Large increases in attractant concentration disrupt the polar localization of bacterial chemoreceptors

Recent Developments in Bacterial Chemotaxis Analysis Based on the Microfluidic System

Bacterial motility in response to chemicals, also called bacterial chemotaxis, is a critical ability to search for the optimal environment to ensure the survival of bacterial species. Recent advances in microbiology have allowed the engineering of bacterial chemotactic properties. Conventional methods for characterizing bacterial motility are not able to fully monitor chemotactic behavior. Developments in microfluidic technology have enabled the designing of new experimental protocols in which spatiotemporal control of the cellular microenvironment can be achieved, and in which bacterial motility can be precisely and quantitatively measured and compared. This review provides an overview of recent developments of and new insights into microfluidic systems for chemotaxis assay.

Lighting up my life: a LOV-based fluorescent reporter for Campylobacter jejuni

In this study, a LOV-based fluorescent reporter (light, oxygen, or voltage-sensing domains of phototropin), termed iLOV, was adapted for Campylobacter jejuni and used to investigate promoter activity via monitoring fluorescence intensity and to study the localisation of two chemotaxis proteins. The pC46 complementation vector contains coding sequence from cj0046, a C. jejuni NCTC11168 pseudo-gene and is used to integrate cloned genes onto the C. jejuni chromosome. The pC46 vector was used to construct plasmids containing iLOV, driven by three different C. jejuni constitutive promoters and plasmids containing transcriptional fusions of the iLOV reporter and two chemoreceptors, tlp5 and tlp8. Expression from the porA promoter, pporA, produced the highest fluorescence signals compared to pfdxA (intermediate level) and pmetK (lowest level). The cellular localisation pattern of transducer-like protein (Tlp) clusters, containing Tlp5 and Tlp8, was predominately polar, with Tlp5 positioned only at one and Tlp8 at both poles. Here, we demonstrate that a iLOV fluorescent reporter can be used as a promoter probe or as a gene fusion reporter in Campylobacter spp. This is a new system uniquely placed for studying Campylobacter spp., as it combines resistance to photobleaching and functionality under microaerobic conditions.

Progress and Potential of Electron Cryotomography as Illustrated by Its Application to Bacterial Chemoreceptor Arrays

Electron cryotomography (ECT) can produce three-dimensional images of biological samples such as intact cells in a near-native, frozen-hydrated state to macromolecular resolution (∼4 nm). Because one of its first and most common applications has been to bacterial chemoreceptor arrays, ECT's contributions to this field illustrate well its past, present, and future. While X-ray crystallography and nuclear magnetic resonance spectroscopy have revealed the structures of nearly all the individual components of chemoreceptor arrays, ECT has revealed the mesoscale information about how the components are arranged within cells. Receptors assemble into a universally conserved 12-nm hexagonal lattice linked by CheA/CheW rings. Membrane-bound arrays are single layered; cytoplasmic arrays are double layered. Images of in vitro reconstitutions have led to a model of how arrays assemble, and images of native arrays in different states have shown that the conformational changes associated with signal transduction are subtle, constraining models of activation and system cooperativity. Phase plates, better detectors, and more stable stages promise even higher resolution and broader application in the near future.

Physiological and transcriptomic analyses reveal mechanistic insight into the adaption of marine Bacillus subtilis C01 to alumina nanoparticles

An increasing number of studies have investigated the effects of nanoparticles (NPs) on microbial systems; however, few existing reports have focused on the defense mechanisms of bacteria against NPs. Whether secondary metabolism biosynthesis is a response to NP stress and contributes to the adaption of bacteria to NPs is unclear. Here, a significant induction in the surfactin production and biofilm formation were detected by adding Al2O3 NPs to the B. subtilis fermentation broth. Physiological analysis showed that Al2O3 NP stress could also affect the cell and colony morphogenesis and inhibit the motility and sporulation. Exogenously adding commercial surfactin restored the swarming motility. Additionally, a suite of toxicity assays analyzing membrane damage, cellular ROS generation, electron transport activity and membrane potential was used to determine the molecular mechanisms of toxicity of Al2O3 NPs. Furthermore, whole transcriptomic analysis was used to elucidate the mechanisms of B. subtilis adaption to Al2O3 NPs. These results revealed several mechanisms by which marine B. subtilis C01 adapt to Al2O3 NPs. Additionally, this study broadens the applications of nanomaterials and describes the important effects on secondary metabolism and multicellularity regulation by using Al2O3 NPs or other nano-products.

The Helicobacter pylori CZB Cytoplasmic Chemoreceptor TlpD Forms an Autonomous Polar Chemotaxis Signaling Complex That Mediates a Tactic Response to Oxidative Stress

Cytoplasmic chemoreceptors are widespread among prokaryotes but are far less understood than transmembrane chemoreceptors, despite being implicated in many processes. One such cytoplasmic chemoreceptor is Helicobacter pylori TlpD, which is required for stomach colonization and drives a chemotaxis response to cellular energy levels. Neither the signals sensed by TlpD nor its molecular mechanisms of action are known. We report here that TlpD functions independently of the other chemoreceptors. When TlpD is the sole chemoreceptor, it is able to localize to the pole and recruits CheW, CheA, and at least two CheV proteins to this location. It loses the normal membrane association that appears to be driven by interactions with other chemoreceptors and with CheW, CheV1, and CheA. These results suggest that TlpD can form an autonomous signaling unit. We further determined that TlpD mediates a repellent chemotaxis response to conditions that promote oxidative stress, including being in the presence of iron, hydrogen peroxide, paraquat, and metronidazole. Last, we found that all tested H. pylori strains express TlpD, whereas other chemoreceptors were present to various degrees. Our data suggest a model in which TlpD coordinates a signaling complex that responds to oxidative stress and may allow H. pylori to avoid areas of the stomach with high concentrations of reactive oxygen species.

