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

Potassium-mediated bacterial chemotactic response

Bacteria in biofilms secrete potassium ions to attract free swimming cells. However, the basis of chemotaxis to potassium remains poorly understood. Here, using a microfluidic device, we found that Escherichia coli can rapidly accumulate in regions of high potassium concentration on the order of millimoles. Using a bead assay, we measured the dynamic response of individual flagellar motors to stepwise changes in potassium concentration, finding that the response resulted from the chemotaxis signaling pathway. To characterize the chemotactic response to potassium, we measured the dose-response curve and adaptation kinetics via an Förster resonance energy transfer (FRET) assay, finding that the chemotaxis pathway exhibited a sensitive response and fast adaptation to potassium. We further found that the two major chemoreceptors Tar and Tsr respond differently to potassium. Tar receptors exhibit a biphasic response, whereas Tsr receptors respond to potassium as an attractant. These different responses were consistent with the responses of the two receptors to intracellular pH changes. The sensitive response and fast adaptation allow bacteria to sense and localize small changes in potassium concentration. The differential responses of Tar and Tsr receptors to potassium suggest that cells at different growth stages respond differently to potassium and may have different requirements for potassium.

Collective responses of bacteria to a local source of conflicting effectors

To cope in complex environments, motile bacteria have developed a chemosensory system that integrates multiple cues and directs their motion toward regions that it deems favorable. However, we have a limited understanding of the principles that govern bacterial behavior in complex stimuli fields. Here, we followed the spatial redistribution of E. coli cells in perplexing environments created by a local source of both beneficial (nutrients) and hazardous (low pH or indole) effectors. We identified two fundamentally distinct collective responses: a ‘trade-off’ response, in which bacteria sharply accumulated at a distance from the source that reflected a trade-off between the propagating effectors, and a ‘bet-hedging’ response, in which part of the bacteria accumulated away from the source, avoiding the hazardous effector, while the other part evaded the repulsive force and accumulated at the source. In addition, we demonstrate that cells lacking the Tsr sensor swim toward both repellents and, surprisingly, even toward pH values well below 7. Using a numerical analysis, we could correlate the collective bacterial responses with fundamentally distinct chemotactic force fields created along the channel by the propagation of the effectors and their unique perception by the chemosensory system.

pH-taxis drives aerobic bacteria in duodenum to migrate into the pancreas with tumors

As oral or intestinal bacteria have been found in pancreatic cystic fluid and tumors, understanding bacterial migration from the duodenum into the pancreas via hepato-pancreatic duct is critical. Mathematical models of migration of aerobic bacteria from the duodenum to the pancreas with tumors were developed. Additionally, the bacterial distributions under the pH gradient and those under flow were measured in double-layer flow based microfluidic device and T-shaped cylinders. Migration of aerobic bacteria from the duodenum into pancreas is counteracted by bile and pancreatic juice flow but facilitated by pH-taxis from acidic duodenum fluid toward more favorable slightly alkaline pH in pancreatic juice. Additionally, the reduced flow velocity in cancer patients, due to compressed pancreatic duct by solid tumor, facilitates migration. Moreover, measured distribution of GFP E. coli under the pH gradient in a microfluidic device validated pH-tactic behaviors. Furthermore, Pseudomonas fluorescens in hydrochloride solution, but not in bicarbonate solution, migrated upstream against bicarbonate flow of > 20 μm/s, with an advancement at approximately 50 μm/s.

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.

The enigma of environmental pH sensing in plants

Environmental pH is a critical parameter for innumerable chemical reactions, myriad biological processes and all forms of life. The mechanisms that underlie the perception of external pH (pH_e) have been elucidated in detail for bacteria, fungi and mammalian cells; however, little information is available on whether and, if so, how pH_e is perceived by plants. This is particularly surprising since hydrogen ion activity of the substrate is of paramount significance for plants, governing the availability of mineral nutrients, the structure of the soil microbiome and the composition of natural plant communities. Rapid changes in soil pH require constant readjustment of nutrient acquisition strategies, which is associated with dynamic alterations in gene expression. Referring to observations made in diverse experimental set-ups that unambiguously show that pH_e per se affects gene expression, we hypothesize that sensing of pH_e in plants is mandatory to prioritize responses to various simultaneously received environmental cues.

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.

FRET Analysis of the Chemotaxis Pathway Response

Most motile bacteria follow spatial gradients of chemical and physical stimuli in their environment. In Escherichia coli and other bacteria, the best characterized chemotaxis is in gradients of amino acids or sugars, but other physiological stimuli such as pH, osmolarity, redox potentials, and temperature are also known to elicit tactic responses. These multiple environmental stimuli are integrated and processed within a highly sophisticated chemotaxis network to generate coordinated chemotaxis behavior, which features high sensitivity, a wide dynamic range, and robustness against variations in background stimulation, protein levels, and temperature. Although early studies relied on behavioral analyses to characterize chemotactic responses in vivo, or on biochemical assays to study the pathway in vitro, we describe here a method to directly measure the intracellular pathway response using Förster resonance energy transfer (FRET). In E. coli, the most commonly used form of the FRET assay relies on the interaction between the phosphorylated response regulator CheY and its phosphatase CheZ to quantify activity of the histidine kinase CheA. We further describe a FRET assay for Bacillus subtilis, which employs CheY and the motor-associated phosphatase FliY as a FRET pair. In particular, we highlight the use of FRET to quantify pathway properties, including signal amplification, dynamic range, and kinetics of adaptation.

