Belt and braces: two escape ways to maintain the cassette reservoir of large chromosomal integrons

Abstract

Integrons are powerful adaptive devices that can capture, stockpile, shuffle and express gene cassettes to sample combinatorial phenotypic diversity. Some integrons called sedentary chromosomal integrons (SCIs) can be massive structures containing hundreds of cassettes. Since most of these cassettes are non-expressed, it is not clear how they remain stable over long evolutionary timescales. Recently, it was found that the experimental inversion of the SCI of Vibrio cholerae led to a dramatic increase of the cassette excision rate linked to a fitness defect. Here, we investigate the outcome of such an active SCI through experimental evolution. We find that the integrase is rapidly inactivated. Strikingly, we also find that the inverted SCI can in part recover its original, more stable orientation by homologous recombination between two insertion sequences (ISs) present in the array. These two possible outcomes of SCI inversion both restore the normal growth and prevent the massive and rapid loss of cassettes, enabling SCIs to retain their roles as reservoirs of valuable functions. These results illustrate a nice interplay between gene orientation, genome rearrangement, bacterial fitness and show how integrons can benefit from their embedded ISs.