IMPORTANCE

Helicobacter pylori senses its environment with proteins called chemoreceptors. Chemoreceptors integrate this sensory information to affect flagellum-based motility in a process called chemotaxis. Chemotaxis is employed during infection and presumably aids H. pylori in encountering and colonizing preferred niches. A cytoplasmic chemoreceptor named TlpD is particularly important in this process, and we report here that this chemoreceptor is able to operate independently of other chemoreceptors to organize a chemotaxis signaling complex and mediate a repellent response to oxidative stress conditions. H. pylori encounters and must cope with oxidative stress during infection due to oxygen and reactive oxygen species produced by host cells. TlpD's repellent response may allow the bacteria to escape niches experiencing inflammation and elevated reactive oxygen species (ROS) production.

Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway

Understanding the principles underlying the plasticity of signal transduction networks is fundamental to decipher the functioning of living cells. In Myxococcus xanthus, a particular chemosensory system (Frz) coordinates the activity of two separate motility systems (the A- and S-motility systems), promoting multicellular development. This unusual structure asks how signal is transduced in a branched signal transduction pathway. Using combined evolution-guided and single cell approaches, we successfully uncoupled the regulations and showed that the A-motility regulation system branched-off an existing signaling system that initially only controlled S-motility. Pathway branching emerged in part following a gene duplication event and changes in the circuit structure increasing the signaling efficiency. In the evolved pathway, the Frz histidine kinase generates a steep biphasic response to increasing external stimulations, which is essential for signal partitioning to the motility systems. We further show that this behavior results from the action of two accessory response regulator proteins that act independently to filter and amplify signals from the upstream kinase. Thus, signal amplification loops may underlie the emergence of new connectivity in signal transduction pathways.

Internal sense of direction: sensing and signaling from cytoplasmic chemoreceptors

SUMMARY

Chemoreceptors sense environmental signals and drive chemotactic responses in Bacteria and Archaea. There are two main classes of chemoreceptors: integral inner membrane and soluble cytoplasmic proteins. The latter were identified more recently than integral membrane chemoreceptors and have been studied much less thoroughly. These cytoplasmic chemoreceptors are the subject of this review. Our analysis determined that 14% of bacterial and 43% of archaeal chemoreceptors are cytoplasmic, based on currently sequenced genomes. Cytoplasmic chemoreceptors appear to share the same key structural features as integral membrane chemoreceptors, including the formations of homodimers, trimers of dimers, and 12-nm hexagonal arrays within the cell. Cytoplasmic chemoreceptors exhibit varied subcellular locations, with some localizing to the poles and others appearing both cytoplasmic and polar. Some cytoplasmic chemoreceptors adopt more exotic locations, including the formations of exclusively internal clusters or moving dynamic clusters that coalesce at points of contact with other cells. Cytoplasmic chemoreceptors presumably sense signals within the cytoplasm and bear diverse signal input domains that are mostly N terminal to the domain that defines chemoreceptors, the so-called MA domain. Similar to the case for transmembrane receptors, our analysis suggests that the most common signal input domain is the PAS (Per-Arnt-Sim) domain, but a variety of other N-terminal domains exist. It is also common, however, for cytoplasmic chemoreceptors to have C-terminal domains that may function for signal input. The most common of these is the recently identified chemoreceptor zinc binding (CZB) domain, found in 8% of all cytoplasmic chemoreceptors. The widespread nature and diverse signal input domains suggest that these chemoreceptors can monitor a variety of cytoplasmically based signals, most of which remain to be determined.

Metabolism Dependent Chemotaxis of Pseudomonas aeruginosa N1 Towards Anionic Detergent Sodium Dodecyl Sulfate

Sodium dodecyl sulfate (SDS) is one of the most commonly used detergent, which exhibits excellent biocidal activity against various bacteria and fungi. It is commonly employed in many detergent formulations and is employed for disinfection purposes. It is shown to be toxic to fishes, aquatic animals and is also inhibitory to microbes and cyanobacteria. We had isolated a strain belonging to Pseudomonas aeruginosa N1, from a detergent contaminated pond situated in Varanasi city India, which was able to degrade and metabolize SDS as a source of carbon. In the present investigation, we have studied chemotactic response of this strain towards SDS. The results clearly indicate that this strain showed chemotactic response towards SDS. The nature of chemotaxis was found to be metabolism dependent as glucose grown cells showed a delayed chemotactic response towards SDS. This is first study that reported chemotaxis response for P. aeruginosa towards anionic detergent SDS.

The mobility of two kinase domains in the Escherichia coli chemoreceptor array varies with signalling state

Motile bacteria sense their physical and chemical environment through highly cooperative, ordered arrays of chemoreceptors. These signalling complexes phosphorylate a response regulator which in turn governs flagellar motor reversals, driving cells towards favourable environments. The structural changes that translate chemoeffector binding into the appropriate kinase output are not known. Here, we apply high-resolution electron cryotomography to visualize mutant chemoreceptor signalling arrays in well-defined kinase activity states. The arrays were well ordered in all signalling states, with no discernible differences in receptor conformation at 2-3 nm resolution. Differences were observed, however, in a keel-like density that we identify here as CheA kinase domains P1 and P2, the phosphorylation site domain and the binding domain for response regulator target proteins. Mutant receptor arrays with high kinase activities all exhibited small keels and high proteolysis susceptibility, indicative of mobile P1 and P2 domains. In contrast, arrays in kinase-off signalling states exhibited a range of keel sizes. These findings confirm that chemoreceptor arrays do not undergo large structural changes during signalling, and suggest instead that kinase activity is modulated at least in part by changes in the mobility of key domains.

