Comparative genomics of the Microviridae. Part 2

Chipman et al predicted that the IN5 trimer structure in VP1 may function as a substitute for spike proteins of the ΦX174-like viruses, which are not found in SpV4 or the Chlamydia phages, and as such may be responsible for receptor recognition. It has also been suggested that the diverse sequence in this region is associated with host range of phages. The presence of a large insertion in ΦCA82 further supports that it is closer to the intracellular phage subfamily and the sequence dissimilarity within this region between the ΦCA82 and various other phages strongly indicates that this domain indeed may function as a host range determinant.

Rep protein of ΦCA82

ORF3 encoded a putative replication initiation protein that was most similar to the SpV4-rep and the Bdellovibrio phage ΦMH2K-rep [36] proteins. Pairwise alignment of the ΦCA82 VP3 (rep) protein and SpV4 p1 (rep) protein revealed the presence of two conserved domains from residues 73 through 176 and 195 through 320 of the ΦCA82 protein. Overall, the two rep proteins only had 22.6% identity, but shared many of the same sequences throughout the conserved regions that were recognized by BLAST as putative replication initiation protein regions. Rep protein plays an essential role in viral DNA replication and binds the origin of replication where it cleaves the dsDNA replicative form I (RFI) and becomes covalently bound to it via phosphotyrosine bond. The conservation of the functional domains between the ΦCA82 phage rep protein and other microviral replication initiation proteins suggests a similar pathway/mechanism for DNA replication and virion packaging.

Full genome comparisons of ΦCA82 with other members of the Microviridae

The ΦCA82 genome is quite different from other members of Microviridae as indicated by comparisons of nucleotide similarity, predicted protein similarity, and functional classifications. Comparisons of ΦCA82 to 14 other Microviridae genomes showed very low correlations of tetra-nucleotide frequencies as a measure of genome similarity. ΦCA82 was most similar to SpV4, but the correlation of tetra-nucleotide frequencies was poor (R2 = 0.33; Figure 4A). Only ΦMH2K had lower similarities to other Microviridae (Figure 4A). Clustering of predicted proteins showed ΦCA82 was most closely related to a clade comprised of the chlamydial phages, but as in the nucleotide comparisons, the predicted proteins of ΦCA82 are quite distinct from those of the other microviruses. Function-based clustering of genomes using pfam categories showed that ΦCA82 was most similar to SpV4, based on shared membership of the ΦCA82 ORF1 in pfam02305, an F super family capsid protein. These results were confirmed by comparisons of predicted proteins from the ΦCA82 genome to a Microviridae pangenome. This analysis showed only three genes with significant similarity as determined by local alignments using blastp with no overlap between ΦCA82 and the Microviridae pangenome based on global alignments at a 40% similarity cutoff. ΦCA82 is only distantly related to other Microviridae, but is most similar to SpV4 and the chlamydial phages. In summary, the whole genome comparisons of ΦCA82 to other Microviridae members indicate a distant evolutionary relationship, perhaps suggesting that the divergence of ΦCA82 from other microviruses reflects unique evolutionary pressures encountered within the turkey gastrointestinal system.