Sequencing and analysis of the DNA genome of the temperate bacteriophage Aa[Phi]23 of "Actinobacillus actinomycetemcomitans"

The entire genomic sequence of the AaΦ23 bacteriophage is presented. Its size is 43,033 bp and it has an overall molar G+C content of 41mol%. 57 potential open reading frames (ORFs) were identified. A putative function could be assigned to 20 of the 57 ORFs, i.e. to 35% of them. While another 25 ORFs share homologies with hypothetical proteins present in several bacteria or bacteriophages, 12 seem to be specific for the phage AaΦ23. Based on the genetic organization of its genome, AaΦ23 shares extensive similarities with lambdoid bacteriophages. Most functions described for lambda are also found on the AaΦ23 genome. We identified potential ORFs coding for the integrase mediating recombination at the attachment sites; the generalized recombination proteins ninB and ninG; both C1 and Cro regulators of lysogeny; the replication proteins O and P; the antitermination protein Q; two components of the lytic system; structural components of the virion head, tail, baseplate and tail fibers and both subunits of the terminase enzyme involved in DNA packaging. The sequence of the phage attachment site (attP) is located 19 bp upstream of the gene coding for the integrase. The attL and attR of two lysogenic A. actinomycetemcomitans strains and the attB sites in two non-lysogenic strains were also identified. The common att core is 49 bp in length. No gene coding for a known virulence factor was detected on the AaΦ23 genome. However, a DNA adenine methylase was characterized that may be functionally expressed from the prophage. This protein is of particular interest because DNA adenine methylase enzymes are involved in the virulence of several bacterial pathogens such as Salmonella typhimurium, Yersinia pseudotuberculosis, and Vibrio cholerae. Still, presence of ORFs coding for proteins modulating the A. actinomycetemcomitans pathogenicity cannot be exclude as no putative function was assigned to 37 ORFs.
Preliminary data on the putative lytic enzyme of AaΦ23 suggest that expression, even at low
level, of the cloned lys gene is lethal for Escherichia coli cells.
Location on the genetic map, amino acid sequence homologies and conservation of structural
key residues strongly suggest that the integrase is coded by orf1. Preliminary data on the
functional characterization were inconclusive. Delineation of the integration elements of
AaΦ23 will allow the construction of an integration vector for A. actinomycetemcomitans.