Evolutionary Repair Experiments as a Window to the Molecular Diversity of Life

Abstract

Comparative genomics reveals an unexpected diversity in the molecular mechanisms underlying conserved cellular functions, such as DNA replication and cytokinesis. However, the genetic bases and evolutionary processes underlying this 'molecular diversity' remain to be explained. Here, we review a tool to generate alternative mechanisms for conserved cellular functions and test hypotheses concerning the generation of molecular diversity - evolutionary repair experiments, in which laboratory microbial populations adapt in response to a genetic perturbation. We summarize the insights gained from evolutionary repair experiments, the spectrum and dynamics of compensatory mutations, and the alternative molecular mechanisms used to repair perturbed cellular functions. We relate these experiments to the modifications of conserved functions that have occurred outside the laboratory. We end by proposing strategies to improve evolutionary repair experiments as a tool to explore the molecular diversity of life.

Figure 1.. Overview of an evolutionary repair experiment.

(A) A genetic perturbation is introduced in an ancestral clone. Isogenic populations are founded by inoculating the ancestral strain in several tubes, representing independent evolutionary lines. Tubes are diluted regularly in fresh media to allow the continuous proliferation to select for mutations that increase reproduction and survival. The sequenced genomes of ancestor and evolved populations are compared. Genes mutated multiple times across independent populations suggest targets of putative adaptive mutations. (B) After an initial drop in relative fitness due to the genetic perturbation, an evolving population gradually recovers fitness over the course of hundreds of generations, ultimately approaching wild-type fitness. (C) Compensatory mutations occur successively in an evolving population and different mutant lineages compete with each other. This plot represents competing lineages within an evolving population, with their vertical extent at each time point proportional to their frequency. The differently colored sectors represent the rise and spread of compensatory mutations, which are indicated with different symbols. A sector nested inside another sector represents a secondary compensatory mutation arising in the background of an existing mutant lineage.

Figure 2.. Conditions where evolutionary repair could happen in nature

Three natural conditions in which the spread of deleterious mutations allows for the compensatory mutations to occur. The red lightning symbol represents an initial genetic perturbation and the black asterisk represents compensatory mutation. The fitness effects of mutations are color-coded: dark gray represents reduced fitness and yellow represents fitness restored by compensatory mutation. (A) Population bottlenecks and genetic drift increase the chance that deleterious mutations accumulate in small populations. (B) A change in the environment alters the fitness effect of a mutation from beneficial to deleterious. (C) The antagonistic interaction between a pathogen and its host selects for the loss of function of a host gene. A mutation that inactivates a host protein, mediating the interaction with a pathogen, allow host cells become resistant to the pathogen. The inactivation of this host protein also selects for secondary mutations that compensate the cellular defect caused by the inactivating mutation.