Phenotypic plasticity as an adaptation to a functional trade-off

Evolution of pH-sensitive transcription termination during adaptation to repeated long-term starvation

Fluctuating environments that consist of regular cycles of co-occurring stress are a common challenge faced by cellular populations. For a population to thrive in constantly changing conditions, an ability to coordinate a rapid cellular response is essential. Here, we identify a mutation conferring an arginine-to-histidine (Arg to His) substitution in the transcription terminator Rho. The rho R109H mutation frequently arose in E. coli populations experimentally evolved under repeated long-term starvation conditions, during which feast and famine result in drastic environmental pH fluctuations. Metagenomic sequencing revealed that populations containing the rho mutation also possess putative loss-of-function mutations in ydcI, which encodes a recently characterized transcription factor associated with pH homeostasis. Genetic reconstructions of these mutations show that the rho allele confers a plastic alkaline-induced reduction of Rho function that, when found in tandem with a ΔydcI allele, leads to intracellular alkalinization and genetic assimilation of Rho mutant function. We further identify Arg to His substitutions at analogous sites in rho alleles from species originating from fluctuating alkaline environments. Our results suggest that Arg to His substitutions in global regulators of gene expression can serve to rapidly coordinate complex responses through pH sensing and shed light on how cellular populations across the tree of life use environmental cues to coordinate rapid responses to complex, fluctuating environments.

Spatial scales of competition and a growth-motility trade-off interact to determine bacterial coexistence

The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth-motility trade-off. To test this hypothesis, we let two Pseudomonas putida strains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth-motility trade-off promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.

Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions

To swim and navigate, motile bacteria synthesize a complex motility machinery involving flagella, motors, and a sensory system. A myriad of studies has elucidated the molecular processes involved, but less is known about the coordination of motility expression with cellular physiology: In Escherichia coli, motility genes are strongly up-regulated in nutrient-poor conditions compared to nutrient-replete conditions; yet a quantitative link to cellular motility has not been developed. Here, we systematically investigated gene expression, swimming behavior, cell growth, and available proteomics data across a broad spectrum of exponential growth conditions. Our results suggest that cells up-regulate the expression of motility genes at slow growth to compensate for reduction in cell size, such that the number of flagella per cell is maintained across conditions. The observed four or five flagella per cell is the minimum number needed to keep the majority of cells motile. This simple regulatory objective allows E. coli cells to remain motile across a broad range of growth conditions, while keeping the biosynthetic and energetic demands to establish and drive the motility machinery at the minimum needed. Given the strong reduction in flagella synthesis resulting from cell size increases at fast growth, our findings also provide a different physiological perspective on bacterial cell size control: A larger cell size at fast growth is an efficient strategy to increase the allocation of cellular resources to the synthesis of those proteins required for biomass synthesis and growth, while maintaining processes such as motility that are only needed on a per-cell basis.

Mechanisms of protein evolution

How do proteins evolve? How do changes in sequence mediate changes in protein structure, and in turn in function? This question has multiple angles, ranging from biochemistry and biophysics to evolutionary biology. This review provides a brief integrated view of some key mechanistic aspects of protein evolution. First, we explain how protein evolution is primarily driven by randomly acquired genetic mutations and selection for function, and how these mutations can even give rise to completely new folds. Then, we also comment on how phenotypic protein variability, including promiscuity, transcriptional and translational errors, may also accelerate this process, possibly via "plasticity-first" mechanisms. Finally, we highlight open questions in the field of protein evolution, with respect to the emergence of more sophisticated protein systems such as protein complexes, pathways, and the emergence of pre-LUCA enzymes.

