Bacterial locomotion and signal transduction

The FilZ Protein Contains a Single PilZ Domain and Facilitates the Swarming Motility of Pseudoalteromonas sp. SM9913

Swarming regulation is complicated in flagellated bacteria, especially those possessing dual flagellar systems. It remains unclear whether and how the movement of the constitutive polar flagellum is regulated during swarming motility of these bacteria. Here, we report the downregulation of polar flagellar motility by the c-di-GMP effector FilZ in the marine sedimentary bacterium Pseudoalteromonas sp. SM9913. Strain SM9913 possesses two flagellar systems, and filZ is located in the lateral flagellar gene cluster. The function of FilZ is negatively controlled by intracellular c-di-GMP. Swarming in strain SM9913 consists of three periods. Deletion and overexpression of filZ revealed that, during the period when strain SM9913 expands quickly, FilZ facilitates swarming. In vitro pull-down and bacterial two-hybrid assays suggested that, in the absence of c-di-GMP, FilZ interacts with the CheW homolog A2230, which may be involved in the chemotactic signal transduction pathway to the polar flagellar motor protein FliM_p, to interfere with polar flagellar motility. When bound to c-di-GMP, FilZ loses its ability to interact with A2230. Bioinformatic investigation indicated that filZ-like genes are present in many bacteria with dual flagellar systems. Our findings demonstrate a novel mode of regulation of bacterial swarming motility.

A Synthetic Overview of Preparation Protocols of Nonmetallic, Contact-Active Antimicrobial Quaternary Surfaces on Polymer Substrates

Antibacterial surfaces have been researched for more than 30 years and remain highly desirable. In particular, there is an interest in providing antimicrobial properties to commodity plastics, because these, in their native state, are excellent substrates for pathogens to adhere and proliferate on. Therefore, efficient strategies for converting surfaces of commodity plastics into contact-active antimicrobial surfaces are of significant interest. Many systems have been prepared and tested for their efficacy. Here, the synthetic approaches to such active surfaces are reviewed, with the restriction to only include systems with tested antibacterial properties. The review focuses on the synthetic approach to surface functionalization of the most common materials used and tested for biomedical applications, which effectively has limited the study to quaternary materials. For future developments in the field, it is evident that there is a need for development of simple methods that permit scalable production of active surfaces. Furthermore, in terms of efficacy, there is an outstanding concern of a lack of universal antimicrobial action as well as rapid deactivation of the antibacterial effect through surface fouling.

Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains

Pan-genome analysis is widely used to study the evolution and genetic diversity of species, particularly in bacteria. However, the impact of strain selection on the outcome of pan-genome analysis is poorly understood. Furthermore, a standard protocol to ensure high-quality pan-genome results is lacking. In this study, we carried out a series of pan-genome analyses of different strain sets of Bacillus subtilis to understand the impact of various strains on the performance and output quality of pan-genome analyses. Consequently, we found that the results obtained by pan-genome analyses of B. subtilis can be influenced by the inclusion of incorrectly classified Bacillus subspecies strains, phylogenetically distinct strains, engineered genome-reduced strains, chimeric strains, strains with a large number of unique genes or a large proportion of pseudogenes, and multiple clonal strains. Since the presence of these confounding strains can seriously affect the quality and true landscape of the pan-genome, we should remove these deviations in the process of pan-genome analyses. Our study provides new insights into the removal of biases from confounding strains in pan-genome analyses at the beginning of data processing, which enables the achievement of a closer representation of a high-quality pan-genome landscape of B. subtilis that better reflects the performance and credibility of the B. subtilis pan-genome. This procedure could be added as an important quality control step in pan-genome analyses for improving the efficiency of analyses, and ultimately contributing to a better understanding of genome function, evolution and genome-reduction strategies for B. subtilis in the future.

The periplasmic sensing domain of Vibrio fischeri chemoreceptor protein A (VfcA): cloning, purification and crystallographic analysis

Flagella-mediated motility and chemotaxis towards nutrients are important characteristics of Vibrio fischeri that play a crucial role in the development of its symbiotic relationship with its Hawaiian squid host Euprymna scolopes. The V. fischeri chemoreceptor A (VfcA) mediates chemotaxis toward amino acids. The periplasmic sensory domain of VfcA has been crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 as a precipitating agent. The crystals belonged to space group P1, with unit-cell parameters a = 39.9, b = 57.0, c = 117.0 Å, α = 88.9, β = 80.5, γ = 89.7°. A complete X-ray diffraction data set has been collected to 1.8 Å resolution using cryocooling conditions and synchrotron radiation.

