A computational investigation into the role of tRNAs encoded by Shigella phage Sf14

Bacteriophage Sf14 infects Shigella flexneri, a major foodborne pathogen that causes shigellosis outbreaks primarily in developing nations. It is a Moogle-like myovirus that encodes 26 tRNAs recognizing 19 different amino acids. The presence of tRNAs in phage genomes have been known for decades, but their functions are still poorly understood and appear to vary between species. This work uses computational methods to test several existing hypotheses regarding phage-encoded tRNAs in the context of Sf14 infection. Analyses of codon usage, tRNA adaptation, and tRNA mutation patterns were performed to test four hypotheses of phage tRNA function: codon usage bias, host range expansion, an all-destructive infection phenotype, and escape from host nucleases.

Data from these analyses excluded hypotheses of host range expansion and escape from host anticodon nucleases. Instead, results suggest phage-encoded tRNAs are likely used during late stages of infection, primarily increasing expression of structural genes. While there are significant differences in codon usage bias between Sf14 gene groups and S. flexneri 2457T, translational efficiency of Sf14 late genes (as estimated by tRNA adaptation index) is highest when using the phage tRNA pool only.

The most likely hypothesis explaining the presence of tRNAs in the Sf14 genome is the possession of an all-destructive infection phenotype, where genes encoding host tRNAs are degraded along with the genome and translation relies heavily or exclusively on the phage tRNAs. The differences in codon usage also suggest phage-encoded tRNAs specifically affect the production of late gene products.