A concentration-dependent switch in the bacterial response to temperature

Non-genetic adaptation by collective migration

Collective behaviors require coordination of individuals. Thus, a population must adjust its phenotypic distribution to adapt to changing environments. How can a population regulate its phenotypic distribution? One strategy is to utilize specialized networks for gene regulation and maintaining distinct phenotypic subsets. Another involves genetic mutations, which can be augmented by stress-response pathways. Here, we studied how a migrating bacterial population regulates its phenotypic distribution to traverse across diverse environments. We generated isogenic Escherichia coli populations with varying distributions of swimming behaviors and observed their phenotype distributions during migration in liquid and porous environments. Surprisingly, we found that during collective migration, the distributions of swimming phenotypes adapt to the environment without mutations or gene regulation. Instead, adaptation is caused by the dynamic and reversible enrichment of high-performing swimming phenotypes within each environment. This adaptation mechanism is supported by a recent theoretical study, which proposed that the phenotypic composition of a migrating population results from a balance between cell growth generating diversity and collective migration eliminating the phenotypes that are unable to keep up with the migrating group. Furthermore, by examining chemoreceptor abundance distributions during migration towards different attractants, we found that this mechanism acts on multiple chemotaxis-related traits simultaneously. Our findings reveal that collective migration itself can enable cell populations with continuous, multi-dimensional phenotypes to flexibly and rapidly adapt their phenotypic composition to diverse environmental conditions.

Significance statement

Conventional cell adaptation mechanisms, like gene regulation and random phenotypic switching, act swiftly but are limited to a few traits, while mutation-driven adaptations unfold slowly. By quantifying phenotypic diversity during bacterial collective migration, we discovered an adaptation mechanism that rapidly and reversibly adjusts multiple traits simultaneously. By dynamically balancing the elimination of phenotypes unable to keep pace with generation of diversity through growth, this process enables populations to tune their phenotypic composition based on the environment, without the need for gene regulation or mutations. Given the prevalence of collective migration in microbes, cancers, and embryonic development, non-genetic adaptation through collective migration may be a universal mechanism for populations to navigate diverse environments, offering insights into broader applications across various fields.

Bacterial battle against acidity

The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.

A Mathematical Description of Bacterial Chemotaxis in Response to Two Stimuli

Bacteria are often exposed to multiple stimuli in complex environments, and their efficient chemotactic decisions are critical to survive and grow in their native environments. Bacterial responses to the environmental stimuli depend on the ratio of their corresponding chemoreceptors. By incorporating the signaling machinery of individual cells, we analyze the collective motion of a population of Escherichia coli bacteria in response to two stimuli, mainly serine and methyl-aspartate (MeAsp), in a one-dimensional and a two-dimensional environment, which is inspired by experimental results in Y. Kalinin et al., J. Bacteriol. 192(7):1796-1800, 2010. Under suitable conditions, we show that if the ratio of the main chemoreceptors of individual cells, namely Tar/Tsr, is less than a specific threshold, the bacteria move to the gradient of serine, and if the ratio is greater than the threshold, the group of bacteria moves toward the gradient of MeAsp. Finally, we examine the theory with Monte Carlo agent-based simulations and verify that our results qualitatively agree well with the experimental results in Y. Kalinin et al. (2010).

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.

Aggregation Temperature of Escherichia coli Depends on Steepness of the Thermal Gradient

Bacterial chemotaxis, the directed migration of bacteria in a gradient of chemoattractant, is one of the most well-studied and well-understood processes in cell biology. On the other hand, bacterial thermotaxis, the directed migration of bacteria in a gradient of temperature, is understood relatively poorly, with somewhat conflicting reports by different groups. One of the reasons for that is the relative technical difficulty of the generation of well-defined gradients of temperature that are sufficiently steep to elicit readily detectable thermotaxis. Here, we used a specially designed microfluidic device to study thermotaxis of Escherichia coli in a broad range of thermal gradients with a high rate of data collection. We found that in shallow temperature gradients with narrow temperature ranges, E. coli tended to aggregate near a sidewall of the gradient channel at either the lowest or the highest temperature. On the other hand, in sufficiently steep gradients with wide temperature ranges, E. coli aggregated at intermediate temperatures, with maximal cell concentrations found away from the sidewalls. We observed this intermediate temperature aggregation in a motility buffer that did not contain any major chemoattractants of E. coli, in contradiction to some previous reports, which suggested that this type of aggregation required the presence of at least one major chemoattractant in the medium. Even more surprisingly, the aggregation temperature strongly depended on the gradient steepness, decreasing by ∼10° as the steepness was increased from 27 to 53°C/mm. Our experiments also highlight the fact that assessments of thermal gradients by changes in fluorescence of temperature-sensitive fluorescent dyes need to account for thermophoresis of the dyes.

Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications

BACKGROUND

Biosafety is a key aspect in the international Genetically Engineered Machine (iGEM) competition, which offers student teams an amazing opportunity to pursue their own research projects in the field of Synthetic Biology. iGEM projects often involve the creation of genetically engineered bacterial strains. To minimize the risks associated with bacterial release, a variety of biosafety systems were constructed, either to prevent survival of bacteria outside the lab or to hinder horizontal or vertical gene transfer.

MAIN BODY

Physical containment methods such as bioreactors or microencapsulation are considered the first safety level. Additionally, various systems involving auxotrophies for both natural and synthetic compounds have been utilized by iGEM teams in recent years. Combinatorial systems comprising multiple auxotrophies have been shown to reduced escape frequencies below the detection limit. Furthermore, a number of natural toxin-antitoxin systems can be deployed to kill cells under certain conditions. Additionally, parts of naturally occurring toxin-antitoxin systems can be used for the construction of 'kill switches' controlled by synthetic regulatory modules, allowing control of cell survival. Kill switches prevent cell survival but do not completely degrade nucleic acids. To avoid horizontal gene transfer, multiple mechanisms to cleave nucleic acids can be employed, resulting in 'self-destruction' of cells. Changes in light or temperature conditions are powerful regulators of gene expression and could serve as triggers for kill switches or self-destruction systems. Xenobiology-based containment uses applications of Xeno-DNA, recoded codons and non-canonical amino acids to nullify the genetic information of constructed cells for wild type organisms. A 'minimal genome' approach brings the opportunity to reduce the genome of a cell to only genes necessary for survival under lab conditions. Such cells are unlikely to survive in the natural environment and are thus considered safe hosts. If suitable for the desired application, a shift to cell-free systems based on Xeno-DNA may represent the ultimate biosafety system.

CONCLUSION

Here we describe different containment approaches in synthetic biology, ranging from auxotrophies to minimal genomes, which can be combined to significantly improve reliability. Since the iGEM competition greatly increases the number of people involved in synthetic biology, we will focus especially on biosafety systems developed and applied in the context of the iGEM competition.