Spatial regulation of cell motility and its fitness effect in a surface-attached bacterial community

On a surface, microorganisms grow into a multi-cellular community. When a community becomes densely populated, cells migrate away to expand the community's territory. How microorganisms regulate surface motility to optimize expansion remains poorly understood. Here, we characterized surface motility of Proteus mirabilis. P. mirabilis is well known for its ability to expand its colony rapidly on a surface. Cursory visual inspection of an expanding colony suggests partial migration, i.e., one fraction of a population migrates while the other is sessile. Quantitative microscopic imaging shows that this migration pattern is determined by spatially inhomogeneous regulation of cell motility. Further analyses reveal that this spatial regulation is mediated by the Rcs system, which represses the expression of the motility regulator (FlhDC) in a nutrient-dependent manner. Alleviating this repression increases the colony expansion speed but results in a rapid drop in the number of viable cells, lowering population fitness. These findings collectively demonstrate how Rcs regulates cell motility dynamically to increase the fitness of an expanding bacterial population, illustrating a fundamental trade-off underlying bacterial colonization of a surface.

Slow expanders invade by forming dented fronts in microbial colonies

Living organisms never cease to evolve, so there is a significant interest in predicting and controlling evolution in all branches of life sciences. The most basic question is whether a trait should increase or decrease in a given environment. The answer seems to be trivial for traits such as the growth rate in a bioreactor or the expansion rate of a tumor. Yet, it has been suggested that such traits can decrease, rather than increase, during evolution. Here, we report a mutant that outcompeted the ancestor despite having a slower expansion velocity when in isolation. To explain this observation, we developed and validated a theory that describes spatial competition between organisms with different expansion rates and arbitrary competitive interactions.

Most organisms grow in space, whether they are viruses spreading within a host tissue or invasive species colonizing a new continent. Evolution typically selects for higher expansion rates during spatial growth, but it has been suggested that slower expanders can take over under certain conditions. Here, we report an experimental observation of such population dynamics. We demonstrate that mutants that grow slower in isolation nevertheless win in competition, not only when the two types are intermixed, but also when they are spatially segregated into sectors. The latter was thought to be impossible because previous studies focused exclusively on the global competitions mediated by expansion velocities, but overlooked the local competitions at sector boundaries. Local competition, however, can enhance the velocity of either type at the sector boundary and thus alter expansion dynamics. We developed a theory that accounts for both local and global competitions and describes all possible sector shapes. In particular, the theory predicted that a slower on its own, but more competitive, mutant forms a dented V-shaped sector as it takes over the expansion front. Such sectors were indeed observed experimentally, and their shapes matched quantitatively with the theory. In simulations, we further explored several mechanisms that could provide slow expanders with a local competitive advantage and showed that they are all well-described by our theory. Taken together, our results shed light on previously unexplored outcomes of spatial competition and establish a universal framework to understand evolutionary and ecological dynamics in expanding populations.

Multiple functions of flagellar motility and chemotaxis in bacterial physiology

Most swimming bacteria are capable of following gradients of nutrients, signaling molecules and other environmental factors that affect bacterial physiology. This tactic behavior became one of the most-studied model systems for signal transduction and quantitative biology, and underlying molecular mechanisms are well characterized in Escherichia coli and several other model bacteria. In this review, we focus primarily on less understood aspect of bacterial chemotaxis, namely its physiological relevance for individual bacterial cells and for bacterial populations. As evident from multiple recent studies, even for the same bacterial species flagellar motility and chemotaxis might serve multiple roles, depending on the physiological and environmental conditions. Among these, finding sources of nutrients and more generally locating niches that are optimal for growth appear to be one of the major functions of bacterial chemotaxis, which could explain many chemoeffector preferences as well as flagellar gene regulation. Chemotaxis might also generally enhance efficiency of environmental colonization by motile bacteria, which involves intricate interplay between individual and collective behaviors and trade-offs between growth and motility. Finally, motility and chemotaxis play multiple roles in collective behaviors of bacteria including swarming, biofilm formation and autoaggregation, as well as in their interactions with animal and plant hosts.