Trg-deficient Salmonella colonize quiescent tumor regions by exclusively penetrating or proliferating

Chemotherapeutics fail to effectively treat tumors because they cannot reach quiescent regions far from blood vessels. Motile Salmonella are an attractive delivery system that could break this therapeutic barrier. However, little is known about the dissemination and tissue penetration of individual bacteria in tumors after intravenous administration. We hypothesized that eliminating the Trg receptor would improve accumulation in tumor quiescence. To test this hypothesis, we deleted the trg gene from nonpathogenic Salmonella. To quantify individual bacterial behavior, we measured tissue penetration in a tumor-on-a-chip device and measured colony localization in mouse tumors using immunofluorescence. In tumors in vitro and in mice, trg(-) Salmonella penetrated farther into tissue than control bacteria. This difference in localization was caused by the inability to sense sugars in well perfused tissue. Three distinct bacterial phenotypes were observed: proliferating, penetrating, and inactive. Large proliferating colonies, containing more than 40% of individual bacteria, only formed less than 60μm from blood vessels. Small colonies, in comparison, were present both near (inactive) and far (penetrating) from vessels. The farthest was 361.2μm from a vessel, demonstrating the ability to target avascular regions. In addition, colonization was most pronounced in poorly vascularized tumor regions. We show that deletion of trg amplifies Salmonella accumulation in quiescent tumor regions, and, for the first time, identify biological processes that control bacterial distribution in tumors. Understanding how Salmonella penetrate tissue, target quiescence and specifically replicate in tumors are essential steps toward creating a tightly controlled, tunable bacterial therapy.

Gimme shelter: how Vibrio fischeri successfully navigates an animal's multiple environments

Bacteria successfully colonize distinct niches because they can sense and appropriately respond to a variety of environmental signals. Of particular interest is how a bacterium negotiates the multiple, complex environments posed during successful infection of an animal host. One tractable model system to study how a bacterium manages a host’s multiple environments is the symbiotic relationship between the marine bacterium, Vibrio fischeri, and its squid host, Euprymna scolopes. V. fischeri encounters many different host surroundings ranging from initial contact with the squid to ultimate colonization of a specialized organ known as the light organ. For example, upon recognition of the squid, V. fischeri forms a biofilm aggregate outside the light organ that is required for efficient colonization. The bacteria then disperse from this biofilm to enter the organ, where they are exposed to nitric oxide, a molecule that can act as both a signal and an antimicrobial. After successfully managing this potentially hostile environment, V. fischeri cells finally establish their niche in the deep crypts of the light organ where the bacteria bioluminesce in a pheromone-dependent fashion, a phenotype that E. scolopes utilizes for anti-predation purposes. The mechanism by which V. fischeri manages these environments to outcompete all other bacterial species for colonization of E. scolopes is an important and intriguing question that will permit valuable insights into how a bacterium successfully associates with a host. This review focuses on specific molecular pathways that allow V. fischeri to establish this exquisite bacteria–host interaction.

A novel dnaJ family gene, sflA, encodes an inhibitor of flagellation in marine Vibrio species

The marine bacterium Vibrio alginolyticus has a single polar flagellum. Formation of that flagellum is regulated positively and negatively by FlhF and by FlhG, respectively. The ΔflhF mutant makes no flagellum, whereas the ΔflhFG double-deletion mutant usually lacks a flagellum. However, the ΔflhFG mutant occasionally reverts to become motile by forming peritrichous flagella. We have isolated a suppressor pseudorevertant from the ΔflhFG strain (ΔflhFG-sup). The suppressor strain forms peritrichous flagella in the majority of cells. We identified candidate suppressor mutations by comparing the genome sequence of the parental strain, VIO5, with the genome sequences of the suppressor strains. Two mutations were mapped to a gene, named sflA (suppressor of ΔflhFG), at the VEA003730 locus of the Vibrio sp. strain EX25 genome. This gene is specific for Vibrio species and is predicted to encode a transmembrane protein with a DnaJ domain. When the wild-type gene was introduced into the suppressor strain, motility was impaired. Introducing a mutant version of the sflA gene into the ΔflhFG strain conferred the suppressor phenotype. Thus, we conclude that loss of the sflA gene is responsible for the suppressor phenotype and that the wild-type SflA protein plays a role in preventing polar-type flagella from forming on the lateral cell wall.

On-chip cellomics assay enabling algebraic and geometric understanding of epigenetic information in cellular networks of living systems. 1. Temporal aspects of epigenetic information in bacteria

A series of studies aimed at developing methods and systems of analyzing epigenetic information in cells and in cell networks, as well as that of genetic information, was examined to expand our understanding of how living systems are determined. Because cells are minimum units reflecting epigenetic information, which is considered to map the history of a parallel-processing recurrent network of biochemical reactions, their behaviors cannot be explained by considering only conventional DNA information-processing events. The role of epigenetic information on cells, which complements their genetic information, was inferred by comparing predictions from genetic information with cell behaviour observed under conditions chosen to reveal adaptation processes, population effects and community effects. A system of analyzing epigenetic information was developed starting from the twin complementary viewpoints of cell regulation as an “algebraic” system (emphasis on temporal aspects) and as a “geometric” system (emphasis on spatial aspects). Exploiting the combination of latest microfabrication technology and measurement technologies, which we call on-chip cellomics assay, we can control and re-construct the environments and interaction of cells from “algebraic” and “geometric” viewpoints. In this review, temporal viewpoint of epigenetic information, a part of the series of single-cell-based “algebraic” and “geometric” studies of celluler systems in our research groups, are summerized and reported. The knowlege acquired from this study may lead to the use of cells that fully control practical applications like cell-based drug screening and the regeneration of organs.

