Aerotactic responses in bacteria to photoreleased oxygen

Harnessing density to control the duration of intermittent Lévy walks in bacterial turbulence

Dense bacterial suspensions display collective motion exhibiting coherent flow structures reminiscent of turbulent flows. However, in contrast to inertial turbulence, the microscopic dynamics underlying bacterial turbulence is only beginning to be understood. Here, we report experiments revealing correlations between microscopic dynamics and the emergence of collective motion in bacterial suspensions. Our results demonstrate the existence of three microscopic dynamical regimes: initial ballistic dynamics followed by an intermittent Lévy walk before the intriguing decay to random Gaussian fluctuations. Our experiments capture that the fluid correlation time earmarks the transition from Lévy to Gaussian fluctuations demonstrating the microscopic reason underlying the observation. By harnessing the flow activity via bacterial concentration, we reveal systematic control over the flow correlation timescales, which, in turn, allows controlling the duration of the Lévy walk.

The Aer2 chemoreceptor from Vibrio vulnificus is a tri-PAS-heme oxygen sensor

The marine pathogen Vibrio vulnificus senses and responds to environmental stimuli via two chemosensory systems and 42-53 chemoreceptors. Here, we present an analysis of the V. vulnificus Aer2 chemoreceptor, VvAer2, which is the first V. vulnificus chemoreceptor to be characterized. VvAer2 is related to the Aer2 receptors of other gammaproteobacteria, but uncharacteristically contains three PAS domains (PAS1-3), rather than one or two. Using an E. coli chemotaxis hijack assay, we determined that VvAer2, like other Aer2 receptors, senses and responds to O₂ . All three VvAer2 PAS domains bound pentacoordinate b-type heme and exhibited similar O₂ affinities. PAS2 and PAS3 both stabilized O₂ via conserved Iβ-Trp residues, but PAS1, which was easily oxidized in vitro, was unaffected by Iβ-Trp replacement. Our results support a model in which PAS1 is largely dispensable for O₂ -mediated signaling, whereas PAS2 modulates PAS3 signaling, and PAS3 signals to the downstream domains. Each PAS domain appeared to be positionally optimized, because PAS swapping caused altered signaling properties, and neither PAS1 nor PAS2 could replace PAS3. Our findings strengthen previous conclusions that Aer2 receptors are O₂ sensors, but with distinct N-terminal domain arrangements that facilitate, modulate and tune responses based on environmental signals.

Defining Two Chemosensory Arrays in Shewanella oneidensis

Shewanella oneidensis has 2 functional chemosensory systems named Che1 and Che3, and 27 chemoreceptors. Che3 is dedicated to chemotaxis while Che1 could be involved in RpoS post-translational regulation. In this study, we have shown that two chemoreceptors Aer2so and McpAso, genetically related to the Che1 system, form distinct core-signaling units and signal to Che1 and Che3, respectively. Moreover, we observed that Aer2so is a cytoplasmic dynamic chemoreceptor that, when in complex with CheA1 and CheW1, localizes at the two poles and the centre of the cells. Altogether, the results obtained indicate that Che1 and Che3 systems are interconnected by these two chemoreceptors allowing a global response for bacterial survival.

New Roles for HAMP Domains: the Tri-HAMP Region of Pseudomonas aeruginosa Aer2 Controls Receptor Signaling and Cellular Localization

