Selective elimination of donor bacteria to analyze plasmid reactions during conjugative transfer

Abstract Bacterial conjugation is an important means of horizontal gene transfer in which DNA is transferred from a donor to a recipient cell by direct cell-to-cell contact. Dissemination of antibiotic resistance in bacteria is very often driven by conjugative plasmids harbouring antibiotic resistance genes. Recent research highlighted the temporal cascade of DNA reactions that are critical for the establishment of a plasmid in the new host, which include prompt and robust induction of anti-defence genes as well as re-formation of double-stranded circular form of the plasmid after transfer as single-stranded linear DNA. Nature of conjugation which occurs in mixture of cell populations constrained the research on plasmid establishment. Since plasmid molecules in before and after transfer are indistinguishable, distinction of donor and recipient/transconjugant cell is required, and physical separation is particularly necessary for the genomic approaches. We established a novel method exploiting a mutant donor which can be expeditiously eliminated from the conjugation mixture with simple manipulation. This method, dubbed as ED-TA for elimination of donor cells for transconjugant analysis, was shown to be a powerful tool to unveil plasmid gene expression profile at the early stages of conjugation (Wen et al. 2025, Nucleic Acids Res, doi: 10.1093/nar/gkaf1299). Here we present an optimized protocol for the ED-TA method which will help our study on plasmid actions during establishment in new host cell, including emerging interests between host defence and plasmid anti-defence systems.