RT Journal Article
SR Electronic
T1 Mobile Integrons Encode Phage Defense Systems
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2024.07.02.601719
DO 10.1101/2024.07.02.601719
A1 Kieffer, Nicolas
A1 Hipólito, Alberto
A1 Blanco, Paula
A1 Delobelle, Thomas
A1 Ortiz-Miravalles, Laura
A1 Ojeda, Francisco Manuel
A1 Jové, Thomas
A1 Jurenas, Dukas
A1 García-Quintanilla, Meritxell
A1 Domingo-Calap, Pilar
A1 Escudero, José Antonio
YR 2024
UL http://biorxiv.org/content/early/2024/07/26/2024.07.02.601719.abstract
AB Integrons are bacterial genetic elements that capture, stockpile and modulate the expression of genes encoded in integron cassettes. Mobile Integrons (MI) are borne on plasmids, acting as a vehicle for hundreds of antimicrobial resistance genes among key pathogens. These elements also carry gene cassettes of unknown function (gcus) whose role and adaptive value remains unexplored. Recent years have witnessed the discovery of a myriad defense systems against bacteriophages, highlighting that viral infection is a major selective pressure for bacteria. We hence sought to explore if gcus could encode phage defense systems. Using the INTEGRALL database, we established a collection of 129 gcus in pMBA, a vector where cassettes are established as part of a class 1 integron. PADLOC and DefenseFinder predicted four phage defense systems in this collection, comprising Lamassu, CBASS and two ABI (abortive infection) systems. We experimentally challenged all cassettes with phages and found eleven additional candidates that were not detected in silico. We have characterized in depth the 15 gcus against a panel of phages in Escherichia coli confirming their role as phage defense integron cassettes (PICs). We used recombination assays to verify that these are bona fide integron cassettes and are therefore mobile. We show that PICs confer resistance in other clinically relevant species, such as Klebsiella pneumoniae and Pseudomonas aeruginosa. Several PICs also limit prophage activation, providing protection at the population-level. Given the stockpiling capacity of integrons, we explored the additivity of phenotypes and found that integrons with two PICs confer multiphage-resistance. Additionally, when combined with antimicrobial resistance genes, integrons confer simultaneously drug and phage resistance. Crucially, we also show that the position of a pic in the array can strongly decrease its cost. Our results prove a role of integrons in phage defense, acting as highly mobile, low-cost defense islands.Competing Interest StatementThe authors have declared no competing interest.