Inversion of thermosensing property of the bacterial receptor Tar by mutations in the second transmembrane region

Mechanism of bidirectional thermotaxis in Escherichia coli

In bacteria various tactic responses are mediated by the same cellular pathway, but sensing of physical stimuli remains poorly understood. Here, we combine an in-vivo analysis of the pathway activity with a microfluidic taxis assay and mathematical modeling to investigate the thermotactic response of Escherichia coli. We show that in the absence of chemical attractants E. coli exhibits a steady thermophilic response, the magnitude of which decreases at higher temperatures. Adaptation of wild-type cells to high levels of chemoattractants sensed by only one of the major chemoreceptors leads to inversion of the thermotactic response at intermediate temperatures and bidirectional cell accumulation in a thermal gradient. A mathematical model can explain this behavior based on the saturation-dependent kinetics of adaptive receptor methylation. Lastly, we find that the preferred accumulation temperature corresponds to optimal growth in the presence of the chemoattractant serine, pointing to a physiological relevance of the observed thermotactic behavior.

Many bacteria can move towards or away from chemicals, heat and other stimuli in their environment. The ability of bacteria to move in response to nutrients and other chemicals, known as chemotaxis, is the best understood of these phenomena. Bacteria generally swim in a fairly random way and frequently change direction. During chemotaxis, however, the bacteria sense changes in the concentrations of a chemical in their surroundings and this biases the direction in which they swim so that they spend more time swimming towards or away from the source of the chemical. The bacteria have various receptor proteins that can detect different chemicals. For example, the Tar and Tsr receptors can recognize chemicals called aspartate and serine, respectively, which are – amongst other things – nutrients that are used to build proteins.

Tar and Tsr are also involved in the response to temperature, referred to as thermotaxis. At low temperatures, a bacterium Escherichia coli will move towards sources of heat. Yet when the bacteria detect both serine and aspartate they may reverse the response and move towards colder areas instead. However, it was not clear why the bacteria do this, and what roles Tar and Tsr play in this response.

Paulick et al. have now combined approaches that directly visualise signalling inside living bacteria and that track the movements of individual bacterial cellswith mathematical modelling to investigate thermotaxis in E. coli. The experiments show that the bacteria’s behaviour could be explained by interplay between the responses mediated by Tar and Tsr. In the absence of both serine and aspartate, both receptors stimulate heat-seeking responses, causing the bacteria to move towards hotter areas. When only aspartate is present, Tsr continues to stimulate the heat-seeking response, but the aspartate causes Tar to switch to promoting a cold-seeking response instead. This leads to the bacteria accumulating in areas of intermediate temperature. In the presence of serine only, the bacteria behave in a similar way because the receptors swap roles so that Tsr stimulates the cold-seeking response, while Tar promotes the heat-seeking one.

The intermediate temperature at which the bacteria accumulate in response to serine is also around the optimal temperature for E.coli growth in presence of this chemical, suggesting that thermotaxis might play an important role in allowing bacteria to survive and grow in many different environments, including in the human body. Thus, understanding how chemotaxis and thermotaxis are regulated may lead to new ways to control how bacteria behave in patients and natural environments.

Bacterial motility measured by a miniature chamber for high-pressure microscopy

Hydrostatic pressure is one of the physical stimuli that characterize the environment of living matter. Many microorganisms thrive under high pressure and may even physically or geochemically require this extreme environmental condition. In contrast, application of pressure is detrimental to most life on Earth; especially to living organisms under ambient pressure conditions. To study the mechanism of how living things adapt to high-pressure conditions, it is necessary to monitor directly the organism of interest under various pressure conditions. Here, we report a miniature chamber for high-pressure microscopy. The chamber was equipped with a built-in separator, in which water pressure was properly transduced to that of the sample solution. The apparatus developed could apply pressure up to 150 MPa, and enabled us to acquire bright-field and epifluorescence images at various pressures and temperatures. We demonstrated that the application of pressure acted directly and reversibly on the swimming motility of Escherichia coli cells. The present technique should be applicable to a wide range of dynamic biological processes that depend on applied pressures.

