The Phage Time Continuum: Genome Organization Constrains Anti-CRISPR Success

Abstract

Bacteria and lytic phages experience antagonistic co-evolution, with bacterial defenses (e.g., CRISPR-Cas) battling phage anti-defenses (e.g., anti-CRISPR (Acr) systems). We investigate whether CRISPR-Cas and Acr engage in a timing-dependent genetic conflict. If anti-CRISPR genes act too late in infection, they risk failing to neutralize CRISPR, if Cas cannot find its target in time, Acr may be able to neutralize it. Because phages typically inject their genomes in a linear manner, location along the genome acts as a proxy for time from start of infection. Given these restrictions, we suggest that phage genomes that contain Acr systems will have a distinct pattern of spacers when compared to those that do not, reflecting the time dependent interaction of infections, we have termed this the Phage Time Continuum. In our analysis of 1462 phage genomes and 105 mobile plasmid genomes infecting Pseudomonas aeruginosa, we found clear distribution of where P. aeruginosa spacers map back onto these mobile genetic elements genomes. Further CRISPR spacers significantly enriched against anti-CRISPR systems over other anti-defense systems from both phage and plasmids. Finally, in genomes with anti-CRISPR, spacers map to earlier positions, suggesting that success hinges not just on targeting a given gene, but where those spacers hit along a genome.