The Aer2 chemoreceptor from Pseudomonas aeruginosa is an O₂ sensor involved in stress responses, virulence, and tuning the behavior of the chemotaxis (Che) system. Aer2 is the sole receptor of the Che2 system. It is soluble, but membrane associated, and forms complexes at the cell pole during stationary phase. The domain arrangement of Aer2 is unusual, with a PAS sensing domain sandwiched between five HAMP domains, followed by a C-terminal kinase-control output domain. The first three HAMP domains form a poly-HAMP chain N-terminal to the PAS sensing domain. HAMP domains are often located between signal input and output domains, where they transduce signals. Given that HAMP1 to 3 reside N-terminal to the input-output pathway, we undertook a systematic examination of their function in Aer2. We found that HAMP1 to 3 influence PAS signaling over a considerable distance, as the majority of HAMP1, 2 and 3 mutations, and deletions of helical phase stutters, led to nonresponsive signal-off or off-biased receptors. PAS signal-on lesions that mimic activated Aer2 also failed to override N-terminal HAMP signal-off replacements. This indicates that HAMP1 to 3 are critical coupling partners for PAS signaling and likely function as a cohesive unit and moveable scaffold to correctly orient and poise PAS dimers for O₂-mediated signaling in Aer2. HAMP1 additionally controlled the clustering and polar localization of Aer2 in P. aeruginosa. Localization was not driven by HAMP1 charge, and HAMP1 signal-off mutants still localized. Employing HAMP as a clustering and localization determinant, as well as a facilitator of PAS signaling, are newly recognized roles for HAMP domains. IMPORTANCE P. aeruginosa is an opportunistic pathogen that interprets environmental stimuli via 26 chemoreceptors that signal through 4 distinct chemosensory systems. The second chemosensory system, Che2, contains a receptor named Aer2 that senses O₂ and mediates stress responses and virulence and tunes chemotactic behavior. Aer2 is membrane associated, but soluble, and has three N-terminal HAMP domains (HAMP1 to 3) that reside outside the signal input-output pathway of Aer2. In this study, we determined that HAMP1 to 3 facilitate O₂-dependent signaling from the PAS sensing domain and that HAMP1 controls the formation of Aer2-containing polar foci in P. aeruginosa. Both of these are newly recognized roles for HAMP domains that may be applicable to other non-signal-transducing HAMP domains and poly-HAMP chains.

Direct measurement of the aerotactic response in a bacterial suspension

Aerotaxis is the ability of motile cells to navigate toward oxygen. A key question is the dependence of the aerotactic velocity with the local oxygen concentration c. Here we combine simultaneous bacteria tracking and local oxygen concentration measurements using Ruthenium encapsulated in micelles to characterize the aerotactic response of Burkholderia contaminans, a motile bacterium ubiquitous in the environment. In our experiments, an oxygen gradient is produced by the bacterial respiration in a sealed glass capillary permeable to oxygen at one end, producing a bacterial band traveling toward the oxygen source. We compute the aerotactic response χ(c) both at the population scale, from the drift velocity in the bacterial band, and at the bacterial scale, from the angular modulation of the run times. Both methods are consistent with a power-law χ∝c^{-2}, in good agreement with existing models based on the biochemistry of bacterial membrane receptors.

Leptospira interrogans Aer2: an Unusual Membrane-Bound PAS-Heme Oxygen Sensor

In this study, we provide the first characterization of a chemoreceptor from Leptospira interrogans, the cause of leptospirosis. This receptor is related to the Aer2 receptors that have been studied in other bacteria. In those organisms, Aer2 is a soluble receptor with one or two PAS-heme domains and signals in response to O₂ binding. In contrast, L. interrogans Aer2 (LiAer2) is an unusual membrane-bound Aer2 with a periplasmic domain and three cytoplasmic PAS-heme domains. Each of the three PAS domains bound b-type heme via conserved Eη-His residues. They also bound O₂ and CO with similar affinities to each other and other PAS-heme domains. However, all three PAS domains were uniquely hexacoordinate in the deoxy-heme state, whereas other Aer2-PAS domains are pentacoordinate. Similar to other Aer2 receptors, LiAer2 could hijack the E. coli chemotaxis pathway but only when it was expressed with an E. coli high-abundance chemoreceptor. Unexpectedly, the response was inverted relative to classic Aer2 receptors. That is, LiAer2 caused E. coli to tumble (it was signal-on) in the absence of O₂ and to stop tumbling in its presence. Thus, an endogenous ligand in the deoxy-heme state was correlated with signal-on LiAer2, and its displacement for gas-binding turned signaling off. This response also occurred in a soluble version of LiAer2 lacking the periplasmic domain, transmembrane (TM) region, and first two PAS domains, meaning that PAS3 alone was sufficient for O₂-mediated control. Future studies are needed to understand the unique signaling mechanisms of this unusual Aer2 receptor. IMPORTANCE Leptospira interrogans, the cause of the zoonotic infection leptospirosis, is found in soil and water contaminated with animal urine. L. interrogans survives in complex environments with the aid of 12 chemoreceptors, none of which has been explicitly studied. In this study, we characterized the first L. interrogans chemoreceptor, LiAer2, and reported its unique characteristics. LiAer2 is membrane-bound, has three cytoplasmic PAS-heme domains that each bound hexacoordinate b-type heme and O₂ turned LiAer2 signaling off. An endogenous ligand in the deoxy-heme state was correlated with signal-on LiAer2 and its displacement for O₂-binding turned signaling off. Our study corroborated previous findings that Aer2 receptors are O₂ sensors, but also demonstrated that they do not all function the same way.