A bacterial antibiotic resistance accelerator and applications

The systematic emergence of drug resistance remains a major problem in the treatment of infectious diseases (antibiotics) and cancer (chemotherapy), with possible common fundamental origins linking bacterial antibiotic resistance and emergence of chemotherapy resistance. The common link may be evolution in a complex fitness landscape with connected small population niches. We report a detailed method for observing bacterial adaptive behavior in heterogeneous microfluidic environment designed to mimic the environmental heterogeneity found in natural microbial niches. First, the device is structured with multiple connected micro-chambers that allow the cell population to communicate and organize into smaller populations. Second, bacteria evolve within an antibiotic gradient generated throughout the micro-chambers that creates a wide range of fitness landscapes. High-resolution images of the adaptive response to the antibiotic stress are captured by epifluorescence microscopy at various levels of the bacterial organization for quantitative analysis. Thus, the experimental setup we have developed provides a powerful frame for visualizing evolution at work: bacterial movement, survival and death. It also presents a basis for exploring the rates at which drug resistance arises in bacteria and other biological contexts such as cancer.

Chemotaxis of Escherichia coli to major hormones and polyamines present in human gut

The microorganisms in the gastrointestinal (GI) tract can influence the metabolism, immunity, and behavior of animal hosts. Increasing evidence suggests that communication between the host and the microbiome also occurs in the opposite direction, with hormones and other host-secreted compounds being sensed by microorganisms. Here, we addressed one key aspect of the host–microbe communication by studying chemotaxis of a model commensal bacterium, Escherichia coli, to several compounds present abundantly in the GI tract, namely catecholamines, thyroid hormones, and polyamines. Our results show that E. coli reacts to five out of ten analyzed chemicals, sensing melatonin, and spermidine as chemorepellents and showing mixed responses to dopamine, norepinephrine and 3,4-dihydroxymandelic acid. The strongest repellent response was observed for the polyamine spermidine, and we demonstrate that this response involves the low-abundance chemoreceptor Trg and the periplasmic binding protein PotD of the spermidine uptake system. The chemotactic effects of the tested compounds apparently correlate with their influence on growth and their stability in the GI tract, pointing to the specificity of the observed behavior. We hypothesize that the repellent responses observed at high concentrations of chemoeffective compounds might enable bacteria to avoid harmful levels of hormones and polyamines in the gut and, more generally, antimicrobial activities of the mucous layer.

Microfluidic Devices Developed for and Inspired by Thermotaxis and Chemotaxis

Taxis has been reported in many cells and microorganisms, due to their tendency to migrate toward favorable physical situations and avoid damage and death. Thermotaxis and chemotaxis are two of the major types of taxis that naturally occur on a daily basis. Understanding the details of the thermo- and chemotactic behavioral response of cells and microorganisms is necessary to reveal the body function, diagnosing diseases and developing therapeutic treatments. Considering the length-scale and range of effectiveness of these phenomena, advances in microfluidics have facilitated taxis experiments and enhanced the precision of controlling and capturing microscale samples. Microfabrication of fluidic chips could bridge the gap between in vitro and in situ biological assays, specifically in taxis experiments. Numerous efforts have been made to develop, fabricate and implement novel microchips to conduct taxis experiments and increase the accuracy of the results. The concepts originated from thermo- and chemotaxis, inspired novel ideas applicable to microfluidics as well, more specifically, thermocapillarity and chemocapillarity (or solutocapillarity) for the manipulation of single- and multi-phase fluid flows in microscale and fluidic control elements such as valves, pumps, mixers, traps, etc. This paper starts with a brief biological overview of the concept of thermo- and chemotaxis followed by the most recent developments in microchips used for thermo- and chemotaxis experiments. The last section of this review focuses on the microfluidic devices inspired by the concept of thermo- and chemotaxis. Various microfluidic devices that have either been used for, or inspired by thermo- and chemotaxis are reviewed categorically.

Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET

We present in vivo single-cell FRET measurements in the Escherichia coli chemotaxis system that reveal pervasive signaling variability, both across cells in isogenic populations and within individual cells over time. We quantify cell-to-cell variability of adaptation, ligand response, as well as steady-state output level, and analyze the role of network design in shaping this diversity from gene expression noise. In the absence of changes in gene expression, we find that single cells demonstrate strong temporal fluctuations. We provide evidence that such signaling noise can arise from at least two sources: (i) stochastic activities of adaptation enzymes, and (ii) receptor-kinase dynamics in the absence of adaptation. We demonstrate that under certain conditions, (ii) can generate giant fluctuations that drive signaling activity of the entire cell into a stochastic two-state switching regime. Our findings underscore the importance of molecular noise, arising not only in gene expression but also in protein networks.

Optogenetic Manipulation of Cyclic Di-GMP (c-di-GMP) Levels Reveals the Role of c-di-GMP in Regulating Aerotaxis Receptor Activity in Azospirillum brasilense

Bacterial chemotaxis receptors provide the sensory inputs that inform the direction of navigation in changing environments. Recently, we described the bacterial second messenger cyclic di-GMP (c-di-GMP) as a novel regulator of a subclass of chemotaxis receptors. In Azospirillum brasilense, c-di-GMP binds to a chemotaxis receptor, Tlp1, and modulates its signaling function during aerotaxis. Here, we further characterize the role of c-di-GMP in aerotaxis using a novel dichromatic optogenetic system engineered for manipulating intracellular c-di-GMP levels in real time. This system comprises a red/near-infrared-light-regulated diguanylate cyclase and a blue-light-regulated c-di-GMP phosphodiesterase. It allows the generation of transient changes in intracellular c-di-GMP concentrations within seconds of irradiation with appropriate light, which is compatible with the time scale of chemotaxis signaling. We provide experimental evidence that binding of c-di-GMP to the Tlp1 receptor activates its signaling function during aerotaxis, which supports the role of transient changes in c-di-GMP levels as a means of adjusting the response of A. brasilense to oxygen gradients. We also show that intracellular c-di-GMP levels in A. brasilense change with carbon metabolism. Our data support a model whereby c-di-GMP functions to imprint chemotaxis receptors with a record of recent metabolic experience, to adjust their contribution to the signaling output, thus allowing the cells to continually fine-tune chemotaxis sensory perception to their metabolic state.IMPORTANCE Motile bacteria use chemotaxis to change swimming direction in response to changes in environmental conditions. Chemotaxis receptors sense environmental signals and relay sensory information to the chemotaxis machinery, which ultimately controls the swimming pattern of cells. In bacteria studied to date, differential methylation has been known as a mechanism to control the activity of chemotaxis receptors and modulates their contribution to the overall chemotaxis response. Here, we used an optogenetic system to perturb intracellular concentrations of the bacterial second messenger c-di-GMP to show that in some chemotaxis receptors, c-di-GMP functions in a similar feedback loop to connect the metabolic status of the cells to the sensory activity of chemotaxis receptors.

