First published 2 September 2013
In silico evolution of transferable genetic elements
Dusan Misevic, Antoine Frenoy and François Taddei
Plasmids are an integral and essential factor in microbial biology and evolution, with broad implications ranging from antibiotic resistance to research tools. Much has been done to describe, quantify, and modify properties of transferable plasmids, including the extensive theoretical work using simulations and models. However, a wide gap between theory and experiments still remains, especially relating to the underlying genetic architecture of transfer as well as coevolutionary dynamics of the plasmid infectivity and susceptibility. Large-scale genomic studies and more biologically accurate models are among different approaches working towards narrowing this gap. Here we describe how Aevol, a digital evolution system, can be effectively used to study plasmid and quantify various aspects of their evolution and its outcomes. Specifically, we find that plasmid maintenance is extremely sensitive to the direct fitness cost of expressing transfer genes. In our study, the genes for donor ability and recipient immunity (which additively describe the probability of plasmid transfer) typically, but not exclusively, evolved on the plasmid itself. Additionally, we find epistatic interactions between genes on plasmids and the chromosome may evolve, a new aspect of their interaction and struggle for control over each other. There is a strong coevolutionary link between donor ability and recipient immunity, with their values tracking and being driven by one another. While plasmids seem to largely behave as selfish genetic elements, they occasionally may also carry metabolic genes and directly increase individual's fitness. With a number of concise questions and results, this initial study of plasmids in Aevol establishes the baseline and opens possibilities for future work, while simultaneously uncovering and describing novel evolutionary trajectories taken by the transferable genetic elements.