The cucurbit pathogenic bacterium Acidovorax citrulli requires a polar flagellum for full virulence before and after host-tissue penetration

Acidovorax citrulli causes seedling blight and bacterial fruit blotch of cucurbits. Previous reports demonstrated the contribution of type IV pili (T4P) to A. citrulli virulence and to systemic infection of melon seedlings. Microfluidic flow-chamber assays demonstrated the involvement of T4P in surface adhesion and biofilm formation, whereas polar flagella did not appear to contribute to either of these features. On the other hand, a transposon mutant impaired in the biosynthesis of polar flagella was identified in screens for reduced virulence of an A. citrulli mutant library. Further characterization of polar flagellum mutants confirmed that A. citrulli requires a polar flagellum for full virulence on melon plants. Foliage and stem inoculation experiments revealed that polar flagella contribute to A. citrulli virulence and growth in planta at both pre- and post-host-tissue penetration. Interestingly, light microscope observations revealed that almost all A. citrulli wild-type cells extracted from the xylem sap of stem-inoculated melon seedlings remained motile, supporting the importance of this organelle in virulence and colonization of the host vascular system. We also report a negative effect of polar flagellum impairment on T4P-mediated twitching motility of A. citrulli and discuss a possible co-regulation of these two motility machineries in this bacterium.

Sensing and adhesion are adaptive functions in the plant pathogenic xanthomonads

Background

Bacterial plant pathogens belonging to the Xanthomonas genus are tightly adapted to their host plants and are not known to colonise other environments. The host range of each strain is usually restricted to a few host plant species. Bacterial strains responsible for the same type of symptoms on the same host range cluster in a pathovar. The phyllosphere is a highly stressful environment, but it provides a selective habitat and a source of substrates for these bacteria. Xanthomonads colonise host phylloplane before entering leaf tissues and engaging in an invasive pathogenic phase. Hence, these bacteria are likely to have evolved strategies to adapt to life in this environment. We hypothesised that determinants responsible for bacterial host adaptation are expressed starting from the establishment of chemotactic attraction and adhesion on host tissue.

Results

We established the distribution of 70 genes coding sensors and adhesins in a large collection of xanthomonad strains. These 173 strains belong to different pathovars of Xanthomonas spp and display different host ranges. Candidate genes are involved in chemotactic attraction (25 genes), chemical environment sensing (35 genes), and adhesion (10 genes). Our study revealed that candidate gene repertoires comprised core and variable gene suites that likely have distinct roles in host adaptation. Most pathovars were characterized by unique repertoires of candidate genes, highlighting a correspondence between pathovar clustering and repertoires of sensors and adhesins. To further challenge our hypothesis, we tested for molecular signatures of selection on candidate genes extracted from sequenced genomes of strains belonging to different pathovars. We found strong evidence of adaptive divergence acting on most candidate genes.

Conclusions

These data provide insight into the potential role played by sensors and adhesins in the adaptation of xanthomonads to their host plants. The correspondence between repertoires of sensor and adhesin genes and pathovars and the rapid evolution of sensors and adhesins shows that, for plant pathogenic xanthomonads, events leading to host specificity may occur as early as chemotactic attraction by host and adhesion to tissues.

TbUNC119 and its binding protein complex are essential for propagation, motility, and morphogenesis of Trypanosoma brucei procyclic form cells

Flagellum-mediated motility of Trypanosoma brucei is considered to be essential for the parasite to complete stage development in the tsetse fly vector, while the mechanism by which flagellum-mediated motility is controlled are not fully understood. We thus compared T. brucei whole gene products (amino acid sequence) with Caenorhabditis elegans UNC (uncoordinated) proteins, in order to find uncharacterized motility-related T. brucei genes. Through in silico analysis, we found 88 gene products which were highly similar to C. elegans UNC proteins and categorized them as TbCEUN (T. brucei gene products which have high similarity to C. elegansUNC proteins). Approximately two thirds of the 88 TbCEUN gene products were kinesin-related molecules. A gene product highly similar to C. elegans UNC119 protein was designated as TbUNC119. RNAi-mediated depletion of TbUNC119 showed no apparent phenotype. However, knock-down analysis of both TbUNC119 and its binding protein (TbUNC119BP) which was found by yeast two-hybrid analysis showed characteristic phenotypes, including reduced motility, morphological change (extended cell shape), and cellular apoptosis. Based on the observed phenotypes, possible function of the TbUNC119 and TbUNC119BP is discussed.

Flagellin: key target of mucosal innate immunity

The mucosal immune system is charged with defending the host's vast interfaces with the outside world from the enormous and diverse group of microbes that colonizes these surfaces. A key means by which the mucosal immune system protects the host from such diverse microbes is using germ-line-encoded receptors that target structurally conserved motifs that mediate important bacterial functions. This review focuses on one embodiment of this notion, namely, the mucosal innate immune targeting of flagellin, the primary structural component of flagella, which afford bacteria the ability of directed locomotion. Specifically, we discuss the mechanisms by which flagellin is recognized by the innate immune system, their role in host defense, chronic inflammatory disease, and potential approaches to pharmacologically manipulate these pathways to benefit the host. Discussion will focus on the intestinal tract but will also incorporate key findings in other mucosal surfaces.

Individuality in bacteria

While traditionally microbiologists have examined bacterial behavior averaged over large populations, increasingly we are becoming aware that bacterial populations can be composed of phenotypically diverse individuals generated by a variety of mechanisms. Though the results of different mechanisms, the phenomena of bistability, persistence, variation in chemotactic response, and phase and antigenic variation are all strategies to develop population-level diversity. The understanding of individuality in bacteria requires an appreciation of their environmental and ecological context, and thus evolutionary theory regarding adaptations to time-variable environments is becoming more applicable to these problems. In particular, the application of game and information theory to bacterial individuality has addressed some interesting problems of bacterial behavior. In this review we discuss the mechanisms of generating population-level variability, and the application of evolutionary theory to problems of individuality in bacteria.

