Isolation, Molecular Characterisation and Genome Sequence of a Bacteriophage (Chp3) from Chlamydophila pecorum

Abstract

Abstract. Chlamydiae are obligate intracellular pathogens that have a unique developmental cycle. Thirty nine viable isolates representing all nine currently recognised chlamydial species were screened by immunofluorescence with a cross-reacting chlamydiaphage monoclonal antibody. A novel chlamydiaphage (Chp3) was detected in C. pecorum, a chlamydial species not previously known to carry bacteriophages. Chp3 belongs to the Microviridae, members of this virus family are characterised by circular, single-stranded DNA genomes and small T ¼ 1 icosahedral capsids. Double-stranded replicative form Chp3 DNA was purified from elementary bodies and used as a template to determine the complete genome sequence. The genome of Chp3 is 4,554 base pairs and encodes eight open reading frames organised in the same genome structure as other chlamydiaphages. An unrooted phylogenetic tree was constructed based on the major coat proteins of 11 members of the Microviridae and Chp3. This showed that the Microviridae are clearly divided into two discrete sub-families; those that infect the Enterobacteriaceae e.g. ØX174 and the bacteriophages that infect obligate intracellular bacteria or mollicutes including SpV4 (Spiroplasma melliferum), ØMH2K (Bdellovibrio bacteriovorus) and the chlamydiaphages. Comparative analyses demonstrate that the chlamydiaphages can be further subdivided into two groupings, one represented by Chp2/Chp3 and the other by ØCPG1/ØCPAR39.

Horizontal Gene Transfer and the Evolution of Microvirid Coliphage Genomes

“…They have been well studied in molecular biology (20) and in experimental evolution (5,6,9,24,53). The 12 previously sequenced microvirid phages were isolated on Escherichia coli, Salmonella, Bdellovibrio (2), Chlamydia, (15,16,28,45), and Spiroplasma (41). The initial studies of microvirid genomes seemed to confirm differences in genome evolution from what has been observed in the dsDNA phages.…”

“…The phylogenetic relationship between our 42 new isolates and the five laboratory strains (X174, S13, G4, ␣3, and K) was estimated using Bayesian inference on the whole-genome alignment. We did not include the seven microvirids that were isolated on hosts other than E. coli (2,16,28,40,41,45) in our analysis, because the degree of sequence divergence precludes any reliable alignment or phylogenetic analysis. The maximum a posteriori probability phylogeny (Fig.…”

Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean

“…Genomic characteristics suggest that these viruses are novel members of the family Microviridae, which are icosahedral viruses with circular ssDNA genomes between 4.4 and 6.1 kb (Fane, 2005). Members of the Microviridae infecting a diverse range of hosts (including proteobacteria, Spiroplasma, Chlamydia) have been isolated and completely sequenced (Sanger et al, 1977;Renaudin et al, 1987;Storey et al, 1989;Lui et al, 2000;Read et al, 2000;Brentlinger et al, 2002;Garner et al, 2004;Rokyta et al, 2006). Genome comparisons have identified two distinct groups of Microviridae (those similar to the chlamydiaphages and those similar to Escherichia coli fX174), leading to the suggestion that ssDNA phages evolve through different mechanisms than dsDNA phages (Brentlinger et al, 2002;Rokyta et al, 2006).…”

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

“…The difference in genome size is reflected in the absence of genes for the major spike protein (G) and the external scaffolding protein (D) in gokushoviruses ( Fig. 3A) (89). A large number of genomes (Ͼ40) from closely related X174-like microvirus isolates infecting Escherichia coli has been sequenced (237).…”