Integrative mobilizable elements are pervasive throughout Pseudomonadota

Abstract Integrative mobilizable elements (IMEs) are mobile genetic elements that reside stably integrated into chromosomes and rely on helper conjugative elements for horizontal transfer. Here, we identify and characterize a widespread family of IMEs, named Pseudomonadota Integrative Mobilizable Elements (PIMEs), which are distributed exclusively in the Pseudomonadota phylum. Genome and phylogenomic analyses reveal ∼1,000 putative PIMEs, comprising at least four distinct PIME subfamilies defined by distinctive genomic organizations and conserved hallmark features. Characterized PIMEs depend on helper conjugative plasmids of the incompatibility group P (IncP) and, upon induction, PIMEs excise, replicate and mobilize intra- and inter-species. Remarkably, the representative PIME and its helper conjugative plasmid engages in cross-complementation, revealing an unrecognized level of functional interplay between hijacker and helper element. We also demonstrate that PIMEs act as reservoirs of known and novel prokaryotic immune systems. Overall, our findings uncover an overlooked and disseminated family of IMEs, which likely plays an important role in bacterial ecology and evolution.