Reconstitution of signaling in bacterial chemotaxis

Dynamic Adaptation in Extant Porins Facilitates Antibiotic Tolerance in Energetic Escherichia coli

Bacteria can tolerate antibiotics despite lacking the genetic components for resistance. The prevailing notion is that tolerance results from depleted cellular energy or cell dormancy. In contrast to this view, many cells in the tolerant population of Escherichia coli can exhibit motility - a phenomenon that requires cellular energy, specifically, the proton-motive force (PMF). As these motile-tolerant cells are challenging to isolate from the heterogeneous tolerant population, their survival mechanism is unknown. Here, we discovered that motile bacteria segregate themselves from the tolerant population under micro-confinement, owing to their unique ability to penetrate micron-sized channels. Single-cell measurements on the motile-tolerant population showed that the cells retained a high PMF, but they did not survive through active efflux alone. By utilizing growth assays, single-cell fluorescence studies, and chemotaxis assays, we showed that the cells survived by dynamically inhibiting the function of existing porins in the outer membrane. A drug transport model for porin-mediated intake and efflux pump-mediated expulsion suggested that energetic tolerant cells withstand antibiotics by constricting their porins. The novel porin adaptation we have uncovered is independent of gene expression changes and may involve electrostatic modifications within individual porins to prevent extracellular ligand entry.

Escherichia coli chemotaxis to competing stimuli in a microfluidic device with a constant gradient

In natural systems bacteria are exposed to many chemical stimulants; some attract chemotactic bacteria as they promote survival, while others repel bacteria because they inhibit survival. When faced with a mixture of chemoeffectors, it is not obvious which direction the population will migrate. Predicting this direction requires an understanding of how bacteria process information about their surroundings. We used a multiscale mathematical model to relate molecular level details of their two-component signaling system to the probability that an individual cell changes its swimming direction to the chemotactic velocity of a bacterial population. We used a microfluidic device designed to maintain a constant chemical gradient to compare model predictions to experimental observations. We obtained parameter values for the multiscale model of Escherichia coli chemotaxis to individual stimuli, α-methylaspartate and nickel ion, separately. Then without any additional fitting parameters, we predicted bacteria response to chemoeffector mixtures. Migration of E. coli toward α-methylaspartate was modulated by adding increasing concentrations of nickel ion. Thus, the migration direction was controlled by the relative concentrations of competing chemoeffectors in a predictable way. This study demonstrated the utility of a multiscale model to predict the migration direction of bacteria in the presence of competing chemoeffectors. This article is protected by copyright. All rights reserved.

The Periplasmic Oxidoreductase DsbA Is Required for Virulence of the Phytopathogen Dickeya solani

In bacteria, the DsbA oxidoreductase is a crucial factor responsible for the introduction of disulfide bonds to extracytoplasmic proteins, which include important virulence factors. A lack of proper disulfide bonds frequently leads to instability and/or loss of protein function; therefore, improper disulfide bonding may lead to avirulent phenotypes. The importance of the DsbA function in phytopathogens has not been extensively studied yet. Dickeya solani is a bacterium from the Soft Rot Pectobacteriaceae family which is responsible for very high economic losses mainly in potato. In this work, we constructed a D. solani dsbA mutant and demonstrated that a lack of DsbA caused a loss of virulence. The mutant bacteria showed lower activities of secreted virulence determinants and were unable to develop disease symptoms in a potato plant. The SWATH-MS-based proteomic analysis revealed that the dsbA mutation led to multifaceted effects in the D. solani cells, including not only lower levels of secreted virulence factors, but also the induction of stress responses. Finally, the outer membrane barrier seemed to be disturbed by the mutation. Our results clearly demonstrate that the function played by the DsbA oxidoreductase is crucial for D. solani virulence, and a lack of DsbA significantly disturbs cellular physiology.

Surveying a Swarm: Experimental Techniques to Establish and Examine Bacterial Collective Motion

The survival and successful spread of many bacterial species hinges on their mode of motility. One of the most distinct of these is swarming, a collective form of motility where a dense consortium of bacteria employ flagella to propel themselves across a solid surface. Surface environments pose unique challenges, derived from higher surface friction/tension and insufficient hydration. Bacteria have adapted by deploying an array of mechanisms to overcome these challenges. Beyond allowing bacteria to colonize new terrain in the absence of bulk liquid, swarming also bestows faster speeds and enhanced antibiotic resistance to the collective. These crucial attributes contribute to the dissemination, and in some cases pathogenicity, of an array of bacteria. This mini-review highlights; 1) aspects of swarming motility that differentiates it from other methods of bacterial locomotion. 2) Facilitatory mechanisms deployed by diverse bacteria to overcome different surface challenges. 3) The (often difficult) approaches required to cultivate genuine swarmers. 4) The methods available to observe and assess the various facets of this collective motion, as well as the features exhibited by the population as a whole.

Curved ratchets improve bacteria rectification in microfluidic devices

We study how bacteria rectification in microfluidics devices can be optimized by performing experiments with eight ratchets of different shape and size. Results show that curved ratchets perform best and that their radius of curvature influences how well they perform, as it affects the time bacteria spend on the ratchet surface. We find that the optimal bacterial ratchet is a 60μm radius semicircle witch 15μm concavities. We also show that the angle at which bacteria leave the ratchets can play an important role in their efficiency. Lastly, we reproduce our experimental conditions in a simple numerical simulation to confirm our findings.

A virtual reality interface for the immersive manipulation of live microscopic systems

For more than three centuries we have been watching and studying microscopic phenomena behind a microscope. We discovered that cells live in a physical environment whose predominant factors are no longer those of our scale and for which we lack a direct experience and consequently a deep intuition. Here we demonstrate a new instrument which, by integrating holographic and virtual reality technologies, allows the user to be completely immersed in a dynamic virtual world which is a simultaneous replica of a real system under the microscope. We use holographic microscopy for fast 3D imaging and real-time rendering on a virtual reality headset. At the same time, hand tracking data is used to dynamically generate holographic optical traps that can be used as virtual projections of the user hands to interactively grab and manipulate ensembles of microparticles or living motile cells.

