The regulatory circuits for hysteretic switching in cellular signal transduction pathways

Hysteresis can be found in many physical systems, and a hysteretic switch has been used for various mechanical and electrical systems. Such a hysteretic switch can be created by using a single positive feedback loop, as often used in engineering systems. It is, however, intriguing that various cellular signaling systems use coupled positive feedback loops to implement the hysteretic switch. A question then arises about the advantage of using coupled positive feedback loops instead of simple isolated positive feedback for an apparently equivalent hysteretic switch. Through mathematical simulations, we determined that cellular systems with coupled positive feedback loops show enhanced hysteretic switching, and can thereby make a more reliable decision under conditions of noisy signaling. As most intracellular processes are accompanied by intrinsic noise, important cellular decisions such as differentiation and apoptosis need to be highly robust to such noises. The coupled positive feedback loops might have been evolutionarily acquired to enable correct cell fate decisions to be made through enhanced hysteretic switching in noisy cellular environments.     

Bet hedging based cooperation can limit kin selection and form a basis for mutualism

Mutualism is a mechanism of cooperation in which partners that differ help each other. As such, mutualism opposes mechanisms of kin selection and tag-based selection (for example the green beard mechanism), which are based on giving exclusive help to partners that are related or carry the same tag. In contrast to kin selection, which is a basis for parochialism and intergroup warfare, mutualism can therefore be regarded as a mechanism that drives peaceful coexistence between different groups and individuals. Here the competition between mutualism and kin (tag) selection is studied. In a model where kin selection and tag-based selection are dominant, mutualism is promoted by introducing environmental fluctuations. These fluctuations cause reduction in reproductive success by the mechanism of variance discount. The best strategy to counter variance discount is to share with agents who experience the most anticorrelated fluctuations, a strategy called bet hedging. In this way, bet hedging stimulates cooperation with the most unrelated partners, which is a basis for mutualism. Analytic results and simulations reveal that, if this effect is large enough, mutualistic strategies can dominate kin selective strategies. In addition, mutants of these mutualistic strategies that experience fluctuations that are more anticorrelated to their partner, can outcompete wild type, which can lead to the evolution of specialization. In this way, the evolutionary success of mutualistic strategies can be explained by bet hedging-based cooperation.     

Early commitment and robust differentiation in colonic crypts

Tissue stem cells produce a constant flux of differentiated cells with distinct proportions. Here, we show that stem cells in colonic crypts differentiate early to form precisely 1:3 ratio of secretory to absorptive cells. This precision is surprising, as there are only eight stem cells making irreversible fate decisions, and so large stochastic effects of this small pool should have yielded much larger noise in cell proportions. We use single molecule FISH, lineage‐tracing mice and simulations to identify the homeostatic mechanisms facilitating robust proportions. We find that Delta‐Notch lateral inhibition operates in a restricted spatial zone to reduce initial noise in cell proportions. Increased dwell time and dispersive migration of secretory cells further averages additional variability added during progenitor divisions and breaks up continuous patches of same‐fate cells. These noise‐reducing mechanisms resolve the trade‐off between early commitment and robust differentiation and ensure spatially uniform spread of secretory cells. Our findings may apply to other cases where small progenitor pools expand to give rise to precise tissue cell proportions.     

When sensing is gambling: An experimental system reveals how plasticity can generate tunable bet‐hedging strategies

Genotypes can persist in unpredictable environments by “hedging their bets” and producing diverse phenotypes. Theoretical studies have shown that the phenotypic variability needed for a bet‐hedging strategy can be generated by factors either inside or outside an organism. However, sensing the environment and bet hedging are frequently treated as distinct evolutionary strategies. Furthermore, nearly all empirical studies of the molecular underpinnings of bet‐hedging strategies to date have focused on internal sources of variability. We took a synthetic approach and constructed an experimental system where a phenotypic trade‐off is mediated by actively sensing a cue present in the environment. We show that active sensing can generate a diversified bet‐hedging strategy. Mutations affecting the norm of reaction to the cue alter the diversification strategy, indicating that bet hedging by active sensing is evolvable. Our results indicate that a broader class of biological systems should be considered as potential examples of bet‐hedging strategies, and that research into the structure of environmental variability is needed to distinguish bet‐hedging strategies from adaptive plasticity.     

