The integrase proteins of phages lambda and HK022 are closely related site-specific recombinases that recognize different nucleotide sequences in the core regions of their substrates, the attachment sites of the two phages. The two proteins differ by 92 amino acid substitutions. We have found that no more than 4 of these substitutions are critical for the different DNA sequence specificities of these enzymes. Two of these substitutions act principally by reducing specificity, while another acts principally by specifically decreasing activity on one of the substrates. Using a variant - integrase with HK022 core binding specificity, we have tested the hypothesis that cleavage of the core region during recombination results from nucleophilic attack on the DNA by an amino acid residue contributed by an integrase protomer bound to a nearby site ("trans cleavage"). Our results show that an integrase protomer bound to the site that is cleaved can contribute the residue used in nucleophilic attack ("cis cleavage"). This result argues that the integrase catalytic site is not shared between protomers. We have continued our studies on the mechanism of transcription antitermination in bacteriophage HK022. The only requirements known for antitermination in this system are cis- acting phage sequences and the integrity of a putative zinc binding region in the -- subunit of E. coli RNA polymerase. We have developed a genetic selection for isolating and characterizing mutants that affect antitermination. Changes affecting the first 80 nt of the phage pL transcript as well as changes within the nontranscribed region of the promoter reduce pL operon antitermination.