Abstract
Abstract
Retrons are unique among bacterial defence systems in using DNA to sense phage infection. They achieve this by producing multicopy single-stranded DNA (msDNA) that monitors the activity of DNA-targeting phage proteins. Although we understand how extensive msDNA perturbations such as degradation activate retrons, activation by subtle chemical modifications remains enigmatic. Here, we used a structure-function approach to elucidate how single-site msDNA methylation activates Retron-Sen2. The cryo-EM structure of Retron-Sen2 features RcaT, the most prevalent retron effector, sequestered as an inactive dimer within a four-component assembly of previously undescribed architecture. Methylation by DNA adenine methyltransferase disrupts the RcaT-msDNA interaction and exposes a previously occluded interface that enables RcaT dimers to form tetramers, leading to retron disassembly. We show that RcaT dimer–dimer assembly is essential for its toxicity. To assess whether this is a conserved RcaT feature, we characterised additional homologues. RcaTs capable of tetramerisation or higher-order oligomerisation are toxic and form distinct phylogenetic clades from RcaTs that remain dimeric and are non-toxic. Together, our findings provide a paradigm for retron activation by single-site msDNA modifications and showcase how variation in an intrinsic protein property can diversify the toxicity of the same bacterial defence effector during evolution.