Evolution of a Plasmid Regulatory Circuit Ameliorates Plasmid Fitness Cost

Abstract

Abstract Plasmids play a major role in bacterial evolution and rapid adaptation by facilitating the horizontal transfer of diverse genes. Understanding how plasmids are transferred and maintained in bacterial populations is important, especially given the increasing plasmid-mediated spread of antibiotic-resistance genes to human pathogens. We investigated why broad-host range plasmid pBP136, originally isolated from clinical samples of Bordetella pertussis, quickly became extinct in laboratory Escherichia coli populations. We found that the inactivation of a previously uncharacterized plasmid gene, upf31 , drastically improved long-term maintenance of the plasmid in E. coli . Loss of this single gene was associated with decreased transcription of numerous genes in the plasmid korA , korB and korC regulons, as well as changes in many chromosomal genes primarily related to metabolism. This change in transcriptome is likely initiated by Upf31 interacting with one of these major plasmid regulators, KorB. Expression of upf31 in trans not only negatively affected the persistence of a pBP136 upf31 deletion mutant, but also of the closely related archetype IncPβ plasmid R751, which is stable in E. coli and natively encodes an internally truncated upf31 allele. This suggests that whereas the upf31 allele in pBP136 might advantageously modulate gene expression in its original host, B. pertussis , the same function can have harmful effects in E. coli . Thus, using multiple hosts to study the effects of knockouts in broad-host-range plasmid genes of unknown function may reveal unexpected mechanisms that determine the fate of that plasmid in bacterial communities.