Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage φKZ

As part of the ongoing renaissance of phage biology, more phage genomes are becoming available through DNA sequencing. However, our understanding of the transcriptome architecture that allows these genomes to be expressed during host infection is generally poor. Transcription start sites (TSSs) and operons have been mapped for very few phages, and an annotated global RNA map of a phage - alone or together with its infected host - is not available at all. Here, we applied differential RNA-seq (dRNA-seq) to study the early, host takeover phase of infection by assessing the transcriptome structure of Pseudomonas aeruginosa jumbo phage phi KZ, a model phage for viral genetics and structural research. This map substantially expands the number of early expressed viral genes, defining TSSs that are active ten minutes after phi KZ infection. Simultaneously, we record gene expression changes in the host transcriptome during this critical metabolism conversion. In addition to previously reported upregulation of genes associated with amino acid metabolism, we observe strong activation of genes with functions in biofilm formation (cdrAB) and iron storage (bfrB), as well as an activation of the antitoxin ParD. Conversely, phi KZ infection rapidly down-regulates complexes IV and V of oxidative phosphorylation (atpCDGHF and cyoABCDE). Taken together, our data provide new insights into the transcriptional organization and infection process of the giant bacteriophage phi KZ and adds a framework for the genome-wide transcriptomic analysis of phage-host interactions.

Automated summary

The study used differential RNA-seq to analyze the transcriptome structure of Pseudomonas aeruginosa jumbo phage phi KZ during host infection, revealing new insights into early viral gene expression. The research also observed changes in host gene expression during the critical metabolism conversion, shedding light on the phage-host interactions at a genome-wide level.