Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage

Abstract

We report DNA and predicted protein sequence similarities, implying homology, among genes of double-stranded DNA (dsDNA) bacteriophages and prophages spanning a broad phylogenetic range of host bacteria. The sequence matches reported here establish genetic connections, not always direct, among the lambdoid phages of Escherichia coli, phage phiC31 of Streptomyces, phages of Mycobacterium, a previously unrecognized cryptic prophage, phiflu, in the Haemophilus influenzae genome, and two small prophage-like elements, phiRv1 and phiRv2, in the genome of Mycobacterium tuberculosis. The results imply that these phage genes, and very possibly all of the dsDNA tailed phages, share common ancestry. We propose a model for the genetic structure and dynamics of the global phage population in which all dsDNA phage genomes are mosaics with access, by horizontal exchange, to a large common genetic pool but in which access to the gene pool is not uniform for all phage.

Figure 1

Sequence connections among phages and prophages. The relationships among phage and prophage sequences are indicated, with the solid lines representing sequence similarities and the dotted lines corresponding to commonalities of gene organization or gene function. Closely related phages are shown in boxes, and bacterial hosts are shown at the perimeter of the web. Sequence comparisons were performed by using blast and gapped blast programs available at the National Center for Biotechnology Information web site (http://www.ncbi.nlm.nih.gov/) and the fasta, tfasta, and bestfit programs within the Genetics Computer Group (Madison, WI) package. Protein sequences were considered to be related (that is, probable homologues) if they could be aligned over a substantial portion of their lengths with 20% or greater amino acid identities or if the blast output reported a high probability of relatedness. A table of the protein similarities is available at http://www.pitt.edu/∼gfh/table.html). Accession numbers for phage genome sequences are HK97, AF069529; HK022, AF069308; φC31, AJ006589; L5, Z18946; D29, AF022214; and TM4, AF068845.

Figure 2

Relationship between mycobacteriophages L5 and D29 and H. influenzae gene HI1415. Segments of the genomes of the closely related mycobacteriophages L5 and D29 are shown, with genes 6–12 represented as boxes (L5 genes 7–9 and D29 genes 7–9; I and II encode tRNAs as indicated). Below is shown a segment of the H. influenzae genome from within the putative cryptic prophage φflu (shown in full in Fig. 3). Gene 10 of D29 is larger than L5 gene 10 because of an additional 600 bp within the coding region that results in a gene product (gp10) that is 200 amino acids larger than L5 gp10. The upstream parts of gp10 (green) are significantly more similar than the downstream segments (blue), having 81 and 50% amino acid identity, respectively. The “insert” in D29 gene 10 (red) encodes a protein sequence that has 34% identity with the product of H. influenzae HI1415.

Figure 3

Organization of φflu, a cryptic prophage of H. influenzae. A 37-kilobase segment of the H. influenzae genome is shown corresponding to coordinates 1484000–1521000 (20). Genes and their putative functions are shown according to the published annotation (20) and are shown either above (leftward) or below (rightward) depending on the direction of transcription. Genes with sequences similar to known phage genes are shown in red. White boxes represent genes that do not give a significant database match. The genetic constitution of the φflu prophage suggests that it is unlikely to form infectious particles, although we cannot rule out the possibility that it can do so under certain conditions.

Figure 4

Cryptic prophages of M. tuberculosis H37Rv. Portions of two segments of the M. tuberculosis H37Rv genome present in cosmids MYCY441 (φRv2) and MTCY336 (φRv1) are shown (accession nos. Z80225 and Z95586, respectively). Horizontal bars represent the genomes with markers at 1-kilobase intervals; numbers correspond to the cosmid coordinates. Genes are shown either above or below the bar, depending on the direction of transcription, with genes below transcribed leftward. Related genes are shown in similar colors. Putative attachment junctions, attL and attR, delineate the boundaries of the cryptic prophages φRv2 and φRv1. The location of genes and their putative functions are from annotations by the Sanger Center, Cambridge, U.K.