Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein

• Published in: The ISME Journal Vol. 4; no. 12; pp. 1568 - 1580
• Main Authors: Sota, Masahiro, Yano, Hirokazu, M Hughes, Julie, Daughdrill, Gary W, Abdo, Zaid, Forney, Larry J, Top, Eva M
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01-12-2010; Nature Publishing Group
• Subjects: 631/158/855; 631/181/2474; 631/326/41/2482; Adaptation, Biological - genetics; Bacterial Proteins - genetics; Biomedical and Life Sciences; DNA Helicases - genetics; DNA Replication; DNA, Bacterial - genetics; Ecology; Evolution, Molecular; Evolutionary Biology; Genetic Fitness; Genotypes; Life Sciences; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Mutation; original-article; Plasmids - genetics; Pseudomonas aeruginosa; Pseudomonas aeruginosa - genetics; Replicon; Sequence Analysis, DNA; Shewanella - genetics; Shewanella oneidensis; Trans-Activators - genetics; replication; plasmid; evolution; copy number; host range; stability
• ISSN: 1751-7362; 1751-7370
• DOI: 10.1038/ismej.2010.72

The ability of bacterial plasmids to adapt to novel hosts and thereby shift their host range is key to their long-term persistence in bacterial communities. Promiscuous plasmids of the incompatibility group P (IncP)-1 can colonize a wide range of hosts, but it is not known if and how they can contract, shift or further expand their host range. To understand the evolutionary mechanisms of host range shifts of IncP-1 plasmids, an IncP-1β mini-replicon was experimentally evolved in four hosts in which it was initially unstable. After 1000 generations in serial batch cultures under antibiotic selection for plasmid maintenance (kanamycin resistance), the stability of the mini-plasmid dramatically improved in all coevolved hosts. However, only plasmids evolved in
Shewanella oneidensis
showed improved stability in the ancestor, indicating that adaptive mutations had occurred in the plasmid itself. Complete genome sequence analysis of nine independently evolved plasmids showed seven unique plasmid genotypes that had various kinds of single mutations at one locus, namely, the N-terminal region of the replication initiation protein TrfA. Such parallel evolution indicates that this region was under strong selection. In five of the seven evolved plasmids, these
trfA
mutations resulted in a significantly higher plasmid copy number. Evolved plasmids were found to be stable in four other naive hosts, but could no longer replicate in
Pseudomonas aeruginosa
. This study shows that plasmids can specialize to a novel host through trade-offs between improved stability in the new host and the ability to replicate in a previously permissive host.