Bacterial flagellar motor as a multimodal biosensor

Bacterial Flagellar Motor is one of nature's rare rotary molecular machines. It enables bacterial swimming and it is the key part of the bacterial chemotactic network, one of the best studied chemical signalling networks in biology, which enables bacteria to direct its movement in accordance with the chemical environment. The network can sense down to nanomolar concentrations of specific chemicals on the time scale of seconds. Motor's rotational speed is linearly proportional to the electrochemical gradients of either proton or sodium driving ions, while its direction is regulated by the chemotactic network. Recently, it has been discovered that motor is also a mechanosensor. Given these properties, we discuss the motor's potential to serve as a multifunctional biosensor and a tool for characterising and studying the external environment, the bacterial physiology itself and single molecular motor biophysics.

A transition to stable one-dimensional swimming enhances E. coli motility through narrow channels

Living organisms often display adaptive strategies that allow them to move efficiently even in strong confinement. With one single degree of freedom, the angle of a rotating bundle of flagella, bacteria provide one of the simplest examples of locomotion in the living world. Here we show that a purely physical mechanism, depending on a hydrodynamic stability condition, is responsible for a confinement induced transition between two swimming states in E. coli. While in large channels bacteria always crash onto confining walls, when the cross section falls below a threshold, they leave the walls to move swiftly on a stable swimming trajectory along the channel axis. We investigate this phenomenon for individual cells that are guided through a sequence of micro-fabricated tunnels of decreasing cross section. Our results challenge current theoretical predictions and suggest effective design principles for microrobots by showing that motility based on helical propellers provides a robust swimming strategy for exploring narrow spaces.

Investigating Flagella-Driven Motility in Escherichia coli by Applying Three Established Techniques in a Series

Motility is crucial to the survival and success of many bacterial species. Many methodologies exist to exploit motility to understand signaling pathways, to elucidate the function and assembly of flagellar parts, and to examine and understand patterns of movement. Here we demonstrate a combination of three of these methodologies. Motility in soft agar is the oldest, offering a strong selection for isolating gain-of-function suppressor mutations in motility-impaired strains, where motility is restored through a second mutation. The cell-tethering technique, first employed to demonstrate the rotary nature of the flagellar motor, can be used to assess the impact of signaling effectors on the motor speed and its ability to switch rotational direction. The "border-crossing" assay is more recent, where swimming bacteria can be primed to transition into moving collectively as a swarm. In combination, these protocols represent a systematic and powerful approach to identifying components of the motility machinery, and to characterizing their role in different facets of swimming and swarming. They can be easily adapted to study motility in other bacterial species.

Under Elevated c-di-GMP in Escherichia coli, YcgR Alters Flagellar Motor Bias and Speed Sequentially, with Additional Negative Control of the Flagellar Regulon via the Adaptor Protein RssB

In Escherichia coli and Salmonella, the c-di-GMP effector YcgR inhibits flagellar motility by interacting directly with the motor to alter both its bias and speed. Here, we demonstrate that in both of these bacteria, YcgR acts sequentially, altering motor bias first and then decreasing motor speed. We show that when c-di-GMP levels are high, deletion of ycgR restores wild-type motor behavior in E. coli, indicating that YcgR is the only motor effector in this bacterium. Yet, motility and chemotaxis in soft agar do not return to normal, suggesting that there is a second mechanism that inhibits motility under these conditions. In Salmonella, c-di-GMP-induced synthesis of extracellular cellulose has been reported to entrap flagella and to be responsible for the YcgR-independent motility defect. We found that this is not the case in E. coli Instead, we found through reversion analysis that deletion of rssB, which codes for a response regulator/adaptor protein that normally directs ClpXP protease to target σ^S for degradation, restored wild-type motility in the ycgR mutant. Our data suggest that high c-di-GMP levels may promote altered interactions between these proteins to downregulate flagellar gene expression.IMPORTANCE Flagellum-driven motility has been studied in E. coli and Salmonella for nearly half a century. Over 60 genes control flagellar assembly and function. The expression of these genes is regulated at multiple levels in response to a variety of environmental signals. Cues that elevate c-di-GMP levels, however, inhibit motility by direct binding of the effector YcgR to the flagellar motor. In this study conducted mainly in E. coli, we show that YcgR is the only effector of motor control and tease out the order of YcgR-mediated events. In addition, we find that the σ^S regulator protein RssB contributes to negative regulation of flagellar gene expression when c-di-GMP levels are elevated.

Invariance properties of bacterial random walks in complex structures

Motile cells often explore natural environments characterized by a high degree of structural complexity. Moreover cell motility is also intrinsically noisy due to spontaneous random reorientations and speed fluctuations. This interplay of internal and external noise sources gives rise to a complex dynamical behavior that can be strongly sensitive to details and hard to model quantitatively. In striking contrast to this general picture we show that the mean residence time of swimming bacteria inside artificial complex microstructures is quantitatively predicted by a generic invariance property of random walks. We find that while external shape and internal disorder have dramatic effects on the distributions of path lengths and residence times, the corresponding mean values are constrained by the sole free surface to perimeter ratio. As a counterintuitive consequence, bacteria escape faster from structures with higher density of obstacles due to the lower accessible surface.

It has been previously shown theoretically that the average path length of random walks inside a closed domain is invariant. Here the authors demonstrate that this invariance property can be used to predict the mean residence time of swimming bacteria exploring structured micro-environments.

3D dynamics of bacteria wall entrapment at a water-air interface

Swimming bacteria can be trapped for prolonged times at the surface of an impenetrable boundary. The subsequent surface confined motility is found to be very sensitive to the physico-chemical properties of the interfaces which determine the boundary conditions for the flow. The quantitative understanding of this complex dynamics requires detailed and systematic experimental data to validate theoretical models for both flagellar propulsion and interfacial dynamics. Using a combination of optical trapping and holographic imaging we study the 3D dynamics of wall entrapment of swimming bacteria that are sequentially released towards a surfactant-covered liquid-air interface. We find that an incompressible surfactant model for the interface quantitatively accounts for the observed normal and tangential speed of bacteria as they approach the boundary. Surprisingly we also find that, although bacteria circulate over the air phase in counterclockwise circular trajectories, typical of free-slip interfaces, the body axis is still tilted "nose down" as found for no-slip interfaces.