Phenol sensing by Escherichia coli chemoreceptors: a nonclassical mechanism

The four transmembrane chemoreceptors of Escherichia coli sense phenol as either an attractant (Tar) or a repellent (Tap, Trg, and Tsr). In this study, we investigated the Tar determinants that mediate its attractant response to phenol and the Tsr determinants that mediate its repellent response to phenol. Tar molecules with lesions in the aspartate-binding pocket of the periplasmic domain, with a foreign periplasmic domain (from Tsr or from several Pseudomonas chemoreceptors), or lacking nearly the entire periplasmic domain still mediated attractant responses to phenol. Similarly, Tar molecules with the cytoplasmic methylation and kinase control domains of Tsr still sensed phenol as an attractant. Additional hybrid receptors with signaling elements from both Tar and Tsr indicated that the transmembrane (TM) helices and HAMP domain determined the sign of the phenol-sensing response. Several amino acid replacements in the HAMP domain of Tsr, particularly attractant-mimic signaling lesions at residue E248, converted Tsr to an attractant sensor of phenol. These findings suggest that phenol may elicit chemotactic responses by diffusing into the cytoplasmic membrane and perturbing the structural stability or position of the TM bundle helices, in conjunction with structural input from the HAMP domain. We conclude that behavioral responses to phenol, and perhaps to temperature, cytoplasmic pH, and glycerol, as well, occur through a general sensing mechanism in chemoreceptors that detects changes in the structural stability or dynamic behavior of a receptor signaling element. The structurally sensitive target for phenol is probably the TM bundle, but other behaviors could target other receptor elements.

Thermosensing function of the Escherichia coli redox sensor Aer

Escherichia coli chemoreceptors can sense changes in temperature for thermotaxis. Here we found that the aerotaxis transducer Aer, a homolog of chemoreceptors lacking a periplasmic domain, mediates thermoresponses. We propose that thermosensing by the chemoreceptors is a general attribute of their highly conserved cytoplasmic domain (or their less conserved transmembrane domain).

Microbial thermosensors

Temperature is among the most important of the parameters that free-living microbes monitor. Microbial physiology needs to be readjusted in response to sudden temperature changes. When the ambient temperature rises or drops to potentially harmful levels, cells mount protective stress responses--so-called heat or cold shock responses, respectively. Pathogenic microorganisms often respond to a temperature of around 37 degrees C by inducing virulence gene expression. There are two main ways in which temperature can be measured. Often, the consequences of a sudden temperature shift are detected. Such indirect signals are known to be the accumulation of denatured proteins (heat shock) or stalled ribosomes (cold shock). However, this article focuses solely on direct thermosensors. Since the conformation of virtually every biomolecule is susceptible to temperature changes, primary sensors include DNA, RNA, proteins and lipids.

Phenotypic Suppression Methods for Analyzing Intra‐ and Inter‐Molecular Signaling Interactions of Chemoreceptors

The receptors that mediate chemotactic behaviors in E. coli and other motile bacteria and archaea are exquisite molecular machines. They detect minute concentration changes in the organism's chemical environment, integrate multiple stimulus inputs, and generate a highly amplified output signal that modulates the cell's locomotor pattern. Genetic dissection and suppression analyses have played an important role in elucidating the molecular mechanisms that underlie chemoreceptor signaling. This chapter discusses three examples of phenotypic suppression analyses of receptor signaling defects. (i) Balancing suppression can occur in mutant receptors that have biased output signals and involves second-site mutations that create an offsetting bias change. Such suppressors can arise in many parts of the receptor and need not involve directly interacting parts of the molecule. (ii) Conformational suppression within a mutant receptor molecule occurs through a mutation that directly compensates for the initial structural defect. This form of suppression should be highly dependent on the nature of the structural alterations caused by the original mutation and its suppressor, but in practice may be difficult to distinguish from balancing suppression without high-resolution structural information about the mutant and pseudorevertant proteins. (iii) Conformational suppression between receptor molecules involves correction of a functional defect in one receptor by a mutational change in a heterologous receptor with which it normally interacts. The suppression patterns exhibit allele-specificity with respect to the compensatory residue positions and amino acid side chains, a hallmark of stereospecific protein-protein interactions.

