Acquisition and erosion of toxin-antitoxin systems in bacterial chromosomes

Toxin-antitoxin systems are widespread in bacterial genomes. Yet, their integration, persistence, and impact on chromosome dynamics remain unclear. Here, we identified 80 type II toxin-antitoxin systems in the single chromosome of Photorhabdus laumondii TT01, 50 of which were experimentally validated. Comparative analysis across the Photorhabdus genus revealed a highly heterogeneous distribution, with toxin-antitoxin systems frequently clustering within discrete genomic regions, either alone or associated with cointegrate-forming transposases and integrases. Toxin-antitoxin systems rarely clustered with other putative defense systems and are preferentially associated with different types of recombinases, suggesting distinct pathways of acquisition for the two types of functions. Functional analyses showed that most validated toxin-antitoxin systems display addictive properties and stabilize plasmids. These addictive toxin-antitoxin systems are preferentially located in genomic regions characterized by high gene turnover, consistent with recent acquisition events. Despite their plasmid-stabilizing capacity, toxin-antitoxin systems do not promote long-term conservation of their immediate chromosomal neighborhoods. Instead, we observed frequent toxin-antitoxin loss, either through complete deletion or toxin pseudogenization, indicating relaxed selection for their persistence in bacterial lineages. We propose a stepwise model for toxin-antitoxin evolution in bacterial chromosomes: initial acquisition mediated by mobile genetic elements, preferential integration into permissive genomic regions, subsequent genetic streamlining of linked loci, and progressive gene loss. The short-lasting linkage between toxin-antitoxin systems and their genomic neighborhoods is consistent with the view that toxin-antitoxin modules can behave as autonomous, selfish genetic elements.