Bacterial Swarming: A Model System for Studying Dynamic Self-assembly

Bacterial swarming is an example of dynamic self-assembly in microbiology in which the collective interaction of a population of bacterial cells leads to emergent behavior. Swarming occurs when cells interact with surfaces, reprogram their physiology and behavior, and adapt to changes in their environment by coordinating their growth and motility with other cells in the colony. This review summarizes the salient biological and biophysical features of this system and describes our current understanding of swarming motility. We have organized this review into four sections: 1) The biophysics and mechanisms of bacterial motility in fluids and its relevance to swarming. 2) The role of cell/molecule, cell/surface, and cell/cell interactions during swarming. 3) The changes in physiology and behavior that accompany swarming motility. 4) A concluding discussion of several interesting, unanswered questions that is particularly relevant to soft matter scientists.

Cross-species cluster co-conservation: a new method for generating protein interaction networks

Cluster Co-Conservation (CCC) has been extended to a method for developing protein interaction networks based on co-conservation between protein pairs across multiple species, Cross-Species Cluster Co-Conservation (CS-CCC).

Co-conservation (phylogenetic profiles) is a well-established method for predicting functional relationships between proteins. Several publicly available databases use this method and additional clustering strategies to develop networks of protein interactions (cluster co-conservation (CCC)). CCC has previously been limited to interactions within a single target species. We have extended CCC to develop protein interaction networks based on co-conservation between protein pairs across multiple species, cross-species cluster co-conservation.

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

Interacting or functionally related protein families tend to have similar phylogenetic trees. Based on this observation, techniques have been developed to predict interaction partners. The observed degree of similarity between the phylogenetic trees of two proteins is the result of many different factors besides the actual interaction or functional relationship between them. Such factors influence the performance of interaction predictions. One aspect that can influence this similarity is related to the fact that a given protein interacts with many others, and hence it must adapt to all of them. Accordingly, the interaction or coadaptation signal within its tree is a composite of the influence of all of the interactors. Here, we introduce a new estimator of coevolution to overcome this and other problems. Instead of relying on the individual value of tree similarity between two proteins, we use the whole network of similarities between all of the pairs of proteins within a genome to reassess the similarity of that pair, thereby taking into account its coevolutionary context. We show that this approach offers a substantial improvement in interaction prediction performance, providing a degree of accuracy/coverage comparable with, or in some cases better than, that of experimental techniques. Moreover, important information on the structure, function, and evolution of macromolecular complexes can be inferred with this methodology.

Toll like receptor-5: protecting the gut from enteric microbes

The intestine is normally colonized by a large and diverse commensal microbiota and is occasionally exposed to a variety of potential pathogens. In recent years, there has been substantial progress made in identifying molecular mechanisms that normally serve to protect the intestine from such enteric bacteria and which may go awry in chronic idiopathic inflammatory diseases of the gut. One specific molecular interaction that appears to play a key role in governing bacterial-intestinal interactions is that of the bacterial protein flagellin with toll-like receptor 5. This article reviews studies performed in vitro, in mice, and in humans that indicate an important role for the flagellin-TLR5 interaction in regulating both the innate and adaptive immune responses in the intestine.

Bacterial lateral flagella: an inducible flagella system

Flagella are complex surface organelles that allow bacteria to move towards favourable environments and that contribute to the virulence of pathogenic bacteria through adhesion and biofilm formation on host surfaces. There are a few bacteria that possess functional dual flagella systems, such as Vibrio parahaemolyticus, some mesophilic Aeromonas spp., Rhodospirillum centenum and Azospirillum brasilense. These bacteria are able to express both a constitutive polar flagellum required for swimming motility and a separate lateral flagella system that is induced in viscous media or on surfaces and is essential for swarming motility. As flagella synthesis and motility have a high metabolic cost for the bacterium, the expression of the inducible lateral flagella system is highly regulated by a number of environmental factors and regulators.

Flagellar motility contributes to cytokinesis in Trypanosoma brucei and is modulated by an evolutionarily conserved dynein regulatory system

The flagellum of Trypanosoma brucei is a multifunctional organelle with critical roles in motility and other aspects of the trypanosome life cycle. Trypanin is a flagellar protein required for directional cell motility, but its molecular function is unknown. Recently, a trypanin homologue in Chlamydomonas reinhardtii was reported to be part of a dynein regulatory complex (DRC) that transmits regulatory signals from central pair microtubules and radial spokes to axonemal dynein. DRC genes were identified as extragenic suppressors of central pair and/or radial spoke mutations. We used RNA interference to ablate expression of radial spoke (RSP3) and central pair (PF16) components individually or in combination with trypanin. Both rsp3 and pf16 single knockdown mutants are immotile, with severely defective flagellar beat. In the case of rsp3, this loss of motility is correlated with the loss of radial spokes, while in the case of pf16 the loss of motility correlates with an aberrant orientation of the central pair microtubules within the axoneme. Genetic interaction between trypanin and PF16 is demonstrated by the finding that loss of trypanin suppresses the pf16 beat defect, indicating that the DRC represents an evolutionarily conserved strategy for dynein regulation. Surprisingly, we discovered that four independent mutants with an impaired flagellar beat all fail in the final stage of cytokinesis, indicating that flagellar motility is necessary for normal cell division in T. brucei. These findings present the first evidence that flagellar beating is important for cell division and open the opportunity to exploit enzymatic activities that drive flagellar beat as drug targets for the treatment of African sleeping sickness.