Solitary modes of bacterial culture in a temperature gradient

We study the behavior of a bacterial culture in a one-dimensional temperature gradient. The bacteria first accumulate near their natural temperature due to thermotaxis. The maximum of the bacterial density profile then drifts to lower temperature with a velocity proportional to the initial concentration of bacteria (typical velocity 0.5 microm/sec). Above a critical concentration of 10(8) cells/cm(3), a new mode develops from the initial accumulation in the form of a sharp pulse moving at a faster velocity ( approximately 3.5 microm/sec). The time of development of this mode diverges as the concentration approaches its critical value. This mode is a result of a positive feedback mechanism provided by interbacterial communication. A theoretical model shows good agreement with the experimental results.

Intracellular and extracellular components as bacterial thermometers, and early warning against thermal stress

Responses induced by cold or heat are triggered following detection of temperature changes by specific sensing molecules, complexes or structures. Low temperature responses are often induced following sensing of cold-induced falls in membrane fluidity, such changes turning-on or -off enzymic activities in membrane proteins, although ribosomes and DNA may also function in cold perception. Many thermal sensors are components of structures damaged by the heat, with sensing involving changes to ribosomes, DNA, intracellular proteins and, less commonly, membrane fluidity. Additionally, secreted proteins (extracellular sensing components, ESCs) detect temperature increases i.e. act as thermometers, with ESC activation in the medium, by the stimulus, converting such sensors to extracellular signalling molecules, the extracellular induction components (EICs), which induce thermal responses. Several ESC/EIC pairs trigger thermal responses, and have the unique property of giving early warning of the stress by diffusing to regions (and organisms) not yet exposed to elevated temperatures.

Making sense of it all: bacterial chemotaxis

Bacteria must be able to respond to a changing environment, and one way to respond is to move. The transduction of sensory signals alters the concentration of small phosphorylated response regulators that bind to the rotary flagellar motor and cause switching. This simple pathway has provided a paradigm for sensory systems in general. However, the increasing number of sequenced bacterial genomes shows that although the central sensory mechanism seems to be common to all bacteria, there is added complexity in a wide range of species.

Multiple light inputs control phototaxis in Synechocystis sp. strain PCC6803

The phototactic behavior of individual cells of the cyanobacterium Synechocystis sp. strain PCC6803 was studied with a glass slide-based phototaxis assay. Data from fluence rate-response curves and action spectra suggested that there were at least two light input pathways regulating phototaxis. We observed that positive phototaxis in wild-type cells was a low fluence response, with peak spectral sensitivity at 645 and 704 nm. This red-light-induced phototaxis was inhibited or photoreversible by infrared light (760 nm). Previous work demonstrated that a taxD1 mutant (Cyanobase accession no. sll0041; also called pisJ1) lacked positive but maintained negative phototaxis. Therefore, the TaxD1 protein, which has domains that are similar to sequences found in both bacteriophytochrome and the methyl-accepting chemoreceptor protein, is likely to be the photoreceptor that mediates positive phototaxis. Wild-type cells exhibited negative phototaxis under high-intensity broad-spectrum light. This phenomenon is predominantly blue light responsive, with a maximum sensitivity at approximately 470 nm. A weakly negative phototactic response was also observed in the spectral region between 600 and 700 nm. A deltataxD1 mutant, which exhibits negative phototaxis even under low-fluence light, has a similar action maximum in the blue region of the spectrum, with minor peaks from green to infrared (500 to 740 nm). These results suggest that while positive phototaxis is controlled by the red light photoreceptor TaxD1, negative phototaxis in Synechocystis sp. strain PCC6803 is mediated by one or more (as yet) unidentified blue light photoreceptors.