Effect of gold nanoparticles on thermal gradient generation and thermotaxis of E. coli cells in microfluidic device

Bacteria responds to changing chemical and thermal environment by moving towards or away from a particular location. In this report, we looked into thermal gradient generation and response of E. coli DH5α cells to thermal gradient in the presence and in the absence of spherical gold nanoparticles (size: 15 to 22 nm) in a static microfluidic environment using a polydimethylsiloxane (PDMS) made microfluidic device. A PDMS-agarose based microfluidic device for generating thermal gradient has been developed and the thermal gradient generation in the device has been validated with the numerical simulation. Our studies revealed that the presence of gold nanoparticles, AuNPs (0.649 μg/mL) has no effect on the thermal gradient generation. The E. coli DH5α cells have been treated with AuNPs of two different concentrations (0.649 μg/mL and 0.008 μg/mL). The thermotaxis behavior of cells in the presence of AuNPs has been studied and compared to the thermotaxis of E.coli DH5α cells in the absence of AuNPs. In case of thermotaxis, in the absence of the AuNPs, the E. coli DH5α cells showed better thermotaxis towards lower temperature range, whereas in the presence of AuNPs (0.649 μg/mL and 0.008 μg/mL) thermotaxis of the E. coli DH5α cells has been inhibited. The results show that the spherical AuNPs intervenes in the themotaxis of E. coli DH5α cells and inhibits the cell migration. The reason for the failure in thermotaxis response mechanism may be due to decreased F-type ATP synthase activity and collapse of membrane potential by AuNPs, which, in turn, leads to decreased ATP levels. This has been hypothesized since both thermotaxis and chemotaxis follows the same response mechanism for migration in which ATP plays critical role.

Mechanism of bidirectional thermotaxis in Escherichia coli

In bacteria various tactic responses are mediated by the same cellular pathway, but sensing of physical stimuli remains poorly understood. Here, we combine an in-vivo analysis of the pathway activity with a microfluidic taxis assay and mathematical modeling to investigate the thermotactic response of Escherichia coli. We show that in the absence of chemical attractants E. coli exhibits a steady thermophilic response, the magnitude of which decreases at higher temperatures. Adaptation of wild-type cells to high levels of chemoattractants sensed by only one of the major chemoreceptors leads to inversion of the thermotactic response at intermediate temperatures and bidirectional cell accumulation in a thermal gradient. A mathematical model can explain this behavior based on the saturation-dependent kinetics of adaptive receptor methylation. Lastly, we find that the preferred accumulation temperature corresponds to optimal growth in the presence of the chemoattractant serine, pointing to a physiological relevance of the observed thermotactic behavior.

Many bacteria can move towards or away from chemicals, heat and other stimuli in their environment. The ability of bacteria to move in response to nutrients and other chemicals, known as chemotaxis, is the best understood of these phenomena. Bacteria generally swim in a fairly random way and frequently change direction. During chemotaxis, however, the bacteria sense changes in the concentrations of a chemical in their surroundings and this biases the direction in which they swim so that they spend more time swimming towards or away from the source of the chemical. The bacteria have various receptor proteins that can detect different chemicals. For example, the Tar and Tsr receptors can recognize chemicals called aspartate and serine, respectively, which are – amongst other things – nutrients that are used to build proteins.

Tar and Tsr are also involved in the response to temperature, referred to as thermotaxis. At low temperatures, a bacterium Escherichia coli will move towards sources of heat. Yet when the bacteria detect both serine and aspartate they may reverse the response and move towards colder areas instead. However, it was not clear why the bacteria do this, and what roles Tar and Tsr play in this response.

Paulick et al. have now combined approaches that directly visualise signalling inside living bacteria and that track the movements of individual bacterial cellswith mathematical modelling to investigate thermotaxis in E. coli. The experiments show that the bacteria’s behaviour could be explained by interplay between the responses mediated by Tar and Tsr. In the absence of both serine and aspartate, both receptors stimulate heat-seeking responses, causing the bacteria to move towards hotter areas. When only aspartate is present, Tsr continues to stimulate the heat-seeking response, but the aspartate causes Tar to switch to promoting a cold-seeking response instead. This leads to the bacteria accumulating in areas of intermediate temperature. In the presence of serine only, the bacteria behave in a similar way because the receptors swap roles so that Tsr stimulates the cold-seeking response, while Tar promotes the heat-seeking one.

The intermediate temperature at which the bacteria accumulate in response to serine is also around the optimal temperature for E.coli growth in presence of this chemical, suggesting that thermotaxis might play an important role in allowing bacteria to survive and grow in many different environments, including in the human body. Thus, understanding how chemotaxis and thermotaxis are regulated may lead to new ways to control how bacteria behave in patients and natural environments.

Interplay of chemical and thermal gradient on bacterial migration in a diffusive microfluidic device

Living systems are constantly under different combinations of competing gradients of chemical, thermal, pH, and mechanical stresses allied. The present work is about competing chemical and thermal gradients imposed on E. coli in a diffusive stagnant microfluidic environment. The bacterial cells were exposed to opposing and aligned gradients of an attractant (1 mM sorbitol) or a repellant (1 mM NiSO4) and temperature. The effects of the repellant/attractant and temperature on migration behavior, migration rate, and initiation time for migration have been reported. It has been observed that under competing gradients of an attractant and temperature, the nutrient gradient (gradient generated by cells itself) initiates directed migration, which, in turn, is influenced by temperature through the metabolic rate. Exposure to competing gradients of an inhibitor and temperature leads to the imposed chemical gradient governing the directed cell migration. The cells under opposing gradients of the repellant and temperature have experienced the longest decision time (∼60 min). The conclusion is that in a competing chemical and thermal gradient environment in the range of experimental conditions used in the present work, the migration of E. coli is always initiated and governed by chemical gradients (either generated by the cells in situ or imposed upon externally), but the migration rate and percentage of migration of cells are influenced by temperature, shedding insights into the importance of such gradients in deciding collective dynamics of such cells in physiological conditions.

E. coli DH5α cell response to a sudden change in microfluidic chemical environment

Motile bacteria respond to changing chemical environment by moving towards or away from a particular location. Bacterial migration under chemical gradient is one of the most studied areas in biomedical field. In this work we looked into how bacterial cells respond to sudden change in the microfluidic chemical environment. E. coli DH5α cells were subjected to an attractant gradient (0.1 mM sorbitol--attractant to E. coli cells) and after 120 min the same cells were exposed to an inhibitor (0.1 mM NiSO4) gradient in the same microfluidic device. Our studies revealed that when the E. coli DH5α cells were exposed to 0.1 mM sorbitol, they showed faster chemotaxis towards the attractant (0.1 mM sorbitol) and achieved steady state by 60 min. When we replaced 0.1 mM sorbitol with 0.1 mM NiSO4 in the device we found that that the E. coli DH5α cells started responding to change in chemical environment within 10 min and achieved steady state at the end of 60 min. This shows that the bacterial cells respond to change in local chemical environment is within few minutes.

