Chemotactic signaling in filamentous cells of Escherichia coli

The switching mechanism of the bacterial rotary motor combines tight regulation with inherent flexibility

Regulatory switches are wide spread in many biological systems. Uniquely among them, the switch of the bacterial flagellar motor is not an on/off switch but rather controls the motor’s direction of rotation in response to binding of the signaling protein CheY. Despite its extensive study, the molecular mechanism underlying this switch has remained largely unclear. Here, we resolved the functions of each of the three CheY‐binding sites at the switch in E. coli, as well as their different dependencies on phosphorylation and acetylation of CheY. Based on this, we propose that CheY motor switching activity is potentiated upon binding to the first site. Binding of potentiated CheY to the second site produces unstable switching and at the same time enables CheY binding to the third site, an event that stabilizes the switched state. Thereby, this mechanism exemplifies a unique combination of tight motor regulation with inherent switching flexibility.

Spatiotemporal Organization of Chemotaxis Pathways in Magnetospirillum gryphiswaldense

Magnetospirillum gryphiswaldense employs iron-rich nanoparticles for magnetic navigation within environmental redox gradients. This behavior termed magneto-aerotaxis was previously shown to rely on the sensory pathway CheOp1, but the precise localization of CheOp1-related chemoreceptor arrays during the cell cycle and its possible interconnection with three other chemotaxis pathways have remained unstudied. Here, we analyzed the localization of chemoreceptor-associated adaptor protein CheW₁ and histidine kinase CheA₁ by superresolution microscopy in a spatiotemporal manner. CheW₁ localized in dynamic clusters that undergo occasional segregation and fusion events at lateral sites of both cell poles. Newly formed smaller clusters originating at midcell before completion of cytokinesis were found to grow in size during the cell cycle. Bipolar CheA₁ localization and formation of aerotactic swim halos were affected depending on the fluorescent protein tag, indicating that CheA₁ localization is important for aerotaxis. Furthermore, polar CheW₁ localization was independent of cheOp2 to cheOp4 but lost in the absence of cheOp1 or cheA₁ Results were corroborated by the detection of a direct protein interaction between CheA₁ and CheW₁ and by the observation that cheOp2- and cheOp3-encoded CheW paralogs localized in spatially distinct smaller clusters at the cell boundary. Although the findings of a minor aerotaxis-related CheOp4 phenotype and weak protein interactions between CheOp1 and CheOp4 by two-hybrid analysis implied that CheW₁ and CheW₄ might be part of the same chemoreceptor array, CheW₄ was localized in spatially distinct polar-lateral arrays independent of CheOp1, suggesting that CheOp1 and CheOp4 are also not connected at the molecular level.IMPORTANCE Magnetotactic bacteria (MTB) use the geomagnetic field for navigation in aquatic redox gradients. However, the highly complex signal transduction networks in these environmental microbes are poorly understood. Here, we analyzed the localization of selected chemotaxis proteins to spatially and temporally resolve chemotaxis array localization in Magnetospirillum gryphiswaldense Our findings suggest that bipolar localization of chemotaxis arrays related to the key signaling pathway CheOp1 is important for aerotaxis and that CheOp1 signaling units assemble independent of the three other chemotaxis pathways present in M. gryphiswaldense Overall, our results provide deeper insights into the complex organization of signaling pathways in MTB and add to the general understanding of environmental bacteria possessing multiple chemotaxis pathways.

Fluctuations in Intracellular CheY-P Concentration Coordinate Reversals of Flagellar Motors in E. coli

Signal transduction utilizing membrane-spanning receptors and cytoplasmic regulator proteins is a fundamental process for all living organisms, but quantitative studies of the behavior of signaling proteins, such as their diffusion within a cell, are limited. In this study, we show that fluctuations in the concentration of the signaling molecule, phosphorylated CheY, constitute the basis of chemotaxis signaling. To analyze the propagation of the CheY-P signal quantitatively, we measured the coordination of directional switching between flagellar motors on the same cell. We analyzed the time lags of the switching of two motors in both CCW-to-CW and CW-to-CCW switching (∆t_CCW-CW and ∆t_CW-CCW). In wild-type cells, both time lags increased as a function of the relative distance of two motors from the polar receptor array. The apparent diffusion coefficient estimated for ∆t values was ~9 µm²/s. The distance-dependency of ∆t_CW-CCW disappeared upon loss of polar localization of the CheY-P phosphatase, CheZ. The distance-dependency of the response time for an instantaneously applied serine attractant signal also disappeared with the loss of polar localization of CheZ. These results were modeled by calculating the diffusion of CheY and CheY-P in cells in which phosphorylation and dephosphorylation occur in different subcellular regions. We conclude that diffusion of signaling molecules and their production and destruction through spontaneous activity of the receptor array generates fluctuations in CheY-P concentration over timescales of several hundred milliseconds. Signal fluctuation coordinates rotation among flagella and regulates steady-state run-and-tumble swimming of cells to facilitate efficient responses to environmental chemical signals.

From indication to decision: A hierarchical approach to model the chemotactic behavior of Escherichia coli

Reducing the complex behavior of living entities to its underlying physical and chemical processes is a formidable task in biology. Complex behaviors can be characterized as decision making: the ability to process the incoming information via an intracellular network and act upon this information to choose appropriate strategies. Motility is one such behavior that has been the focus many modeling efforts in the past. Our aim is to reduce the chemotactic behavior in Escherichia coli to its molecular constituents in order to paint a comprehensive and end-to-end picture of this intricate behavior. We utilize a hierarchical approach, consisting of three layers, to achieve this goal: at the first level, chemical reactions involved in chemotaxis are simulated. In the second level, the chemical reactions give rise to the mechanical movement of six independent flagella. At the last layer, the two lower layers are combined to allow a digital bacterium to receive information from its environment and swim through it with verve. Our results are in concert with the experimental studies concerning the motility of E.coli cells. In addition, we show that our detailed model of chemotaxis is reducible to a non-homogeneous Markov process.