Dynamic density shaping of photokinetic E. coli

Many motile microorganisms react to environmental light cues with a variety of motility responses guiding cells towards better conditions for survival and growth. The use of spatial light modulators could help to elucidate the mechanisms of photo-movements while, at the same time, providing an efficient strategy to achieve spatial and temporal control of cell concentration. Here we demonstrate that millions of bacteria, genetically modified to swim smoothly with a light controllable speed, can be arranged into complex and reconfigurable density patterns using a digital light projector. We show that a homogeneous sea of freely swimming bacteria can be made to morph between complex shapes. We model non-local effects arising from memory in light response and show how these can be mitigated by a feedback control strategy resulting in the detailed reproduction of grayscale density images.

Many bacteria can move in response to environmental signals. This helps guide them towards better conditions for growth and survival. Escherichia coli is a bacterium that can swim quickly through liquid, using tiny propeller-like structures that rotate many times per second. These ‘propellers’ are powered by a cellular motor, called the flagellar motor, which similar to an electric motor, requires an energy source to drive movement.

Proteorhodopsin, a protein originally isolated from free-swimming micro-organisms in the ocean, is an alternative energy source that helps bacteria move. The protein is located close to the surface of the cell, where it acts like a solar panel and captures energy from light. In cells powered by proteorhodopsin, the intensity of light from their environment determines their swimming speed: brighter light means faster movement, and less light, slower movement. Proteorhodopsin is now also a useful tool in the laboratory. For example, genetically engineering bacteria to produce proteorhodopsin provides a way to control their movement remotely, using a light source.

Swimming bacteria, much like cars in city traffic, are known to accumulate in areas where their speed decreases. By controlling swimming speed with proteorhodopsin, researchers can manipulate the local density of bacteria simply by projecting different patterns of light.

To study the factors influencing this phenomenon, Frangipane et al. used genetically modified E. coli that could respond to light via proteorhodopsin to make layers of cells that could then have light patterns projected onto them. The results showed that the bacteria responded slowly to these stimuli, which was the main factor limiting the resolution of the final pattern they formed. A simple feedback mechanism, which compared the pattern formed by the cells to the desired image and updated the projected light accordingly, was enough to solve this problem. This way, the layers of E.coli could be turned into a near-perfect copy of the original image.

This work allows us to control the movement of large populations of bacteria more precisely than ever before. This could be extremely valuable for building the next generation of microscopic devices. For example, bacteria could be made to surround a larger object such as a machine part or a drug carrier, and then used as living propellers to transport it where it is needed.

Light controlled 3D micromotors powered by bacteria

Self-propelled bacteria can be integrated into synthetic micromachines and act as biological propellers. So far, proposed designs suffer from low reproducibility, large noise levels or lack of tunability. Here we demonstrate that fast, reliable and tunable bio-hybrid micromotors can be obtained by the self-assembly of synthetic structures with genetically engineered biological propellers. The synthetic components consist of 3D interconnected structures having a rotating unit that can capture individual bacteria into an array of microchambers so that cells contribute maximally to the applied torque. Bacterial cells are smooth swimmers expressing a light-driven proton pump that allows to optically control their swimming speed. Using a spatial light modulator, we can address individual motors with tunable light intensities allowing the dynamic control of their rotational speeds. Applying a real-time feedback control loop, we can also command a set of micromotors to rotate in unison with a prescribed angular speed.

Nitric Oxide Regulation of H-NOX Signaling Pathways in Bacteria

Nitric oxide (NO) is a freely diffusible, radical gas that has now been established as an integral signaling molecule in eukaryotes and bacteria. It has been demonstrated that NO signaling is initiated upon ligation to the heme iron of an H-NOX domain in mammals and in some bacteria. Bacterial H-NOX proteins have been found to interact with enzymes that participate in signaling pathways and regulate bacterial processes such as quorum sensing, biofilm formation, and symbiosis. Here, we review the biochemical characterization of these signaling pathways and, where available, describe how ligation of NO to H-NOX specifically regulates the activity of these pathways and their associated bacterial phenotypes.

Quantitative analysis of chemotaxis towards toluene by Pseudomonas putida in a convection-free microfluidic device

Chemotaxis has been shown to be beneficial for the migration of soil-inhabiting bacteria towards industrial chemical pollutants, which they degrade. Many studies have demonstrated the importance of this microbial property under various circumstances; however, few quantitative analyses have been undertaken to measure the two essential parameters that characterize the chemotaxis of bioremediation bacteria: the chemotactic sensitivity coefficient χ(0) and the chemotactic receptor constant K(c). The main challenge to determine these parameters is that χ(0) and K(c) are coupled together in non-linear mathematical models used to evaluate them. In this study we developed a method to accurately measure these parameters for Pseudomonas putida in the presence of toluene, an important pollutant in groundwater contamination. Our approach uses a multilayer microfluidic device to expose bacteria to a convection-free linear chemical gradient of toluene that is stable over time. The bacterial distribution within the gradient is measured in terms of fluorescence intensity, and is then used to fit the parameters Kc and χ(0) with mathematical models. Critically, bacterial distributions under chemical gradients at two different concentrations were used to solve for both parameters independently. To validate the approach, the chemotaxis parameters of Escherichia coli strains towards α-methylaspartate were experimentally derived and were found to be consistent with published results from related work.

