Methods to Study Fitness and Compensatory Adaptation in Plasmid-Carrying Bacteria

Mobile genetic elements such as plasmids mediate horizontal gene transfer in prokaryotes, promoting bacterial adaptation and evolution. Despite the potential advantages conferred by these genetic elements, plasmids can also produce a fitness cost when they arrive to a new host. This initial burden is one of the main limits to the spread of plasmids in bacterial populations. However, plasmid costs can be ameliorated over time through compensatory mutations in the plasmid or the chromosome (compensatory adaptation). Understanding the origin of the cost produced by plasmids and the potential for compensatory adaptation is crucial to predict the spread and evolution of plasmid-mediated traits, such as antibiotic resistance. Here, we describe a simple protocol designed to analyze the fitness effects of a plasmid in a new host bacterium. We also provide a method to examine the potential for compensatory adaptation, using experimental evolution, and to elucidate if compensation originates in the plasmid, the bacterium, or both.

Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation

Understanding the mechanisms governing innovation is a central element of evolutionary theory. Novel traits usually arise through mutations in existing genes, but trade-offs between new and ancestral protein functions are pervasive and constrain the evolution of innovation. Classical models posit that evolutionary innovation circumvents the constraints imposed by trade-offs through genetic amplifications, which provide functional redundancy. Bacterial multicopy plasmids provide a paradigmatic example of genetic amplification, yet their role in evolutionary innovation remains largely unexplored. Here, we reconstructed the evolution of a new trait encoded in a multicopy plasmid using TEM-1 β-lactamase as a model system. Through a combination of theory and experimentation, we show that multicopy plasmids promote the coexistence of ancestral and novel traits for dozens of generations, allowing bacteria to escape the evolutionary constraints imposed by trade-offs. Our results suggest that multicopy plasmids are excellent platforms for evolutionary innovation, contributing to explain their extreme abundance in bacteria.