Spirochete Flagella and Motility

Spirochetes can be distinguished from other flagellated bacteria by their long, thin, spiral (or wavy) cell bodies and endoflagella that reside within the periplasmic space, designated as periplasmic flagella (PFs). Some members of the spirochetes are pathogenic, including the causative agents of syphilis, Lyme disease, swine dysentery, and leptospirosis. Furthermore, their unique morphologies have attracted attention of structural biologists; however, the underlying physics of viscoelasticity-dependent spirochetal motility is a longstanding mystery. Elucidating the molecular basis of spirochetal invasion and interaction with hosts, resulting in the appearance of symptoms or the generation of asymptomatic reservoirs, will lead to a deeper understanding of host-pathogen relationships and the development of antimicrobials. Moreover, the mechanism of propulsion in fluids or on surfaces by the rotation of PFs within the narrow periplasmic space could be a designing base for an autonomously driving micro-robot with high efficiency. This review describes diverse morphology and motility observed among the spirochetes and further summarizes the current knowledge on their mechanisms and relations to pathogenicity, mainly from the standpoint of experimental biophysics.

Bacterial-mediated recovery of copper from low-grade copper sulphide using acid-processed rice straw

Bacteria community and copper recovery in presence of acid-processed rice straw (ARW) were explored during low-grade copper sulphide bioleaching. The results indicated a strongly promoting response of appropriate-quality ARW with improved bacteria concentration and enhanced copper recovery. The highest bacteria concentration reached 9.54 × 10⁷ cells·mL^-1 with an increase by 69.15%. And a maximum of 95.32% copper leaching rate with a relatively low Fe³⁺ concentration (329.00 mg·L^-1) was obtained in presence of 1.0 g powdered ARW compared to only 83.40% in its absence. That is due to less development of passivation layer formed by Fe³⁺ hydrolysis, which is contributed by reducing ARW. 16S rDNA analysis illustrated the dominant leaching bacteria (Acidithiobacillus ferrooxidans) was influenced significantly, whose proportion reached 40.38% to the total bacteria when the ARW was added compared to 15.92% in its absence. And Stenotrophomonas accounted for the highest proportion of the bacteria community throughout bioleaching process.

Functional Regulators of Bacterial Flagella

Bacteria move by a variety of mechanisms, but the best understood types of motility are powered by flagella (72). Flagella are complex machines embedded in the cell envelope that rotate a long extracellular helical filament like a propeller to push cells through the environment. The flagellum is one of relatively few biological machines that experience continuous 360° rotation, and it is driven by one of the most powerful motors, relative to its size, on earth. The rotational force (torque) generated at the base of the flagellum is essential for motility, niche colonization, and pathogenesis. This review describes regulatory proteins that control motility at the level of torque generation.

Positioning of the Motility Machinery in Halophilic Archaea

Archaea are ubiquitous single cellular microorganisms that play important ecological roles in nature. The intracellular organization of archaeal cells is among the unresolved mysteries of archaeal biology. With this work, we show that cells of haloarchaea are polarized. The cellular positioning of proteins involved in chemotaxis and motility is spatially and temporally organized in these cells. This suggests the presence of a specific mechanism responsible for the positioning of macromolecular protein complexes in archaea.

Bacteria and archaea exhibit tactical behavior and can move up and down chemical gradients. This tactical behavior relies on a motility structure, which is guided by a chemosensory system. Environmental signals are sensed by membrane-inserted chemosensory receptors that are organized in large ordered arrays. While the cellular positioning of the chemotaxis machinery and that of the flagellum have been studied in detail in bacteria, we have little knowledge about the localization of such macromolecular assemblies in archaea. Although the archaeal motility structure, the archaellum, is fundamentally different from the flagellum, archaea have received the chemosensory machinery from bacteria and have connected this system with the archaellum. Here, we applied a combination of time-lapse imaging and fluorescence and electron microscopy using the model euryarchaeon Haloferax volcanii and found that archaella were specifically present at the cell poles of actively dividing rod-shaped cells. The chemosensory arrays also had a polar preference, but in addition, several smaller arrays moved freely in the lateral membranes. In the stationary phase, rod-shaped cells became round and chemosensory arrays were disassembled. The positioning of archaella and that of chemosensory arrays are not interdependent and likely require an independent form of positioning machinery. This work showed that, in the rod-shaped haloarchaeal cells, the positioning of the archaellum and of the chemosensory arrays is regulated in time and in space. These insights into the cellular organization of H. volcanii suggest the presence of an active mechanism responsible for the positioning of macromolecular protein complexes in archaea.

Understanding Protein Mobility in Bacteria by Tracking Single Molecules

Protein diffusion is crucial for understanding the formation of protein complexes in vivo and has been the subject of many fluorescence microscopy studies in cells; however, such microscopy efforts are often limited by low sensitivity and resolution. During the past decade, these limitations have been addressed by new super-resolution imaging methods, most of which rely on single-particle tracking and single-molecule detection; these methods are revolutionizing our understanding of molecular diffusion inside bacterial cells by directly visualizing the motion of proteins and the effects of the local and global environment on diffusion. Here we review key methods that made such experiments possible, with particular emphasis on versions of single-molecule tracking based on photo-activated fluorescent proteins. We also discuss studies that provide estimates of the time a diffusing protein takes to locate a target site, as well as studies that examined the stoichiometries of diffusing species, the effect of stable and weak interactions on diffusion, and the constraints of large macromolecular structures on the ability of proteins and their complexes to access the entire cytoplasm.

Cell morphology governs directional control in swimming bacteria

The ability to rapidly detect and track nutrient gradients is key to the ecological success of motile bacteria in aquatic systems. Consequently, bacteria have evolved a number of chemotactic strategies that consist of sequences of straight runs and reorientations. Theoretically, both phases are affected by fluid drag and Brownian motion, which are themselves governed by cell geometry. Here, we experimentally explore the effect of cell length on control of swimming direction. We subjected Escherichia coli to an antibiotic to obtain motile cells of different lengths, and characterized their swimming patterns in a homogeneous medium. As cells elongated, angles between runs became smaller, forcing a change from a run-and-tumble to a run-and-stop/reverse pattern. Our results show that changes in the motility pattern of microorganisms can be induced by simple morphological variation, and raise the possibility that changes in swimming pattern may be triggered by both morphological plasticity and selection on morphology.