Cell division resets polarity and motility for the bacterium Myxococcus xanthus

Links between cell division and other cellular processes are poorly understood. It is difficult to simultaneously examine division and function in most cell types. Most of the research probing aspects of cell division has experimented with stationary or immobilized cells or distinctly asymmetrical cells. Here we took an alternative approach by examining cell division events within motile groups of cells growing on solid medium by time-lapse microscopy. A total of 558 cell divisions were identified among approximately 12,000 cells. We found an interconnection of division, motility, and polarity in the bacterium Myxococcus xanthus. For every division event, motile cells stop moving to divide. Progeny cells of binary fission subsequently move in opposing directions. This behavior involves M. xanthus Frz proteins that regulate M. xanthus motility reversals but is independent of type IV pilus "S motility." The inheritance of opposing polarity is correlated with the distribution of the G protein RomR within these dividing cells. The constriction at the point of division limits the intracellular distribution of RomR. Thus, the asymmetric distribution of RomR at the parent cell poles becomes mirrored at new poles initiated at the site of division.

A nitric oxide-responsive quorum sensing circuit in Vibrio harveyi regulates flagella production and biofilm formation

Cell signaling plays an important role in the survival of bacterial colonies. They use small molecules to coordinate gene expression in a cell density dependent manner. This process, known as quorum sensing, helps bacteria regulate diverse functions such as bioluminescence, biofilm formation and virulence. In Vibrio harveyi, a bioluminescent marine bacterium, four parallel quorum-sensing systems have been identified to regulate light production. We have previously reported that nitric oxide (NO), through the H-NOX/HqsK quorum sensing pathway contributes to light production in V. harveyi through the LuxU/LuxO/LuxR quorum sensing pathway. In this study, we show that nitric oxide (NO) also regulates flagellar production and enhances biofilm formation. Our data suggest that V. harveyi is capable of switching between lifestyles to be able to adapt to changes in the environment.

Bacterial microsystems and microrobots

Microorganisms and specifically motile bacteria have been recently added to the list of micro-actuators typically considered for the implementation of microsystems and microrobots. Such trend has been motivated by the fact these microorganisms are self-powered actuators with overall sizes at the lower end of the micrometer range and which have proven to be extremely effective in low Reynolds number hydrodynamic regime of usually less than 10(-2). Furthermore, the various sensors or taxes in bacteria influencing their movements can also be exploited to perform tasks that were previously considered only for futuristic artificial microrobots. Bacterial implementations and related issues are not only reviewed, but this paper also proposes many techniques and approaches that can be considered as building blocks for the implementations of more sophisticated microsystems and microrobots.

Elucidation of the multiple roles of CheD in Bacillus subtilis chemotaxis

Chemotaxis by Bacillus subtilis requires the CheD protein for proper function. In a cheD mutant when McpB was the sole chemoreceptor in B. subtilis, chemotaxis to asparagine was quite good. When McpC was the sole chemoreceptor in a cheD mutant, chemotaxis to proline was very poor. The reason for the difference between the chemoreceptors is because CheD deamidates Q609 in McpC and does not deamidate McpB. When mcpC-Q609E is expressed as the sole chemoreceptor in a cheD background, chemotaxis is almost fully restored. Concomitantly, in vitro McpC activates the CheA kinase poorly, whereas McpC-Q609E activates it much more. Moreover, CheD, which activates chemoreceptors, binds better to McpC-Q609E compared with unmodified McpC. Using hydroxyl radical susceptibility in the presence or absence of CheD, the most likely sites of CheD binding were the modification sites where CheD, CheB and CheR carry out their catalytic activities. Thus, CheD appears to have two separate roles in B. subtilis chemotaxis - to bind to chemoreceptors to activate them as part of the CheC/CheD/CheYp adaptation system and to deamidate selected residues to activate the chemoreceptors and enable them to mediate amino acid chemotaxis.

A parallel diffusion-based microfluidic device for bacterial chemotaxis analysis

We developed a multiple-channel microfluidic device for bacterial chemotaxis detection. Some characteristics such as easy operation, parallel sample adding design and fast result readout make this device convenient for most biology labs. The characteristic feature of the design is the agarose gel channels, which serve as a semi-permeable membrane. They can stop the fluid flow and prevent bacteria getting across, but permit the diffusion of small molecules. In the device fabrication process a novel thermal-based method was used to control the shape of agarose gel in the microfluidic channel. The chemical gradient is established by diffusion which can be precisely controlled and measured. Combined with an 8-channel pipette, different attractants, repellent chemicals or different bacteria were analyzed by a two step operation with a readout time of one hour. This device may be useful in the high throughput detection of chemotaxis related molecules and genes.

Phase separation and rotor self-assembly in active particle suspensions

Adding a nonadsorbing polymer to passive colloids induces an attraction between the particles via the "depletion" mechanism. High enough polymer concentrations lead to phase separation. We combine experiments, theory, and simulations to demonstrate that using active colloids (such as motile bacteria) dramatically changes the physics of such mixtures. First, significantly stronger interparticle attraction is needed to cause phase separation. Secondly, the finite size aggregates formed at lower interparticle attraction show unidirectional rotation. These micro-rotors demonstrate the self-assembly of functional structures using active particles. The angular speed of the rotating clusters scales approximately as the inverse of their size, which may be understood theoretically by assuming that the torques exerted by the outermost bacteria in a cluster add up randomly. Our simulations suggest that both the suppression of phase separation and the self-assembly of rotors are generic features of aggregating swimmers and should therefore occur in a variety of biological and synthetic active particle systems.

Two component systems: physiological effect of a third component

Signal transduction systems mediate the response and adaptation of organisms to environmental changes. In prokaryotes, this signal transduction is often done through Two Component Systems (TCS). These TCS are phosphotransfer protein cascades, and in their prototypical form they are composed by a kinase that senses the environmental signals (SK) and by a response regulator (RR) that regulates the cellular response. This basic motif can be modified by the addition of a third protein that interacts either with the SK or the RR in a way that could change the dynamic response of the TCS module. In this work we aim at understanding the effect of such an additional protein (which we call "third component") on the functional properties of a prototypical TCS. To do so we build mathematical models of TCS with alternative designs for their interaction with that third component. These mathematical models are analyzed in order to identify the differences in dynamic behavior inherent to each design, with respect to functionally relevant properties such as sensitivity to changes in either the parameter values or the molecular concentrations, temporal responsiveness, possibility of multiple steady states, or stochastic fluctuations in the system. The differences are then correlated to the physiological requirements that impinge on the functioning of the TCS. This analysis sheds light on both, the dynamic behavior of synthetically designed TCS, and the conditions under which natural selection might favor each of the designs. We find that a third component that modulates SK activity increases the parameter space where a bistable response of the TCS module to signals is possible, if SK is monofunctional, but decreases it when the SK is bifunctional. The presence of a third component that modulates RR activity decreases the parameter space where a bistable response of the TCS module to signals is possible.

