Nucleotide sequence of cloned DNA segments of the Haemophilus influenzae bacteriophage HP1c1

Restriction fragments obtained by digestion of Haemophilus influenzae phage HP1c1 DNA with HaeIII have been cloned by insertion into the HindIII site of pBR322 using synthetic linkers. The nucleotide sequences have been determined for three adjacent fragments, HaeIII-E, HaeIII-C and HaeIII-K, which comprise an 8.2-kb segment of the HP1c1 genome. The distribution and location of restriction sites in the sequenced region were determined. Restriction sites containing the dinucleotides -GG- and -CC- occurred infrequently in the sequence. The region contains numerous sequences which are subsets of the high-affinity recognition sequence of Haemophilus transformation, including five sites which direct high-affinity uptake of fragments containing them. Shorter subsets of the uptake sequence, including those with little or no measurable affinity for the DNA transport system, are considerably over-represented in HP1c1 DNA. Nine open reading frames (ORFs) corresponding to presumed polypeptides longer than 90 amino acid residues were identified; all of these shared a common orientation, suggesting the probable direction of transcription in this segment of the phage genome. These ORFs were preceded by appropriately spaced polypurine stretches which might function as ribosome-binding sites. One ORF coincides with the site of a mutation affecting the production of phage tails.