Proteomic and Genomic Evolution of Phicbkviruses

It is estimated that there are 1031 phages in the global population. They continue to maintain their populations by undergoing 1024 infections per second. Every time these phages replicate, there is potential for genetic exchange and mutations. Because of this potential, it has been assumed that phage evolution is heavily influenced by mosaicism. However, it is now clear that phage evolution varies by host type and phage type. Here, we use genomic and proteomic analyses to study the evolution of phages that infect Caulobacter crescentus. The study began by comparing six bacteriophage genomes that were larger than 250 kbp and had diverged from those of the majority of Phicbkviruses. We found that these diverse genomes share a set of 69 core genes, but they have divergent accessory genes as well as genes unique to each phage genome. The core genes were associated with both the structural proteins and the proteins needed for DNA replication. A phylogenetic analysis indicated that these diverse phage genomes were descended from a common ancestor and could be grouped into four distinct branches of a phylogenetic tree. Phage genomes that shared a branch had 80% nucleotide identity throughout their whole genomes. Furthermore, the highly diverged nucleotide sequences observed between genomes on different branches of the phylogenetic tree and the absence of evidence for horizontal gene transfer indicate that these four branches of Phicbkviruses have independently evolved from one another for millions of generations. We then compared the structural proteins of two Phicbkviruses that had similar morphology but the most diverse genomes. We were able to detect the majority of the predicted structural proteins in both types of phage particles as well as proteins that were associated with only one of the two lineages. These results validated the theory that the genes predicted to code for the proteins required to make the phage particle were located within a single region of each genome. In addition, we discovered that the proteins involved in phiCbK DNA replication may form a physical complex that can be observed in phage lysates