Cholera stool bacteria repress chemotaxis to increase infectivity

Factors that enhance the transmission of pathogens are poorly understood. We show that Vibrio cholerae shed in human 'rice-water' stools have a 10-fold lower oral infectious dose in an animal model than in vitro grown V. cholerae, which may aid in transmission during outbreaks. Furthermore, we identify a bacterial factor contributing to this enhanced infectivity: The achievement of a transient motile but chemotaxis-defective state upon shedding from humans. Rice-water stool V. cholerae have reduced levels of CheW-1, which is essential for chemotaxis, and were consequently shown to have a chemotaxis defect when tested in capillary assays. Through mutational analyses, such a state is known to enhance the infectivity of V. cholerae. This is the first report of a pathogen altering its chemotactic state in response to human infection in order to enhance its transmission.

Chemotaxis in the green flagellate alga Chlamydomonas

Behavior of the green flagellate alga Chlamydomonas changes in response to a number of chemical stimuli. Specific sensitivity of the cells to different substances might appear only at certain stages of the life cycle. The heterogamous species C. allensworthii demonstrates chemotaxis of male gametes towards pheromones excreted by female gametes. In C. reinhardtii chemotaxis towards tryptone occurs only in gametes, whereas chemotaxis towards ammonium, on the contrary, only in vegetative cells. Chemotaxis to different chemical stimuli might involve different mechanisms of reception and signal transduction, elucidation of which has only recently begun. Indirect evidences show that the cells likely respond to tryptone with changes in the membrane electrical conductance. The recently completed project of sequencing the whole nuclear genome of C. reinhardtii provides the basis for future identification of molecular elements of the chemosensory cascade in this alga.

A double exponential model for biochemical oxygen demand

Biochemical oxygen demand (BOD) exertion patterns in anaerobically treated farm dairy wastewater were investigated on a laboratory scale. Oxygen uptake was typically characterised by a period of rapid oxygen exertion, a transitional "shoulder" phase and a period of slower activity. A multi-species model, involving rapidly degradable and slowly degradable material, was developed, leading to a double exponential model of BOD exertion as follows:where t is time, BOD(u1)(') and BOD(u2)(') are apparent ultimate BOD (BOD(u)) values, and k(1) and k(2) are rate constants. The model provided an improved description of BOD exertion patterns in anaerobically treated farm dairy wastewater in comparison to a conventional single exponential model, with rapidly degradable rate constant values (k(1)) ranging from 2.74 to 17.36d(-1), whilst slowly degradable rate constant values (k(2)) averaged 0.25d(-1) (range 0.20-0.29). Rapidly and slowly degradable apparent BOD(u) estimates ranged from 20 to 140g/m(3) and 225 to 500g/m(3), respectively, giving total BOD(u) levels of 265-620g/m(3). The mean square error in the curve fitting procedure ranged between 20 and 60g(2)/m(6), with values on average 70% lower (range 31-91%) than those obtained for the single exponential model. When applied to existing data for a range of other wastewaters, the double exponential model demonstrated a superior fit to the conventional single exponential model and provided a marginally better fit than a mixed order model. It is proposed that the presence of rapidly degradable material may be indicated from the value of the first rate constant (k1) and the time to 95% saturation of the first exponential function. Further model development is required to describe observed transitional and lag phases.

An introduction to cell motility for the physical scientist

Directed, purposeful movement is one of the qualities that we most closely associate with living organisms, and essentially all known forms of life on this planet exhibit some type of self-generated movement or motility. Even organisms that remain sessile most of the time, like flowering plants and trees, are quite busy at the cellular level, with large organelles, including chloroplasts, constantly racing around within cellular boundaries. Directed biological movement requires that the cell be able to convert its abundant stores of chemical energy into mechanical energy. Understanding how this mechanochemical energy transduction takes place and understanding how small biological forces generated at the molecular level are marshaled and organized for large-scale cellular or organismal movements are the focus of the field of cell motility. This tutorial, aimed at readers with a background in physical sciences, surveys the state of current knowledge and recent advances in modeling cell motility.

Going against the grain: chemotaxis and infection in Vibrio cholerae

Chemotaxis is the process by which motile cells move in a biased manner both towards favourable and away from unfavourable environments. The requirement of this process for infection has been examined in several bacterial pathogens, including Vibrio cholerae. The single polar flagellum of Vibrio species is powered by a sodium-motive force across the inner membrane, and can rotate to produce speeds of up to 60 cell-body lengths (approximately 60microm) per second. Investigating the role of the chemotactic control of rapid flagellar motility during V. cholerae infection has revealed some unexpected and intriguing results.

