Erez Dekel

Optimality and evolutionary tuning of the expression level of a protein.

Different proteins have different expression levels. It is unclear to what extent these expression levels are optimized to their environment. Evolutionary theories suggest that protein expression levels maximize fitness, but the fitness as a function of protein level has seldom been directly measured. To address this, we studied the lac system of Escherichia coli, which allows the cell to use the sugar lactose for growth. We experimentally measured the growth burden due to production and maintenance of the Lac proteins (cost), as well as the growth advantage (benefit) conferred by the Lac proteins when lactose is present. The fitness function, given by the difference between the benefit and the cost, predicts that for each lactose environment there exists an optimal Lac expression level that maximizes growth rate. We then performed serial dilution evolution experiments at different lactose concentrations. In a few hundred generations, cells evolved to reach the predicted optimal expression levels. Thus, protein expression from the lac operon seems to be a solution of a cost–benefit optimization problem, and can be rapidly tuned by evolution to function optimally in new environments.

Oscillations and variability in the p53 system

Understanding the dynamics and variability of protein circuitry requires accurate measurements in living cells as well as theoretical models. To address this, we employed one of the best‐studied protein circuits in human cells, the negative feedback loop between the tumor suppressor p53 and the oncogene Mdm2. We measured the dynamics of fluorescently tagged p53 and Mdm2 over several days in individual living cells. We found that isogenic cells in the same environment behaved in highly variable ways following DNA‐damaging gamma irradiation: some cells showed undamped oscillations for at least 3 days (more than 10 peaks). The amplitude of the oscillations was much more variable than the period. Sister cells continued to oscillate in a correlated way after cell division, but lost correlation after about 11 h on average. Other cells showed low‐frequency fluctuations that did not resemble oscillations. We also analyzed different families of mathematical models of the system, including a novel checkpoint mechanism. The models point to the possible source of the variability in the oscillations: low‐frequency noise in protein production rates, rather than noise in other parameters such as degradation rates. This study provides a view of the extensive variability of the behavior of a protein circuit in living human cells, both from cell to cell and in the same cell over time.

Alternating electric fields arrest cell proliferation in animal tumor models and human brain tumors

We have recently shown that low intensity, intermediate frequency, electric fields inhibit by an anti-microtubule mechanism of action, cancerous cell growth in vitro. Using implanted electrodes, these fields were also shown to inhibit the growth of dermal tumors in mice. The present study extends these findings to additional cell lines [human breast carcinoma; MDA-MB-231, and human non-small-cell lung carcinoma (H1299)] and to animal tumor models (intradermal B16F1 melanoma and intracranial F-98 glioma) using external insulated electrodes. These findings led to the initiation of a pilot clinical trial of the effects of TTFields in 10 patients with recurrent glioblastoma (GBM). Median time to disease progression in these patients was 26.1 weeks and median overall survival was 62.2 weeks. These time to disease progression and OS values are more than double the reported medians of historical control patients. No device-related serious adverse events were seen after >70 months of cumulative treatment in all of the patients. The only device-related side effect seen was a mild to moderate contact dermatitis beneath the field delivering electrodes. We conclude that TTFields are a safe and effective new treatment modality which effectively slows down tumor growth in vitro, in vivo and, as demonstrated here, in human cancer patients.

Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy

Latency and ongoing replication have both been proposed to explain the drug-insensitive human immunodeficiency virus (HIV) reservoir maintained during antiretroviral therapy. Here we explore a novel mechanism for ongoing HIV replication in the face of antiretroviral drugs. We propose a model whereby multiple infections per cell lead to reduced sensitivity to drugs without requiring drug-resistant mutations, and experimentally validate the model using multiple infections per cell by cell-free HIV in the presence of the drug tenofovir. We then examine the drug sensitivity of cell-to-cell spread of HIV, a mode of HIV transmission that can lead to multiple infection events per target cell. Infections originating from cell-free virus decrease strongly in the presence of antiretrovirals tenofovir and efavirenz whereas infections involving cell-to-cell spread are markedly less sensitive to the drugs. The reduction in sensitivity is sufficient to keep multiple rounds of infection from terminating in the presence of drugs. We examine replication from cell-to-cell spread in the presence of clinical drug concentrations using a stochastic infection model and find that replication is intermittent, without substantial accumulation of mutations. If cell-to-cell spread has the same properties in vivo, it may have adverse consequences for the immune system, lead to therapy failure in individuals with risk factors, and potentially contribute to viral persistence and hence be a barrier to curing HIV infection.

Adaptive prediction of environmental changes by microorganisms.

Natural habitats of some microorganisms may fluctuate erratically, whereas others, which are more predictable, offer the opportunity to prepare in advance for the next environmental change. In analogy to classical Pavlovian conditioning, microorganisms may have evolved to anticipate environmental stimuli by adapting to their temporal order of appearance. Here we present evidence for environmental change anticipation in two model microorganisms, Escherichia coli and Saccharomyces cerevisiae. We show that anticipation is an adaptive trait, because pre-exposure to the stimulus that typically appears early in the ecology improves the organism’s fitness when encountered with a second stimulus. Additionally, we observe loss of the conditioned response in E. coli strains that were repeatedly exposed in a laboratory evolution experiment only to the first stimulus. Focusing on the molecular level reveals that the natural temporal order of stimuli is embedded in the wiring of the regulatory network—early stimuli pre-induce genes that would be needed for later ones, yet later stimuli only induce genes needed to cope with them. Our work indicates that environmental anticipation is an adaptive trait that was repeatedly selected for during evolution and thus may be ubiquitous in biology.

Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space

Managing Trade-Offs Most organisms experience selection on a host of traits to determine their likelihood to succeed evolutionarily. However, specific traits may experience trade-offs in determining an organisms optimal phenotype. Shoval et al. (p. 1157; see the Perspective by Noor and Milo) relate physical traits to the task that they are optimizing using a Pareto curve, a power law probability distribution, to show that a single set of trait values optimizes performance at a given task and that performance decreases as an organisms phenotype moves away from this set of trait values. The results suggest how selection makes the best trade-offs for an arbitrary number of tasks and traits and may explain examples of evolutionary variation. The fitness of an organism can be modeled graphically to determine how phenotypic trade-offs are maximized. Biological systems that perform multiple tasks face a fundamental trade-off: A given phenotype cannot be optimal at all tasks. Here we ask how trade-offs affect the range of phenotypes found in nature. Using the Pareto front concept from economics and engineering, we find that best–trade-off phenotypes are weighted averages of archetypes—phenotypes specialized for single tasks. For two tasks, phenotypes fall on the line connecting the two archetypes, which could explain linear trait correlations, allometric relationships, as well as bacterial gene-expression patterns. For three tasks, phenotypes fall within a triangle in phenotype space, whose vertices are the archetypes, as evident in morphological studies, including on Darwin’s finches. Tasks can be inferred from measured phenotypes based on the behavior of organisms nearest the archetypes.

The mirror game as a paradigm for studying the dynamics of two people improvising motion together

Joint improvisation is the creative action of two or more people without a script or designated leader. Examples include improvisational theater and music, and day-to-day activities such as conversations. In joint improvisation, novel action is created, emerging from the interaction between people. Although central to creative processes and social interaction, joint improvisation remains largely unexplored due to the lack of experimental paradigms. Here we introduce a paradigm based on a theater practice called the mirror game. We measured the hand motions of two people mirroring each other at high temporal and spatial resolution. We focused on expert actors and musicians skilled in joint improvisation. We found that players can jointly create novel complex motion without a designated leader, synchronized to less than 40 ms. In contrast, we found that designating one player as leader deteriorated performance: The follower showed 2–3 Hz oscillation around the leaders smooth trajectory, decreasing synchrony and reducing the range of velocities reached. A mathematical model suggests a mechanism for these observations based on mutual agreement on future motion in mirrored reactive–predictive controllers. This is a step toward understanding the human ability to create novelty by improvising together.

The incoherent feed‐forward loop can generate non‐monotonic input functions for genes

Gene regulation networks contain recurring circuit patterns called network motifs. One of the most common network motif is the incoherent type 1 feed‐forward loop (I1‐FFL), in which an activator controls both gene and repressor of that gene. This motif was shown to act as a pulse generator and response accelerator of gene expression. Here we consider an additional function of this motif: the I1‐FFL can generate a non‐monotonic dependence of gene expression on the input signal. Here, we study this experimentally in the galactose system of Escherichia coli, which is regulated by an I1‐FFL. The promoter activity of two of the gal operons, galETK and galP, peaks at intermediate levels of the signal cAMP. We find that mutants in which the I1‐FFL is disrupted lose this non‐monotonic behavior, and instead display monotonic input functions. Theoretical analysis suggests that non‐monotonic input functions can be achieved for a wide range of parameters by the I1‐FFL. The models also suggest regimes where a monotonic input‐function can occur, as observed in the mglBAC operon regulated by the same I1‐FFL. The present study thus experimentally demonstrates how upstream circuitry can affect gene input functions and how an I1‐FFL functions within its natural context in the cell.

Cost of Unneeded Proteins in E. coli Is Reduced after Several Generations in Exponential Growth

When E. coli cells express unneeded protein, they grow more slowly. Such penalty to fitness associated with making proteins is called protein cost. Protein cost is an important component in the cost-benefit tradeoffs that underlie the evolution of protein circuits, but its origins are still poorly understood. Here, we ask how the protein cost varies during the exponential growth phase of E. coli. We find that cells growing exponentially following an upshift from overnight culture show a large cost when producing unneeded proteins. However, after several generations, while still in exponential growth, the cells enter a phase where cost is much reduced despite vigorous unneeded protein production. We find that this reduced-cost phase depends on the ppGpp system, which adjusts the amount of ribosomes in the cell and does not occur after a downshift from rich to poor medium. These findings suggest that protein cost is a transient phenomenon that happens upon an upshift in conditions and that cost is reduced when ribosomes and other cellular systems have increased to their appropriate steady-state level in the new condition.

Diverse Two-Dimensional Input Functions Control Bacterial Sugar Genes

Cells respond to signals by regulating gene expression. The relation between the level of input signals and the transcription rate of the gene is called the genes input function. Because most genes are regulated by more than one signal, the input functions are usually multidimensional. To understand cellular responses, it is essential to know the shapes of these functions. Here, we map the two-dimensional input functions of 19 sugar-utilization genes at high resolution in living E. coli cells. We find diverse, intricately shaped input functions, despite the similarity in the regulatory circuitry of these genes. Surprisingly, some of the input functions are nonmonotonic, peaking at intermediate signal levels. Furthermore, most of the input functions show separation of variables, in the sense that they can be described as the product of simple functions that depend on a single input. This first broad survey of two-dimensional input functions can be extended to map the logic of gene regulation in other systems.