Stress Dependent Biofilm Formation and Bioactive Melanin Pigment Production by a Thermophilic Bacillus Species from Chilean Hot Spring

Thermophilic bacteria able to survive extreme temperature stress are of great biotechnological interest due to their extracellular production of bioactive molecules as a part of a survival strategy, or by intracellular modifications. In the present study, thermophilic Bacillus haynesii CamB6, isolated from a Chilean hot spring, was studied for the formation of different stress response molecules. The polymeric pigment produced by the bacterial strain was characterized by different physicochemical techniques. On exposure to ranges of temperature (50–60 °C), pH (5.0–7.0), and sources of nitrogen and carbon (1–5 g·L⁻¹), the bacteria responded with a biofilm network formation in a hydrophobic polystyrene surface. Biofilm formation under fed-batch conditions was also statistically validated. The bacteria showed a planktonic pellicle network formation in the presence of induced hypoxia and salinity stress (19.45 g·L⁻¹) under static conditions. Salinity stress also resulted in the intracellular response of brown pigment production. The pigment was structurally and functionally characterized by UV-Vis absorbance and the presence of different characteristic peaks via FTIR analysis (bacterial pyomelanin fingerprints) were assessed. A high thermal stability and TGA profile indicated the brown pigment was a probable pyomelanin candidate. Micropyrolysis (Py-GC/MS) showed that isoprene, pyrrole, benzene, pyridine, and their derivatives were the major components detected. In addition, acetic acid, indole, phenol, and its derivatives were observed. The absence of sulfocompounds in the pyrolyzed products agreed with those reported in the literature for pyomelanin. The pigment surface morphology was analyzed via SEM, and the elemental composition via EDS also demonstrated the similarity of the brown pigment to that of the melanin family. The pyomelanin pigment was observed to be bioactive with promising antioxidant capacity (H₂O₂, Fe²⁺) compared to the standard antioxidant molecules. In conclusion, B. haynesii CamB6 demonstrated the formation of several biomolecules as a stress response mechanism that is bioactive, showing its probable biotechnological applications in future.

Oxygen-Induced Conformational Changes in the PAS-Heme Domain of the Pseudomonas aeruginosa Aer2 Receptor

