Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

Abstract

Pseudomonas virus vB_PaeM_PA5oct is a compelling model phage to investigate phage-bacteria interactions and is a potent candidate for phage therapy. Combining hybrid genome sequencing, RNA-Seq, and mass spectrometry of virion-associated proteins allowed us to accurately assemble and annotate PA5octs 286,783 bp genome. It encodes 461 coding regions, of which 93 were identified as virion-associated proteins using ESI-MS/MS. RNA-seq revealed twelve tRNA genes, four ncRNA regions, and a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. Although PA5oct is not organized into strictly contiguous regions of temporal transcription, defined genomic regions are expressed in early, middle, and late phases of infection. Interestingly, we observed distinct regions showing limited transcription activity throughout the infection cycle. The infection of Pseudomonas aeruginosa by PA5oct triggers the upregulation of bacterial operons related to NAD biosynthesis, Psl exopolysaccharide, and periplasmic nitrate reductase production and downregulates Type IV pili gene products, suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position this isolate amongst other phages using a protein-sharing network. This study expands our understanding of the molecular diversity of jumbo viruses and opens new questions towards cellular regulation and phage-encoded hijacking mechanisms.