Type III secretion systems: the bacterial flagellum and the injectisome

The flagellum and the injectisome are two of the most complex and fascinating bacterial nanomachines. At their core, they share a type III secretion system (T3SS), a transmembrane export complex that forms the extracellular appendages, the flagellar filament and the injectisome needle. Recent advances, combining structural biology, cryo-electron tomography, molecular genetics, in vivo imaging, bioinformatics and biophysics, have greatly increased our understanding of the T3SS, especially the structure of its transmembrane and cytosolic components, the transcriptional, post-transcriptional and functional regulation and the remarkable adaptivity of the system. This review aims to integrate these new findings into our current knowledge of the evolution, function, regulation and dynamics of the T3SS, and to highlight commonalities and differences between the two systems, as well as their potential applications.

The Role of Adaptation in Bacterial Speed Races

Evolution of biological sensory systems is driven by the need for efficient responses to environmental stimuli. A paradigm among prokaryotes is the chemotaxis system, which allows bacteria to navigate gradients of chemoattractants by biasing their run-and-tumble motion. A notable feature of chemotaxis is adaptation: after the application of a step stimulus, the bacterial running time relaxes to its pre-stimulus level. The response to the amino acid aspartate is precisely adapted whilst the response to serine is not, in spite of the same pathway processing the signals preferentially sensed by the two receptors Tar and Tsr, respectively. While the chemotaxis pathway in E. coli is well characterized, the role of adaptation, its functional significance and the ecological conditions where chemotaxis is selected, are largely unknown. Here, we investigate the role of adaptation in the climbing of gradients by E. coli. We first present theoretical arguments that highlight the mechanisms that control the efficiency of the chemotactic up-gradient motion. We discuss then the limitations of linear response theory, which motivate our subsequent experimental investigation of E. coli speed races in gradients of aspartate, serine and combinations thereof. By using microfluidic techniques, we engineer controlled gradients and demonstrate that bacterial fronts progress faster in equal-magnitude gradients of serine than aspartate. The effect is observed over an extended range of concentrations and is not due to differences in swimming velocities. We then show that adding a constant background of serine to gradients of aspartate breaks the adaptation to aspartate, which results in a sped-up progression of the fronts and directly illustrate the role of adaptation in chemotactic gradient-climbing.

Biological sensory pathways are presumed to evolve for the processing of environmental information, yet quantitative evidence is scant. Chemotaxis allows bacteria to sense chemical gradients but their ecological distribution, e.g. whether natural gradients sensed by E. coli change slowly or rapidly in space and time, is unknown. That distribution matters, as it controls constraints and selective pressure acting on the pathway. We used microfluidic devices to generate controlled chemoattractant gradients and measure the speed of bacterial climbing of those gradients. We could thereby assay the impact of adaptation properties of the chemotaxis pathway onto the progression of gradient climbing. We specifically show that loss of adaptation, induced by adding a background of serine to gradients of aspartate, leads to a faster progression of the bacteria along the chemoattractant gradient. We finally discuss why our experiments suggest that ecological conditions are likely to involve chemoattractant profiles more complex than constant gradients usually considered in the laboratory.

Dose-Response Analysis of Chemotactic Signaling Response in Salmonella typhimurium LT2 upon Exposure to Cysteine/Cystine Redox Pair

The chemotaxis system enables motile bacteria to search for an optimum level of environmental factors. Salmonella typhimurium senses the amino acid cysteine as an attractant and its oxidized dimeric form, cystine, as a repellent. We investigated the dose-response dependence of changes in chemotactic signaling activity upon exposure to cysteine and cystine of S. typhimurium LT2 using in vivo fluorescence resonance energy transfer (FRET) measurements. The dose-response curve of the attractant response to cysteine had a sigmoidal shape, typical for receptor-ligand interactions. However, in a knockout strain of the chemoreceptor genes tsr and tar, we detected a repellent response to cysteine solutions, scaling linearly with the logarithm of the cysteine concentration. Interestingly, the magnitude of the repellent response to cystine also showed linear dependence to the logarithm of the cystine concentration. This linear dependence was observed over more than four orders of magnitude, where detection started at nanomolar concentrations. Notably, low concentrations of another oxidized compound, benzoquinone, triggered similar responses. In contrast to S. typhimurium 14028, where no response to cystine was observed in a knockout strain of chemoreceptor genes mcpB and mcpC, here we showed that McpB/McpC-independent responses to cystine existed in the strain S. typhimurium LT2 even at nanomolar concentrations. Additionally, knocking out mcpB and mcpC did not affect the linear dose-response dependence, whereas enhanced responses were only observed to solutions that where not pH neutral (>100 μM cystine) in the case of McpC overexpression. We discuss that the linear dependence of the response on the logarithm of cystine concentrations could be a result of a McpB/C-independent redox-sensing pathway that exists in S. typhimurium LT2. We supported this hypothesis with experiments with defined cysteine/cystine mixed solutions, where a transition from repellent to attractant response occurred depending on the estimated redox potential.

Disorder-mediated crowd control in an active matter system

Living active matter systems such as bacterial colonies, schools of fish and human crowds, display a wealth of emerging collective and dynamic behaviours as a result of far-from-equilibrium interactions. The dynamics of these systems are better understood and controlled considering their interaction with the environment, which for realistic systems is often highly heterogeneous and disordered. Here, we demonstrate that the presence of spatial disorder can alter the long-term dynamics in a colloidal active matter system, making it switch between gathering and dispersal of individuals. At equilibrium, colloidal particles always gather at the bottom of any attractive potential; however, under non-equilibrium driving forces in a bacterial bath, the colloids disperse if disorder is added to the potential. The depth of the local roughness in the environment regulates the transition between gathering and dispersal of individuals in the active matter system, thus inspiring novel routes for controlling emerging behaviours far from equilibrium.

Many living systems, such as bacterial colonies, exhibit collective and dynamic behaviours that are sensitive to the change in environmental conditions. Here, the authors show that a colloidal active matter system switches between gathering and dispersal of individuals in response to a disordered potential.

Precision and variability in bacterial temperature sensing

In Escherichia coli, the ratio of the two most abundant chemoreceptors, Tar/Tsr, has become the focus of much attention in bacterial taxis studies. This ratio has been shown to change under various growth conditions and to determine the response of the bacteria to the environment. Here, we present a study that makes a quantitative link between the ratio Tar/Tsr and the favored temperature of the cell in a temperature gradient and in various chemical environments. From the steady-state density-profile of bacteria with one dominant thermo-sensor, Tar or Tsr, we deduce the response function of each receptor to temperature changes. Using the response functions of both receptors, we determine the relationship between the favored temperature of wild-type bacteria with mixed clusters of receptors and the receptor ratio. Our model is based on the assumption that the behavior of a wild-type bacterium in a temperature gradient is determined by a linear combination of the independent responses of the two receptors, factored by the receptor's relative abundance in the bacterium. This is confirmed by comparing our model predictions with measurements of the steady-state density-profile of several bacterial populations in a temperature gradient. Our results reveal that the density-profile of wild-type bacteria can be accurately described by measuring the distribution of the ratio Tar/Tsr in the population, which is then used to divide the population into groups with distinct Tar/Tsr values, whose behavior can be described in terms of independent Gaussian distributions. Each of these Gaussians is centered about the favored temperature of the subpopulation, which is determined by the receptor ratio, and has a width defined by the temperature-dependent speed and persistence time.

