The Role of Phage tRNAs in the Evolution of Codon Usage Biases in Giant Pseudomonas Phage phiKZ and EL

As the most abundant and diverse biological agents in the biosphere phage have significant roles in microbial ecology, acting both as lethal bacterial parasites and vehicles of horizontal gene transfer. Phage/host coevolution drives optimization of phage codon usage for use of host translational machinery, thus lowered correspondence between phage and host codon usage reduces viral fitness. Some phage may partially bypass host translational selection on their codon usage by encoding their own tRNAs, although the effects of these tRNAs on phage codon usage and translation has not been well examined. This work explores the influence of phage encoded tRNAs on viral codon usage via 1) codon usage analysis of Pseudomonas aeruginosa phage phiKZ and EL; 2) attempted engineering of phiKZ populations with deoptimized proline tRNAs; and 3) engineering and experimental evolution of mutant phiKZ strain, B1, with duplicated aspartic acid, methionine, and proline tRNAs