We have studied the mechanism of site specific recombination promoted by a system derived from a small bacteriophage, HP1 of Haemophilus influenzae. The key steps are the protein-mediated association of DNA molecules with limited homology, and the reciprocal conservative breakage and rejoining of the DNA strands. These processes, like many other important genetic transactions, are mediated by complex nucleoproteins; these complexes are transiently assembled on DNA scaffolds by binding to separated nucleotide sites. HP1 integration is targeted to the anticodon stem-loop sequence of a host tRNA gene which is part of an operon of three tRNA genes.

We have purified the proteins required for the integration and excision reactions: HP1 integrase, the bacterial DNA bending protein IHF, and the HP1 Cox protein. The Cox protein is a modulator of recombination, activating excision and inhibiting integration; it also is a transcriptional regulator, inhibiting the expression of genes from the lysogenic promoter of HP1. We are investigating the structure and functions of the HP1 integrase and of Cox. The interactions of these proteins with DNA produce their activities. The orchestration of recombination with other complex transactions of the bacterial chromosome remains to be clarified.

(Although Dr. Scocca is not accepting students he will remain as a consulting faculty for the training program).

Biochemistry and molecular biology, mechanisms of site specific recombination

Hickman, A. B., Waninger, S., Scocca, J. J., and Dyda, F. (1997). Molecular organization in sitespecific recombination: The catalytic domain of bacteriophage HP1 integrase at 2.7 A resolution. Cell 89: 227-237.

Esposito, D. and Scocca, J. J. (1997). Purification and characterization of HP1 Cox and definition of its role in controlling the direction of site-specific recombination. J. Biol. Chem. 272: 8660-8670.

Hakimi, J. M. and Scocca, J. J. (1996). Purification and characterization of the integrase from the Haemophilus influenzae bacteriophage HP1. Identification of a four-stranded intermediate and the order of strand exchange. Mol. Microbiol. 21: 147-158.

Esposito, D., Benjamin, R. C., Fitzmaurice, W.P., Goodman, S. D., Waldman, A. S., and Scocca, J. J. (1996). The complete nucleotide sequence of bacteriophage HP1 DNA. Nucleic Acids Res. 24: 2360-2368.