Thermal control of virulence factors in bacteria: a hot topic

Pathogenic bacteria sense environmental cues, including the local temperature, to control the production of key virulence factors. Thermal regulation can be achieved at the level of DNA, RNA or protein and although many virulence factors are subject to thermal regulation, the exact mechanisms of control are yet to be elucidated in many instances. Understanding how virulence factors are regulated by temperature presents a significant challenge, as gene expression and protein production are often influenced by complex regulatory networks involving multiple transcription factors in bacteria. Here we highlight some recent insights into thermal regulation of virulence in pathogenic bacteria. We focus on bacteria which cause disease in mammalian hosts, which are at a significantly higher temperature than the outside environment. We outline the mechanisms of thermal regulation and how understanding this fundamental aspect of the biology of bacteria has implications for pathogenesis and human health.

Relation between chemotaxis and consumption of amino acids in bacteria

Chemotaxis enables bacteria to navigate chemical gradients in their environment, accumulating toward high concentrations of attractants and avoiding high concentrations of repellents. Although finding nutrients is likely to be an important function of bacterial chemotaxis, not all characterized attractants are nutrients. Moreover, even for potential nutrients, the exact relation between the metabolic value of chemicals and their efficiency as chemoattractants has not been systematically explored. Here we compare the chemotactic response of amino acids with their use by bacteria for two well‐established models of chemotactic behavior, Escherichia coli and Bacillus subtilis. We demonstrate that in E. coli chemotaxis toward amino acids indeed strongly correlates with their utilization. However, no such correlation is observed for B. subtilis, suggesting that in this case, the amino acids are not followed because of their nutritional value but rather as environmental cues.

Fast, high-throughput measurement of collective behaviour in a bacterial population

Swimming bacteria explore their environment by performing a random walk, which is biased in response to, for example, chemical stimuli, resulting in a collective drift of bacterial populations towards 'a better life'. This phenomenon, called chemotaxis, is one of the best known forms of collective behaviour in bacteria, crucial for bacterial survival and virulence. Both single-cell and macroscopic assays have investigated bacterial behaviours. However, theories that relate the two scales have previously been difficult to test directly. We present an image analysis method, inspired by light scattering, which measures the average collective motion of thousands of bacteria simultaneously. Using this method, a time-varying collective drift as small as 50 nm s(-1) can be measured. The method, validated using simulations, was applied to chemotactic Escherichia coli bacteria in linear gradients of the attractant α-methylaspartate. This enabled us to test a coarse-grained minimal model of chemotaxis. Our results clearly map the onset of receptor methylation, and the transition from linear to logarithmic sensing in the bacterial response to an external chemoeffector. Our method is broadly applicable to problems involving the measurement of collective drift with high time resolution, such as cell migration and fluid flows measurements, and enables fast screening of tactic behaviours.

Universal response-adaptation relation in bacterial chemotaxis

The bacterial strategy of chemotaxis relies on temporal comparisons of chemical concentrations, where the probability of maintaining the current direction of swimming is modulated by changes in stimulation experienced during the recent past. A short-term memory required for such comparisons is provided by the adaptation system, which operates through the activity-dependent methylation of chemotaxis receptors. Previous theoretical studies have suggested that efficient navigation in gradients requires a well-defined adaptation rate, because the memory time scale needs to match the duration of straight runs made by bacteria. Here we demonstrate that the chemotaxis pathway of Escherichia coli does indeed exhibit a universal relation between the response magnitude and adaptation time which does not depend on the type of chemical ligand. Our results suggest that this alignment of adaptation rates for different ligands is achieved through cooperative interactions among chemoreceptors rather than through fine-tuning of methylation rates for individual receptors. This observation illustrates a yet-unrecognized function of receptor clustering in bacterial chemotaxis.

Behaviors and strategies of bacterial navigation in chemical and nonchemical gradients

Navigation of cells to the optimal environmental condition is critical for their survival and growth. Escherichia coli cells, for example, can detect various chemicals and move up or down those chemical gradients (i.e., chemotaxis). Using the same signaling machinery, they can also sense other external factors such as pH and temperature and navigate from both sides toward some intermediate levels of those stimuli. This mode of precision sensing is more sophisticated than the (unidirectional) chemotaxis strategy and requires distinctive molecular mechanisms to encode and track the preferred external conditions. To systematically study these different bacterial taxis behaviors, we develop a continuum model that incorporates microscopic signaling events in single cells into macroscopic population dynamics. A simple theoretical result is obtained for the steady state cell distribution in general. In particular, we find the cell distribution is controlled by the intracellular sensory dynamics as well as the dependence of the cells' speed on external factors. The model is verified by available experimental data in various taxis behaviors (including bacterial chemotaxis, pH taxis, and thermotaxis), and it also leads to predictions that can be tested by future experiments. Our analysis help reveal the key conditions/mechanisms for bacterial precision-sensing behaviors and directly connects the cellular taxis performances with the underlying molecular parameters. It provides a unified framework to study bacterial navigation in complex environments with chemical and non-chemical stimuli.

Bacteria, such as E. coli, live in a complex environment with varying chemical and/or non-chemical stimuli. They constantly seek for and migrate to optimal environmental conditions. A well-known example is E. coli chemotaxis which direct cell movements up or down chemical gradients. Using the same machinery, E. coli can also respond to non-chemical factors (e.g., pH and temperature) and navigate toward certain intermediate, optimal levels of those stimuli. Such taxis behaviors are more sophisticated and require distinctive sensing mechanisms. In this paper, we develop a unified model for different bacterial taxis strategies. This multiscale model incorporates intracellular signaling pathways into population dynamics and leads to a simple theoretical result regarding the steady-state population distribution. Our model can be applied to reveal the key mechanisms for different taxis behaviors and quantitatively account for various experimental data. New predictions can be made within this new model framework to direct future experiments.

Emotion: The Self-regulatory Sense

While emotion is a central component of human health and well-being, traditional approaches to understanding its biological function have been wanting. A dynamic systems model, however, broadly redefines and recasts emotion as a primary sensory system-perhaps the first sensory system to have emerged, serving the ancient autopoietic function of "self-regulation." Drawing upon molecular biology and revelations from the field of epigenetics, the model suggests that human emotional perceptions provide an ongoing stream of "self-relevant" sensory information concerning optimally adaptive states between the organism and its immediate environment, along with coupled behavioral corrections that honor a universal self-regulatory logic, one still encoded within cellular signaling and immune functions. Exemplified by the fundamental molecular circuitry of sensorimotor control in the E coli bacterium, the model suggests that the hedonic (affective) categories emerge directly from positive and negative feedback processes, their good/bad binary appraisals relating to dual self-regulatory behavioral regimes-evolutionary purposes, through which organisms actively participate in natural selection, and through which humans can interpret optimal or deficit states of balanced being and becoming. The self-regulatory sensory paradigm transcends anthropomorphism, unites divergent theoretical perspectives and isolated bodies of literature, while challenging time-honored assumptions. While suppressive regulatory strategies abound, it suggests that emotions are better understood as regulating us, providing a service crucial to all semantic language, learning systems, evaluative decision-making, and fundamental to optimal physical, mental, and social health.