Single-cell E. coli response to an instantaneously applied chemotactic signal

In response to an attractant or repellant, an Escherichia coli cell controls the rotational direction of its flagellar motor by a chemotaxis system. When an E. coli cell senses an attractant, a reduction in the intracellular concentration of a chemotaxis protein, phosphorylated CheY (CheY-P), induces counterclockwise (CCW) rotation of the flagellar motor, and this cellular response is thought to occur in several hundred milliseconds. Here, to measure the signaling process occurring inside a single E. coli cell, including the recognition of an attractant by a receptor cluster, the inactivation of histidine kinase CheA, and the diffusion of CheY and CheY-P molecules, we applied a serine stimulus by instantaneous photorelease from a caged compound and examined the cellular response at a temporal resolution of several hundred microseconds. We quantified the clockwise (CW) and CCW durations immediately after the photorelease of serine as the response time and the duration of the response, respectively. The results showed that the response time depended on the distance between the receptor and motor, indicating that the decreased CheY-P concentration induced by serine propagates through the cytoplasm from the receptor-kinase cluster toward the motor with a timing that is explained by the diffusion of CheY and CheY-P molecules. The response time included 240 ms for enzymatic reactions in addition to the time required for diffusion of the signaling molecule. The measured response time and duration of the response also revealed that the E. coli cell senses a similar serine concentration regardless of whether the serine concentration is increasing or decreasing. These detailed quantitative findings increase our understanding of the signal transduction process that occurs inside cells during bacterial chemotaxis.

Comparative Analysis of Extremely Thermophilic Caldicellulosiruptor Species Reveals Common and Unique Cellular Strategies for Plant Biomass Utilization

Microbiological, genomic and transcriptomic analyses were used to examine three species from the bacterial genus Caldicellulosiruptor with respect to their capacity to convert the carbohydrate content of lignocellulosic biomass at 70°C to simple sugars, acetate, lactate, CO2, and H2. Caldicellulosiruptor bescii, C. kronotskyensis, and C. saccharolyticus solubilized 38%, 36%, and 29% (by weight) of unpretreated switchgrass (Panicum virgatum) (5 g/liter), respectively, which was about half of the amount of crystalline cellulose (Avicel; 5 g/liter) that was solubilized under the same conditions. The lower yields with C. saccharolyticus, not appreciably greater than the thermal control for switchgrass, were unexpected, given that its genome encodes the same glycoside hydrolase 9 (GH9)-GH48 multidomain cellulase (CelA) found in the other two species. However, the genome of C. saccharolyticus lacks two other cellulases with GH48 domains, which could be responsible for its lower levels of solubilization. Transcriptomes for growth of each species comparing cellulose to switchgrass showed that many carbohydrate ABC transporters and multidomain extracellular glycoside hydrolases were differentially regulated, reflecting the heterogeneity of lignocellulose. However, significant differences in transcription levels for conserved genes among the three species were noted, indicating unexpectedly diverse regulatory strategies for deconstruction for these closely related bacteria. Genes encoding the Che-type chemotaxis system and flagellum biosynthesis were upregulated in C. kronotskyensis and C. bescii during growth on cellulose, implicating motility in substrate utilization. The results here show that capacity for plant biomass deconstruction varies across Caldicellulosiruptor species and depends in a complex way on GH genome inventory, substrate composition, and gene regulation.

Positioning of bacterial chemoreceptors

For optimum growth, bacteria must adapt to their environment, and one way that many species do this is by moving towards favourable conditions. To do so requires mechanisms to both physically drive movement and provide directionality to this movement. The pathways that control this directionality comprise chemoreceptors, which, along with an adaptor protein (CheW) and kinase (CheA), form large hexagonal arrays. These arrays can be formed around transmembrane receptors, resulting in arrays embedded in the inner membrane, or they can comprise soluble receptors, forming arrays in the cytoplasm. Across bacterial species, chemoreceptor arrays (both transmembrane and soluble) are localised to a variety of positions within the cell; some species with multiple arrays demonstrate this variety within individual cells. In many cases, the positioning pattern of the arrays is linked to the need for segregation of arrays between daughter cells on division, ensuring the production of chemotactically competent progeny. Multiple mechanisms have evolved to drive this segregation, including stochastic self-assembly, cellular landmarks, and the utilisation of ParA homologues. The variety of mechanisms highlights the importance of chemotaxis to motile species.

Filamentous Escherichia coli cells swimming in tapered microcapillaries

This study analyzed the swimming characteristics of filamentous Escherichia coli cells inside tapered capillaries with a diameter decreasing from 700 μm to 4 μm and a mean body length of 27.8 μm ± 11.9 μm. Cells that were pre-oriented towards the narrower diameter section of the tapered capillary swam with high directional persistence, following conical-helix trajectories along the capillary wall. The confinement of the tapered capillary significantly diminished the mean swimming speed of filamentous cells when compared to their unrestricted mean swimming speed. The cell body rotation of individual filamentous bacteria decreased along the tapered direction, likely due to increased steric interactions with the capillary wall. Filamentous cells that swam under imposed flow rates ranging from 0.2 μl/min to 0.8 μl/min showed positive rheotaxis inside the 150 μm-350 μm diameter region of the tapered capillary. Depending on the imposed flow rate, none of the bacteria could advance beyond a critical diameter in the tapered capillary. This critical diameter is likely to be the position of the maximum shear rate they can tolerate without being flushed away. This work showed experimental evidence of how a simple flow constriction such as a tapered tube forms a hydrodynamic barrier that can deter the advance of bacterial rheotaxis.

