Significant Differences in Terms of Codon Usage Bias between Early and Late Bacteriophages Gene

Deciphering the way gene expression regulatory aspects are encoded in viral genomes is a challenging mission with ramifications related to all biomedical disciplines. Here we aimed to understand how the evolution shapes bacteriophages genes by performing a high resolution analysis of ribosomal profiling data and gene expression related synonymous/silent information encoded in bacteriophage coding regions.
Gene expression within different DNA viruses, such as herpeses, lenti-retro, polyoma, papilloma, adeno, parvo and various families of bacteriophages is regulated in a temporal fashion and can be divided into early and late stages with respect to the viral replication cycle.
It has been suggested that viral coding sequences are shaped by evolution to improve their expression and fitness. Several works have implicated codon usage in the temporal regulation of viral gene expression, specifically showing that the composition of codons in coding sequences of viruses is regulated.
We demonstrated evidence of selection for distinct compositions of synonymous codons in early and late viral genes related to the adaptation of translation efficiency to different bacteriophage developmental stages. Specifically, we showed that evolution of viral coding regions is driven, among others, by selection for codons with higher decoding rates; during the initial/progressive stages of infection the decoding rates in early/late genes were found to be superior to those in late/early genes respectively. Moreover, we argued that selection for translation efficiency could be partially explained by adaptation to the host tRNA pool and the fact that it can change during the bacteriophage life cycle.