How do plasmids overcome the defense systems of recipient bacteria?

Microbes have developed diverse defense systems against exogenous DNA, including CRISPR-Cas and restriction-modification systems. Hence, it is not surprising that plasmids and other conjugative elements have developed various “anti-defense” genes that can counteract microbial defenses, such as anti-CRISPRs and anti-restriction genes. Here, we found that the first plasmid genes transferred to the recipient bacterial cell are highly enriched with anti-defense functions. Our analysis relies on a dataset of hundreds of thousands of genomes and metagenomes. We found that anti-defense systems were significantly overrepresented in the leading region of conjugative elements, which is the first region of the plasmid transferred to the recipient cell during conjugation. Further, we found that anti-defense systems tend to cluster into “islands” that contain various combinations of anti-defense and anti-defense-related proteins. Early expression of the leading regions’ genes, even before the transfer is complete, is enabled by special single-stranded promoters, which are prevalent in the islands we identified. Our results suggest that anti-defense islands on conjugative elements are expressed upon entry, promoting rapid protection against host defense systems. Uncovering these islands and characterizing them may considerably improve our understanding of the repertoire of anti-defense genes, plasmid dissemination and the intricate co-evolution of plasmids and their hosts.