Theoretical insights into bacterial chemotaxis

Research into understanding bacterial chemotactic systems has become a paradigm for Systems Biology. Experimental and theoretical researchers have worked hand-in-hand for over 40 years to understand the intricate behavior driving bacterial species, in particular how such small creatures, usually not more than 5 µm in length, detect and respond to small changes in their extracellular environment. In this review we highlight the importance that theoretical modeling has played in providing new insight and understanding into bacterial chemotaxis. We begin with an overview of the bacterial chemotaxis sensory response, before reviewing the role of theoretical modeling in understanding elements of the system on the single cell scale and features underpinning multiscale extensions to population models.

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.

Coordinated reversal of flagellar motors on a single Escherichia coli cell

An Escherichia coli cell transduces extracellular stimuli sensed by chemoreceptors to the state of an intracellular signal molecule, which regulates the switching of the rotational direction of the flagellar motors from counterclockwise (CCW) to clockwise (CW) and from CW back to CCW. Here, we performed high-speed imaging of flagellar motor rotation and show that the switching of two different motors on a cell is controlled coordinatedly by an intracellular signal protein, phosphorylated CheY (CheY-P). The switching is highly coordinated with a subsecond delay between motors in clear correlation with the distance of each motor from the chemoreceptor patch localized at a cell pole, which would be explained by the diffusive motion of CheY-P molecules in the cell. The coordinated switching becomes disordered by the expression of a constitutively active CheY mutant that mimics the CW-rotation stimulating function. The coordinated switching requires CheZ, which is the phosphatase for CheY-P. Our results suggest that a transient increase and decrease in the concentration of CheY-P caused by a spontaneous burst of its production by the chemoreceptor patch followed by its dephosphorylation by CheZ, which is probably a wavelike propagation in a subsecond timescale, triggers and regulates the coordinated switching of flagellar motors.

Reaction-diffusion systems in intracellular molecular transport and control

Chemical reactions make cells work only if the participating chemicals are delivered to desired locations in a timely and precise fashion. Most research to date has focused on active-transport mechanisms, although passive diffusion is often equally rapid and energetically less costly. Capitalizing on these advantages, cells have developed sophisticated reaction-diffusion (RD) systems that control a wide range of cellular functions-from chemotaxis and cell division, through signaling cascades and oscillations, to cell motility. These apparently diverse systems share many common features and are "wired" according to "generic" motifs such as nonlinear kinetics, autocatalysis, and feedback loops. Understanding the operation of these complex (bio)chemical systems requires the analysis of pertinent transport-kinetic equations or, at least on a qualitative level, of the characteristic times of the constituent subprocesses. Therefore, in reviewing the manifestations of cellular RD, we also describe basic theory of reaction-diffusion phenomena.

Cloning and characterization of three cheB genes in Leptospira interrogans

Motility and chemotaxis systems are critical for the virulence of leptospires. There were multiple copies of putative chemotaxis homologs located at leptospires large chromosome. CheB1 and CheB3 from Leptospira interrogans strain Lai are predicted to have a global CheB-like domain, but CheB2 is predicted to have a C-terminal effector domain only. In order to verify the function of three putative cheB genes, they were cloned into pQE31 vector and then expressed, respectively, in wild-type Escherichia coli strain RP437 and cheB defective strain RP4972. The results of swarming assays and the predicted ternary structures of CheB1 and CheB3 of L. interrogans strain Lai suggested that the absence of an N-terminal regulatory domain may be one of the reasons for the failure of CheB2 to complement an E. coli cheB mutant. Furthermore, CheB2 links solely to CheR1 and CheR3 in the interaction network of leptospires. Taken together, these results indicated that CheB2 may not function alone, and under certain physiological conditions, it may require CheB3 and CheR1 to function. The existence of multiple copies of chemotaxis gene homologs suggested that L. interrogans strain Lai might have a more complex chemosensory pathway.

Millisecond timescale slimfield imaging and automated quantification of single fluorescent protein molecules for use in probing complex biological processes

Fluorescence microscopy offers a minimally perturbative approach to probe biology in vivo. However, available techniques are limited both in sensitivity and temporal resolution for commonly used fluorescent proteins. Here we present a new imaging system with a diagnostic toolkit that caters for the detection and quantification of fluorescent proteins for use in fast functional imaging at the single-molecule level. It utilizes customized microscopy with a mode of illumination we call "slimfield" suitable for rapid (approximately millisecond) temporal resolution on a range of common fluorescent proteins. Slimfield is cheap and simple, allowing excitation intensities approximately 100 times greater than those of widefield imaging, permitting single-molecule detection at high speed. We demonstrate its application on several purified fluorescent proteins in standard use as genetically-encoded reporter molecules. Controlled in vitro experiments indicate single protein molecules over a field of view of approximately 30 microm(2) area, large enough to encapsulate complete prokaryotic and small eukaryotic cells. Using a novel diagnostic toolkit we demonstrate automated detection and quantification of single molecules with maximum imaging rates for a 128 x 128 pixel array of approximately 500 frames per second with a localization precision for these photophysically poor fluorophores to within 50 nm. We report for the first time the imaging of the dim enhanced cyan fluorescent protein (ECFP) and CyPet at the single-molecule level. Applying modifications, we performed simultaneous dual-colour slimfield imaging for use in co-localization and FRET. We present preliminary in vivo imaging on bacterial cells and demonstrate approximately millisecond timescale functional imaging at the single-molecule level with negligible photodamage.

Spatiotemporal modelling of CheY complexes in Escherichia coli chemotaxis

The chemotaxis pathway of Escherichia coli is one of the best studied and modelled biological signalling pathways. Here we extend existing modelling approaches by explicitly including a description of the formation and subcellular localization of intermediary complexes in the phosphotransfer pathway. The inclusion of these complexes shows that only about 60% of the total output response regulator (CheY) is uncomplexed at any moment and hence free to interact with its target, the flagellar motor. A clear strength of this model is its ability to predict the experimentally observable subcellular localization of CheY throughout a chemotactic response. We have found good agreement between the model output and experimentally determined CheY localization patterns.