The Aer2 receptor from Pseudomonas aeruginosa has an O₂-binding PAS-heme domain that stabilizes O₂ via a Trp residue in the distal heme pocket. Trp rotates ∼90° to bond with the ligand and initiate signaling. Although the isolated PAS domain is monomeric, both in solution and in a cyanide-bound crystal structure, an unliganded structure forms a dimer. An overlay of the two structures suggests possible signaling motions but also predicts implausible clashes at the dimer interface when the ligand is bound. Moreover, in a full-length Aer2 dimer, PAS is sandwiched between multiple N- and C-terminal HAMP domains, which would feasibly restrict PAS motions. To explore the PAS dimer interface and signal-induced motions in full-length Aer2, we introduced Cys substitutions and used thiol-reactive probes to examine in vivo accessibility and residue proximities under both aerobic and anaerobic conditions. In vivo, PAS dimers were retained in full-length Aer2 in the presence and absence of O₂, and the dimer interface was consistent with the isolated PAS dimer structure. O₂-mediated changes were also consistent with structural predictions in which the PAS N-terminal caps move apart and the C-terminal DxT region moves closer together. The DxT motif links PAS to the C-terminal HAMP domains and was critical for PAS-HAMP signaling. Removing the N-terminal HAMP domains altered the distal PAS dimer interface and prevented signaling, even after signal-on lesions were introduced into PAS. The N-terminal HAMP domains thus facilitate the O₂-dependent shift of PAS to the signal-on conformation, clarifying their role upstream of the PAS-sensing domain.

A bacterial antibiotic resistance accelerator and applications

The systematic emergence of drug resistance remains a major problem in the treatment of infectious diseases (antibiotics) and cancer (chemotherapy), with possible common fundamental origins linking bacterial antibiotic resistance and emergence of chemotherapy resistance. The common link may be evolution in a complex fitness landscape with connected small population niches. We report a detailed method for observing bacterial adaptive behavior in heterogeneous microfluidic environment designed to mimic the environmental heterogeneity found in natural microbial niches. First, the device is structured with multiple connected micro-chambers that allow the cell population to communicate and organize into smaller populations. Second, bacteria evolve within an antibiotic gradient generated throughout the micro-chambers that creates a wide range of fitness landscapes. High-resolution images of the adaptive response to the antibiotic stress are captured by epifluorescence microscopy at various levels of the bacterial organization for quantitative analysis. Thus, the experimental setup we have developed provides a powerful frame for visualizing evolution at work: bacterial movement, survival and death. It also presents a basis for exploring the rates at which drug resistance arises in bacteria and other biological contexts such as cancer.

THE AER2 RECEPTOR FROM VIBRIO CHOLERAE IS A DUAL PAS-HEME OXYGEN SENSOR

The diarrheal pathogen Vibrio cholerae navigates complex environments using three chemosensory systems and 44-45 chemoreceptors. Chemosensory cluster II modulates chemotaxis, whereas clusters I and III have unknown functions. Ligands have been identified for only five V. cholerae chemoreceptors. Here we report that the cluster III receptor, VcAer2, binds and responds to O₂ . VcAer2 is an ortholog of Pseudomonas aeruginosa Aer2 (PaAer2), but differs in that VcAer2 has two, rather than one, N-terminal PAS domain. We have determined that both PAS1 and PAS2 form homodimers and bind penta-coordinate b-type heme via an Eη-His residue. Heme binding to PAS1 required the entire PAS core, but receptor function also required the N-terminal cap. PAS2 functioned as an O₂ -sensor [K_d(O2) , 19 μM], utilizing the same Iβ Trp (W276) as PaAer2 to stabilize O₂ . The crystal structure of PAS2-W276L was similar to that of PaAer2-PAS, but resided in an active conformation mimicking the ligand-bound state, consistent with its signal-on phenotype. PAS1 also bound O₂ [K_d(O2), 12 μM], although O₂ binding was stabilized by either a Trp or Tyr residue. Moreover, PAS1 appeared to function as a signal modulator, regulating O₂ -mediated signaling from PAS2, and resulting in activation of the cluster III chemosensory pathway. This article is protected by copyright. All rights reserved.

