viral promoters, in cluding those for the oncogenes E6 and E7. Structural and biochemical studies have shown that E2 proteins bend the DNA to which they specifi cally bind. Atomic resolution structures of complexes of the bovine pa pillomavirus strain 1 (BPV-1) E2 protein and DNA show that the protein does not contact the spacer DNA. A direct comparison of the binding o f the DNA-binding domains of the E2 proteins from BPV-1 and human papi llomavirus strain 16 (HPV-16) to a series of binding sites as a functi on of the sequence of their central spacer and/or the presence of a ni ck or gap in one strand of the spacer DNA is presented in this paper. The BPV-1 E2 DNA-binding domain is only moderately sensitive to the na ture of the central spacer; less than several fold differences in affi nity were observed when the DNA sequence of the spacer was varied and/ or a nick or gap was introduced. Ln contrast, the HPV-16 E2 DNA-bindin g domain binds to sites containing A:T-rich central spacers with signi ficantly increased affinity. The introduction of a nick or gap into th e spacer of these high affinity sequences is very detrimental to HPV-1 6 E2 binding while comparable nicks or gaps have only small effects in the low affinity sequences. These results suggest that the HPV-16 E2 protein recognizes the structure of the DNA spacer and that the mechan ism of DNA-sequence specific binding of the homologous HPV-16 E2 and B PV-1 E2 proteins is significantly different. (C) 1998 Academic Press L imited.