Positioning of chemosensory clusters in E. coli and its relation to cell division

Chemotaxis receptors and associated signalling proteins in Escherichia coli form clusters that consist of thousands of molecules and are the largest native protein complexes described to date in bacteria. Clusters are located at the cell poles and laterally along the cell body, and play an important role in signal transduction. Much work has been done to study the structure and function of receptor clusters, but the significance of their positioning and the underlying mechanisms are not understood. Here, we used fluorescence imaging to study cluster distribution and follow cluster dynamics during cell growth. Our data show that lateral clusters localise to specific periodic positions along the cell body, which mark future division sites and are involved in the localisation of the replication machinery. The chemoreceptor cluster positioning is thus intricately related to the overall structure and division of an E. coli cell.

Identification of specific chemoattractants and genetic complementation of a Borrelia burgdorferi chemotaxis mutant: flow cytometry-based capillary tube chemotaxis assay

Measuring the chemotactic response of Borrelia burgdorferi, the bacterial species that causes Lyme disease, is relatively more difficult than measuring that of other bacteria. Because these spirochetes have long generation times, enumerating cells that swim up a capillary tube containing an attractant by using colony counts is impractical. Furthermore, direct counts with a Petroff-Hausser chamber is problematic, as this method has a low throughput and necessitates a high cell density; the latter can lead to misinterpretation of results when assaying for specific attractants. Only rabbit serum and tick saliva have been reported to be chemoattractants for B. burgdorferi. These complex biological mixtures are limited in their utility for studying chemotaxis on a molecular level. Here we present a modified capillary tube chemotaxis assay for B. burgdorferi that enumerates cells by flow cytometry. Initial studies identified N-acetylglucosamine as a chemoattractant. The assay was then optimized with respect to cell concentration, incubation time, motility buffer composition, and growth phase. Besides N-acetylglucosamine, glucosamine, glucosamine dimers (chitosan), glutamate, and glucose also elicited significant chemoattractant responses, although the response obtained with glucose was weak and variable. Serine and glycine were nonchemotactic. To further validate and to exploit the use of this assay, a previously described nonchemotactic cheA2 mutant was shown to be nonchemotactic by this assay; it also regained the wild-type phenotype when complemented in trans. This is the first report that identifies specific chemical attractants for B. burgdorferi and the use of flow cytometry for spirochete enumeration. The method should also be useful for assaying chemotaxis for other slow-growing prokaryotic species and in specific environments in nature.

Characterization of the cheY genes from Leptospira interrogans and their effects on the behavior of Escherichia coli

The motility and chemotaxis system are critical for the virulence of pathogenic leptospire, which enable them to penetrate host tissue barriers during infection. The completed genome sequence of a representative virulent serovar type strain (Lai) of Leptospira interrogans serogroups Icterohaemorrhagiae (L. interrogans strain Lai) suggested that there were multiple copies of putative chemotaxis homologues located at its large chromosome. In order to verify the function of these proteins, the putative cheY genes were cloned into pQE31 vector and then expressed, respectively, in wild-type Escherichia coli strain RP437 and cheY defective strain RP5232. The results showed that all the five cheYs could restore the swarming of RP5232 strain to some extend. Overexpression of CheYs in RP437 showed inhibited swarming of RP437. To investigate the mechanism of chemotaxis signaling in L. interrogans strain Lai, certain aspartates (Asp-53, Asp-61, Asp-70, Asp-62, and Asp-66 for L. interrogans strain Lai CheY1, CheY2, CheY3, CheY4, and CheY5, respectively) were mutated. Expression of these mutated cheYs manifested neither restoration of the swarming ability of RP5232 nor inhibition on swarming ability of RP437. Multiple amino acid sequence alignment predicted ternary structures and the result of mutation experiment suggested that these conserved aspartate residues of L. interrogans were analogous to that in E. coli CheY in function and structure. So, L. interrogans and E. coli may have similar mechanisms of activation of the chemotaxis phosphorelay pathway, but there are differences in their control by signal terminator.

Changing cellular location of CheZ predicted by molecular simulations

In the chemotaxis pathway of the bacterium Escherichia coli, signals are carried from a cluster of receptors to the flagellar motors by the diffusion of the protein CheY-phosphate (CheYp) through the cytoplasm. A second protein, CheZ, which promotes dephosphorylation of CheYp, partially colocalizes with receptors in the plasma membrane. CheZ is normally dimeric in solution but has been suggested to associate into highly active oligomers in the presence of CheYp. A model is presented here and supported by Brownian dynamics simulations, which accounts for these and other experimental data: A minority component of the receptor cluster (dimers of CheA_short) nucleates CheZ oligomerization and CheZ molecules move from the cytoplasm to a bound state at the receptor cluster depending on the current level of cellular stimulation. The corresponding simulations suggest that dynamic CheZ localization will sharpen cellular responses to chemoeffectors, increase the range of detectable ligand concentrations, and make adaptation more precise and robust. The localization and activation of CheZ constitute a negative feedback loop that provides a second tier of adaptation to the system. Subtle adjustments of this kind are likely to be found in many other signaling pathways.

In order to function effectively, a living cell must not only synthesize the correct molecules but also put them in the correct place. Understanding how this positioning occurs, and what its consequences are, is a matter of great interest and concern to contemporary biologists. The author here proposes a novel mechanism that will enhance the ability of a bacterial cell to perform chemotaxis—the ability to swim toward sources of food or away from noxious substances. In this hypothesis, a key protein in the chemotaxis pathway moves dynamically between the membrane and the cytoplasm depending on the presence of attractants or repellents. This idea is explored and tested by means of detailed molecular simulations in which all of the relevant molecules are shown in their correct location in the cell. The simulations show that the proposed shift in location of the key molecule will improve the speed, range, and robustness of the cell's response. It seems likely that similar movements of proteins will occur in many other signaling pathways.

Controlling the shape of filamentous cells of Escherichia coli

This paper describes a technique for growing filamentous cells of Escherichia coli with defined shapes, including crescents, zigzags, sinusoids, and spirals. The procedure begins with the fabrication of embossed microchambers in agarose. Cells are trapped in the chambers by placing a flat, flexible "ceiling", either a slab of agarose or poly(dimethylsiloxane), against an agarose mold on which a suspension of cells has been added; the use of agarose keeps cells hydrated and allows nutrients to diffuse into the chambers. Cells grown in microchambers in the presence of cephalexin grow into a multinucleate, nonseptate, filamentous phenotype and adopt the shape of the microchambers. The resulting cells are motile and can be released by removing the "ceiling" from the agarose microchambers and rinsing the cells into solution.

