Improving phage genome annotation to understand phage biology: the case of Pseudomonas aeruginosa LES prophages

Pseudomonas aeruginosais an important opportunistic pathogen, causing nosocomial infections. The Liverpool Epidemic Strain (LES), a major cause of mortality and morbidity in cystic fibrosis patients, harbours five prophages associated with increased fitness and survival in models of infection. However, ~76.5% of the LES prophage genes are hypothetical proteins. Also, little is known about the LES prophage interactions with the lysogen and other prophages. In this study, we used the VIral Genome Annotation (VIGA) pipeline to re-annotate the LES prophage genomes and improve the prediction of gene function. The RefSeq viral proteins database was used for homology-based gene prediction and the Prokaryotic Virus Orthologous Genes (PVOGs) and Reference Viral DataBase (RVDB) were used for HMM-based protein function prediction. InterProScan 5.47-5.82 and Infernal 1.1.3 (with Rfam 14.3) were applied to enrich the gene function prediction for all genes and ncRNA elements, respectively. The number of putative coding sequences had increased by 1.17-1.43 times. Multiple genes related to DNA recombination and host cell lysis were identified in this reannotation. Also, we have identified new ncRNA elements in these prophages, such astRNAs in prophages 2 and 5 and a putative regulatory ncRNA, a Hammerhead-II ribozyme, in prophage 4. All this new information will be combined with data from future RNAseq experiments to map the expression profiles of each LES prophage under inducing and non-inducing conditions to characterise interactions between the prophages and their lysogen host.