Complete genomic sequence of bacteriophage B3, a Mu-like phage of Pseudomonas aeruginosa

Abstract

Bacteriophage B3 is a transposable phage of Pseudomonas aeruginosa. In this report, we present the complete DNA sequence and annotation of the B3 genome. DNA sequence analysis revealed that the B3 genome is 38,439 bp long with a G+C content of 63.3%. The genome contains 59 proposed open reading frames (ORFs) organized into at least three operons. Of these ORFs, the predicted proteins from 41 ORFs (68%) display significant similarity to other phage or bacterial proteins. Many of the predicted B3 proteins are homologous to those encoded by the early genes and head genes of Mu and Mu-like prophages found in sequenced bacterial genomes. Only two of the predicted B3 tail proteins are homologous to other well-characterized phage tail proteins; however, several Mu-like prophages and transposable phage D3112 encode approximately 10 highly similar proteins in their predicted tail gene regions. Comparison of the B3 genomic organization with that of Mu revealed evidence of multiple genetic rearrangements, the most notable being the inversion of the proposed B3 immunity/early gene region, the loss of Mu-like tail genes, and an extreme leftward shift of the B3 DNA modification gene cluster. These differences illustrate and support the widely held view that tailed phages are genetic mosaics arising by the exchange of functional modules within a diverse genetic pool.

FIG. 1.

Comparison of the genome organization for phages B3 and Mu. The genomes of B3 and Mu are shown as thick lines and are drawn approximately to scale, with tick marks at 1-kb intervals. ORFs are shown as boxes; their positions were derived from GenBank accession numbers AF083977 and NC_000929 for the Mu genome and this work for B3 (GenBank accession number AF232233). The direction of transcription is indicated by an arrow; in addition, genes transcribed rightward are shown above the line, and those transcribed leftward are positioned below the line. Relevant Mu genes are identified by their gene names or sequential genome gp numbers, and functions if known. The predicted B3 gene functions shown were deduced from the known functions of homologous genes in Mu or other phages; for B3 genes with Mu homologues, the identity of the homologous Mu gene is also given.

FIG. 2.

Potential regulatory elements in untranslated regions. The sequences for both DNA strands in relevant predicted untranslated regions are shown. The beginning or end of the flanking ORFs are shown by the large brackets; the ORFs continue in the directions of the broken lines. Potential −10 and −35 hexamers are indicated by bullets, which are pointed in the direction of transcription.

FIG. 3.

Diagrammatic representation of the degree of relatedness for B3 genes with homologues in other Mu-like phages and prophages. The B3 map, ORFs, and predicted protein functions are shown as in Fig. 1, except that all ORFs are shown above the kilobase line. Phages and prophages with homology to at least six B3 genes are included, and their names are listed on the left. Horizontal lines drawn below a B3 gene indicate the presence of a homologue in the corresponding Mu-like phage or prophage. The thickness of the line indicates the degree of similarity, achieved by dividing the BLAST expect values in Table S2 in the supplemental material into five groups, with the thickest line representing the greatest similarity (group I) and decreasing thickness indicating decreasing similarity. The expect value boundaries for the five groups are as follows: e-50 or better for group I, e-49 to e-15 for group II, e-14 to e-4 for group III, 0.001 to 5.0 for group IV, and >5.0 for group V on PSI-BLAST iteration 1 but 1.0 or better on PSI-BLAST iteration 2.