Mutational analysis of a conserved signal-transducing element: the HAMP linker of the Escherichia coli nitrate sensor NarX

The HAMP linker, a predicted structural element observed in sensor proteins from all domains of life, is proposed to transmit signals between extracellular sensory input domains and cytoplasmic output domains. HAMP (histidine kinase, adenylyl cyclase, methyl-accepting chemotaxis protein, and phosphatase) linkers are located just inside the cytoplasmic membrane and are projected to form two short amphipathic alpha-helices (AS-1 and AS-2) joined by an unstructured connector. The presumed helices are comprised of hydrophobic residues in heptad repeats, with only three positions exhibiting strong conservation. We generated missense mutations at these three positions and throughout the HAMP linker in the Escherichia coli nitrate sensor kinase NarX and screened the resulting mutants for defective responses to nitrate. Most missense mutations in this region resulted in a constitutive phenotype mimicking the ligand-bound state, and only one residue (a conserved Glu before AS-2) was essential for HAMP linker function. We also scanned the narX HAMP linker with an overlapping set of seven-residue deletions. Deletions in AS-1 and the connector resulted in constitutive phenotypes. Two deletions in AS-2 resulted in a novel reversed response phenotype in which the response to ligand was the opposite of that seen for the narX(+) strain. These observations are consistent with the proposed HAMP linker structure, show that the HAMP linker plays an active role in transmembrane signal transduction, and indicate that the two amphipathic alpha-helices have different roles in signal transduction.

Bacterial cold shock responses

As a measure for molecular motion, temperature is one of the most important environmental factors for life as it directly influences structural and hence functional properties of cellular components. After a sudden increase in ambient temperature, which is termed heat shock, bacteria respond by expressing a specific set of genes whose protein products are designed to mainly cope with heat-induced alterations of protein conformation. This heat shock response comprises the expression of protein chaperones and proteases, and is under central control of an alternative sigma factor (sigma 32) which acts as a master regulator that specifically directs RNA polymerase to transcribe from the heat shock promotors. In a similar manner, bacteria express a well-defined set of proteins after a rapid decrease in temperature, which is termed cold shock. This protein set, however, is different from that expressed under heat shock conditions and predominantly comprises proteins such as helicases, nucleases, and ribosome-associated components that directly or indirectly interact with the biological information molecules DNA and RNA. Interestingly, in contrast to the heat shock response, to date no cold-specific sigma factor has been identified. Rather, it appears that the cold shock response is organized as a complex stimulon in which post-transcriptional events play an important role. In this review, we present a summary of research results that have been acquired in recent years by examinations of bacterial cold shock responses. Important processes such as cold signal perception, membrane adaptation, and the modification of the translation apparatus are discussed together with many other cold-relevant aspects of bacterial physiology and first attempts are made to dissect the cold shock stimulon into less complex regulatory subunits. Special emphasis is placed on findings concerning the nucleic acid-binding cold shock proteins which play a fundamental role not only during cold shock adaptation but also under optimal growth conditions.

Sensing of cytoplasmic pH by bacterial chemoreceptors involves the linker region that connects the membrane-spanning and the signal-modulating helices