The protein interaction network of a taxis signal transduction system in a halophilic archaeon

Background

The taxis signaling system of the extreme halophilic archaeon Halobacterium (Hbt.) salinarum differs in several aspects from its model bacterial counterparts Escherichia coli and Bacillus subtilis. We studied the protein interactions in the Hbt. salinarum taxis signaling system to gain an understanding of its structure, to gain knowledge about its known components and to search for new members.

Results

The interaction analysis revealed that the core signaling proteins are involved in different protein complexes and our data provide evidence for dynamic interchanges between them. Fifteen of the eighteen taxis receptors (halobacterial transducers, Htrs) can be assigned to four different groups depending on their interactions with the core signaling proteins. Only one of these groups, which contains six of the eight Htrs with known signals, shows the composition expected for signaling complexes (receptor, kinase CheA, adaptor CheW, response regulator CheY). From the two Hbt. salinarum CheW proteins, only CheW1 is engaged in signaling complexes with Htrs and CheA, whereas CheW2 interacts with Htrs but not with CheA. CheY connects the core signaling structure to a subnetwork consisting of the two CheF proteins (which build a link to the flagellar apparatus), CheD (the hub of the subnetwork), two CheC complexes and the receptor methylesterase CheB.

Conclusions

Based on our findings, we propose two hypotheses. First, Hbt. salinarum might have the capability to dynamically adjust the impact of certain Htrs or Htr clusters depending on its current needs or environmental conditions. Secondly, we propose a hypothetical feedback loop from the response regulator to Htr methylation made from the CheC proteins, CheD and CheB, which might contribute to adaptation analogous to the CheC/CheD system of B. subtilis.

Tandem adaptation with a common design in Escherichia coli chemotaxis

We analyze a model for motor-level adaptation in Escherichia coli based upon the premise that clockwise (CW) and counter-clockwise (CCW) states have different preferred numbers of FliM subunits. We show that this model provides a simple mechanism for the recently observed motor-level adaptation, and it also explains the long-lasting puzzle on the thresholds observed when tethered cells are used to monitor responses to temporal ramps. We note that the motor-level adaptation has the same negative-feedback network design as the upstream receptor-level adaptation, and the tandem architecture of one control circuit followed by the other mitigates the effects of cell-to-cell variation and broadens the range of stimuli over which cells optimally respond.

Ligand affinity and kinase activity are independent of bacterial chemotaxis receptor concentration: insight into signaling mechanisms

Binding of attractant to bacterial chemotaxis receptors initiates a transmembrane signal that inhibits the kinase CheA bound ~300 Å distant at the other end of the receptor. Chemoreceptors form large clusters in many bacterial species, and the extent of clustering has been reported to vary with signaling state. To test whether ligand binding regulates kinase activity by modulating a clustering equilibrium, we measured the effects of two-dimensional receptor concentration on kinase activity in proteoliposomes containing the purified Escherichia coli serine receptor reconstituted into vesicles over a range of lipid:protein molar ratios. The IC(50) of kinase inhibition was unchanged despite a 10-fold change in receptor concentration. Such a change in concentration would have produced a measurable shift in the IC(50) if receptor clustering were involved in kinase regulation, based on a simple model in which the receptor oligomerization and ligand binding equilibria are coupled. These results indicate that the primary signal, ligand control of kinase activity, does not involve a change in receptor oligomerization state. In combination with previous work on cytoplasmic fragments assembled on vesicle surfaces [Besschetnova, T. Y., et al. (2008) Proc. Natl. Acad. Sci. U.S.A.105, 12289-12294], this suggests that binding of ligand to chemotaxis receptors inhibits the kinase by inducing a conformational change that expands the membrane area occupied by the receptor cytoplasmic domain, without changing the number of associated receptors in the signaling complex.

Activated chemoreceptor arrays remain intact and hexagonally packed

Bacterial chemoreceptors cluster into exquisitively sensitive, tunable, highly ordered, polar arrays. While these arrays serve as paradigms of cell signalling in general, it remains unclear what conformational changes transduce signals from the periplasmic tips, where attractants and repellents bind, to the cytoplasmic signalling domains. Conflicting reports support and contest the hypothesis that activation causes large changes in the packing arrangement of the arrays, up to and including their complete disassembly. Using electron cryotomography, here we show that in Caulobacter crescentus, chemoreceptor arrays in cells grown in different media and immediately after exposure to the attractant galactose all exhibit the same 12 nm hexagonal packing arrangement, array size and other structural parameters. ΔcheB and ΔcheR mutants mimicking attractant- or repellent-bound states prior to adaptation also show the same lattice structure. We conclude that signal transduction and amplification must be accomplished through only small, nanoscale conformational changes.

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.

Cellular stoichiometry of the chemotaxis proteins in Bacillus subtilis

The chemoreceptor-CheA kinase-CheW coupling protein complex, with ancillary associated proteins, is at the heart of chemotactic signal transduction in bacteria. The goal of this work was to determine the cellular stoichiometry of the chemotaxis signaling proteins in Bacillus subtilis. Quantitative immunoblotting was used to determine the total number of chemotaxis proteins in a single cell of B. subtilis. Significantly higher levels of chemoreceptors and much lower levels of CheA kinase were measured in B. subtilis than in Escherichia coli. The resulting cellular ratio of chemoreceptor dimers per CheA dimer in B. subtilis is roughly 23.0 ± 4.5 compared to 3.4 ± 0.8 receptor dimers per CheA dimer observed in E. coli, but the ratios of the coupling protein CheW to the CheA dimer are nearly identical in the two organisms. The ratios of CheB to CheR in B. subtilis are also very similar, although the overall levels of modification enzymes are higher. When the potential binding partners of CheD are deleted, the levels of CheD drop significantly. This finding suggests that B. subtilis selectively degrades excess chemotaxis proteins to maintain optimum ratios. Finally, the two cytoplasmic receptors were observed to localize among the other receptors at the cell poles and appear to participate in the chemoreceptor complex. These results suggest that there are many novel features of B. subtilis chemotaxis compared with the mechanism in E. coli, but they are built on a common core.

