Bacteriophage PAK_P3 genome structuration and dynamics during infection of Pseudomonas aeruginosa reveal specific interaction patterns

While the dynamic changes in genome organization in cellular organisms have been well described, the three-dimensional (3D) folding of phage genomes during the infection of their host is extremely limited. Understanding how phage genomes fold, invade, and rearrange the genome of their host to functionally organize the optimal expression of their genes remains unknown. Here, we explore the spatial dynamics of the virulent double-stranded DNA phage PAK_P3 during infection of its host Pseudomonas aeruginosa and reveal how its genome rapidly decondenses to adopt a specific 3D organization that reflects its transcriptional program. Concomitantly, the host genome decondenses as gene expression wanes and transcription-induced domains vanish. We also uncover specific contacts of the phage genome with host chromosome, showing how the phage genome exploits the spatial genome architecture of its host to succeed in its infection cycle. Our data highlight an unprecedented level of genome folding and gene expression regulation during a viral infection.