Antitermination increases the transcription of genes that are located downstream of terminators. Phage HK022 antiterminates transcription of its early genes by converting host RNA polymerase to a terminator- resistant form. This requires cis-acting phage sequences called nut sites. The isolation and characterization of nut region mutants argue that the sites are about 70 bases long and act as RNA transcripts consisting of two adjacent stem-loops. These transcripts presumably interact with a recognition site on RNA polymerase. The properties of polymerase mutants that are unable to antiterminate HK022 early transcription but are normal in all other respects tested suggest that the recognition site is located in a zinc-binding domain of the beta' subunit. The modified polymerase is capable of reading through at least three successive strong transcription terminators with much increased efficiency. The efficiency is greater than 90% per terminator in vivo and about 50% in vitro, consistent with the hypothesis that the requirements for persistent antitermination in the HK022 system are extraordinarily simple. 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 5 of these substitutions are critical for the different DNA sequence specificities of these enzymes. Two of these substitutions act principally by reducing specificity, while the other three act principally by specifically decreasing activity on one of the substrates.