The Role of Ancestral Duplicated Genes in Adaptation to Growth on Lactate, a Non-Fermentable Carbon Source for the Yeast Saccharomyces cerevisiae

The cell central metabolism has been shaped throughout evolutionary times when facing challenges from the availability of resources. In the budding yeast, Saccharomyces cerevisiae, a set of duplicated genes originating from an ancestral whole-genome and several coetaneous small-scale duplication events drive energy transfer through glucose metabolism as the main carbon source either by fermentation or respiration. These duplicates (~a third of the genome) have been dated back to approximately 100 MY, allowing for enough evolutionary time to diverge in both sequence and function. Gene duplication has been proposed as a molecular mechanism of biological innovation, maintaining balance between mutational robustness and evolvability of the system. However, some questions concerning the molecular mechanisms behind duplicated genes transcriptional plasticity and functional divergence remain unresolved. In this work we challenged S. cerevisiae to the use of lactic acid/lactate as the sole carbon source and performed a small adaptive laboratory evolution to this non-fermentative carbon source, determining phenotypic and transcriptomic changes. We observed growth adaptation to acidic stress, by reduction of growth rate and increase in biomass production, while the transcriptomic response was mainly driven by repression of the whole-genome duplicates, those implied in glycolysis and overexpression of ROS response. The contribution of several duplicated pairs to this carbon source switch and acidic stress is also discussed.

Photosynthetic compensation of non-leaf organ stems of the invasive species Sphagneticola trilobata (L.) Pruski at low temperature

Biological invasion is a hot topic in ecological research. Most studies on the physiological mechanisms of plants focus on leaves, but few studies focus on stems. To study the tolerance of invasive plant (Sphagneticola trilobata L.) to low temperature, relevant physiological indicators (including anthocyanin and chlorophyll) in different organs (leaves and stems) were analyzed, using a native species (Sphagneticola calendulacea L.) as the control. The results showed that, upon exposure to low temperature for 15 days, the stems of two Sphagneticola species were markedly reddened, their anthocyanin content increased, chlorophyll and chlorophyll fluorescence parameters decreased, and the accumulation of reactive oxygen species in the stem increased. The percentage increases of antioxidants and total antioxidant capacities in stems were significantly higher in S. trilobata than in S. calendulacea. This showed that S. trilobata had higher cold tolerance in stems while leaves were opposite. To further verify the higher cold tolerance of the stem of S. trilobata, a defoliation experiment was designed. We found that the defoliated stem of S. trilobata reduced anthocyanin accumulation and increased chlorophyll content, while alleviating membrane lipid damage and electrical conductivity, and the defoliated stem still showed an increase in stem diameter and biomass under low temperature. The discovery of the physiological and adaptive mechanisms of the stem of S. trilobata to low temperature will provide a theoretical basis for explaining how S. trilobata maintains its annual growth in South China. This is of great significance for predicting the future spread of cloned and propagated invasive plants.

Rampant False Detection of Adaptive Phenotypic Optimization by ParTI-Based Pareto Front Inference

Organisms face tradeoffs in performing multiple tasks. Identifying the optimal phenotypes maximizing the organismal fitness (or Pareto front) and inferring the relevant tasks allow testing phenotypic adaptations and help delineate evolutionary constraints, tradeoffs, and critical fitness components, so are of broad interest. It has been proposed that Pareto fronts can be identified from high-dimensional phenotypic data, including molecular phenotypes such as gene expression levels, by fitting polytopes (lines, triangles, tetrahedrons, and so on), and a program named ParTI was recently introduced for this purpose. ParTI has identified Pareto fronts and inferred phenotypes best for individual tasks (or archetypes) from numerous data sets such as the beak morphologies of Darwin’s finches and mRNA concentrations in human tumors, implying evolutionary optimizations of the involved traits. Nevertheless, the reliabilities of these findings are unknown. Using real and simulated data that lack evolutionary optimization, we here report extremely high false-positive rates of ParTI. The errors arise from phylogenetic relationships or population structures of the organisms analyzed and the flexibility of data analysis in ParTI that is equivalent to p-hacking. Because these problems are virtually universal, our findings cast doubt on almost all ParTI-based results and suggest that reliably identifying Pareto fronts and archetypes from high-dimensional phenotypic data are currently generally difficult.