Ligand specificity determined by differentially arranged common ligand-binding residues in bacterial amino acid chemoreceptors Tsr and Tar

Escherichia coli has closely related amino acid chemoreceptors with distinct ligand specificity, Tar for l-aspartate and Tsr for l-serine. Crystallography of the ligand-binding domain of Tar identified the residues interacting with aspartate, most of which are conserved in Tsr. However, swapping of the nonconserved residues between Tsr and Tar did not change ligand specificity. Analyses with chimeric receptors led us to hypothesize that distinct three-dimensional arrangements of the conserved ligand-binding residues are responsible for ligand specificity. To test this hypothesis, the structures of the apo- and serine-binding forms of the ligand-binding domain of Tsr were determined at 1.95 and 2.5 Å resolutions, respectively. Some of the Tsr residues are arranged differently from the corresponding aspartate-binding residues of Tar to form a high affinity serine-binding pocket. The ligand-binding pocket of Tsr was surrounded by negatively charged residues, which presumably exclude negatively charged aspartate molecules. We propose that all these Tsr- and Tar-specific features contribute to specific recognition of serine and aspartate with the arrangement of the side chain of residue 68 (Asn in Tsr and Ser in Tar) being the most critical.

Mutational analysis of N381, a key trimer contact residue in Tsr, the Escherichia coli serine chemoreceptor

Chemoreceptors such as Tsr, the serine receptor, function in trimer-of-dimer associations to mediate chemotactic behavior in Escherichia coli. The two subunits of each receptor homodimer occupy different positions in the trimer, one at its central axis and the other at the trimer periphery. Residue N381 of Tsr contributes to trimer stability through interactions with its counterparts in a central cavity surrounded by hydrophobic residues at the trimer axis. To assess the functional role of N381, we created and characterized a full set of amino acid replacements at this Tsr residue. We found that every amino acid replacement at N381 destroyed Tsr function, and all but one (N381G) of the mutant receptors also blocked signaling by Tar, the aspartate chemoreceptor. Tar jamming reflects the formation of signaling-defective mixed trimers of dimers, and in vivo assays with a trifunctional cross-linking reagent demonstrated trimer-based interactions between Tar and Tsr-N381 mutants. Mutant Tsr molecules with a charged amino acid or proline replacement exhibited the most severe trimer formation defects. These trimer-defective receptors, as well as most of the trimer-competent mutant receptors, were unable to form ternary signaling complexes with the CheA kinase and with CheW, which couples CheA to receptor control. Some of the trimer-competent mutant receptors, particularly those with a hydrophobic amino acid replacement, may not bind CheW/CheA because they form conformationally frozen or distorted trimers. These findings indicate that trimer dynamics probably are important for ternary complex assembly and that N381 may not be a direct binding determinant for CheW/CheA at the trimer periphery.

In Rhodobacter sphaeroides, chemotactic operon 1 regulates rotation of the flagellar system 2

Rhodobacter sphaeroides is able to assemble two different flagella, the subpolar flagellum (Fla1) and the polar flagella (Fla2). In this work, we report the swimming behavior of R. sphaeroides Fla2(+) cells lacking each of the proteins encoded by chemotactic operon 1. A model proposing how these proteins control Fla2 rotation is presented.

Effective interactions between colloidal particles suspended in a bath of swimming cells

The dynamics of passive colloidal tracers in a bath of self-propelled particles is receiving a lot of attention in the context of nonequilibrium statistical mechanics. Here we demonstrate that active baths are also capable of mediating effective interactions between suspended bodies. In particular we observe that a bath of swimming bacteria gives rise to a short range attraction similar to depletion forces in equilibrium colloidal suspensions. Using numerical simulations and experiments we show how the features of this interaction arise from the combination of nonequilibrium dynamics (peculiar of bacterial baths) and excluded volume effects.

Protein footprinting in a complex milieu: identifying the interaction surfaces of the chemotaxis adaptor protein CheW

Characterizing protein-protein interactions in a biologically relevant context is important for understanding the mechanisms of signal transduction. Most signal transduction systems are membrane associated and consist of large multiprotein complexes that undergo rapid reorganization--circumstances that present challenges to traditional structure determination methods. To study protein-protein interactions in a biologically relevant complex milieu, we employed a protein footprinting strategy based on isotope-coded affinity tag (ICAT) reagents. ICAT reagents are valuable tools for proteomics. Here, we show their utility in an alternative application--they are ideal for protein footprinting in complex backgrounds because the affinity tag moiety allows for enrichment of alkylated species prior to analysis. We employed a water-soluble ICAT reagent to monitor cysteine accessibility and thereby to identify residues involved in two different protein-protein interactions in the Escherichia coli chemotaxis signaling system. The chemotaxis system is an archetypal transmembrane signaling pathway in which a complex protein superstructure underlies sophisticated sensory performance. The formation of this superstructure depends on the adaptor protein CheW, which mediates a functionally important bridging interaction between transmembrane receptors and histidine kinase. ICAT footprinting was used to map the surfaces of CheW that interact with the large multidomain histidine kinase CheA, as well as with the transmembrane chemoreceptor Tsr in native E. coli membranes. By leveraging the affinity tag, we successfully identified CheW surfaces responsible for CheA-Tsr interaction. The proximity of the CheA and Tsr binding sites on CheW suggests the formation of a composite CheW-Tsr surface for the recruitment of the signaling kinase to the chemoreceptor complex.