Attractant binding induces distinct structural changes to the polar and lateral signaling clusters in Bacillus subtilis chemotaxis

Bacteria employ a modified two-component system for chemotaxis, where the receptors form ternary complexes with CheA histidine kinases and CheW adaptor proteins. These complexes are arranged in semi-ordered arrays clustered predominantly at the cell poles. The prevailing models assume that these arrays are static and reorganize only locally in response to attractant binding. Recent studies have shown, however, that these structures may in fact be much more fluid. We investigated the localization of the chemotaxis signaling arrays in Bacillus subtilis using immunofluorescence and live cell fluorescence microscopy. We found that the receptors were localized in clusters at the poles in most cells. However, when the cells were exposed to attractant, the number exhibiting polar clusters was reduced roughly 2-fold, whereas the number exhibiting lateral clusters distinct from the poles increased significantly. These changes in receptor clustering were reversible as polar localization was reestablished in adapted cells. We also investigated the dynamic localization of CheV, a hybrid protein consisting of an N-terminal CheW-like adaptor domain and a C-terminal response regulator domain that is known to be phosphorylated by CheA, using immunofluorescence. Interestingly, we found that CheV was localized predominantly at lateral clusters in unstimulated cells. However, upon exposure to attractant, CheV was found to be predominantly localized to the cell poles. Moreover, changes in CheV localization are phosphorylation-dependent. Collectively, these results suggest that the chemotaxis signaling arrays in B. subtilis are dynamic structures and that feedback loops involving phosphorylation may regulate the positioning of individual proteins.

Site-specific methylation in Bacillus subtilis chemotaxis: effect of covalent modifications to the chemotaxis receptor McpB

The Bacillus subtilis chemotaxis pathway employs a receptor methylation system that functions differently from the one in the canonical Escherichia coli pathway. Previously, we hypothesized that B. subtilis employs a site-specific methylation system for adaptation where methyl groups are added and removed at different sites. This study investigated how covalent modifications to the adaptation region of the chemotaxis receptor McpB altered its apparent affinity for its cognate ligand, asparagine, and also its ability to activate the CheA kinase. This receptor has three closely spaced adaptation sites located at residues Gln371, Glu630 and Glu637. We found that amidation, a putative methylation mimic, of site 371 increased the receptor's apparent affinity for asparagine and its ability to activate the CheA kinase. Conversely, amidation of sites 630 and 637 reduced the receptor's ability to activate the kinase but did not affect the apparent affinity for asparagine, suggesting that activity and sensitivity are independently controlled in B. subtilis. We also examined how electrostatic interactions may underlie this behaviour, using homology models. These findings further our understanding of the site-specific methylation system in B. subtilis by demonstrating how the modification of specific sites can have varying effects on receptor function.

CheV: CheW-like coupling proteins at the core of the chemotaxis signaling network

Microbes have chemotactic signaling systems that enable them to detect and follow chemical gradients in their environments. The core of these sensory systems consists of chemoreceptor proteins coupled to the CheA kinase via the scaffold or coupler protein CheW. Some bacterial chemotaxis systems replace or augment CheW with a related protein, CheV, which is less well understood. CheV consists of a CheW domain fused to a receiver domain that is capable of being phosphorylated. Our review of the literature, as well as comparisons of the CheV and CheW sequence and structure, suggest that CheV proteins conserve CheW residues that are crucial for coupling. Phosphorylation of the CheV receiver domain might adjust the efficiency of its coupling and thus allow the system to modulate the response to chemical stimuli in an adaptation process.

Structure of the ternary complex formed by a chemotaxis receptor signaling domain, the CheA histidine kinase, and the coupling protein CheW as determined by pulsed dipolar ESR spectroscopy

The signaling apparatus that controls bacterial chemotaxis is composed of a core complex containing chemoreceptors, the histidine autokinase CheA, and the coupling protein CheW. Site-specific spin labeling and pulsed dipolar ESR spectroscopy (PDS) have been applied to investigate the structure of a soluble ternary complex formed by Thermotoga maritima CheA (TmCheA), CheW, and receptor signaling domains. Thirty-five symmetric spin-label sites (SLSs) were engineered into the five domains of the CheA dimer and CheW to provide distance restraints within the CheA:CheW complex in the absence and presence of a soluble receptor that inhibits kinase activity (Tm14). Additional PDS restraints among spin-labeled CheA, CheW, and an engineered single-chain receptor labeled at six different sites allow docking of the receptor structure relative to the CheA:CheW complex. Disulfide cross-linking between selectively incorporated Cys residues finds two pairs of positions that provide further constraints within the ternary complex: one involving Tm14 and CheW and another involving Tm14 and CheA. The derived structure of the ternary complex indicates a primary site of interaction between CheW and Tm14 that agrees well with previous biochemical and genetic data for transmembrane chemoreceptors. The PDS distance distributions are most consistent with only one CheW directly engaging one dimeric Tm14. The CheA dimerization domain (P3) aligns roughly antiparallel to the receptor-conserved signaling tip but does not interact strongly with it. The angle of the receptor axis with respect to P3 and the CheW-binding P5 domains is bound by two limits differing by approximately 20 degrees . In one limit, Tm14 aligns roughly along P3 and may interact to some extent with the hinge region near the P3 hairpin loop. In the other limit, Tm14 tilts to interact with the P5 domain of the opposite subunit in an interface that mimics that observed with the P5 homologue CheW. The time domain ESR data can be simulated from the model only if orientational variability is introduced for the P5 and, especially, P3 domains. The Tm14 tip also binds beside one of the CheA kinase domains (P4); however, in both bound and unbound states, P4 samples a broad range of distributions that are only minimally affected by Tm14 binding. The CheA P1 domains that contain the substrate histidine are also broadly distributed in space under all conditions. In the context of the hexagonal lattice formed by trimeric transmembrane chemoreceptors, the PDS structure is best accommodated with the P3 domain in the center of a honeycomb edge.