The two major chemoreceptors of Escherichia coli, Tsr and Tar, mediate opposite responses to the same changes in cytoplasmic pH (pH(i)). We set out to identify residues involved in pH(i) sensing to gain insight into the general mechanisms of signaling employed by the chemoreceptors. Characterization of various chimeras of Tsr and Tar localized the pH(i)-sensing region to Arg(259)-His(267) of Tar and Gly(261)-Asp(269) of Tsr. This region of Tar contains three charged residues (Arg(259)-Ser(261), Asp(263), and His(267)) that have counterparts of opposite charge in Tsr (Gly(261)-Glu(262), Arg(265), and Asp(269)). The replacement of all of the three charged residues in Tar or Arg(259)-Ser(260) alone by the corresponding residues of Tsr reversed the polarity of pH(i) response, whereas the replacement of Asp(263) or His(267) did not change the polarity but altered the time course of pH(i) response. These results suggest that the electrostatic properties of a short cytoplasmic region within the linker region that connects the second transmembrane helix to the first methylation helix is critical for switching the signaling state of the chemoreceptors during pH sensing. Similar conformational changes of this region in response to external ligands may be critical components of transmembrane signaling.

The thermostability of an alpha-helical coiled-coil protein and its potential use in sensor applications

Coiled-coil proteins are assemblies of two to four alpha-helices that pack together in a parallel or anti-parallel fashion. Coiled-coil structures can confer a variety of functional capabilities, which include enabling proteins, such as myosin, to function in the contractile apparatus of muscle and non-muscle cells. The TlpA protein encoded by the virulence plasmid of Salmonella is an alpha-helical protein that forms an elongated coiled-coil homodimer. A number of studies have clearly established the role of TlpA as a temperature-sensing gene regulator, however the potential use of a TlpA in a thermo-sensor application outside of the organism has not been exploited. In this paper, we demonstrate that TlpA has several characteristics that are common with alpha-helical coiled-coils and its thermal folding and unfolding is reversible and rapid. TlpA is extremely sensitive to changes in temperature. We have also compared the heat-stability of TlpA with other structurally similar proteins. Using a folding reporter, in which TlpA is expressed as a C-terminal fusion with green fluorescent protein (GFP), we were able to use fluorescence as an indicator of folding and unfolding of the fusion protein. Our results on the rapid conformational changes inherent in TlpA support the previous findings and we present here preliminary data on the use of a GFP-TlpA fusion protein as temperature sensor.

Evidence that both ligand binding and covalent adaptation drive a two-state equilibrium in the aspartate receptor signaling complex

The transmembrane aspartate receptor of bacterial chemotaxis regulates an associated kinase protein in response to both attractant binding to the receptor periplasmic domain and covalent modification of four adaptation sites on the receptor cytoplasmic domain. The existence of at least 16 covalent modification states raises the question of how many stable signaling conformations exist. In the simplest case, the receptor could have just two stable conformations ("on" and "off") yielding the two-state behavior of a toggle-switch. Alternatively, covalent modification could incrementally shift the receptor between many more than two stable conformations, thereby allowing the receptor to function as a rheostatic switch. An important distinction between these models is that the observed functional parameters of a toggle-switch receptor could strongly covary as covalent modification shifts the equilibrium between the on- and off-states, due to population-weighted averaging of the intrinsic on- and off-state parameters. By contrast, covalent modification of a rheostatic receptor would create new conformational states with completely independent parameters. To resolve the toggle-switch and rheostat models, the present study has generated all 16 homogeneous covalent modification states of the receptor adaptation sites, and has compared their effects on the attractant affinity and kinase activity of the reconstituted receptor-kinase signaling complex. This approach reveals that receptor covalent modification modulates both attractant affinity and kinase activity up to 100-fold, respectively. The regulatory effects of individual adaptation sites are not perfectly additive, indicating synergistic interactions between sites. The three adaptation sites at positions 295, 302, and 309 are more important than the site at position 491 in regulating attractant affinity and kinase activity, thereby explaining the previously observed dominance of the former three sites in in vivo studies. The most notable finding is that covalent modification of the adaptation sites alters the receptor attractant affinity and the receptor-regulated kinase activity in a highly correlated fashion, strongly supporting the toggle-switch model. Similarly, certain mutations that drive the receptor into the kinase activating state are found to have correlated effects on attractant affinity. Together these results provide strong evidence that chemotaxis receptors possess just two stable signaling conformations and that the equilibrium between these pure on- and off-states is modulated by both attractant binding and covalent adaptation. It follows that the attractant and adaptation signals drive the same conformational change between the two settings of a toggle. An approach that quantifies the fractional occupancy of the on- and off-states is illustrated.