Biophysical and kinetic characterization of HemAT, an aerotaxis receptor from Bacillus subtilis

HemAT from Bacillus subtilis is a new type of heme protein responsible for sensing oxygen. The structural and functional properties of the full-length HemAT protein, the sensor domain (1-178), and Tyr-70 mutants have been characterized. Kinetic and equilibrium measurements reveal that both full-length HemAT and the sensor domain show two distinct O(2) binding components. The high-affinity component has a K(dissociation) approximately 1-2 microM and a normal O(2) dissociation rate constant, k(O2) = 50-80 s(-1). The low-affinity component has a K(dissociation) approximately 50-100 microM and a large O(2) dissociation rate constant equal to approximately 2000 s(-1). The low n-value and biphasic character of the equilibrium curve indicate that O(2) binding to HemAT involves either independent binding to high- and low-affinity subunits in the dimer or negative cooperativity. Replacement of Tyr-70(B10) with Phe, Leu, or Trp in the sensor domain causes dramatic increases in k(O2) for both the high- and low-affinity components. In contrast, the rates and affinity for CO binding are little affected by loss of the Tyr-70 hydroxyl group. These results suggest highly dynamic behavior for the Tyr-70 side chain and the fraction of the "up" versus "down" conformation is strongly influenced by the nature of the iron-ligand complex. As a result of having both high- and low-affinity components, HemAT can respond to oxygen concentration gradients under both hypoxic (0-10 microM) and aerobic (50-250 microM) conditions, a property which could, in principle, be important for a robust sensing system. The unusual ligand-binding properties of HemAT suggest that asymmetry and apparent negative cooperativity play an important role in the signal transduction pathway.

Simultaneous measurement of sensor-protein dynamics and motility of a single cell by on-chip microcultivation system

Measurement of the correlation between sensor-protein expression, motility and environmental change is important for understanding the adaptation process of cells during their change of generation. We have developed a novel assay exploiting the on-chip cultivation system, which enabled us to observe the change of the localization of expressed sensor-protein and the motility for generations. Localization of the aspartate sensitive sensor protein at two poles in Escherichia coli decreased quickly after the aspartate was added into the cultivation medium. However, it took more than three generations for recovering the localization after the removal of aspartate from the medium. Moreover, the tumbling frequency was strongly related to the localization of the sensor protein in a cell. The results indicate that the change of the spatial localization of sensor protein, which was inherited for more than three generations, may contribute to cells, motility as the inheritable information.

Nitrobenzoates and aminobenzoates are chemoattractants for Pseudomonas strains

Three Pseudomonas strains were tested for the ability to sense and respond to nitrobenzoate and aminobenzoate isomers in chemotaxis assays. Pseudomonas putida PRS2000, a strain that grows on benzoate and 4-hydroxybenzoate by using the beta-ketoadipate pathway, has a well-characterized beta-ketoadipate-inducible chemotactic response to aromatic acids. PRS2000 was chemotactic to 3- and 4-nitrobenzoate and all three isomers of aminobenzoate when grown under conditions that induce the benzoate chemotactic response. P. putida TW3 and Pseudomonas sp. strain 4NT grow on 4-nitrotoluene and 4-nitrobenzoate by using the ortho (beta-ketoadipate) and meta pathways, respectively, to complete the degradation of protocatechuate derived from 4-nitrotoluene and 4-nitrobenzoate. However, based on results of catechol 1,2-dioxygenase and catechol 2,3-dioxygenase assays, both strains were found to use the beta-ketoadipate pathway for the degradation of benzoate. Both strains were chemotactic to benzoate, 3- and 4-nitrobenzoate, and all three aminobenzoate isomers after growth with benzoate but not succinate. Strain TW3 was chemotactic to the same set of aromatic compounds after growth with 4-nitrotoluene or 4-nitrobenzoate. In contrast, strain 4NT did not respond to any aromatic acids when grown with 4-nitrotoluene or 4-nitrobenzoate, apparently because these substrates are not metabolized to the inducer (beta-ketoadipate) of the chemotaxis system. The results suggest that strains TW3 and 4NT have a beta-ketoadipate-inducible chemotaxis system that responds to a wide range of aromatic acids and is quite similar to that present in PRS2000. The broad specificity of this chemotaxis system works as an advantage in strains TW3 and 4NT because it functions to detect diverse carbon sources, including 4-nitrobenzoate.

Motility of Escherichia coli cells in clusters formed by chemotactic aggregation

Cells of Escherichia coli under conditions of certain cellular stresses excrete attractants. Cells of chemotactic strains respond to these excreted signaling molecules by moving up their local concentration gradients and forming different types of stable multicellular structures. Multicellular clusters are the simplest among these structures. Fluorescence microscopy was used to characterize the macroscopic properties of the clusters and to track individual E. coli cells in the clusters in real time. A quantitative analysis reveals that the equilibrium cluster size is only weakly dependent on the total number of cells in the cluster. The tumble frequency of an individual cell strongly depends on the position of the cell within the cluster and its direction of movement. In the central region of the cluster, tumbles are strongly suppressed whereas near the edge of the cluster, the tumble frequency is restored for exiting cells, thereby preventing them from leaving the cluster, resulting in the maintenance of sharp cluster boundaries. A simulation based on a model of the sensory memory of E. coli reproduces the experimental data and indicates that the tumble rate and consequently the morphology of the cluster are determined by the sensory memory of cells.

Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry

Much is now known about chemotaxis signaling transduction for Escherichia coli and Salmonella typhimurium. The mechanism of chemotaxis of Bacillus subtilis is, in a sense, reversed. Attractant binding strengthens the activity of histidine kinase in B. subtilis, instead of an inhibition reaction. The HemAT from B. subtilis can detect oxygen and transmit the signal to regulatory proteins that control the direction of flagella rotation. We have determined the crystal structures of the HemAT sensor domain in liganded and unliganded forms at 2.15 A and 2.7 A resolution, respectively. The liganded structure reveals a highly symmetrical organization. Tyrosine70 shows distinct conformational changes on one subunit when ligands are removed. Our study suggests that disruption of the symmetry of HemAT plays an important role in initiating the chemotaxis signaling transduction cascade.

Helicobacter pylori strain ATCC700392 encodes a methyl-accepting chemotaxis receptor protein (MCP) for arginine and sodium bicarbonate

Helicobacter pylori ATCC43504 responds chemotactically to aspartic acid and serine, but not to arginine, nor to sodium bicarbonate. In contrast, H. pylori ATCC700392 (strain 26695) shows chemotaxis to all four attractants. Open reading frame HP0099 from H. pylori 26695 is predicted to encode one of three methyl-accepting chemotaxis receptor proteins (MCPs). When Escherichia coli is transformed with a plasmid carrying HP0099 from strain 26695, the recombinants acquire chemotaxis to arginine, bicarbonate, and urea. In H. pylori 43504, the HP0099 gene is interrupted with a mini-IS605 insertion, which accounts for its inability to recognize arginine and bicarbonate as attractants. Together, these results argue that the H. pylori HP0099 gene encodes an MCP for arginine and bicarbonate.

The flagellum of Legionella pneumophila and its link to the expression of the virulent phenotype

Legionalla pneumophila is a human pathogen causing atypical pneumonia. It is a monopolar flagellated gram-negative bacterium. Flagellation of L. pneumophila is life cycle dependent and the expression of flagella is genetically linked to the virulence phenotype. Non-flagellated mutants of L. pneumophila are less infectious for macrophages and amoebae compared to the wild type. The flagellar operon is expressed in a hierarchical manner, and different sigma factors and transcriptional regulators are involved in this cascade of gene regulation. The genome sequence of L. pneumophila was used to identify putative regulatory elements of various flagellar operons. Preliminary reports about regulators which are involved in the link between virulence gene regulation and flagellation are discussed.

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.

The DeltafliD mutant of Pseudomonas syringae pv. tabaci, which secretes flagellin monomers, induces a strong hypersensitive reaction (HR) in non-host tomato cells

To investigate the role of flagella and monomer flagellin in the interaction between Pseudomonas syringae pv. tabaci and plants, non-polar fliC and fliD mutants were produced. The ORFs for fliC and fliD are deleted in the DeltafliC and DeltafliD mutants, respectively. Both mutants lost all flagella and were non-motile. The DeltafliC mutant did not produce flagellin, whereas the DeltafliD mutant, which lacks the HAP2 protein, secreted large amounts of monomer flagellin into the culture medium. Inoculation of non-host tomato leaves with wild-type P. syringae pv. tabaci or the DeltafliD mutant induced a hypersensitive reaction (HR), whereas the DeltafliC mutant propagated and caused characteristic symptom-like changes. In tomato cells in suspension culture, wild-type P. syringae pv. tabaci induced slight, visible HR-like changes. The DeltafliC mutant did not induce HR, but the DeltafliD mutant induced a remarkably strong HR. Expression of the hsr203J gene was rapidly and strongly induced by inoculation with the DeltafliD mutant, compared to inoculation with wild-type P. syringae pv. tabaci. Furthermore, introduction of the fliC gene into the DeltafliC mutant restored motility and HR-inducing ability in tomato. These results, together with our previous study, suggest that the flagellin monomer of pv. tabaci acts as a strong elicitor to induce HR-associated cell death in non-host tomato cells.

Characterization of the nodulation plasmid encoded chemoreceptor gene mcpG from Rhizobium leguminosarum

BACKGROUND

In general, chemotaxis in Rhizobium has not been well characterized. Methyl accepting chemotaxis proteins are sensory proteins important in chemotaxis of numerous bacteria, but their involvement in Rhizobium chemotaxis is unclear and merits further investigation.

RESULTS

A putative methyl accepting chemotaxis protein gene (mcpG) of Rhizobium leguminosarum VF39SM was isolated and characterized. The gene was found to reside on the nodulation plasmid, pRleVF39d. The predicted mcpG ORF displayed motifs common to known methyl-accepting chemotaxis proteins, such as two transmembrane domains and high homology to the conserved methylation and signaling domains of well-characterized MCPs. Phenotypic analysis of mcpG mutants using swarm plates did not identify ligands for this putative receptor. Additionally, gene knockouts of mcpG did not affect a mutant strain's ability to compete for nodulation with the wild type. Notably, mcpG was found to be plasmid-encoded in all strains of R. leguminosarum and R. etli examined, though it was found on the nodulation plasmid only in a minority of strains.

CONCLUSIONS

Based on sequence homology R. leguminosarum mcpG gene codes for a methyl accepting chemotaxis protein. The gene is plasmid localized in numerous Rhizobium spp. Although localized to the sym plasmid of VF39SM mcpG does not appear to participate in early nodulation events. A ligand for McpG remains to be found. Apparent McpG orthologs appear in a diverse range of proteobacteria. Identification and characterization of mcpG adds to the family of mcp genes already identified in this organism.