Evolution of chemotactic hitchhiking

Bacteria typically reside in heterogeneous environments with various chemogradients where motile cells can gain an advantage over nonmotile cells. Since motility is energetically costly, cells must optimize their swimming speed and behaviour to maximize their fitness. Here, we investigate how cheating strategies might evolve where slow or nonmotile microbes exploit faster ones by sticking together and hitching a ride. Starting with physical and biological first principles, we computationally study the effects of sticking on the evolution of motility in a controlled chemostat environment. We find that stickiness allows for slow cheaters to dominate when chemoattractants are dispersed at intermediate distances. In this case, slow microbes exploit faster ones until they consume the population, leading to a tragedy of commons. For long races, slow microbes do gain an initial advantage from sticking, but eventually fall behind. Here, fast microbes are more likely to stick to other fast microbes and co-operate to increase their own population. We therefore conclude that whether the nature of the hitchhiking interaction is parasitic or mutualistic, depends on the chemoattractant distribution.

A universal trade-off between growth and lag in fluctuating environments

The rate of cell growth is crucial for bacterial fitness and a main driver of proteome allocation^1,2, but it is unclear what ultimately determines growth rates in different environmental conditions. Increasing evidence suggests that other objectives also play key roles^3–7, such as the rate of physiological adaptation to changing environments^8,9. The challenge for cells is that these objectives often cannot be independently optimized, and maximizing one often reduces another. Many such tradeoffs have indeed been hypothesized, based on qualitative correlative studies^8–11. Here we report the occurrence of a tradeoff between steady-state growth rate and physiological adaptability for Escherichia coli, upon abruptly shifting a growing culture from a preferred carbon source to fermentation products such as acetate. Such transitions, common for enteric bacteria, are often accompanied by multi-hour lags before growth resumes. Metabolomic analysis revealed that the long lags resulted from the depletion of key metabolites due to the sudden reversal of central carbon flux imposed by these nutrient shifts. A model of sequential flux limitation not only explained the observed universal tradeoff between growth and adaptability, but also generated quantitative predictions that were validated experimentally. The observed trade-off reflects the opposing enzyme requirements for glycolysis versus gluconeogenesis.

Effects of auxin derivatives on phenotypic plasticity and stress tolerance in five species of the green alga Desmodesmus (Chlorophyceae, Chlorophyta)

Green microalgae of the genus Desmodesmus are characterized by a high degree of phenotypic plasticity (i.e. colony morphology), allowing them to be truly cosmopolitan and withstand environmental fluctuations. This flexibility enables Desmodesmus to produce a phenotype–environment match across a range of environments broader compared to algae with more fixed phenotypes. Indoles and their derivatives are a well-known crucial class of heterocyclic compounds and are widespread in different species of plants, animals, and microorganisms. Indole-3-acetic acid (IAA) is the most common, naturally occurring plant hormone of the auxin class. IAA may behave as a signaling molecule in microorganisms, and the physiological cues of IAA may also trigger phenotypic plasticity responses in Desmodesmus. In this study, we demonstrated that the changes in colonial morphs (cells per coenobium) of five species of the green alga Desmodesmus were specific to IAA but not to the chemically more stable synthetic auxins, naphthalene-1-acetic acid and 2,4-dichlorophenoxyacetic acid. Moreover, inhibitors of auxin biosynthesis and polar auxin transport inhibited cell division. Notably, different algal species (even different intraspecific strains) exhibited phenotypic plasticity different to that correlated to IAA. Thus, the plasticity involving individual-level heterogeneity in morphological characteristics may be crucial for microalgae to adapt to changing or novel conditions, and IAA treatment potentially increases the tolerance of Desmodesmus algae to several stress conditions. In summary, our results provide circumstantial evidence for the hypothesized role of IAA as a diffusible signal in the communication between the microalga and microorganisms. This information is crucial for elucidation of the role of plant hormones in plankton ecology.

