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bioRxiv · 10.1101/2022.11.11.516204

Core Defense Hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems

Johnson, M. C.·Laderman, E.·Huiting, E. C.·Zhang, C.·Davidson, A. R.·Bondy-Denomy, J. R.
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Abstract

Bacteria use a diverse arsenal of anti-phage immune systems, including CRISPR-Cas and restriction enzymes. Identifying the full defense repertoire of a given species is still challenging, however. Here, we developed a computational tool to broadly identify anti-phage systems, which was applied to >180,000 genomes available on NCBI, revealing Pseudomonas aeruginosa to possess the most diverse anti-phage arsenal of any species with >200 sequenced genomes. Using network analysis to identify the common neighbors of anti-phage systems, we surprisingly identified two highly conserved core defense hotspot loci (cDHS1 and cDHS2). Across more than 1,000 P. aeruginosa strains, cDHS1 is up to 224 kb (mean: 34 kb) with varied arrangements of at least 31 immune systems while cDHS2 has 24 distinct systems (mean: 15.4 kb). cDHS1/2 are present in most P. aeruginosa isolates, in contrast to highly variable mobile DHSs. Most cDHS genes are of unknown function potentially representing new anti-phage systems, which we validated by identifying a novel anti-phage system (Shango) commonly encoded in cDHS1. Identification of core gene markers that flank immune islands could be a simple approach for immune system discovery and may represent popular landing spots for diverse MGEs carrying anti-phage systems.

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Johnson, M. C., Laderman, E., Huiting, E. C., Zhang, C., Davidson, A. R., Bondy-Denomy, J. R.. 2022-11-11. Core Defense Hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems. https://doi.org/10.1101/2022.11.11.516204

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