Ratcheting and transitions: short granular chain in a gradient of vibration

We report our experimental work on a one-dimensional gradient of vibration with a short granular chain. The system exhibits transitions of ratcheting dynamics from passive monotonic creeping against the gradient, to rapid stochastic head swinging with a reversed bias in its direction, and to seemingly random fluctuations. The spontaneously emerged spatial pattern reflects bifurcations of the state of the chain. Evidence from counterpart experiments using uniform vibrations confirms a nonmonotonic development of accessible modes behind the transitions, whereas the reversed ratcheting reflects an interesting dialogue between the size of the object and the spatial gradient.

Precision sensing by two opposing gradient sensors: how does Escherichia coli find its preferred pH level?

It is essential for bacteria to find optimal conditions for their growth and survival. The optimal levels of certain environmental factors (such as pH and temperature) often correspond to some intermediate points of the respective gradients. This requires the ability of bacteria to navigate from both directions toward the optimum location and is distinct from the conventional unidirectional chemotactic strategy. Remarkably, Escherichia coli cells can perform such a precision sensing task in pH taxis by using the same chemotaxis machinery, but with opposite pH responses from two different chemoreceptors (Tar and Tsr). To understand bacterial pH sensing, we developed an Ising-type model for a mixed cluster of opposing receptors based on the push-pull mechanism. Our model can quantitatively explain experimental observations in pH taxis for various mutants and wild-type cells. We show how the preferred pH level depends on the relative abundance of the competing sensors and how the sensory activity regulates the behavioral response. Our model allows us to make quantitative predictions on signal integration of pH and chemoattractant stimuli. Our study reveals two general conditions and a robust push-pull scheme for precision sensing, which should be applicable in other adaptive sensory systems with opposing gradient sensors.

Sensing temperature

Temperature is an omnipresent physical variable reflecting the rotational, vibrational and translational motion of matter, what Richard Feynman called the "jiggling" of atoms. Temperature varies across space and time, and this variation has dramatic effects on the physiology of living cells. It changes the rate and nature of chemical reactions, and it alters the configuration of the atoms that make up nucleic acids, proteins, lipids and other biomolecules, significantly affecting their activity. While life may have started in a "warm little pond", as Charles Darwin mused, the organisms that surround us today have only made it this far by devising sophisticated systems for sensing and responding to variations in temperature, and by using these systems in ways that allow them to persist and thrive in the face of thermal fluctuation.

Thermosensing to adjust bacterial virulence in a fluctuating environment

The lifecycle of most microbial pathogens can be divided into two states: existence outside and inside their hosts. The sudden temperature upshift experienced upon entry from environmental or vector reservoirs into a warm-blooded host is one of the most crucial signals informing the pathogens to adjust virulence gene expression and their host-stress survival program. This article reviews the plethora of sophisticated strategies that bacteria have evolved to sense temperature, and outlines the molecular signal transduction mechanisms used to modulate synthesis of crucial virulence determinants. The molecular details of thermal control through conformational changes of DNA, RNA and proteins are summarized, complex and diverse thermosensing principles are introduced and their potential as drug targets or synthetic tools are discussed.

Bacterial thermotaxis by speed modulation

Naturally occurring gradients often extend over relatively long distances such that their steepness is too small for bacteria to detect. We studied the bacterial behavior in such thermal gradients. We find that bacteria migrate along shallow thermal gradients due to a change in their swimming speed resulting from the effect of temperature on the intracellular pH, which also depends on the chemical environment. When nutrients are scarce in the environment the bacteria's intracellular pH decreases with temperature. As a result, the swimming speed of the bacteria decreases with temperature, which causes them to slowly drift toward the warm end of the thermal gradient. However, when serine is added to the medium at concentrations >300 μM, the intracellular pH increases causing the swimming speed to increase continuously with temperature, and the bacteria to drift toward the cold end of the temperature gradient. This directional migration is not a result of bacterial thermotaxis in the classical sense, because the steepness of the gradients applied is below the sensing threshold of bacteria. Nevertheless, our results show that the directional switch requires the presence of the bacterial sensing receptors. This seems to be due to the involvement of the receptors in regulating the intracellular pH.

MetR-regulated Vibrio cholerae metabolism is required for virulence

LysR-type transcriptional regulators (LTTRs) are the largest, most diverse family of prokaryotic transcription factors, with regulatory roles spanning metabolism, cell growth and division, and pathogenesis. Using a sequence-defined transposon mutant library, we screened a panel of V. cholerae El Tor mutants to identify LTTRs required for host intestinal colonization. Surprisingly, out of 38 LTTRs, only one severely affected intestinal colonization in the suckling mouse model of cholera: the methionine metabolism regulator, MetR. Genetic analysis of genes influenced by MetR revealed that glyA1 and metJ were also required for intestinal colonization. Chromatin immunoprecipitation of MetR and quantitative reverse transcription-PCR (qRT-PCR) confirmed interaction with and regulation of glyA1, indicating that misregulation of glyA1 is likely responsible for the colonization defect observed in the metR mutant. The glyA1 mutant was auxotrophic for glycine but exhibited wild-type trimethoprim sensitivity, making folate deficiency an unlikely cause of its colonization defect. MetJ regulatory mutants are not auxotrophic but are likely altered in the regulation of amino acid-biosynthetic pathways, including those for methionine, glycine, and serine, and this misregulation likely explains its colonization defect. However, mutants defective in methionine, serine, and cysteine biosynthesis exhibited wild-type virulence, suggesting that these amino acids can be scavenged in vivo. Taken together, our results suggest that glycine biosynthesis may be required to alleviate an in vivo nutritional restriction in the mouse intestine; however, additional roles for glycine may exist. Irrespective of the precise nature of this requirement, this study illustrates the importance of pathogen metabolism, and the regulation thereof, as a virulence factor.

Vibrio cholerae continues to be a severe cause of morbidity and mortality in developing countries. Identification of V. cholerae factors critical to disease progression offers the potential to develop or improve upon therapeutics and prevention strategies. To increase the efficiency of virulence factor discovery, we employed a regulator-centric approach to multiplex our in vivo screening capabilities and allow whole regulons in V. cholerae to be interrogated for pathogenic potential. We identified MetR as a new virulence regulator and serine hydroxymethyltransferase GlyA1 as a new MetR-regulated virulence factor, both required by V. cholerae to colonize the infant mouse intestine. Bacterial metabolism is a prerequisite to virulence, and current knowledge of in vivo metabolism of pathogens is limited. Here, we expand the known role of amino acid metabolism and regulation in virulence and offer new insights into the in vivo metabolic requirements of V. cholerae within the mouse intestine.