Involvement of in vivo induced cheY-4 gene of Vibrio cholerae in motility, early adherence to intestinal epithelial cells and regulation of virulence factors

Using a global transcription profile approach cheY-4 of Vibrio cholerae was identified as an in vivo induced gene. In the present study, duplication of the gene in the chromosome resulted in increased motility, increased chemotactic response towards isolated intestinal mucus layer and stronger adhesion to human intestinal epithelial cell line at an early phase of infection compared to wild type and a null mutant strain. In contrast to the cheY-4 null mutant, duplication of cheY-4 gene resulted in increased expression of ctxAB and tcpA, the two major virulence genes of V. cholerae.

CheA kinase and chemoreceptor interaction surfaces on CheW

Chemotactic responses of Escherichia coli to aspartic acid are initiated by a ternary protein complex composed of Tar (chemoreceptor), CheA (kinase), and CheW (a coupling protein that binds to both Tar and CheA and links their activities). We used a genetic selection based on the yeast two-hybrid assay to identify nine cheW point mutations that specifically disrupted CheW interaction with CheA but not with Tar. We sequenced these single point mutants and purified four of the mutant CheW proteins for detailed biochemical characterizations that demonstrated the weakened affinity of the mutant CheW proteins for CheA, but not for Tar. In the three-dimensional structure of CheW, the positions affected by these mutations cluster on one face of the protein, defining a potential binding interface for interaction of CheW with CheA. We used a similar two-hybrid approach to identify four mutation sites that disrupted CheW binding to Tar. Mapping of these "Tar-sensitive" mutation sites and those from previous suppressor analysis onto the structure of CheW defined an extended surface on a face of the protein that is adjacent to the CheA-binding surface and that may serve as an interface for CheW binding to Tar.

CheW binding interactions with CheA and Tar. Importance for chemotaxis signaling in Escherichia coli

The initial signaling events underlying the chemotactic response of Escherichia coli to aspartic acid occur within a ternary complex that includes Tar (an aspartate receptor), CheA (a protein kinase), and CheW. Because CheW can bind to CheA and to Tar, it is thought to serve as an adapter protein in this complex. The functional importance of CheW binding interactions, however, has not been investigated. To better define the role of CheW and its binding interactions, we performed biochemical characterization of six mutant variants of CheW. We examined the ability of the purified mutant CheW proteins to bind to CheA and Tar, to promote formation of active ternary complexes, and to support chemotaxis in vivo. Our results indicate that mutations which eliminate CheW binding to Tar (V36M) or to CheA (G57D) result in a complete inability to form active ternary complexes in vitro and render the CheW protein incapable of mediating chemotaxis in vivo. The in vivo signaling pathway can, however, tolerate moderate changes in CheW-Tar and CheW-CheA affinities observed with several of the mutants (G133E, G41D, and 154ocr). One mutant (R62H) provided surprising results that may indicate a role for CheW in addition to binding CheA/receptors and promoting ternary complex formation.

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.

Hydrogen exchange reveals a stable and expandable core within the aspartate receptor cytoplasmic domain

Intensive study of bacterial chemoreceptors has not yet revealed how receptor methylation and ligand binding alter the interactions between the receptor cytoplasmic domain and the CheA kinase to control kinase activity. Both monomeric and dimeric forms of an Asp receptor cytoplasmic fragment have been shown to be highly dynamic, with a small core of slowly exchanging amide hydrogens (Seeley, S. K., Weis, R. M., and Thompson, L. K. (1996) Biochemistry 35, 5199-5206). Hydrogen exchange studies of the wild-type cytoplasmic fragment and an S461L mutant thought to mimic the kinase-inactivating state are used to investigate the relationship between the stable core and dimer dissociation. Our results establish that (i) decreasing pH stabilizes the dimeric state, (ii) the stable core is present also in the transition state for dissociation, and (iii) this core is expanded significantly by small changes in electrostatic and hydrophobic interactions. These kinase-inactivating changes stabilize both the monomeric and the dimeric states of the protein, which has interesting implications for the mechanism of kinase activation. We conclude that the cytoplasmic domain is a flexible region poised for stabilization by small changes in electrostatic and hydrophobic interactions such as those caused by methylation of glutamate residues and by ligand-induced conformational changes during signaling.

Motility and chemotaxis in tissue penetration of oral epithelial cell layers by Treponema denticola

The ability to penetrate tissue is an important virulence factor for pathogenic spirochetes. Previous studies have recognized the role of motility in allowing pathogenic spirochetes to invade tissues and migrate to sites favorable for bacterial proliferation. However, the nature of the movements, whether they are random or controlled by chemotaxis systems, has yet to be established. In this study, we addressed the role of motility and chemotaxis in tissue penetration by the periodontal disease-associated oral spirochete Treponema denticola using an oral epithelial cell line-based experimental approach. Wild-type T. denticola ATCC 35405 was found to penetrate the tissue layers effectively, whereas a nonmotile mutant was unable to overcome the tissue barrier. Interestingly, the chemotaxis mutants also showed impaired tissue penetration. A cheA mutant that is motile but lacks the central kinase of the chemotaxis pathway showed only about 2 to 3% of the wild-type penetration rate. The two known chemoreceptors of T. denticola, DmcA and DmcB, also appear to be involved in the invasion process. The dmc mutants were actively motile but exhibited reduced tissue penetration of about 30 and 10% of the wild-type behavior, respectively. These data suggest that not only motility but also chemotaxis is involved in the tissue penetration by T. denticola.