Interim report on genomics of Escherichia coli

We present a summary of recent progress in understanding Escherichia coli K-12 gene and protein functions. New information has come both from classical biological experimentation and from using the analytical tools of functional genomics. The content of the E. coli genome can clearly be seen to contain elements acquired by horizontal transfer. Nevertheless, there is probably a large, stable core of >3500 genes that are shared among all E. coli strains. The gene-enzyme relationship is examined, and, in many cases, it exhibits complexity beyond a simple one-to-one relationship. Also, the E. coli genome can now be seen to contain many multiple enzymes that carry out the same or closely similar reactions. Some are similar in sequence and may share common ancestry; some are not. We discuss the concept of a minimal genome as being variable among organisms and obligatorily linked to their life styles and defined environmental conditions. We also address classification of functions of gene products and avenues of insight into the history of protein evolution.

Attractant regulation of the aspartate receptor-kinase complex: limited cooperative interactions between receptors and effects of the receptor modification state

The manner by which the bacterial chemotaxis system responds to a wide range of attractant concentrations remains incompletely understood. In principle, positive cooperativity between chemotaxis receptors could explain the ability of bacteria to respond to extremely low attractant concentrations. By utilizing an in vitro receptor-coupled kinase assay, the attractant-dependent response curve has been measured for the Salmonella typhimurium aspartate chemoreceptor. The attractant chosen, alpha-methyl aspartate, was originally used to quantitate high receptor sensitivity at low attractant concentrations by Segall, Block, and Berg [(1986) Proc. Natl. Acad. Sci. U.S.A. 83, 8987-8991]. The attractant response curve exhibits limited positive cooperativity, yielding a Hill coefficient of 1.7-2.4, and this Hill coefficient is relatively independent of both the receptor modification state and the mole ratio of CheA to receptor. These results disfavor models in which there are strong cooperative interactions between large numbers of receptor dimers in an extensive receptor array. Instead, the results are consistent with cooperative interactions between a small number of coupled receptor dimers. Because the in vitro receptor-coupled kinase assay utilizes higher than native receptor densities arising from overexpression, the observed positive cooperativity may overestimate that present in native receptor populations. Such positive cooperativity between dimers is fully compatible with the negative cooperativity previously observed between the two symmetric ligand binding sites within a single dimer. The attractant affinity of the aspartate receptor is found to depend on the modification state of its covalent adaptation sites. Increasing the the level of modification decreases the apparent attractant affinity at least 10-fold in the in vitro receptor-coupled kinase assay. This observation helps explain the ability of the chemotaxis pathway to respond to a broad range of attractant concentrations in vivo.

Genetics of chemotaxis and thermotaxis in the nematode Caenorhabditis elegans

Molecular genetic analysis of chemotaxis and theramotaxis in Caenorhabditis elegans has revealed the molecular bases of olfaction, taste, and thermosensation, which, in turn, has demonstrated that sensory signaling in C. elegans is very similar to that in vertebrates. A cyclic nucleotide-gated channel (TAX-2/TAX-4) that is highly homologous to the olfactory and photoreceptor channels in vertebrates is required for taste and thermosensation, in addition to olfaction. A cation channel (OSM-9) that is closely related to a capsaicin receptor channel is required for olfactory adaptation in one olfactory neuron and olfactory sensation in the other olfactory neuron. A novel G alpha protein (ODR-3) is essential for olfactory responses in all olfactory neurons and aversive responses in a polymodal sensory neuron. A G protein-coupled seven-transmembrane receptor (ODR-10) is the first olfactory receptor whose ligand was elucidated. Using chemotaxis and thermotaxis as behavioral paradigms, neural plasticity including learning and memory can be studied genetically in C. elegans.