Idling time of motile bacteria contributes to retardation and dispersion in sand porous medium

The motility of microorganisms affects their transport in natural systems by altering their interactions with the solid phase of the soil matrix. To assess the effect of these interactions on transport parameters, a series of breakthrough curves (BTCs) for motile and nonmotile bacteria, including E. coli and P. putida species, were measured from a homogeneously packed sand column under three different interstitial velocities of 1 m/d, 5 m/d, and 10 m/d. BTCs for the nonmotile bacteria were nearly identical for all three flow rates, except that the recovery percentage at 1 m/d was reduced by 5% compared to the higher flow rates. In contrast, for the motile bacteria, the recovery percentages were not affected by flow rate, but their BTCs exhibited a higher degree of retardation and dispersion as the flow velocity decreased, which was consistent with increased idling times of the motile strains. The smooth-swimming mutant E. coli HCB437, which is unable to change its swimming direction after encountering the solid surfaces and thus has the largest idling time, also exhibited the greatest degree of retardation and dispersion. All of the experimental observations were compared to results from an advection-dispersion transport model with three fitting parameters: retardation factor (R), longitudinal dispersivity (α(L)), and attachment rate coefficient (k(att)). In addition, the single-collector efficiency (η₀) and collision efficiency (α) were calculated according to the colloid filtration theory (CFT), and confirmed that motile bacteria had lower collision efficiencies than nonmotile bacteria. This is consistent with previously reported observations that motile bacteria can avoid attachment to a solid surface by their active swimming capabilities. By quantifying the effect of bacterial motility on various transport parameters, more robust fate and transport models can be developed for decision-making related to environmental remediation strategies and risk assessment.

From SELEX to cell dual selections for synthetic riboswitches

Synthetic riboswitches have emerged as useful tools for controlling gene expression to reprogram cellular behavior. However, advancing beyond proof-of-principle experiments requires the ability to quickly generate new synthetic riboswitches from RNA libraries. In this chapter, we provide a step-by-step overview of the process of obtaining synthetic riboswitches for use in Escherichia coli, starting from a randomized RNA library.

Idling time of swimming bacteria near particulate surfaces contributes to apparent adsorption coefficients at the macroscopic scale under static conditions

Static capillary assays were performed to observe the distribution of Escherichia coli and several mutant strains at the interface between an aqueous solution and a Gelrite particulate suspension, used as a model porous medium. Motile smooth-swimming mutant bacteria (E. coli HCB437) accumulated at the interface, but did not penetrate very far into the Gelrite suspension. Motile wild-type bacteria (E. coli HCB1) penetrated much further than the smooth-swimming mutant, but did not accumulate to the same extent at the interface. Nonmotile tumbly mutant bacteria (E. coli HCB359) did not accumulate or penetrate to a significant degree. Computer simulations using a Monte Carlo algorithm, with input parameters based on bacterial swimming properties in static bulk aqueous systems, appeared to underestimate the bacterial idling time associated with solid surfaces. To account for physicochemical, biological and geometrical influences, an additional component of the bacterial idling time was included. The third component of the idling time was further analyzed semiquantitatively with a 1-D population-scale transport model with first-order association (k(on)) and dissociation (k(off)) adsorption-like kinetics. Computer simulation results suggested that this additional bacterial idling time not only increased the magnitudes of k(on) and k(off), but also enhanced the ratio of k(on) to k(off). This further implies that motile bacteria may tend to accumulate at the boundaries of low-permeable regions in groundwater systems, which is beneficial for bioremediation of residual contamination that may not be accessible by conventional remediation approaches.

Transverse bacterial migration induced by chemotaxis in a packed column with structured physical heterogeneity

The significance of chemotaxis in directing bacterial migration toward contaminants in natural porous media was investigated under groundwater flow conditions. A laboratory-scale column, with a coarse-grained sand core surrounded by a fine-grained annulus, was used to simulate natural aquifers with strata of different hydraulic conductivities. A chemoattractant source was placed along the central axis of the column to model contaminants trapped in the heterogeneous subsurface. Chemotactic bacterial strains, Escherichia coli HCB1 and Pseudomonas putida F1, introduced into the column by a pulse injection, were found to alter their transport behaviors under the influence of the attractant chemical emanating from the central source. For E. coil HCB1, approximately 18% more of the total population relative to the control without attractant exited the column from the coarse sand layer due to the chemotactic effects of alpha-methylaspartate under an average fluid velocity of 5.1 m/d. Although P. putida F1 demonstrated no observable changes in migration pathways with the model contaminant acetate under the same flow rate, when the flow rate was reduced to 1.9 m/d, approximately 6-10% of the population relative to the control migrated from the fine sand layer toward attractant into the coarse sand layer. Microbial transport properties were further quantified by a mathematical model to examine the significance of bacterial motility and chemotaxis under different hydrodynamic conditions, which suggested important considerations for strain selection and practical operation of bioremediation schemes.

Surface association of motile bacteria at granular porous media interfaces

Bacterial populations were observed using dark-field light scattering at porous media interfaces comprised of a dilute solution containing the polymer additives methylcellulose and a transparent particulate suspension composed of mechanically agitated Gelrite gellan gum. Population-scale experiments with a nonchemotactic smooth-swimming mutant, Escherichia col HCB 437, yielded a variety of distinct and reproducible bacterial distributions that included highly concentrated bands of bacteria near the interface. While no physical attachment was observed between the bacteria and granular Gelrite media, the population exhibited surface associations characterized by reversible physical obstructions of the motile bacteria at the solid granular surfaces. These interactions decreased translational motion, which reduced bacterial migration and concentrated bacterial populations near the interface. Results from glass bead experiments indicated similar surface associations in high-surface area glass bead environments. Experimental results were semiquantitatively analyzed using a one-dimensional population-scale transport model. Theoretical profiles were generated using a single set of parameters and simultaneously compared with averaged bacterial distributions from multiple interface configurations. Parameter estimates were consistent with expected values. The agreement between the theoretical and experimental data suggests a quantifiable approach for modeling bacterial migration within high-surface area granular media environments.

