Sequence of the Genome of the Temperate, Serotype-Converting, Pseudomonas aeruginosa Bacteriophage D3

Abstract

Temperate bacteriophage D3, a member of the virus family Siphoviridae, is responsible for serotype conversion in its host, Pseudomonas aeruginosa. The complete sequence of the double-stranded DNA genome has been determined. The 56,426 bp contains 90 putative open reading frames (ORFs) and four genes specifying tRNAs. The latter are specific for methionine (AUG), glycine (GGA), asparagine (AAC), and threonine (ACA). The tRNAs may function in the translation of certain highly expressed proteins from this relatively AT-rich genome. D3 proteins which exhibited a high degree of sequence similarity to previously characterized phage proteins included the portal, major head, tail, and tail tape measure proteins, endolysin, integrase, helicase, and NinG. The layout of genes was reminiscent of lambdoid phages, with the exception of the placement of the endolysin gene, which parenthetically also lacked a cognate holin. The greatest sequence similarity was found in the morphogenesis genes to coliphages HK022 and HK97. Among the ORFs was discovered the gene encoding the fucosamine O-acetylase, which is in part responsible for the serotype conversion events.Upon infection of sensitive cells, the genomes of temperate bacteriophages have two pathways open to them: development associated with cell lysis and the release of progeny (lytic response), or repression of lytic development usually associated with integration into the host chromosome and maintenance in a quiescent state (lysogenic response). The best studied of the temperate phages is bacteriophage lambda, which infects Escherichia coli strains. This phage is the archetype of a group of phylogenetically related viruses called the lambdoid phages. In many cases temperate phages also alter the phenotype of the lysogenized cells, resulting in the production of toxins or expression of surface components resulting in alterations to the cells' antigenicity. This phenomenon is called lysogenic conversion.Bacteriophage D3 was obtained from a clinical isolate of Pseudomonas aeruginosa by Holloway et al. (35), who noted subsequently that lysogenization of host cells by phage D3 resulted in a change in the cells' serological properties (34). Kuzio and Kropinski showed that the lipopolysaccharide isolated from the lysogens [PAO(D3)] lacked receptor activity for this phage and that the O-antigenic polysaccharide side chains were chemically altered (41). Specifically, the hydroxyl group at position 4 of the D-fucosamine residues became acetylated, and the bonding between the trisaccharide repeats changed from ␣134 to ␤134. This results in the change of serotype from International Antigenic Typing Scheme O5 to O16/20 (42, 43). Simultaneously, the cells become both immune and resistant to superinfection by D3. Extrapolating from the work with Salmonella phage ε15 (6, 45, 46), I hypothesized that three phage gene products might be involved in the conversion: an inhibitor of the ␣-polymerase, a new ␤-polymerase, and a fucosamine O-acetylase. Extensive early attempts to clone the conversi...

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

“…Preliminary experiments suggested that unlike those in other phages (23,41,82), the attPPЈ site might not be located close to the int gene (unpublished data). An excisionase-encoding gene (xis) was not identified in either the PH15 or CNPH82 genome, similar to the case for other phages where the xis gene is absent but an int gene is predicted (23,32,82).…”

Prophage Genomics

“…It has been involved in serotype conversion of its lysogenic host by changing the O-antigenic polysaccharide side chain of the lipopolysaccharide. An O-acetylase responsible for part of the seroconversion was located on phage D3 upstream of the lysis cassette (107). D3 shows a genome organization characteristic of lambda-like coliphages, except that the lysis module has changed its position.…”

Nucleotide Sequence and Evolution of the Five-Plasmid Complement of the Phytopathogen Pseudomonas syringae pv. maculicola ES4326

“…Plasmid pPMA4326A does not appear to encode any identifiable virulence genes, but it does possess several putative transposases. ORFs A09 and A10 appear to constitute an IS3-like element that is most closely related to IS222 from the D3 bacteriophage of Pseudomonas aeruginosa (49), and ORF A17 encodes an IS1406 transposase of the IS5 family. The putative borders of both IS elements encompass only their respective transposases.…”