Intracellular competitions reveal the combination of active partitioning and addiction mechanisms as most advantageous for low-copy plasmid fitness

Extrachromosomal and mobile genetic elements, including transposable elements, plasmids, and accessory chromosomes, are found across all domains of life. The replication and segregation of elements integrated into the host chromosome are ensured by the host life cycle. In contrast, the persistence of autonomously replicating elements relies on their ability to remain within the host population. Here, we compare the evolutionary advantage of different persistence strategies found in prokaryotic plasmids. Through intracellular competitions between plasmid genotypes, we find that the combination of active partitioning during cell division with a toxin-antitoxin (TA) system for post-segregational killing increases plasmid fitness more than either strategy alone. Mathematical modeling of long-term plasmid evolution, calibrated with empirical plasmid loss dynamics, further supports these findings. A survey of enterobacterial genomes indicates that partitioning and TA systems are core features of large conjugative plasmids. Indeed, we confirm the presence of a previously unrecognized type I TA system in IncX3 plasmids, which serve as important vectors of antibiotic resistance in human pathogens. These findings suggest that large conjugative plasmids encode TA systems, including those yet to be identified. The combination of TA and partitioning systems emerges as the most effective strategy for the evolutionary success of low-copy extrachromosomal elements.