High-throughput screens to discover synthetic riboswitches

Synthetic riboswitches constructed from RNA aptamers provide a means to control bacterial gene expression using exogenous ligands. A common theme among riboswitches that function at the translational level is that the RNA aptamer interacts with the ribosome-binding site (RBS) of a gene via an intervening sequence known as an expression platform. Structural rearrangements of the expression platform convert ligand binding into a change in gene expression. While methods for selecting RNA aptamers that bind ligands are well established, few general methods have been reported for converting these aptamers into synthetic riboswitches with desirable properties. We have developed two such methods that not only provide the throughput of genetic selections, but also feature the quantitative nature of genetic screens. One method, based on cell motility, is operationally simple and requires only standard consumables; while the other, based on fluorescence-activated cell sorting (FACS), is particularly adept at identifying synthetic riboswitches that are highly dynamic and display very low levels of background expression in the absence of the ligand. Here we present detailed procedures for screening libraries for riboswitches using the two methods.

In vivo acetylation of CheY, a response regulator in chemotaxis of Escherichia coli

CheY, the excitatory response regulator in the chemotaxis system of Escherichia coli, can be modulated by two covalent modifications: phosphorylation and acetylation. Both modifications have been detected in vitro only. The role of CheY acetylation is still obscure, although it is known to be involved in chemotaxis and to occur in vitro by two mechanisms--acetyl-CoA synthetase-catalyzed transfer of acetyl groups from acetate to CheY and autocatalyzed transfer from AcCoA. Here, we succeeded in detecting CheY acetylation in vivo by three means--Western blotting with a specific anti-acetyl-lysine antibody, mass spectrometry, and radiolabeling with [(14)C]acetate in the presence of protein-synthesis inhibitor. Unexpectedly, the level and rate of CheY acetylation in vivo were much higher than that in vitro. Thus, before any treatment, 9-13% of the lysine residues were found acetylated, depending on the growth phase, meaning that, on average, essentially every CheY molecule was acetylated in vivo. This high level was mainly the outcome of autoacetylation. Addition of acetate caused an incremental increase in the acetylation level, in which acetyl-CoA synthetase was involved too. These findings may have far-reaching implications for the structure-function relationship of CheY.

Bacterial motility: handedness and symmetry

Many bacteria swim by rotating thin helical filaments that extend into the external medium, as with common bacteria, or run beneath the outer membrane, as with spirochetes. Each filament is driven at its base by a motor that turns alternately clockwise and counterclockwise. The motor-filament complex is called a flagellum. Other kinds of bacteria glide, but their organelles of locomotion are not known. Since bacteria are microscopic and live in an aqueous environment, they swim at low Reynolds' number; cyclic motion works (e.g. rotation of a helix) but reciprocal motion does not (e.g. stroking of a singly hinged oar). By measuring concentrations of certain chemicals as they move through their environment, making temporal comparisons and modulating the direction of flagellar rotation, bacteria accumulate in regions that they find more favourable. Studies of bacterial chemotaxis are highly advanced, particularly for the peritrichously flagellated species Escherichia coli. A great deal is known about chemoreception, receptor-flagellar coupling and adaptation. Recently it has been found that E. coli can aggregate in response to signals generated by the cells themselves. Complex patterns form with remarkable symmetries.

Salmonella typhimurium lacking ribose chemoreceptors localize in tumor quiescence and induce apoptosis

The effectiveness of most chemotherapeutics is limited by their inability to penetrate deep into tumor tissue and their ineffectiveness against quiescent cells. Motile Salmonella typhimurium, which are specifically attracted to compounds produced by quiescent cancer cells, could overcome this therapeutic barrier. We hypothesized that individual chemoreceptors target S. typhimurium to specific tumor microenvironments. To test this hypothesis, we used time-lapse fluorescent microscopy and tumor cylindroids to quantify the accumulation of chemotaxis machinery knockouts, including strains lacking individual cell surface chemoreceptors, chemotaxis signal transduction pathway enzymes, and the flagella and motor assemblies. To measure the extent of apoptosis induced by individual bacterial strains, caspase-3 activity was measured as a function of time. Our results showed how chemoreceptors directed bacterial chemotaxis within cylindroids: the aspartate receptor initiated chemotaxis toward cylindroids, the serine receptor initiated penetration, and the ribose/galactose receptor directed S. typhimurium toward necrosis. In addition, strains lacking proper flagella constructs, signal transduction proteins, or active motor function did not chemotax toward tumor cylindroids, indicating that directed chemotaxis is necessary to promote accumulation in tumors. By deleting the ribose/galactose receptor, bacterial accumulation localized to tumor quiescence and had a greater individual effect on inducing apoptosis than wild-type S. typhimurium. This new understanding of the mechanisms of Salmonella migration in tumors will allow for the development of bacterial therapies with improved targeting to therapeutically inaccessible regions of tumors.

Characterization of the Thermotoga maritima chemotaxis methylation system that lacks pentapeptide-dependent methyltransferase CheR:MCP tethering

Sensory adaptation in bacterial chemotaxis is mediated by covalent modifications of specific glutamate and glutamine residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins (MCPs). In Escherichia coli and Salmonella enterica, efficient methylation of MCPs depends on the localization of methyltransferase CheR to MCP clusters through an interaction between the CheR beta-subdomain and a pentapeptide sequence (NWETF or NWESF) at the C-terminus of the MCP. In vitro methylation analyses utilizing S. enterica and Thermotoga maritima CheR proteins and MCPs indicate that MCP methylation in T. maritima occurs independently of a pentapeptide-binding motif. Kinetic and binding measurements demonstrate that despite efficient methylation, the interaction between T. maritima CheR and T. maritima MCPs is of relatively low affinity. Comparative protein sequence analyses of CheR beta-subdomains from organisms having MCPs that contain and/or lack pentapeptide-binding motifs identified key similarities and differences in residue conservation, suggesting the existence of two distinct classes of CheR proteins: pentapeptide-dependent and pentapeptide-independent methyltransferases. Analysis of MCP C-terminal ends showed that only approximately 10% of MCPs contain a putative C-terminal binding motif, the majority of which are restricted to the different proteobacteria classes (alpha, beta, gamma, delta). These findings suggest that tethering of CheR to MCPs is a relatively recent event in evolution and that the pentapeptide-independent methylation system is more common than the well-characterized pentapeptide-dependent methylation system.

