Toxin-antitoxin systems propagate through addictive selection during bacterial chromosome-plasmid conflicts

Plasmids are obligate genetic parasites that significantly influence bacterial host adaptation, ecology, and clinically relevant traits such as antibiotic resistance. They persist within host populations primarily through self-maintenance mechanisms, most notably Toxin-Antitoxin (TA) systems, which are autoregulated poison-antidote operons mediating genomic conflict. Plasmid-encoded TAs act as "addiction modules," promoting plasmid stability via post-segregational killing of daughter cells that fail to inherit the plasmid. However, the widespread and abundant presence of TAs on bacterial chromosomes remains an evolutionary puzzle. We conducted comprehensive bioinformatics analyses of 11 000 bacterial chromosomes and 1300 plasmids, focusing on Type II TAs in Escherichia and Shigella species, to elucidate their prevalence, distribution, and ecological significance. Our results reveal distinct horizontal gene transfer patterns and strongly support the antiaddiction hypothesis, which posits that chromosomal TAs protect host cells by neutralizing TA-plasmid addiction effects. This neutralization allows for plasmid loss without the toxin-mediated lethal consequences, resulting in a pattern of mutual exclusivity between identical chromosomal and plasmid TAs. This study reinforces the view that chromosomal Type II TA systems play a significant role in counteracting addiction processes within bacterial chromosomes.