Bacterial coexistence driven by motility and spatial competition

Elucidating elementary mechanisms that underlie bacterial diversity is central to ecology^1,2 and microbiome research³. Bacteria are known to coexist by metabolic specialization⁴, cooperation⁵ and cyclic warfare^6-8. Many species are also motile⁹, which is studied in terms of mechanism^10,11, benefit^12,13, strategy^14,15, evolution^16,17 and ecology^18,19. Indeed, bacteria often compete for nutrient patches that become available periodically or by random disturbances^2,20,21. However, the role of bacterial motility in coexistence remains unexplored experimentally. Here we show that-for mixed bacterial populations that colonize nutrient patches-either population outcompetes the other when low in relative abundance. This inversion of the competitive hierarchy is caused by active segregation and spatial exclusion within the patch: a small fast-moving population can outcompete a large fast-growing population by impeding its migration into the patch, while a small fast-growing population can outcompete a large fast-moving population by expelling it from the initial contact area. The resulting spatial segregation is lost for weak growth-migration trade-offs and a lack of virgin space, but is robust to population ratio, density and chemotactic ability, and is observed in both laboratory and wild strains. These findings show that motility differences and their trade-offs with growth are sufficient to promote diversity, and suggest previously undescribed roles for motility in niche formation and collective expulsion-containment strategies beyond individual search and survival.

An evolutionarily stable strategy to colonize spatially extended habitats

The ability of a species to colonize newly available habitas is crucial to its overall fitness. Generally, motility and fast expansion is expected to be beneficial to the colonization process and hence to organismal fitness. Here we apply a unique evolution protocol to investigate phenotypical requirements for colonizing habitats of different sizes during range expansion of chemotaxing bacteria. Contrary to the intuitive expectation that faster is better, we show the existence of an optimal expansion speed associated with a given habitat size. Our analysis showed this effect to arise from interactions among pioneering cells at the front of the expanding population, and revealed a simple, evolutionary stable strategy for colonizing a habitat of a specific size: to expand at a speed given by the product of the growth rate and habitat size. These results illustrates stability-to-invasion as a powerful principle for the selection of phenotypes in complex ecological processes.

Single nucleotide mapping of trait space reveals Pareto fronts that constrain adaptation

Trade-offs constrain the improvement of performance of multiple traits simultaneously. Such trade-offs define Pareto fronts, which represent a set of optimal individuals that cannot be improved in any one trait without reducing performance in another. Surprisingly, experimental evolution often yields genotypes with improved performance in all measured traits, perhaps indicating an absence of trade-offs at least in the short term. Here we densely sample adaptive mutations in Saccharomyces cerevisiae to ask whether first-step adaptive mutations result in trade-offs during the growth cycle. We isolated thousands of adaptive clones evolved under carefully chosen conditions and quantified their performances in each part of the growth cycle. We too find that some first-step adaptive mutations can improve all traits to a modest extent. However, our dense sampling allowed us to identify trade-offs and establish the existence of Pareto fronts between fermentation and respiration, and between respiration and stationary phases. Moreover, we establish that no single mutation in the ancestral genome can circumvent the detected trade-offs. Finally, we sequenced hundreds of these adaptive clones, revealing new targets of adaptation and defining the genetic basis of the identified trade-offs.

Adaptive Landscapes in the Age of Synthetic Biology

For nearly a century adaptive landscapes have provided overviews of the evolutionary process and yet they remain metaphors. We redefine adaptive landscapes in terms of biological processes rather than descriptive phenomenology. We focus on the underlying mechanisms that generate emergent properties such as epistasis, dominance, trade-offs and adaptive peaks. We illustrate the utility of landscapes in predicting the course of adaptation and the distribution of fitness effects. We abandon aged arguments concerning landscape ruggedness in favor of empirically determining landscape architecture. In so doing, we transform the landscape metaphor into a scientific framework within which causal hypotheses can be tested.