Helical distribution of the bacterial chemoreceptor via colocalization with the Sec protein translocation machinery

In Escherichia coli, chemoreceptor clustering at a cell pole seems critical for signal amplification and adaptation. However, little is known about the mechanism of localization itself. Here we examined whether the aspartate chemoreceptor (Tar) is inserted directly into the polar membrane by using its fusion to green fluorescent protein (GFP). After induction of Tar–GFP, fluorescent spots first appeared in lateral membrane regions, and later cell poles became predominantly fluorescent. Unexpectedly, Tar–GFP showed a helical arrangement in lateral regions, which was more apparent when a Tar–GFP derivative with two cysteine residues in the periplasmic domain was cross-linked to form higher oligomers. Moreover, similar distribution was observed even when the cytoplasmic domain of the double cysteine Tar–GFP mutant was replaced by that of the kinase EnvZ, which does not localize to a pole. Observation of GFP–SecE and a translocation-defective MalE–GFP mutant, as well as indirect immunofluorescence microscopy on SecG, suggested that the general protein translocation machinery (Sec) itself is arranged into a helical array, with which Tar is transiently associated. The Sec coil appeared distinct from the MreB coil, an actin-like cytoskeleton. These findings will shed new light on the mechanisms underlying spatial organization of membrane proteins in E. coli.

Control of chemotactic signal gain via modulation of a pre-formed receptor array

The remarkably wide dynamic range of the chemotactic pathway of Escherichia coli, a model signal transduction system, is achieved by methylation/amidation of the transmembrane chemoreceptors that regulate the histidine kinase CheA in response to extracellular stimuli. The chemoreceptors cluster at a cell pole together with CheA and the adaptor CheW. Several lines of evidence have led to models that assume high cooperativity and sensitivity via collaboration of receptor dimers within a cluster. Here, using in vivo disulfide cross-linking assays, we have demonstrated a well defined arrangement of the aspartate chemoreceptor (Tar). The differential effects of amidation on cross-linking at different positions indicate that amidation alters the relative orientation of Tar dimers to each other (presumably inducing rotational displacements) without much affecting the conformation of the periplasmic domains. Interestingly, the effect of aspartate on cross-linking at any position tested was roughly opposite to that of receptor amidation. Furthermore, amidation attenuated the effects of aspartate by several orders of magnitude. These results suggest that receptor covalent modification controls signal gain by altering the arrangement or packing of receptor dimers in a pre-formed cluster.

Differential recognition of citrate and a metal-citrate complex by the bacterial chemoreceptor Tcp

The chemoreceptor Tcp of Salmonella enterica serovar Typhimurium can sense citrate and a metal-citrate complex as distinct attractants. In this study, we tried to investigate the molecular mechanism of this discrimination. That citrate binds directly to Tcp was verified by the site-specific thiol modification assays using membrane fractions prepared from Escherichia coli cells expressing the mutant Tcp receptors in which single Cys residues were introduced at positions in the putative ligand-binding pocket. To determine the region responsible for the ligand discrimination, we screened for mutations defective in taxis to magnesium in the presence of citrate. All of the isolated mutants from random mutagenesis with hydroxylamine were defective in both citrate and metal-citrate sensing, and the mutated residues are located in or near the alpha1-alpha2 and alpha3-alpha4 loops within the periplasmic domain. Further analyses with site-directed replacements around these regions demonstrated that the residue Asn(67), which is presumed to lie at the subunit interface of the Tcp homodimer, plays a critical role in the recognition of the metal-citrate complex but not that of citrate. Various amino acids at this position differentially affect the citrate and metal-citrate sensing abilities. Thus, for the first time, the abilities to sense the two attractants were genetically dissected. Based on the results obtained in this study, we propose models in which the discrimination of the metal-citrate complex from citrate involves cooperative interaction at Asn(67) and allosteric switching.

Swimming in circles: motion of bacteria near solid boundaries

Near a solid boundary, Escherichia coli swims in clockwise circular motion. We provide a hydrodynamic model for this behavior. We show that circular trajectories are natural consequences of force-free and torque-free swimming and the hydrodynamic interactions with the boundary, which also leads to a hydrodynamic trapping of the cells close to the surface. We compare the results of the model with experimental data and obtain reasonable agreement. In particular, the radius of curvature of the trajectory is observed to increase with the length of the bacterium body.

Stabilization of polar localization of a chemoreceptor via its covalent modifications and its communication with a different chemoreceptor

In the chemotaxis of Escherichia coli, polar clustering of the chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW is thought to be involved in signal amplification and adaptation. However, the mechanism that leads to the polar localization of the receptor is still largely unknown. In this study, we examined the effect of receptor covalent modification on the polar localization of the aspartate chemoreceptor Tar fused to green fluorescent protein (GFP). Amidation (and presumably methylation) of Tar-GFP enhanced its own polar localization, although the effect was small. The slight but significant effect of amidation on receptor localization was reinforced by the fact that localization of a noncatalytic mutant version of GFP-CheR that targets to the C-terminal pentapeptide sequence of Tar was similarly facilitated by receptor amidation. Polar localization of the demethylated version of Tar-GFP was also enhanced by increasing levels of the serine chemoreceptor Tsr. The effect of covalent modification on receptor localization by itself may be too small to account for chemotactic adaptation, but receptor modification is suggested to contribute to the molecular assembly of the chemoreceptor/histidine kinase array at a cell pole, presumably by stabilizing the receptor dimer-to-dimer interaction.