Motility and chemotaxis in alkaliphilic Bacillus species

Alkaliphilic Bacillus species grow at pH values up to approximately 11. Motile alkaliphilic Bacillus use electrochemical gradients of Na(+) (sodium-motive force) to power ion-coupled, flagella-mediated motility as opposed to the electrochemical gradients of H(+) (proton-motive force) used by most neutralophilic bacteria. Membrane-embedded stators of bacterial flagella contain ion channels through which either H(+) or Na(+) flow to energize flagellar rotation. Stators of the major H(+)-coupled type, MotAB, are distinguishable from Na(+)-coupled stators, PomAB of marine bacteria and MotPS of alkaliphilic Bacillus. Dual ion-coupling capacity is found in neutralophilic Bacillus strains with both MotAB and MotPS. There is also a MotAB variant that uses both coupling ions, switching as a function of pH. Chemotaxis of alkaliphilic Bacillus depends upon flagellar motility but also requires a distinct voltage-gated NaChBac-type channel. The two alkaliphile Na(+) channels provide new vistas on the diverse adaptations of sensory responses in bacteria.

Flow cytometry reveals that multivalent chemoattractants effect swarmer cell dedifferentiation

Bacterial cells can differentiate into states that allow them to respond efficiently to their environment. An example of such a transformation is the differentiation of planktonic bacteria into highly motile swarmer cells. The hyperflagellated, filamentous swarmer cells can use coordinated movement to seek out and colonize new sites for pathogenic infection. Because the chemotaxis proteins are essential for swarmer differentiation, we sought to probe the relationship between differentiation and chemoattractants. To this end, we developed a method to screen large populations of swarmer cells using flow cytometry. Using this approach, we found that highly potent multivalent chemoattractants can induce the dedifferentiation of swarmer cells. Our results indicate that chemotactic signaling functions as a target for agents that interfere with bacterial swarming. In addition, the identification of ligands that promote the dedifferentiation of swarmer cells offers new strategies for modulating this multicellular behavior.

Flow-based microfluidic device for quantifying bacterial chemotaxis in stable, competing gradients

Chemotaxis is the migration of cells in gradients of chemoeffector molecules. Although multiple, competing gradients must often coexist in nature, conventional approaches for investigating bacterial chemotaxis are suboptimal for quantifying migration in response to gradients of multiple signals. In this work, we developed a microfluidic device for generating precise and stable gradients of signaling molecules. We used the device to investigate the effects of individual and combined chemoeffector gradients on Escherichia coli chemotaxis. Laminar flow-based diffusive mixing was used to generate gradients, and the chemotactic responses of cells expressing green fluorescent protein were determined using fluorescence microscopy. Quantification of the migration profiles indicated that E. coli was attracted to the quorum-sensing molecule autoinducer-2 (AI-2) but was repelled from the stationary-phase signal indole. Cells also migrated toward higher concentrations of isatin (indole-2,3-dione), an oxidized derivative of indole. Attraction to AI-2 overcame repulsion by indole in equal, competing gradients. Our data suggest that concentration-dependent interactions between attractant and repellent signals may be important determinants of bacterial colonization of the gut.

Polar chemoreceptor clustering by coupled trimers of dimers

Receptors of bacterial chemotaxis form clusters at the cell poles, where clusters act as "antennas" to amplify small changes in ligand concentration. It is worthy of note that chemoreceptors cluster at multiple length scales. At the smallest scale, receptors form dimers, which assemble into stable timers of dimers. At a large scale, trimers form large polar clusters composed of thousands of receptors. Although much is known about the signaling properties emerging from receptor clusters, it is unknown how receptors localize at the cell poles and what the determining factors are for cluster size. Here, we present a model of polar receptor clustering based on coupled trimers of dimers, where cluster size is determined as a minimum of the cluster-membrane free energy. This energy has contributions from the cluster-membrane elastic energy, penalizing large clusters due to their high intrinsic curvature, and receptor-receptor coupling that favors large clusters. We find that the reduced cluster-membrane curvature mismatch at the curved cell poles leads to large and robust polar clusters, in line with experimental observation, whereas lateral clusters are efficiently suppressed.