Bet‐hedging as a mechanism for the evolution of polyandry,revisited

Females that mate with multiple males (polyandry) may reduce the risk that their eggs are fertilized by a single unsuitable male. About 25 years ago it was hypothesized that bet‐hedging could function as a mechanism favoring the evolution of polyandry, but this idea is controversial because theory indicates that bet‐hedging via polyandry can compensate the costs of mating only in small populations. Nevertheless, populations are often spatially structured, and even in the absence of spatial structure, mate‐choice opportunity can be limited to a few potential partners. We examined the effectiveness of bet‐hedging in such situations with simulations carried out under two scenarios: (1) intrinsic male quality, with offspring survival determined by male phenotype (male's ability to generate viable offspring), and (2) genetic incompatibility (offspring fitness determined nonadditively by parental genotypes). We find higher fixation probabilities for a polyandrous strategy compared to a monandrous strategy if complete reproductive failure due to male effects or parental incompatibility is pervasive in the population. Our results also indicate that bet‐hedging polyandry can delay the extinction of small demes. Our results underscore the potential for bet‐hedging to provide benefits to polyandrous females and have valuable implications for conservation biology.     

Subpopulations of sensorless bacteria drive fitness in fluctuating environments

Populations of bacteria often undergo a lag in growth when switching conditions. Because growth lags can be large compared to typical doubling times, variations in growth lag are an important but often overlooked component of bacterial fitness in fluctuating environments. We here explore how growth lag variation is determined for the archetypical switch from glucose to lactose as a carbon source in Escherichia coli. First, we show that single-cell lags are bimodally distributed and controlled by a single-molecule trigger. That is, gene expression noise causes the population before the switch to divide into subpopulations with zero and nonzero lac operon expression. While “sensorless” cells with zero preexisting lac expression at the switch have long lags because they are unable to sense the lactose signal, any nonzero lac operon expression suffices to ensure a short lag. Second, we show that the growth lag at the population level depends crucially on the fraction of sensorless cells and that this fraction in turn depends sensitively on the growth condition before the switch. Consequently, even small changes in basal expression can significantly affect the fraction of sensorless cells, thereby population lags and fitness under switching conditions, and may thus be subject to significant natural selection. Indeed, we show that condition-dependent population lags vary across wild E. coli isolates. Since many sensory genes are naturally low expressed in conditions where their inducer is not present, bimodal responses due to subpopulations of sensorless cells may be a general mechanism inducing phenotypic heterogeneity and controlling population lags in switching environments. This mechanism also illustrates how gene expression noise can turn even a simple sensory gene circuit into a bet hedging module and underlines the profound role of gene expression noise in regulatory responses.

Is ignorance bliss for some bacterial cells? Single-cell analysis of the archetypical switch from glucose to lactose as a carbon source in E. coli shows that bacteria can exhibit stochastic bimodal responses to external stimuli because the corresponding sensory circuit is so lowly expressed that some cells are effectively blind to the stimulus.     

Playing smart vs. playing safe: the joint expression of phenotypic plasticity and potential bet hedging across and within thermal environments

Adaptive phenotypic plasticity evolves when cues reliably predict fitness consequences of life‐history decisions, whereas bet hedging evolves when environments are unpredictable. These modes of response should be jointly expressed, because environmental variance is composed of both predictable and unpredictable components. However, little attention has been paid to the joint expression of plasticity and bet hedging. Here, I examine the simultaneous expression of plasticity in germination rate and two potential bet‐hedging traits – germination fraction and within‐season diversification in timing of germination – in seeds from multiple seed families of five geographically distant populations of Lobelia inflata (L.) subjected to a thermal gradient. Populations differ in germination plasticity to temperature, in total germination fraction and in the expression of potential diversification in the timing of germination. The observation of a negative partial correlation between the expression of plasticity and germination variance (potential diversification), and a positive correlation between plasticity and germination fraction is suggestive of a trade‐off between modes of response to environmental variance. If the observed correlations are indicative of those between adaptive plasticity and bet hedging, we expect an optimal balance to exist and differ among populations. I discuss the challenges involved in testing whether the balance between plasticity and bet hedging depends on the relative predictability of environmental variance.     