Biophysical constraints determine the selection of phenotypic fluctuations during directed evolution

Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in populations from microbes to higher animals. Phenotypic fluctuations can provide a basis for adaptation and be the target of selection. Here we present a theoretical and experimental investigation of the fate of phenotypic fluctuations in directed evolution experiments where phenotypes are subject to constraints. We show that selecting bacterial populations for fast migration through a porous environment drives a reduction in cell-to-cell variation across the population. Using sequencing and genetic engineering we study the genetic basis for this reduction in phenotypic fluctuations. We study the generality of this reduction by developing a simple, abstracted, numerical simulation model of the evolution of phenotypic fluctuations subject to constraints. Using this model we find that strong and weak selection generally lead respectively to increasing or decreasing cell-to-cell variation as a result of a bound on the selected phenotype under a wide range of parameters. However, other behaviors are also possible, and we describe the outcome of selection simulations for different model parameters and suggest future experiments. We analyze the mechanism of the observed reduction of phenotypic fluctuations in our experimental system, discuss the relevance of our abstract model to the experiment and explore its broader implications for evolution.

Maximizing Growth Yield and Dispersal via Quorum Sensing Promotes Cooperation in Vibrio Bacteria

Quorum sensing (QS) is a form of bacterial chemical communication that regulates cellular phenotypes, including certain cooperative behaviors, in response to environmental and demographic changes. Despite the existence of proposed mechanisms that stabilize QS against defector exploitation, it is unclear if or how QS cooperators can proliferate in some model systems in populations mostly consisting of defectors. We predicted that growth in fragmented subpopulations could allow QS cooperators to invade a QS defector population. This could occur despite cooperators having lower relative fitnesses than defectors due to favored weighting of genotypes that produce larger populations of bacteria. Mixed metapopulations of Vibrio QS-proficient or unconditional cooperators and QS defectors were diluted and fragmented into isolated subpopulations in an environment that requires QS-regulated public good production to achieve larger population yields. Under these conditions, we observed global invasions of both cooperator genotypes into populations composed of primarily defectors. This spatially dependent increase in cooperator frequency was replicated for QS cooperators when mixed populations were competed in soft agar motility plates under conditions that allowed cooperators to disperse and outcompete defectors at the population edge, despite being less motile in isolation than defectors. These competition results show that the coordinated growth and dispersal of QS cooperators to additional resources is heavily favored in comparison to unconditional cooperation, and that dispersal of cooperators by motility into new environments, examined here in laboratory populations, constitutes a key mechanism for maintaining QS-regulated cooperation in the face of defection.IMPORTANCE Behaviors that are cooperative in nature are at risk of exploitation by cheating and are thus difficult to maintain by natural selection alone. While bacterial cell-cell communication, known as quorum sensing (QS), can stabilize microbial cooperative behaviors and is widespread in Vibrio species, it is unclear how QS can increase the frequency of cooperative strains in the presence of defectors without additional mechanisms. In this study, we demonstrate under multiple conditions that QS-mediated cooperation can increase in populations of Vibrio strains when cells experience narrow population bottlenecks or disperse from defectors. This occurred for both conditional cooperation mediated by QS and for unconditional cooperation, although conditional cooperators were better able to stabilize cooperation over a much wider range of conditions. Thus, we observed that population structuring allowed for assortment of competing genotypes and promoted cooperation via kin selection in microbes in a QS-dependent manner.

Stimulus sensing and signal processing in bacterial chemotaxis

Motile bacteria use chemotaxis to migrate towards environments that are favorable for growth and survival. The signaling pathway that mediates this behavior is largely conserved among prokaryotes, with Escherichia coli chemotaxis system being one of the simplest and the best studied. At the core of this pathway are the arrays of clustered chemoreceptors that detect, amplify and integrate various stimuli. Recent work provided deeper understanding of spatial organization and signal processing by these clusters and uncovered the variety of sensory mechanisms used to detect environmental stimuli. Moreover, studies of bacteria with different lifestyles have led to new insights into the diversity and evolutionary conservation of the chemotaxis pathway, as well as the physiological relevance of chemotactic behavior in different environments.