Receptor density balances signal stimulation and attenuation in membrane-assembled complexes of bacterial chemotaxis signaling proteins

All cells possess transmembrane signaling systems that function in the environment of the lipid bilayer. In the Escherichia coli chemotaxis pathway, the binding of attractants to a two-dimensional array of receptors and signaling proteins simultaneously inhibits an associated kinase and stimulates receptor methylation--a slower process that restores kinase activity. These two opposing effects lead to robust adaptation toward stimuli through a physical mechanism that is not understood. Here, we provide evidence of a counterbalancing influence exerted by receptor density on kinase stimulation and receptor methylation. Receptor signaling complexes were reconstituted over a range of defined surface concentrations by using a template-directed assembly method, and the kinase and receptor methylation activities were measured. Kinase activity and methylation rates were both found to vary significantly with surface concentration--yet in opposite ways: samples prepared at high surface densities stimulated kinase activity more effectively than low-density samples, whereas lower surface densities produced greater methylation rates than higher densities. FRET experiments demonstrated that the cooperative change in kinase activity coincided with a change in the arrangement of the membrane-associated receptor domains. The counterbalancing influence of density on receptor methylation and kinase stimulation leads naturally to a model for signal regulation that is compatible with the known logic of the E. coli pathway. Density-dependent mechanisms are likely to be general and may operate when two or more membrane-related processes are influenced differently by the two-dimensional concentration of pathway elements.

Variable sizes of Escherichia coli chemoreceptor signaling teams

Like many sensory receptors, bacterial chemotaxis receptors form clusters. In bacteria, large-scale clusters are subdivided into signaling teams that act as ‘antennas' allowing detection of ligands with remarkable sensitivity. The range of sensitivity is greatly extended by adaptation of receptors to changes in concentrations through covalent modification. However, surprisingly little is known about the sizes of receptor signaling teams. Here, we combine measurements of the signaling response, obtained from in vivo fluorescence resonance energy transfer, with the statistical method of principal component analysis, to quantify the size of signaling teams within the framework of the previously successful Monod–Wyman–Changeux model. We find that size of signaling teams increases 2- to 3-fold with receptor modification, indicating an additional, previously unrecognized level of adaptation of the chemotaxis network. This variation of signaling-team size shows that receptor cooperativity is dynamic and likely optimized for sensing noisy ligand concentrations.

Stochastic assembly of chemoreceptor clusters in Escherichia coli

Chemoreceptors and cytoplasmic chemotaxis proteins in Escherichia coli form clusters that play a key role in signal processing. These clusters localize at cell poles and at specific positions along the cell body which correspond to future division sites, but the details of cluster formation and the mechanism of cluster distribution remain unclear. Here, we used fluorescence microscopy to investigate how the numbers and sizes of receptor clusters depend on the expression level of chemotaxis proteins and on the cell length. We show that the average cluster number saturates at high levels of protein expression at approximately 3.7 clusters per cell, well below the number of available positioning sites. Correspondingly, distances between clusters in filamentous cells saturate at an average of 1 mum but, even at saturating expression levels, individual cluster numbers and distances show a broad distribution around the mean. Our data imply a stochastic mode of cluster assembly, where a defined average interval between clusters along the cell body arises from competition between nucleation of new clusters and growth of existing clusters. Upon subsequent anchorage to defined lateral sites, clusters grow with rates that inversely depend on their size, and become polar upon several rounds of cell division.

The voltage-gated Na+ channel NaVBP co-localizes with methyl-accepting chemotaxis protein at cell poles of alkaliphilic Bacillus pseudofirmus OF4

Na(V)BP, found in alkaliphilic Bacillus pseudofirmus OF4, is a member of the bacterial voltage-gated Na(+) channel superfamily. The alkaliphile requires Na(V)BP for normal chemotaxis responses and for optimal pH homeostasis during a shift to alkaline conditions at suboptimally low Na(+) concentrations. We hypothesized that interaction of Na(V)BP with one or more other proteins in vivo, specifically methyl-accepting chemotaxis proteins (MCPs), is involved in activation of the channel under the pH conditions that exist in the extremophile and could underpin its role in chemotaxis; MCPs transduce chemotactic signals and generally localize to cell poles of rod-shaped cells. Here, immunofluorescence microscopy and fluorescent protein fusion studies showed that an alkaliphile protein (designated McpX) that cross-reacts with antibodies raised against Bacillus subtilis McpB co-localizes with Na(V)BP at the cell poles of B. pseudofirmus OF4. In a mutant in which Na(V)BP-encoding ncbA is deleted, the content of McpX was close to the wild-type level but McpX was significantly delocalized. A mutant of B. pseudofirmus OF4 was constructed in which cheAW expression was disrupted to assess whether this mutation impaired polar localization of McpX, as expected from studies in Escherichia coli and Salmonella, and, if so, whether Na(V)BP would be similarly affected. Polar localization of both McpX and Na(V)BP was decreased in the cheAW mutant. The results suggest interactions between McpX and Na(V)BP that affect their co-localization. The inverse chemotaxis phenotype of ncbA mutants may result in part from MCP delocalization.

Chemical probes of bacterial signal transduction reveal that repellents stabilize and attractants destabilize the chemoreceptor array

The signal transduction cascade responsible for bacterial chemotaxis serves as a model for understanding how cells perceive and respond to their environments. Bacteria react to chemotactic signals by migrating toward attractants and away from repellents. Recent data suggest that the amplification of attractant stimuli depends on receptor collaboration: occupied and unoccupied chemoreceptors act together to relay attractant signals. Attractant signal transmission, therefore, depends on the organization of the chemoreceptors into a lattice of signaling proteins. The importance of this lattice for transducing repellent signals was unexplored. Here, we investigate the role of inter-receptor communication on repellent responses in Escherichia coli. Previously, we found that multivalent displays of attractants are more potent than their monovalent counterparts. To examine the importance of the chemoreceptor lattice in repellent signaling, we synthesized ligands displaying multiple copies of the repellent leucine. Monomeric leucine and low-valency leucine-displaying polymers were sensed as repellents. In contrast, multivalent displays of leucine capable of binding multiple chemoreceptors function not as potent repellents but as attractants. Intriguingly, chemical cross-linking studies indicate that these multivalent ligands, like monovalent attractants, disrupt the cellular chemoreceptor lattice. Thus, repellents stabilize the intrinsic chemoreceptor lattice, and attractants destabilize it. These results indicate that signals can be transmitted with high sensitivity via the disruption of protein-protein interactions. Moreover, our data demonstrate that repellents can be transformed into attractants merely by their multivalent display. These results have implications for designing agonists and antagonists for other signaling systems.