Tunable Stochastic Pulsing in the Escherichia coli Multiple Antibiotic Resistance Network from Interlinked Positive and Negative Feedback Loops

Cells live in uncertain, dynamic environments and have many mechanisms for sensing and responding to changes in their surroundings. However, sudden fluctuations in the environment can be catastrophic to a population if it relies solely on sensory responses, which have a delay associated with them. Cells can reconcile these effects by using a tunable stochastic response, where in the absence of a stressor they create phenotypic diversity within an isogenic population, but use a deterministic response when stressors are sensed. Here, we develop a stochastic model of the multiple antibiotic resistance network of Escherichia coli and show that it can produce tunable stochastic pulses in the activator MarA. In particular, we show that a combination of interlinked positive and negative feedback loops plays an important role in setting the dynamics of the stochastic pulses. Negative feedback produces a pulsatile response that is tunable, while positive feedback serves to amplify the effect. Our simulations show that the uninduced native network is in a parameter regime that is of low cost to the cell (taxing resistance mechanisms are expressed infrequently) and also elevated noise strength (phenotypic variability is high). The stochastic pulsing can be tuned by MarA induction such that variability is decreased once stresses are sensed, avoiding the detrimental effects of noise when an optimal MarA concentration is needed. We further show that variability in the expression of MarA can act as a bet hedging mechanism, allowing for survival in time-varying stress environments, however this effect is tunable to allow for a fully induced, deterministic response in the presence of a stressor.     

Within‐generation bet hedging: a seductive explanation?

Bet hedging occurs when a single genotype shows a variety of phenotypes in the same environment, and each phenotype is successful only when the particular circumstances to which it is adapted occur. The time scale of between-generation bet hedging ensures that all individuals with a given phenotype suffer the same fate – circumstances such as drought exert homogenous pressure on all members of a population. Under within-generation bet hedging, however, individuals with the same phenotype are subject to heterogeneous selection pressure – predation, for example, will affect some individuals but not others. An important consequence of this difference is that conditions favoring the evolution of within-generation bet hedging are very restricted. While a single lineage may realize increased fitness via within-generation bet hedging, this fitness advantage varies inversely with population size and becomes vanishingly small at even modest population sizes. Although several reviews and analyses have highlighted the differences between these two types of bet hedging, confusion persists regarding their respective definitions and evolutionary justification. Bet hedging is a seductive explanation because most students of evolution are trained to focus on costs and benefits at the individual level, and tend to seek adaptive explanations for individual traits. Although this focus is often successful, it leads us astray in the case of within-generation bet hedging. Only by assessing the fitness effects of a trait in the context of whole populations can one accurately identify traits that can and cannot be favored by within-generation bet hedging.     

Bet hedging in yeast by heterogeneous, age-correlated expression of a stress protectant

Genetically identical cells grown in the same culture display striking cell-to-cell heterogeneity in gene expression and other traits. A crucial challenge is to understand how much of this heterogeneity reflects the noise tolerance of a robust system and how much serves a biological function. In bacteria, stochastic gene expression results in cell-to-cell heterogeneity that might serve as a bet-hedging mechanism, allowing a few cells to survive through an antimicrobial treatment while others perish. Despite its clinical importance, the molecular mechanisms underlying bet hedging remain unclear. Here, we investigate the mechanisms of bet hedging in Saccharomyces cerevisiae using a new high-throughput microscopy assay that monitors variable protein expression, morphology, growth rate, and survival outcomes of tens of thousands of yeast microcolonies simultaneously. We find that clonal populations display broad distributions of growth rates and that slow growth predicts resistance to heat killing in a probabalistic manner. We identify several gene products that are likely to play a role in bet hedging and confirm that Tsl1, a trehalose-synthesis regulator, is an important component of this resistance. Tsl1 abundance correlates with growth rate and replicative age and predicts survival. Our results suggest that yeast bet hedging results from multiple epigenetic growth states determined by a combination of stochastic and deterministic factors.