Incompatibility Groups Of Pseudomonas Plasmids Revisited: Comprehensive Analysis Of R-Factors And Their Replicons
Nishimura, Y.; Kaneko, K.; Kamijo, T.; Isogai, N.; Tokuda, M.; Xie, H.; Tsuda, Y.; Hirabayashi, A.; Moriuchi, R.; Dohra, H.; Kimbara, K.; Suzuki-Minakuchi, C.; Nojiri, H.; Suzuki, H.; Suzuki, M.; Shintani, M.
Show abstract
Plasmids are key for the acquisition of new traits in bacterial cells, including antimicrobial resistance. The rep gene and its encoding replication initiation protein (RIP) are essential for plasmid autonomous replication. Here, we reconstructed a large-scale phylogeny of RIPs containing a conserved winged-helix domain (WH), encompassing 34,724 plasmids including 5,369 yet unclassified ones, together with RIPs likely derived from unrecognized plasmids. The phylogeny incorporates macroevolutionary perspectives into plasmid replication systems and resolves evolutionary relationships among replicon types including existing and newly defined ones. Integration of the knowledge of genetic organization, taxonomic and environmental distribution of plasmids, RIP sequences illuminates the diversification history of plasmids and their replication proteins, including an early event of domain arrangement of WH RIPs. The WH RIP phylogeny opens a new door for plasmid macroclassification centered on the replication system and provides valuable insights into plasmid evolution.
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