How the "melting" and "freezing" of protein molecules may be used in cell signaling

The motile response of Escherichia coli bacteria to attractants and repellents is one of the best-understood examples of a signal transduction pathway. A number of recent studies suggest that the receptors in this system undergo major changes in both their degree of structural order and their state of aggregation in the membrane. We discuss the thermodynamic basis for this effect and argue that the "freezing" or "melting" of protein structure may be the language of signaling.

Formation and activity of template-assembled receptor signaling complexes

Problems in membrane biology require methods to recreate the interactions between receptors and cytoplasmic signaling proteins at the membrane surface. Here, unilamellar vesicles composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine and a nickel-chelating lipid were used as templates to direct the assembly of proteins from the Escherichia coli chemotaxis signaling pathway. The bacterial chemoreceptors are known to form clusters, which promote the binding of the adaptor protein (CheW) and the kinase (CheA). When CheA was incubated with vesicles, CheW, and a histidine-tagged cytoplasmic domain fragment of the aspartate chemoreceptor (CF), the kinase activity was stimulated approximately 300-fold. Activity and pull-down assays were used with dynamic light scattering and electron microscopy to characterize the protein-vesicle compositions that were correlated with the high levels of activity, which demonstrated that CF-CheW-CheA complexes on the vesicle surface were the active entities. Assembly and stimulation occurred with vesicles of different sizes and CFs in different extents of glutamine substitution (in place of glutamate) at physiologically relevant sites. An exception was the combination of sonicated vesicles with the unsubstituted CF, which displayed lower CheA activity. The lower activity was attributed to the high curvature of the sonicated vesicles and a weaker tendency of the unsubstituted CF to self-assemble. Electron micrographs of the vesicle-protein assemblies revealed that protein binding induced pronounced changes in vesicle shape, which was consistent with the introduction of positive curvature in the outer leaflet of the bilayer. Overall, vesicle-mediated template-directed assembly is shown to be an effective way to form functional complexes of membrane-associated proteins and suggests that significant changes in membrane shape can be involved in the process of transmembrane signaling.

Spatial organization of the bacterial chemotaxis system

Sensory complexes in bacterial chemotaxis are organized in large clusters, building complex signal-processing machinery. Interactions among chemoreceptors are the main determinant of cluster formation and create an allosteric network that is able to integrate and amplify stimuli, before transmitting the signal to downstream proteins. Association of the other proteins with the receptor cluster creates a signalling scaffold, which enhances the efficiency and specificity of the pathway. Clusters localize to specific locations inside the cell, perhaps to ensure their proper distribution during cell division. Clustering is conserved among all studied prokaryotic chemotaxis systems and exemplifies a growing number of bacterial pathways with a reported sub-cellular spatial organization. Moreover, because allostery provides a simple mechanism to achieve very high response sensitivity, it is probable that clustering-based signal amplification is not limited to bacterial chemotaxis but also exists in other prokaryotic and eukaryotic pathways.

Determinants of chemoreceptor cluster formation in Escherichia coli

Chemotactic stimuli in bacteria are sensed by large sensory complexes, or receptor clusters, that consist of tens of thousands of proteins. Receptor clusters appear to play a key role in signal processing, but their structure remains poorly understood. Here we used fluorescent protein fusions to study in vivo formation of the cluster core, which consists of receptors, a kinase CheA and an assisting protein CheW. We show that receptors aggregate through their cytoplasmic domains even in the absence of other chemotaxis proteins. Clustering is further enhanced by the binding of CheW. Surprisingly, we observed that some fragments of CheA bind receptor clusters well in the absence of CheW, although the latter does assist the binding of full-length CheA. The resulting mode of receptor cluster formation is consistent with an experimentally observed flexible stoichiometry of chemosensory complexes and with assumptions of recently proposed computer models of signal processing in chemotaxis.

Different subcellular locations of secretome components of Gram-positive bacteria

Gram-positive bacteria contain different types of secretion systems for the transport of proteins into or across the cytoplasmic membrane. Recent studies on subcellular localization of specific components of these secretion systems and their substrates have shown that they can be present at various locations in the cell. The translocons of the general Sec secretion system in the rod-shaped bacteriumBacillus subtilishave been shown to localize in spirals along the cytoplasmic membrane, whereas the translocons in the coccoidStreptococcus pyogenesare located in a microdomain near the septum. In both bacteria the Sec translocons appear to be located near the sites of cell wall synthesis. The Tat secretion system, which is used for the transport of folded proteins, probably localizes in the cytoplasmic membrane and at the cell poles ofB. subtilis. InLactococcus lactisthe ABC transporter dedicated to the transport of a small antimicrobial peptide is distributed throughout the membrane. Possible mechanisms for maintaining the localization of these secretion machineries involve their interaction with proteins of the cytoskeleton or components of the cell wall synthesis machinery, or the presence of lipid subdomains surrounding the transport systems.