Phosphatase localization in bacterial chemotaxis: divergent mechanisms, convergent principles

Chemotaxis is the process by which cells sense changes in their chemical environment and move towards more favorable conditions. In divergent species of bacteria, the chemotaxis proteins localize to the poles of the cell and information is transferred to the flagellar motors through the phosphorylation of a soluble protein CheY. Using mathematical models and computer simulation, we demonstrate that phosphatase localization controls the spatial distribution of CheY-P in the cytosol at steady state. Remarkably, the location of the phosphatase is not conserved in different species of bacteria. The sole phosphatase in Escherichia coli is localized with the signaling complex and the primary phosphatase in Bacillus subtilis is localized at the flagellar motors. Despite these alternate pathway structures, both designs minimize differences in the concentration of phosphorylated CheY proximal to each motor unlike a design where the phosphatase is freely diffusing in the cytoplasm. These results suggest that motile bacteria have evolved alternate mechanisms to ensure that each motor receives roughly the same signal at steady state. The hypothesis is that complex networks have evolved to satisfy certain design principles in order to function robustly. While specific mechanisms are different, the underlying principles of phosphatase localization in E. coli and B. subtilis appear to be the same.

Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coli

We describe the use of a computational model to study the effects of cellular architecture and macromolecular crowding on signal transduction in Escherichia coli chemotaxis. A newly developed program, Smoldyn, allows the movement and interaction of a large number of individual molecules in a structured environment to be simulated (S. S. Andrews and D. Bray, Phys. Biol., in press). With Smoldyn, we constructed a three-dimensional model of an E. coli cell and examined the diffusion of CheYp from the cluster of receptors to the flagellar motors under control conditions and in response to attractant and repellent stimuli. Our simulations agree well with experimental observations of cell swimming responses and are consistent with the diffusive behavior expected in wild-type and mutant cells. The high resolution available to us in the new program allows us to calculate the loci of individual CheYp molecules in a cell and the distribution of their lifetimes under different cellular conditions. We find that the time delay between stimulus and response differs for flagellar motors located at different positions in the cell. We explore different possible locations for the phosphatase CheZ and show conditions under which a gradient of CheYp exists in the cell. The introduction of inert blocks into the cytoplasm, representing impenetrable structures such as the nucleoid and large protein complexes, produces a fall in the apparent diffusion coefficient of CheYp and enhances the differences between motors. These and other results are left as predictions for future experiments.

Genetics of motility and chemotaxis of a fascinating group of bacteria: the spirochetes

Spirochetes are a medically important and ecologically significant group of motile bacteria with a distinct morphology. Outermost is a membrane sheath, and within this sheath is the protoplasmic cell cylinder and subterminally attached periplasmic flagella. Here we address specific and unique aspects of their motility and chemotaxis. For spirochetes, translational motility requires asymmetrical rotation of the two internally located flagellar bundles. Consequently, they have swimming modalities that are more complex than the well-studied paradigms. In addition, coordinated flagellar rotation likely involves an efficient and novel signaling mechanism. This signal would be transmitted over the length of the cell, which in some cases is over 100-fold greater than the cell diameter. Finally, many spirochetes, including Treponema, Borrelia, and Leptospira, are highly invasive pathogens. Motility is likely to play a major role in the disease process. This review summarizes the progress in the genetics of motility and chemotaxis of spirochetes, and points to new directions for future experimentation.

Bacteria are not too small for spatial sensing of chemical gradients: an experimental evidence

By analyzing the chemotactic behavior of a recently described marine bacterial species, we provide experimental evidence that bacteria are not too small for sensing chemical gradients spatially. The bipolar flagellated vibrioid bacteria (typical size 2 x 6 microm) exhibit a unique motility pattern as they translate along as well as rotate around their short axis, i.e., the pathways of the cell poles describe a double helix. The natural habitat of the bacteria is characterized by steep oxygen gradients where they accumulate in a band at their preferred oxygen concentration of approximately 2 microM. Single cells leaving the band toward the oxic region typically return to the band within 16 s following a U-shaped track. A detailed analysis of the tracks reveals that the cells must be able to sense the oxygen gradient perpendicular to their swimming direction. Thus, they can detect oxygen gradients along a distance of approximately 5 microm corresponding to the extension of their long axis. The observed behavior can be explained by the presence of two independent sensor regions at either cell pole that modulate the rotation speed of the polar flagellar bundles, i.e., the flagellar bundle at the cell pole exposed to higher oxygen concentration is rotating faster than the other bundle. A mathematical model based on these assumptions reproduces the observed swimming behavior of the bacteria.

Binding of the Escherichia coli response regulator CheY to its target measured in vivo by fluorescence resonance energy transfer

In Escherichia coli chemotaxis, signaling depends on modulation of the level of phosphorylation of CheY, a small protein that couples receptors and flagellar motors. Working in vivo, we used fluorescence resonance energy transfer (FRET) to measure the interaction of CheY approximately P with its target, FliM. Binding of CheY approximately P to FliM was found to be much less cooperative than motor switching; however, under the conditions of our experiment, most of the FliM appeared to be in the cytoplasm. We studied signal processing times in the chemotaxis pathway by measuring the changes in CheY approximately P binding to FliM on flash release of caged chemoeffectors. Following sudden addition of attractant, the amount of CheY approximately P bound to FliM decayed exponentially with a rate constant of about 2 s(-1). Following sudden addition of repellent, FliM occupancy increased with a rate constant of about 20 s(-1). Using these data, we were able to construct a simple model for the chemotactic pathway and to estimate values of rate constants for several key reactions.