Bacterial motility measured by a miniature chamber for high-pressure microscopy

Hydrostatic pressure is one of the physical stimuli that characterize the environment of living matter. Many microorganisms thrive under high pressure and may even physically or geochemically require this extreme environmental condition. In contrast, application of pressure is detrimental to most life on Earth; especially to living organisms under ambient pressure conditions. To study the mechanism of how living things adapt to high-pressure conditions, it is necessary to monitor directly the organism of interest under various pressure conditions. Here, we report a miniature chamber for high-pressure microscopy. The chamber was equipped with a built-in separator, in which water pressure was properly transduced to that of the sample solution. The apparatus developed could apply pressure up to 150 MPa, and enabled us to acquire bright-field and epifluorescence images at various pressures and temperatures. We demonstrated that the application of pressure acted directly and reversibly on the swimming motility of Escherichia coli cells. The present technique should be applicable to a wide range of dynamic biological processes that depend on applied pressures.

Responding to chemical gradients: bacterial chemotaxis

Chemotaxis allows bacteria to follow gradients of nutrients and other environmental stimuli. The bacterium Escherichia coli performs chemotaxis via a run-and-tumble strategy in which sensitive temporal comparisons lead to a biased random walk, with longer runs in the preferred gradient direction. The chemotaxis network of E. coli has developed over the years into one of the most thoroughly studied model systems for signal transduction and behavior, yielding general insights into such properties of cellular networks as signal amplification, signal integration, and robustness. Despite its relative simplicity, the operation of the E. coli chemotaxis network is highly refined and evolutionarily optimized at many levels. For example, recent studies revealed that the network adjusts its signaling properties dependent on the extracellular environment, apparently to optimize chemotaxis under particular conditions. The network can even utilize potentially detrimental stochastic fluctuations in protein levels and reaction rates to maximize the chemotactic performance of the population.

Effects of population density and chemical environment on the behavior of Escherichia coli in shallow temperature gradients

In shallow temperature gradients, changes in temperature that bacteria experience occur over long time scales. Therefore, slow processes such as adaptation, metabolism, chemical secretion and even gene expression become important. Since these are cellular processes, the cell density is an important parameter that affects the bacteria's response. We find that there are four density regimes with distinct behaviors. At low cell density, bacteria do not cause changes in their chemical environment; however, their response to the temperature gradient is strongly influenced by it. In the intermediate cell-density regime, the consumption of nutrients becomes significant and induces a gradient of nutrients opposing the temperature gradient due to higher consumption rate at the high temperature. This causes the bacteria to drift toward low temperature. In the high cell-density regime, interactions among bacteria due to secretion of an attractant lead to a strong local accumulation of bacteria. This together with the gradient of nutrients, resulted from the differential consumption rate, creates a fast propagating pulse of bacterial density. These observations are a result of classical nonlinear population dynamics. At extremely high cell density, a change in the physiological state of the bacteria is observed. The bacteria, at the individual level, become cold seeking. This appears initially as a result of a change in the methylation level of the two most abundant sensing receptors, Tsr and Tar. It is further enforced at an even higher cell density by a change in the expression level of these receptors.

Directional persistence of chemotactic bacteria in a traveling concentration wave

Chemotactic bacteria are known to collectively migrate towards sources of attractants. In confined convectionless geometries, concentration "waves" of swimming Escherichia coli can form and propagate through a self-organized process involving hundreds of thousands of these microorganisms. These waves are observed in particular in microcapillaries or microchannels; they result from the interaction between individual chemotactic bacteria and the macroscopic chemical gradients dynamically generated by the migrating population. By studying individual trajectories within the propagating wave, we show that, not only the mean run length is longer in the direction of propagation, but also that the directional persistence is larger compared to the opposite direction. This modulation of the reorientations significantly improves the efficiency of the collective migration. Moreover, these two quantities are spatially modulated along the concentration profile. We recover quantitatively these microscopic and macroscopic observations with a dedicated kinetic model.

Thermal robustness of signaling in bacterial chemotaxis

Temperature is a global factor that affects the performance of all intracellular networks. Robustness against temperature variations is thus expected to be an essential network property, particularly in organisms without inherent temperature control. Here, we combine experimental analyses with computational modeling to investigate thermal robustness of signaling in chemotaxis of Escherichia coli, a relatively simple and well-established model for systems biology. We show that steady-state and kinetic pathway parameters that are essential for chemotactic performance are indeed temperature-compensated in the entire physiological range. Thermal robustness of steady-state pathway output is ensured at several levels by mutual compensation of temperature effects on activities of individual pathway components. Moreover, the effect of temperature on adaptation kinetics is counterbalanced by preprogrammed temperature dependence of enzyme synthesis and stability to achieve nearly optimal performance at the growth temperature. Similar compensatory mechanisms are expected to ensure thermal robustness in other systems.

Precision and kinetics of adaptation in bacterial chemotaxis

The chemotaxis network of the bacterium Escherichia coli is perhaps the most studied model for adaptation of a signaling system to persistent stimuli. Although adaptation in this system is generally considered to be precise, there has been little effort to quantify this precision, or to understand how and when precision fails. Using a Förster resonance energy transfer-based reporter of signaling activity, we undertook a systematic study of adaptation kinetics and precision in E. coli cells expressing a single type of chemoreceptor (Tar). Quantifiable loss of precision of adaptation was observed at levels of the attractant MeAsp as low 10 μM, with pronounced differences in both kinetics and precision of adaptation between addition and removal of attractant. Quantitative modeling of the kinetic data suggests that loss of precise adaptation is due to a slowing of receptor methylation as available modification sites become scarce. Moreover, the observed kinetics of adaptation imply large cell-to-cell variation in adaptation rates-potentially providing genetically identical cells with the ability to "hedge their bets" by pursuing distinct chemotactic strategies.

Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis

In chemotaxis of Escherichia coli and other bacteria, extracellular stimuli are perceived by transmembrane receptors that bind their ligands either directly, or indirectly through periplasmic-binding proteins (BPs). As BPs are also involved in ligand uptake, they provide a link between chemotaxis and nutrient utilization by cells. However, signalling by indirectly binding ligands remains much less understood than signalling by directly binding ligands. Here, we compared intracellular responses mediated by both types of ligands and developed a new mathematical model for signalling by indirectly binding ligands. We show that indirect binding allows cells to better control sensitivity to specific ligands in response to their nutrient environment and to coordinate chemotaxis with ligand transport, but at the cost of the dynamic range being much narrower than for directly binding ligands. We further demonstrate that signal integration by the chemosensory complexes does not depend on the type of ligand. Overall, our data suggest that the distinction between signalling by directly and indirectly binding ligands is more physiologically important than the traditional distinction between high- and low-abundance receptors.