Experimental evolution and proximate mechanisms in biology

Biological functions – studied by molecular, systems and behavioral biology – are referred to as proximate mechanisms. Why and how they have emerged from the course of evolution are referred to as ultimate mechanisms. Despite the conceptual and technical schism between the disciplines that focus on each, studies from one side can benefit the other. Experimental evolution is an emerging field at the crossroads of functional and evolutionary biology. Herein microorganisms and mammalian cell lines evolve in well-controlled laboratory environments over multiple generations. Phenotypic changes arising from the process are then characterized in genetics and function to understand the evolutionary process. While providing empirical tests to evolutionary questions, such studies also offer opportunities of new insights into proximate mechanisms. Experimental evolution optimizes biological systems by means of adaptation; the adapted systems with their mutations present unique perturbed states of the systems that generate new and often unexpected output/performance. Hence, learning about these states not only adds to but also might deepen knowledge on the proximate processes. To demonstrate this point, five examples in experimental evolution are introduced, and their relevance to functional biology explicated. In some examples, from evolution experiments, updates were made to known proximate processes – gene regulation and cell polarization. In some examples, new contexts were found for known proximate processes – cell division and drug resistance of cancer. In one example, a new cellular mechanism was discovered. These cases identify ways the approach of experimental evolution can be used to ask questions in functional biology.

Emergent properties of bacterial chemotaxis pathway

The chemotaxis pathway of Escherichia coli is the most studied sensory system in prokaryotes. The highly conserved general architecture of this pathway consists of two modules which mediate signal transduction and adaptation. The signal transduction module detects and amplifies changes in environmental conditions and rapidly transmits these signals to control bacterial swimming behavior. The adaptation module gradually resets the activity and sensitivity of the first module after initial stimulation and thereby enables the temporal comparisons necessary for bacterial chemotaxis. Recent experimental and theoretical work has unraveled multiple quantitative features emerging from the interplay between these two modules. This has laid the groundwork for rationalization of these emerging properties in the context of the evolutionary optimization of the chemotactic behavior.

Environment determines evolutionary trajectory in a constrained phenotypic space

Constraints on phenotypic variation limit the capacity of organisms to adapt to the multiple selection pressures encountered in natural environments. To better understand evolutionary dynamics in this context, we select Escherichia coli for faster migration through a porous environment, a process which depends on both motility and growth. We find that a trade-off between swimming speed and growth rate constrains the evolution of faster migration. Evolving faster migration in rich medium results in slow growth and fast swimming, while evolution in minimal medium results in fast growth and slow swimming. In each condition parallel genomic evolution drives adaptation through different mutations. We show that the trade-off is mediated by antagonistic pleiotropy through mutations that affect negative regulation. A model of the evolutionary process shows that the genetic capacity of an organism to vary traits can qualitatively depend on its environment, which in turn alters its evolutionary trajectory.

DOI:http://dx.doi.org/10.7554/eLife.24669.001

In nature organisms face many challenges, and species adapt to their environment by changing heritable traits over the course of many generations. How organisms adapt is often limited by trade-offs, in which improving one trait can only come at the expense of another.

In the laboratory, scientists use well-controlled environments to study how populations adapt to specific challenges without interference from their natural habitat. Most experiments, however, only look at simple challenges and do not take into account that organisms in the wild face many pressures at the same time. Fraebel et al. wanted to know what happens when an organism’s performance depends on two traits that are restricted by a trade-off. The experiments used populations of the bacterium Escherichia coli, which can go through hundreds of generations in a week, providing ample opportunity to study mutations and their impact on heritable traits.

Through a combination of mathematical modeling and experiments, Fraebel et al. found that the environment is crucial for determining how bacteria adapt when their swimming speed and population growth rate are restricted by a trade-off. When nutrients are plentiful, E. coli populations evolve to spread faster by swimming more quickly despite growing more slowly. Yet, if nutrients are scarcer, the bacteria evolve to spread faster by growing more quickly despite swimming more slowly. In each scenario, the experiments identified single mutations that changed both swimming speed and growth rate by modifying regulatory activity in the cell.

A better understanding of how an organism’s genetic architecture, its environment and trade-offs are connected may help identify the traits that are most easily changed by mutations. The ultimate goal would be to be able to predict evolutionary responses to complex selection pressures.

DOI:http://dx.doi.org/10.7554/eLife.24669.002