Construction and characterization of a cheA mutant of Treponema denticola

The Treponema denticola cheA gene, encoding the central kinase of the general chemotaxis pathway, was analyzed for its role in chemotaxis and tissue penetration. The cheA gene was interrupted by insertion of an ermF-ermAM gene cassette. Reverse transcription-PCR confirmed that the other downstream chemotaxis genes within the same operon (cheW, cheX, and cheY) were still expressed in the cheA mutant strain. Lack of cheA resulted in decreased swarming on soft-agar swarm plates and failure to respond chemotactically to a mixture of nutrients. Behavioral analyses using video microscopy revealed that the cheA mutant exhibited coordinated cell movement. The cellular reversal frequency, however, was severely reduced, indicating that CheA in T. denticola mainly controls cellular reversal and that active chemotaxis signaling input is not required for coordination of flagellar rotation at both cell poles.

Evolutionary conservation of methyl-accepting chemotaxis protein location in Bacteria and Archaea

The methyl-accepting chemotaxis proteins (MCPs) are concentrated at the cell poles in an evolutionarily diverse panel of bacteria and an archeon. In elongated cells, the MCPs are located both at the poles and at regions along the length of the cells. Together, these results suggest that MCP location is evolutionarily conserved.

Effects of organic antagonists of Ca(2+), Na(+), and K(+) on chemotaxis and motility of escherichia coli

Various Ca(2+) antagonists used in animal research, many of them known to be Ca(2+) channel blockers, inhibited Escherichia coli chemotaxis (measured as entry of cells into a capillary containing attractant). The most effective of these, acting in the nanomolar range, was omega-conotoxin GVIA. The next most effective were gallopamil and verapamil. At concentrations around 100-fold higher than that needed for inhibition of chemotaxis, each of these antagonists inhibited motility (measured as entry of cells into a capillary lacking attractant). Various other Ca(2+) antagonists were less effective, though chemotaxis was almost always more sensitive to inhibition than was motility. Cells treated with each of these Ca(2+) antagonists swam with a running bias, i.e., tumbling was inhibited. Similarly, some Na(+) antagonists used in animal research inhibited bacterial chemotaxis. E. coli chemotaxis was inhibited by saxitoxin at concentrations above 10(-7) M, while more than 10(-4) M was needed to inhibit motility. Cells treated with saxitoxin swam with a tumbling bias. In the case of other Na(+) antagonists in animals, aconitine inhibited bacterial chemotaxis 10 times more effectively than it inhibited motility, and two others inhibited chemotaxis and motility at about the same concentration. In the case of K(+) antagonists used in animal research, 4-aminopyridine blocked E. coli chemotaxis between 10(-3) M and, totally, 10(-2) M, while motility was not affected at 10(-2) M; on the other hand, tetraethylammonium chloride failed to inhibit either chemotaxis or motility at 10(-2) M.

Motility and chemotaxis of filamentous cells of Escherichia coli

Filamentous cells of Escherichia coli can be produced by treatment with the antibiotic cephalexin, which blocks cell division but allows cell growth. To explore the effect of cell size on chemotactic activity, we studied the motility and chemotaxis of filamentous cells. The filaments, up to 50 times the length of normal E. coli organisms, were motile and had flagella along their entire lengths. Despite their increased size, the motility and chemotaxis of filaments were very similar to those properties of normal-sized cells. Unstimulated filaments of chemotactically normal bacteria ran and stopped repeatedly (while normal-sized bacteria run and tumble repeatedly). Filaments responded to attractants by prolonged running (like normal-sized bacteria) and to repellents by prolonged stopping (unlike normal-sized bacteria, which tumble), until adaptation restored unstimulated behavior (as occurs with normal-sized cells). Chemotaxis mutants that always ran when they were normal sized always ran when they were filament sized, and those mutants that always tumbled when they were normal sized always stopped when they were filament sized. Chemoreceptors in filaments were localized to regions both at the poles and at intervals along the filament. We suggest that the location of the chemoreceptors enables the chemotactic responses observed in filaments. The implications of this work with regard to the cytoplasmic diffusion of chemotaxis components in normal-sized and filamentous E. coli are discussed.

Effect of cellular filamentation on adventurous and social gliding motility of Myxococcus xanthus

Filamentous bacterial cells often provide biological information that is not readily evident in normal-size cells. In this study, the effect of cellular filamentation on gliding motility of Myxococcus xanthus, a Gram-negative social bacterium, was investigated. Elongation of the cell body had different effects on adventurous and social motility of M. xanthus. The rate of A-motility was insensitive to cell-body elongation whereas the rate of S-motility was reduced dramatically as the cell body got longer, indicating that these two motility systems work in different ways. The study also showed that filamentous wild-type cells glide smoothly with relatively straight, long cell bodies. However, filamentous cells of certain social motility mutants showed zigzag, tangled cell bodies on a solid surface, apparently a result of a lack of coordination between different fragments within the filaments. Further genetic and biochemical analyses indicated that the uncoordinated movements of these mutant filaments were correlated with the absence of cell surface fibril materials, indicating a possible new function for fibrils.

Protein mobility in the cytoplasm of Escherichia coli

The rate of protein diffusion in bacterial cytoplasm may constrain a variety of cellular functions and limit the rates of many biochemical reactions in vivo. In this paper, we report noninvasive measurements of the apparent diffusion coefficient of green fluorescent protein (GFP) in the cytoplasm of Escherichia coli. These measurements were made in two ways: by photobleaching of GFP fluorescence and by photoactivation of a red-emitting fluorescent state of GFP (M. B. Elowitz, M. G. Surette, P. E. Wolf, J. Stock, and S. Leibler, Curr. Biol. 7:809-812, 1997). The apparent diffusion coefficient, Da, of GFP in E. coli DH5alpha was found to be 7.7 +/- 2.5 microm2/s. A 72-kDa fusion protein composed of GFP and a cytoplasmically localized maltose binding protein domain moves more slowly, with Da of 2.5 +/- 0.6 microm2/s. In addition, GFP mobility can depend strongly on at least two factors: first, Da is reduced to 3.6 +/- 0.7 microm2/s at high levels of GFP expression; second, the addition to GFP of a small tag consisting of six histidine residues reduces Da to 4.0 +/- 2.0 microm2/s. Thus, a single effective cytoplasmic viscosity cannot explain all values of Da reported here. These measurements have implications for the understanding of intracellular biochemical networks.