Membrane thickness cue for cold sensing in a bacterium

Thermosensors are ubiquitous integral membrane proteins found in all kinds of life. They are involved in many physiological roles, including membrane remodeling, chemotaxis, touch, and pain [1-3], but, the mechanism by which their transmembrane (TM) domains transmit temperature signals is largely unknown. The histidine kinase DesK from Bacillus subtilis is the paradigmatic example of a membrane-bound thermosensor suited to remodel membrane fluidity when the temperature drops below approximately 30°C [1, 4] providing, thus, a tractable system for investigating the mechanism of TM-mediated input-output control of thermal adaptation. Here we show that the multimembrane-spanning domain from DesK can be simplified into a chimerical single-membrane-spanning minimal sensor (MS) that fully retains, in vivo and in vitro, the sensing properties of the parental system. The MS N terminus contains three hydrophilic amino acids near the lipid-water interface creating an instability hot spot. Mutational analysis of this boundary-sensitive beacon revealed that membrane thickness controls the signaling state of the sensor by dictating the hydration level of the metastable hydrophilic spot. Guided by these results we biochemically demonstrated that the MS signal transmission activity is sensitive to bilayer thickness. Membrane thickness could be a general cue for sensing temperature in many organisms.

Coupling metabolism and chemotaxis-dependent behaviours by energy taxis receptors

Bacteria have evolved the ability to monitor changes in various physico-chemical parameters and to adapt their physiology and metabolism by implementing appropriate cellular responses to these changes. Energy taxis is a metabolism-dependent form of taxis and is the directed movement of motile bacteria in gradients of physico-chemical parameters that affect metabolism. Energy taxis has been described in diverse bacterial species and several dedicated energy sensors have been identified. The molecular mechanism of energy taxis has not been studied in as much detail as chemotaxis, but experimental evidence indicates that this behaviour differs from metabolism-independent taxis only by the presence of dedicated energy taxis receptors. Energy taxis receptors perceive changes in energy-related parameters, including signals related to the redox and/or intracellular energy status of the cell. The best-characterized energy taxis receptors are those that sense the redox state of the electron transport chain via non-covalently bound FAD cofactors. Other receptors shown to mediate energy taxis lack any recognizable redox cofactor or conserved energy-sensing motif, and some have been suggested to monitor changes in the proton motive force. The exact energy-sensing mechanism(s) involved are yet to be elucidated for most of these energy sensors. By monitoring changes in energy-related parameters, energy taxis receptors allow cells to couple motility behaviour with metabolism under diverse environmental conditions. Energy taxis receptors thus provide fruitful models to decipher how cells integrate sensory behaviours with metabolic activities.

Responses of Escherichia coli bacteria to two opposing chemoattractant gradients depend on the chemoreceptor ratio

Escherichia coli chemotaxis has long served as a simple model of environmental signal processing, and bacterial responses to single chemical gradients are relatively well understood. Less is known about the chemotactic behavior of E. coli in multiple chemical gradients. In their native environment, cells are often exposed to multiple chemical stimuli. Using a recently developed microfluidic chemotaxis device, we exposed E. coli cells to two opposing but equally potent gradients of major attractants, methyl-aspartate and serine. The responses of E. coli cells demonstrated that chemotactic decisions depended on the ratio of the respective receptor number of Tar/Tsr. In addition, the ratio of Tar to Tsr was found to vary with cells' growth conditions, whereby it depended on the culture density but not on the growth duration. These results provide biological insights into the decision-making processes of chemotactic bacteria that are subjected to multiple chemical stimuli and demonstrate the importance of the cellular microenvironment in determining phenotypic behavior.

Information processing and signal integration in bacterial quorum sensing

Bacteria communicate using secreted chemical signaling molecules called autoinducers in a process known as quorum sensing. The quorum-sensing network of the marine bacterium Vibrio harveyi uses three autoinducers, each known to encode distinct ecological information. Yet how cells integrate and interpret the information contained within these three autoinducer signals remains a mystery. Here, we develop a new framework for analyzing signal integration on the basis of information theory and use it to analyze quorum sensing in V. harveyi. We quantify how much the cells can learn about individual autoinducers and explain the experimentally observed input–output relation of the V. harveyi quorum-sensing circuit. Our results suggest that the need to limit interference between input signals places strong constraints on the architecture of bacterial signal-integration networks, and that bacteria probably have evolved active strategies for minimizing this interference. Here, we analyze two such strategies: manipulation of autoinducer production and feedback on receptor number ratios.

A mechanism for precision-sensing via a gradient-sensing pathway: a model of Escherichia coli thermotaxis

Thermotaxis is the phenomenon where an organism directs its movement toward its preferred temperature. So far, the molecular origin for this precision-sensing behavior remains a puzzle. We propose a model of Escherichia coli thermotaxis and show that the precision-sensing behavior in E. coli thermotaxis can be carried out by the gradient-sensing chemotaxis pathway under two general conditions. First, the thermosensor response to temperature is inverted by its internal adaptation state. For E. coli, chemoreceptor Tar changes from a warm sensor to a cold sensor on increase of its methylation level. Second, temperature directly affects the adaptation kinetics. The adapted activity in E. coli increases with temperature in contrast to the perfect adaptation to chemical stimuli. Given these two conditions, E. coli thermotaxis is achieved by the cryophilic and thermophilic responses for temperature above and below a critical temperature Tc, which is encoded by internal pathway parameters. Our model results are supported by both experiments with adaptation-disabled mutants and the recent temperature impulse response measurements for wild-type cells. Tc is predicted to decrease with the background attractant concentration. This mechanism for precision sensing in an adaptive gradient-sensing system may apply to other organisms, such as Dictyostelium discoideum and Caenorhabditis elegans.

Structural plasticity and catalysis regulation of a thermosensor histidine kinase

Temperature sensing is essential for the survival of living cells. A major challenge is to understand how a biological thermometer processes thermal information to optimize cellular functions. Using structural and biochemical approaches, we show that the thermosensitive histidine kinase, DesK, from Bacillus subtilis is cold-activated through specific interhelical rearrangements in its central four-helix bundle domain. As revealed by the crystal structures of DesK in different functional states, the plasticity of this helical domain influences the catalytic activities of the protein, either by modifying the mobility of the ATP-binding domains for autokinase activity or by modulating binding of the cognate response regulator to sustain the phosphotransferase and phosphatase activities. The structural and biochemical data suggest a model in which the transmembrane sensor domain of DesK promotes these structural changes through conformational signals transmitted by the membrane-connecting two-helical coiled-coil, ultimately controlling the alternation between output autokinase and phosphatase activities. The structural comparison of the different DesK variants indicates that incoming signals can take the form of helix rotations and asymmetric helical bends similar to those reported for other sensing systems, suggesting that a similar switching mechanism could be operational in a wide range of sensor histidine kinases.

Microbial thermosensors

Temperature is among the most important of the parameters that free-living microbes monitor. Microbial physiology needs to be readjusted in response to sudden temperature changes. When the ambient temperature rises or drops to potentially harmful levels, cells mount protective stress responses--so-called heat or cold shock responses, respectively. Pathogenic microorganisms often respond to a temperature of around 37 degrees C by inducing virulence gene expression. There are two main ways in which temperature can be measured. Often, the consequences of a sudden temperature shift are detected. Such indirect signals are known to be the accumulation of denatured proteins (heat shock) or stalled ribosomes (cold shock). However, this article focuses solely on direct thermosensors. Since the conformation of virtually every biomolecule is susceptible to temperature changes, primary sensors include DNA, RNA, proteins and lipids.