Competitive and cooperative interactions in receptor signaling complexes

In bacterial chemotaxis, clustered transmembrane receptors and the adaptor protein CheW regulate the kinase CheA. Receptors outnumber CheA, yet it is poorly understood how interactions among receptors contribute to regulation. To address this problem, receptor clusters were simulated using liposomes decorated with the cytoplasmic domains of receptors, which supported CheA binding and stimulation. Competitive and cooperative interactions were revealed through the use of known receptor signaling mutants, which were used in mixtures with the wild type domain. Competitive effects among the receptor domains sorted cleanly into two categories defined by either stronger or weaker interactions with CheA. Cooperative effects were also evident in CheA binding and activity. In the transition from the stimulating to the inhibiting states, both the cooperativity of the transition and the persistence of stimulation by the wild type domain increased with receptor modification, as in the intact receptor. We conclude that competitive and cooperative receptor interactions both contribute to CheA regulation and that liposome-mediated assembly is effective in addressing these general membrane phenomena.

Inch by inch, row by row

Bacterial chemotaxis systems have cooperatively interacting clusters of transmembrane receptors and signaling proteins to detect, amplify, integrate and adapt to environmental signals. A recent study provides experimental data to construct a new model of the signaling complex.

Cysteine-scanning analysis of the chemoreceptor-coupling domain of the Escherichia coli chemotaxis signaling kinase CheA

The C-terminal P5 domain of the histidine kinase CheA is essential for coupling CheA autophosphorylation activity to chemoreceptor control through a binding interaction with the CheW protein. To locate P5 determinants critical for CheW binding and chemoreceptor control, we surveyed cysteine replacements at 39 residues predicted to be at or near the P5 surface in Escherichia coli CheA. Two-thirds of the Cys replacement proteins exhibited in vitro defects in CheW binding, either before or after modification with a bulky fluorescein group. The binding-defective sites were widely distributed on the P5 surface and were often interspersed with sites that caused no functional defects, implying that relatively minor structural perturbations, often far from the actual binding site, can influence its conformation or accessibility. The most likely CheW docking area included loop 2 in P5 folding subdomain 1. All but four of the binding-defective P5-Cys proteins were defective in receptor-mediated activation, suggesting that CheW binding, as measured in vitro, is necessary for assembly of ternary signaling complexes and/or subsequent CheA activation. Other Cys sites specifically affected receptor-mediated activation or deactivation of CheA, demonstrating that CheW binding is not sufficient for assembly and/or operation of receptor signaling complexes. Because P5 is quite similar to CheW, whose structure is known to be dynamic, we suggest that conformational flexibility and dynamic motions govern the signaling activities of the P5 domain. In addition, relative movements of the CheA domains may be involved in CheW binding, in ternary complex assembly, and in subsequent stimulus-induced conformational changes in receptor signaling complexes.

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.

Reconstruction of the chemotaxis receptor–kinase assembly

In bacterial chemotaxis, an assembly of transmembrane receptors, the CheA histidine kinase and the adaptor protein CheW processes environmental stimuli to regulate motility. The structure of a Thermotoga maritima receptor cytoplasmic domain defines CheA interaction regions and metal ion-coordinating charge centers that undergo chemical modification to tune receptor response. Dimeric CheA-CheW, defined by crystallography and pulsed ESR, positions two CheWs to form a cleft that is lined with residues important for receptor interactions and sized to clamp one receptor dimer. CheW residues involved in kinase activation map to interfaces that orient the CheW clamps. CheA regulatory domains associate in crystals through conserved hydrophobic surfaces. Such CheA self-contacts align the CheW receptor clamps for binding receptor tips. Linking layers of ternary complexes with close-packed receptors generates a lattice with reasonable component ratios, cooperative interactions among receptors and accessible sites for modification enzymes.

Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters

Receptor coupling is believed to explain the high sensitivity of the Escherichia coli chemotaxis network to small changes in levels of chemoattractant. We compare in detail the activity response of coupled two-state receptors for different models of receptor coupling: weakly-coupled extended one-dimensional and two-dimensional lattice models and the Monod-Wyman-Changeux model of isolated strongly-coupled clusters. We identify features in recent data that distinguish between the models. Specifically, researchers have measured the receptor activity response to steps of chemoattractant for a variety of engineered E. coli strains using in vivo fluorescence resonance energy transfer. We find that the fluorescence resonance energy transfer results for wild-type and for a low-activity mutant are inconsistent with the lattice models of receptor coupling, but consistent with the Monod-Wyman-Changeux model of receptor coupling, suggesting that receptors form isolated strongly-coupled clusters.

Insights into the organization and dynamics of bacterial chemoreceptor clusters through in vivo crosslinking studies

The team signaling model for bacterial chemoreceptors proposes that receptor dimers of different detection specificities form mixed trimers of dimers that bind the cytoplasmic proteins CheA and CheW to form ternary signaling complexes clustered at the cell poles. We used a trifunctional crosslinking reagent targeted to cysteine residues in the aspartate (Tar) and serine (Tsr) receptors to obtain in vivo snapshots of trimer composition in the receptor population. To analyze the dynamics of trimer formation, we followed the appearance of mixed trimers when cells expressing Tar were induced for the expression of Tsr and treated with the crosslinker shortly after the onset of induction. In the absence of CheA or CheW, preformed Tar trimers exchanged partners readily with newly made Tsr. Conversely, in the presence of CheA and CheW, receptor trimers seldom exchanged partners, irrespective of the presence or absence of attractants. The C-terminal receptor-coupling domain of the CheA kinase, which contains binding determinants for the CheW protein, was essential for conferring low exchangeability to the preformed trimers of dimers. CheW also was required for this effect, but, unlike CheA, overexpression of CheW interfered with trimer formation and chemotactic behavior. The CheW effect probably occurs through binding interactions that mask the receptor sites needed for trimer formation. We propose that clustered receptors are organized in mixed trimers of dimers through binding interactions with CheA and CheW, which play distinctly different architectural roles. Moreover, once complete signaling teams have formed, they no longer undergo dynamic exchange of receptor members.