CheZ has no effect on flagellar motors activated by CheY13DK106YW

The behaviors of both cheZ-deleted and wild-type cells of Escherichia coli were found to be very sensitive to the level of expression of CheZ, a protein known to accelerate the dephosphorylation of the response regulator CheY-phosphate (CheY-P). However, cells induced to run and tumble by the unphosphorylated mutant protein CheY13DK106YW (CheY**) failed to respond to CheZ, even when CheZ was expressed at high levels. Therefore, CheZ neither affects the flagellar motors directly nor sequesters CheY**. In in vitro cross-linking studies, CheY** promoted trimerization of CheZ to the same extent as wild-type CheY but failed to induce the formation of complexes of higher molecular weight observed with CheY-P. Also, CheY** could be cross-linked to FliM, the motor receptor protein, nearly as well as CheY-P. Thus, to CheZ, CheY** looks like CheY, but to FliM, it looks like CheY-P.

Oligomerization of the phosphatase CheZ upon interaction with the phosphorylated form of CheY. The signal protein of bacterial chemotaxis

Earlier studies have suggested that CheZ, the phosphatase of the signaling protein CheY in bacterial chemotaxis, may be in an oligomeric state both when bound to phosphorylated CheY (CheY approximately P) (Blat, Y., and Eisenbach, M. (1994) Biochemistry 33, 902-906) or free (Stock, A., and Stock, J. B. (1987) J. Bacteriol. 169, 3301-3311). The purpose of the current study was to determine the oligomeric state of free CheZ and to investigate whether it changes upon binding to CheY approximately P. By using either one of two different sets of cross-linking agents, free CheZ was found to be a dimer. The formation of the dimer was specific, as it was prevented by SDS which does not interfere with cross-linking mediated by random collisions. The dimeric form of CheZ was confirmed by sedimentation analysis, a cross-linking-free technique. In the presence of CheY approximately P (but not in the presence of non-phosphorylated CheY), a high molecular size cross-linked complex (90-200 kDa) was formed, in which the CheZ:CheY ratio was 2:1. The size of the oligomeric complex was estimated by fluorescence depolarization to be 4-5-fold larger than the dimer, suggesting that its size is in the order of 200 kDa. These results indicate that CheZ oligomerizes upon interaction with CheY approximately P. This phosphorylation-dependent oligomerization may be a mechanism for regulating CheZ activity.

Chemotactic signal integration in bacteria

Chemotactic signaling in Escherichia coli involves transmission of both negative and positive signals. In order to examine mechanisms of signal processing, behavioral responses to dual inputs have been measured by using photoactivable "caged" compounds, computer video analysis, and chemoreceptor deletion mutants. Signaling from Tar and Tsr, two receptors that sense amino acids and pH, was studied. In a Tar deletion mutant the photoactivated release of protons, a Tsr repellent, and of serine, a Tsr attractant, in separate experiments at pH 7.0 resulted in tumbling (negative) or smooth-swimming (positive) responses in ca. 50 and 140 ms, respectively. Simultaneous photorelease of protons and serine resulted in a single tumbling or smooth-swimming response, depending on the relative amounts of the two effectors. In contrast, in wild-type E. coli, proton release at pH 7.0 resulted in a biphasic response that was attributed to Tsr-mediated tumbling followed by Tar-mediated smooth-swimming. In wild-type E. coli at more alkaline pH values the Tar-mediated signal was stronger than the Tsr signal, resulting in a strong smooth-swimming response preceded by a diminished tumbling response. These observations imply that (i) a single receptor time-averages the binding of different chemotactic ligands generating a single response; (ii) ligand binding to different receptors can result in a nonintegrated response with the tumbling response preceding the smooth-swimming response; (iii) however, chemotactic signals of different intensities derived from different receptors can also result in an apparently integrated response; and (iv) the different chemotactic responses to protons at neutral and alkaline pH may contribute to E. coli migration toward neutrality.

CheZ mutants with enhanced ability to dephosphorylate CheY, the response regulator in bacterial chemotaxis

CheZ is a component of the chemotaxis signal-transduction pathway in Escherichia coli and Salmonella typhimurium. It is responsible for accelerating dephosphorylation of CheY and thereby antagonizing the tumble-promoting activity of CheY. In the absence of functional CheZ, cells are non-chemotactic and tumble constantly. We characterized the effects of two mutations in CheZ, R54C and V166G, that are unusual in that they cause cells to have a smooth swimming bias. These mutations were isolated as second-site suppressors of mutations in the switch complex responsible for regulating the direction of flagellar rotation (Yamaguchi, S., Aizawa, S.-I., Kihara, M. Isomura, M., Jones, C.J. and Macnab, R.M. (1986) J. Bacteriol. 168, 1172-1179). When produced at low levels in a delta cheZ host strain, CheZ R54C and CheZ V166G supported chemotaxis. However, when moderately overproduced they markedly inhibited chemotactic ability. In vitro studies revealed that these mutations enhanced the ability of CheZ to accelerate dephosphorylation of CheY. These results are discussed in relation to the possible roles and interactions of CheZ in the chemotaxis system.

Behavioral responses of Escherichia coli to changes in temperature caused by electric shock

The behavioral response of Escherichia coli to electric shock in 10(-2) M potassium phosphate plus 10(-4) M potassium EDTA was studied. When presented with a 150-V/cm electric shock that lasted 250 ms, the bacteria at first exclusively ran, then exclusively tumbled, and finally returned to their original running and tumbling. This response is due to increased temperature caused by the electric shock, i.e., to thermotaxis, and it is mediated by the chemotaxis machinery. A more severe electric shock, 150 V/cm for 550 ms, caused cells to tumble immediately, and then they went back to their original running and tumbling. The mechanism of that response is unknown since, unlike known thermotaxis, it does not require the chemotaxis machinery.