Prophage genomics reveals patterns in phage genome organization and replication

Han Suh Kang; Katelyn McNair; Daniel A. Cuevas; Barbara A. Bailey; Anca M. Segall; Robert A. Edwards

Many phages encode tRNA genes, which enhance phage fecundity (47, 48) . Several hypotheses have been proposed to explain the presence of tRNA genes in phage genomes, including providing The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/114819 doi: bioRxiv preprint tRNAs to compensate for missing or weakly expressed genes in the host (49) . A previous study of 37 phage genomes from 15 bacterial genomes demonstrated that phage tRNA genes compensate for codon bias between host and phage, especially when a codon is common in the phage and rare in the host (50) . In addition, tRNA genes carried by the phage may replace those interrupted during phage insertion into the genome at tRNA genes (51, 52) . It is also possible that encoding multiple tRNA genes provides the phage genome alternative attachment sites to integrate into the host's genome in case the preferred attachment site is mutated and/or occupied by another phage.