Cellular fitness depends on multiple phenotypes that must be balanced during evolutionary adaptation. For instance, coordinating growth and motility is critical for microbial colonization and cancer invasiveness. In bacteria, these phenotypes are controlled by local regulators that target single operons, as well as by global regulators that impact hundreds of genes. However, how the different levels of regulation interact during evolution is unclear. Here, we measured in Escherichia coli how CRISPR-mediated knockdowns of global and local transcription factors impact growth and motility in three environments. We found that local regulators mostly modulate motility, whereas global regulators jointly modulate growth and motility. Simulated evolutionary trajectories indicate that local regulators are typically altered first to improve motility before global regulators adjust growth and motility following their trade-off. These findings highlight the role of pleiotropic regulators in the adaptation of multiple phenotypes.

Gene regulation networks allow organisms to adapt to diverse environmental niches. However, the constraints underlying the evolution of gene regulation remain ill defined. Here, we show that partial order—a concept that ranks network output levels as a function of different input signals—identifies such constraints. We tested our predictions by experimentally evolving an engineered signal-integrating network in multiple environments. We find that populations: (1) expand in fitness space along the Pareto-optimal front associated with conflicts in regulatory demands, by fine-tuning binding affinities within the network, and (2) expand beyond the Pareto-optimal front through changes in the network structure. Our constraint predictions are based only on partial order and do not require information on the network architecture or underlying genetics. Overall, our findings show that limited knowledge of current regulatory phenotypes can provide predictions on future evolutionary constraints. To predict evolutionary constraints in regulatory networks, we developed a new network approach based on partial order and verified it by evolving a genetic network in Escherichia coli in variable environments.

The limits of evolution have long fascinated biologists. However, the causes of evolutionary constraint have remained elusive due to a poor mechanistic understanding of studied phenotypes. Recently, a range of innovative approaches have leveraged mechanistic information on regulatory networks and cellular biology. These methods combine systems biology models with population and single-cell quantification and with new genetic tools, and they have been applied to a range of complex cellular functions and engineered networks. In this article, we review these developments, which are revealing the mechanistic causes of epistasis at different levels of biological organization-in molecular recognition, within a single regulatory network, and between different networks-providing first indications of predictable features of evolutionary constraint.

Advances in our ability to zoom in on single cells have revealed striking heterogeneity within isogenic populations. Attention has so far focussed predominantly on underlying stochastic variability in regulatory pathways and downstream differentiation events. In contrast, the role of stochasticity in metabolic processes and networks has long remained unaddressed. Here we review recent studies that have begun to overcome key technical challenges in addressing this issue. First findings have already demonstrated that metabolic networks are stochastic in nature, and highlight the plethora of cellular processes that are critically affected by it.

Sign epistasis is a central evolutionary constraint, but its causal factors remain difficult to predict. Here we use the notion of parameterised optima to explain epistasis within a signalling cascade, and test these predictions in Escherichia coli. We show that sign epistasis arises from the benefit of tuning phenotypic parameters of cascade genes with respect to each other, rather than from their complex and incompletely known genetic bases. Specifically, sign epistasis requires only that the optimal phenotypic parameters of one gene depend on the phenotypic parameters of another, independent of other details, such as activating or repressing nature, position within the cascade, intra-genic pleiotropy or genotype. Mutational effects change sign more readily in downstream genes, indicating that optimising downstream genes is more constrained. The findings show that sign epistasis results from the inherent upstream-downstream hierarchy between signalling cascade genes, and can be addressed without exhaustive genotypic mapping.