A coordinated sequence of distinct flagellar waveforms enables a sharp flagellar turn mediated by squid sperm pH-taxis

Animal spermatozoa navigate by sensing ambient chemicals to reach the site of fertilization. Generally, such chemicals derive from the female reproductive organs or cells. Exceptionally, squid spermatozoa mutually release and perceive carbon dioxide to form clusters after ejaculation. We previously identified the pH-taxis by which each spermatozoon can execute a sharp turn, but how flagellar dynamics enable this movement remains unknown. Here, we show that initiation of the turn motion requires a swim down a steep proton gradient (a theoretical estimation of ≥0.025 pH/s), crossing a threshold pH value of ~5.5. Time-resolved kinematic analysis revealed that the turn sequence results from the rhythmic exercise of two flagellar motions: a stereotypical flagellar ‘bent-cane’ shape followed by asymmetric wave propagation, which enables a sharp turn in the realm of low Reynolds numbers. This turning episode is terminated by an ‘overshoot’ trajectory that differs from either straight-line motility or turning. As with bidirectional pH-taxes in some bacteria, squid spermatozoa also showed repulsion from strong acid conditions with similar flagellar kinematics as in positive pH-taxis. These findings indicate that squid spermatozoa might have a unique reorientation mechanism, which could be dissimilar to that of classical egg-guided sperm chemotaxis in other marine invertebrates.

Merging orthogonal microfluidic flows to generate multi-profile concentration gradients

This work describes a novel microfluidic device capable of generating multi-profile gradients that include sigmoidal, parabolic, and exponential concentration variations across its main channel.

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.

pH-Taxis of Biohybrid Microsystems

The last decade has seen an increasing number of studies developing bacteria and other cell-integrated biohybrid microsystems. However, the highly stochastic motion of these microsystems severely limits their potential use. Here, we present a method that exploits the pH sensing of flagellated bacteria to realize robust drift control of multi-bacteria propelled microrobots. Under three specifically configured pH gradients, we demonstrate that the microrobots exhibit both unidirectional and bidirectional pH-tactic behaviors, which are also observed in free-swimming bacteria. From trajectory analysis, we find that the swimming direction and speed biases are two major factors that contribute to their tactic drift motion. The motion analysis of microrobots also sheds light on the propulsion dynamics of the flagellated bacteria as bioactuators. It is expected that similar driving mechanisms are shared among pH-taxis, chemotaxis, and thermotaxis. By identifying the mechanism that drives the tactic behavior of bacteria-propelled microsystems, this study opens up an avenue towards improving the control of biohybrid microsystems. Furthermore, assuming that it is possible to tune the preferred pH of bioactuators by genetic engineering, these biohybrid microsystems could potentially be applied to sense the pH gradient induced by cancerous cells in stagnant fluids inside human body and realize targeted drug delivery.

Bacterial chemoreceptors and chemoeffectors

Bacteria use chemotaxis signaling pathways to sense environmental changes. Escherichia coli chemotaxis system represents an ideal model that illustrates fundamental principles of biological signaling processes. Chemoreceptors are crucial signaling proteins that mediate taxis toward a wide range of chemoeffectors. Recently, in deep study of the biochemical and structural features of chemoreceptors, the organization of higher-order clusters in native cells, and the signal transduction mechanisms related to the on-off signal output provides us with general insights to understand how chemotaxis performs high sensitivity, precise adaptation, signal amplification, and wide dynamic range. Along with the increasing knowledge, bacterial chemoreceptors can be engineered to sense novel chemoeffectors, which has extensive applications in therapeutics and industry. Here we mainly review recent advances in the E. coli chemotaxis system involving structure and organization of chemoreceptors, discovery, design, and characterization of chemoeffectors, and signal recognition and transduction mechanisms. Possible strategies for changing the specificity of bacterial chemoreceptors to sense novel chemoeffectors are also discussed.

Predicting chemical environments of bacteria from receptor signaling

Sensory systems have evolved to respond to input stimuli of certain statistical properties, and to reliably transmit this information through biochemical pathways. Hence, for an experimentally well-characterized sensory system, one ought to be able to extract valuable information about the statistics of the stimuli. Based on dose-response curves from in vivo fluorescence resonance energy transfer (FRET) experiments of the bacterial chemotaxis sensory system, we predict the chemical gradients chemotactic Escherichia coli cells typically encounter in their natural environment. To predict average gradients cells experience, we revaluate the phenomenological Weber's law and its generalizations to the Weber-Fechner law and fold-change detection. To obtain full distributions of gradients we use information theory and simulations, considering limitations of information transmission from both cell-external and internal noise. We identify broad distributions of exponential gradients, which lead to log-normal stimuli and maximal drift velocity. Our results thus provide a first step towards deciphering the chemical nature of complex, experimentally inaccessible cellular microenvironments, such as the human intestine.

Outside the laboratory, bacteria live in complex microenvironments characterized by competition for space and available nutrients. Although often inaccessible by experiments, understanding the spatio-temporal dynamics of bacterial microenvironments is biomedically important. For instance, the chemical environment that symbiotic Escherichia coli encounter in the human gut relates to health of the gastrointestinal tract, gut metabolism, immune response, and tissue homeostasis. Other complex microenvironments include soil and biofilms. Assuming that bacterial sensory systems have evolved to optimally sense typical gradients, we treat signaling data, the signaling pathway with its architecture and reaction rates, and computer simulations of swimming bacteria in different gradients as “prior knowledge” to “reverse engineer” E. coli's habitat. Our identified gradients are exponentially shaped with wide-ranging rate values. These microenvironments most likely stem from local fluctuating nutrient sources and degradation by competing species, in which bacteria have evolved to swim with optimal performance.

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.