Influence of Different Transposon Families on Genomic Stability of Shewanella oneidensis MR1

Shewanella oneidensis, recognised as an important model organism for exoelectrogenic electron transport, has been extensively studied for its potential applications in bioelectrochemical systems. To date, the activity of transposable elements in this organism has not been conclusively investigated. This study focused on transposases, specifically insertion sequences (IS), which make up approximately 4.7% of the organism's genome, and evaluated their impact on genome stability under stress conditions. Using whole genome sequencing, two IS families, ISSOD1 and ISSOD2, were identified as the most active, both showing similar transposition patterns across all tested stressors. A CRISPR/dCas9 cytosine deaminase system was used to introduce stop codons in the ISSOD2 transposase genes, resulting in a significant reduction of transposition events under stress conditions. Analysis of transposition patterns revealed a high frequency of insertions occurring on the megaplasmid, which predominantly carries non-essential genes. Experiments performed here to delete the megaplasmid resulted in the elimination of approximately 35% of its sequence, including an unexpected complete loss of the ori/repA region. Therefore, it was hypothesised that the megaplasmid either exists in a metastable state, possibly representing a cointegrated intermediate within the ISSOD9 (Tn3 member) transposition mechanism, or consists of two replicons that have been combined in previous assemblies due to long overlapping homologies resulting from the presence of ISSOD9. These findings highlight the dynamics of transposable elements in S. oneidensis and suggest strategies to improve strain stability by inactivating these elements and at least reducing megaplasmid sequences. Such approaches could improve the suitability of the organism for industrial applications.