Visualizing Bacteriophage Evolution Through Sequence and Structural Phylogeny of Lysin A and Terminase Proteins: An Analysis of Protein Structure Across Phage Clusters

Understanding how genes evolve and persist is a critical part of viral genomics. Bacteriophages can provide unique insight about viral evolution because of their abundance and largely unexplored history. Traditionally, phylogenetic trees have used DNA sequence comparison to visualize evolutionary paths between organisms. However, DNA sequence similarity does not refl ect key alterations to protein structure and therefore how the protein performs its function. Phylogenetic trees based on predicted protein structure could provide an alternative lens through which to view evolutionary paths. From each of the 10 largest clusters included in the Actinobacteriophage Database, three mycobacteriophage genomes were selected. Lysin A and terminase proteins are encoded by all of the mycobacteriophage genomes and were therefore selected for analysis. Protein structural predictions were generated from amino acid sequences using Phyre2 and compared with the PyMol Molecular Graphics System, Version 2.0. Structural alignment scores from PyMol were used to quantify the structural homology of lysin A and terminase across diff erent clusters. Five phylogenetic trees were constructed: one was based on structural homology of lysin A, one was based on structural homology of terminase, two were based on amino acid sequence of these individual proteins, and one was based on overall genomic sequence alignment. Phylogenetic trees were compared to evaluate diff erences between amino acid sequence and structural homology. Visualizing the predicted relationships from amino acid sequences and structural analysis of phage proteins will provide a new perspective on the evolution of the virosphere.