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

Bacteriophages, or phages, are highly abundant and diverse genomic entities that play an important role in microbial ecology, evolution, and horizontal gene transfer. While the dynamic changes in genome organization in cellular organisms have been well described, the 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 and discrete bridging of the host and the phage genomes, showing how the phage genome exploits the spatial genome architecture of its host to succeed in its infection cycle. Our data highlights an unprecedented level of genome folding and gene expression regulation during a viral infection.