Experimental evolution for cell biology

Abstract

Evolutionary cell biology explores the origins, principles, and core functions of cellular features and regulatory networks through the lens of evolution. This emerging field relies heavily on comparative experiments and genomic analyses that focus exclusively on extant diversity and historical events, providing limited opportunities for experimental validation. In this opinion article, we explore the potential for experimental laboratory evolution to augment the evolutionary cell biology toolbox, drawing inspiration from recent studies that combine laboratory evolution with cell biological assays. Primarily focusing on approaches for single cells, we provide a generalizable template for adapting experimental evolution protocols to provide fresh insight into long-standing questions in cell biology.

Keywords: adaptation; evolutionary cell biology; evolutionary dynamics; evolutionary innovation; experimental design.

Figure 1 |. Evolutionary cell biology: integrating evolutionary biology and cell biology.

A. Evolutionary cell biology tries to integrate the fields of evolutionary biology and cell biology, each composed of their own sub-disciplines. B. Example highlighting the power of combining comparative phylogenetics with cell biological characterizations across different species. By mapping specific cellular features such as the presence or absence of centrioles and cilia on phylogenetic trees and correlating them back to the species’ genotypes, genotypes can be linked to phenotypes, even for complex cellular processes. This example highlights how the presence (black circles) and absence (white circles) of particular genes coding for proteins involved in centriolar structure correlates with the occurrence of centrioles and cilia/flagella. Gray circles denote instances where a similar, non-orthologous gene is present. Figure modified from [2].

Figure 2 |. Different types of evolutionary repair experiments, using the kinetochore as an example of a cellular feature that can be perturbed.

A. Classic evolutionary repair experiments: one specific perturbation is introduced, after which the strain is evolved. Evolved strains are then characterised to evaluate how cells compensated for the perturbation. B. Homolog swap evolutionary repair experiments. Instead of introducing a defect (e.g. by removing the gene), proteins are replaced by orthologs, paralogs, or sometimes even reconstructed ancestral versions of the protein. C. Systems-level evolutionary repair experiments. This type of experiment follows the same basic scheme, but uses a more systematic approach by perturbing different components of the complex or process.

Figure 3 |. Example of integrated experimental design for evolutionary cell biology.

By integrating computational and experimental approaches, we can systematically probe how specific cellular features evolve. A. A combination of comparative phylogenetics and cell biological characterizations in different species gives us an idea of how variation in particular gene products translates into specific phenotypes (here: cellular features). ETO: experimentally-tractable organism. Red outline: ancestral reconstructed states. Figure is simplified and only shows presence/absence of genes, but in reality we can look at variation in protein sequences. B. By introducing the observed genetic variation in ETOs, we can evaluate the validity of the inferred genotype-phenotype links. ETOs with different perturbations are evolved, after which their C. mutations and D. cellular features are characterised, allowing us to test the role of natural variation in the evolution of cellular features in real time. E. To learn more about the relationships between different cellular features and trade-offs within an evolutionary context, a broader set of cellular features can be assayed.

Figure 4 |. Adding evolutionary dynamics to evolutionary cell biology.

Combining a fluorescent readout of the cellular phenotype of interest (here represented by shades of gray and green) and a conventional lineage tracking technique using DNA barcodes would be a powerful way of coupling evolutionary dynamics to evolutionary cell biology. FACS can be used to sort the population based on their cellular phenotypes, allowing us to link variation in specific cellular features to lineage trajectories and the mutations that arise throughout adaptation. This technique also allows us to add an additional dimension to conventional Muller plots (here represented by shades of gray and green).