L'integron chromosomique sédentaire de Vibrio cholerae en tant que biobanque de systèmes de défense anti-phages

Integrons are bacterial genetic platforms capable of capturing, stockpiling and expressing diverse genes embedded into cassettes. Cassettes are recruited at the beginning of their cassette array, where they can be expressed from a common promoter. By shuffling the order of cassettes, integrons modulate gene expression and offer selective advantage to their host under various stressful conditions. This mechanism accelerates adaptation by enabling the costless accumulation and reuse of cassettes, bypassing slower de novo innovation and risky horizontal gene transfer. Although mobile integrons carried by mobile genetic elements have been extensively studied for their role in antibiotic resistance, the role of sedentary chromosomal integrons (SCIs) remains poorly understood. These large, chromosomally encoded structures contain hundreds of gene cassettes, most with unknown functions. Bacteria constantly face pressures from phages and have evolved a wide array of defense systems. We hypothesized that the features of integrons make them ideal reservoirs to accumulate anti-phage defense functions. To test this, we focused on the SCI of Vibrio cholerae, the causative agent of cholera. By systematically cloning and expressing 88 cassettes from the SCI of V. cholerae strain N16961, we identified 16 with anti-phage activity, none of which could be predicted by current bioinformatic tools. Our broader analysis showed that defense systems are common in SCIs and tend to be compact, making them promising sources of novel defense systems with potential biotechnological relevance. We then confirmed that anti-phage cassettes could be mobilized and expressed thanks to integrase overexpression. We also found that many defense systems, especially abortive infection (abi) systems, require high population frequency to be effective, as they do not protect individual cells. However, spatially structured conditions allowed selection of both abi and non-abi systems. Altogether, this work demonstrates that SCIs act as biobanks of uncharacterized anti-phage defenses and highlights how their expression and selection are shaped by genetic and ecological contexts.