Gas Sensing and Signaling in the PAS-Heme Domain of the Pseudomonas aeruginosa Aer2 Receptor

The Aer2 chemoreceptor from Pseudomonas aeruginosa contains a PAS sensing domain that coordinates b-type heme and signals in response to the binding of O₂, CO, or NO. PAS-heme structures suggest that Aer2 uniquely coordinates heme via a His residue on a 3₁₀ helix (H234 on Eη), stabilizes O₂ binding via a Trp residue (W283), and signals via both W283 and an adjacent Leu residue (L264). Ligand binding may displace L264 and reorient W283 for hydrogen bonding to the ligand. Here, we clarified the mechanisms by which Aer2-PAS binds heme, regulates ligand binding, and initiates conformational signaling. H234 coordinated heme, but additional hydrophobic residues in the heme cleft were also critical for stable heme binding. O₂ appeared to be the native Aer2 ligand (dissociation constant [K_d ] of 16 μM). With one exception, mutants that bound O₂ could signal, whereas many mutants that bound CO could not. W283 stabilized O₂ binding but not CO binding, and it was required for signal initiation; W283 mutants that could not stabilize O₂ were rapidly oxidized to Fe(III). W283F was the only Trp mutant that bound O₂ with wild-type affinity. The size and nature of residue 264 was important for gas binding and signaling: L264W blocked O₂ binding, L264A and L264G caused O₂-mediated oxidation, and L264K formed a hexacoordinate heme. Our data suggest that when O₂ binds to Aer2, L264 moves concomitantly with W283 to initiate the conformational signal. The signal then propagates from the PAS domain to regulate the C-terminal HAMP and kinase control domains, ultimately modulating a cellular response.IMPORTANCEPseudomonas aeruginosa is a ubiquitous environmental bacterium and opportunistic pathogen that infects multiple body sites, including the lungs of cystic fibrosis patients. P. aeruginosa senses and responds to its environment via four chemosensory systems. Three of these systems regulate biofilm formation, twitching motility, and chemotaxis. The role of the fourth system, Che2, is unclear but has been implicated in virulence. The Che2 system contains a chemoreceptor called Aer2, which contains a PAS sensing domain that binds heme and senses oxygen. Here, we show that Aer2 uses unprecedented mechanisms to bind O₂ and initiate signaling. These studies provide both the first functional corroboration of the Aer2-PAS signaling mechanism previously proposed from structure as well as a signaling model for Aer2-PAS receptors.

A Microfluidic Platform for High-Throughput Screening of Small Mutant Libraries

The screening and isolation of target microorganisms from mutated recombinant libraries are crucial for the advancement of synthetic biology and metabolic engineering. However, conventional screening tools present several limitations in throughput, cost, and labor. Herein, we describe a novel microfluidic high-throughput screening (HTS) platform with several advantages. The platform utilizes a fluid array to compartmentalize bacterial cells in well-ordered separated microwells and allows long-term cell culture with high throughput. The platform enables the extraction of selected target cells from the fluid array for additional culture and postanalysis by using a capillary-driven sample relocation method. To confirm the feasibility of the platform, we demonstrated two different types of HTS methods based on the levels of reporter gene expression and cellular growth rate difference. For the reporter gene-based HTS, a spike recovery approach was taken to demonstrate that target cells are successfully screened out from a mixture containing nontarget cells by repeating the culture and extraction processes. Additionally, the same platform allowed us to screen and sort target cells according to their cellular growth rate difference, which seems hard in conventional screening methods. Hence, the platform could be used for various microbiological assays, including the detection of cell-excreted metabolites, microbial biosensors, and other HTS systems.

Delineating PAS-HAMP interaction surfaces and signalling-associated changes in the aerotaxis receptor Aer

The Escherichia coli aerotaxis receptor, Aer, monitors cellular oxygen and redox potential via FAD bound to a cytosolic PAS domain. Here, we show that Aer-PAS controls aerotaxis through direct, lateral interactions with a HAMP domain. This contrasts with most chemoreceptors where signals propagate along the protein backbone from an N-terminal sensor to HAMP. We mapped the interaction surfaces of the Aer PAS, HAMP and proximal signalling domains in the kinase-off state by probing the solvent accessibility of 129 cysteine substitutions. Inaccessible PAS-HAMP surfaces overlapped with a cluster of PAS kinase-on lesions and with cysteine substitutions that crosslinked the PAS β-scaffold to the HAMP AS-2 helix. A refined Aer PAS-HAMP interaction model is presented. Compared to the kinase-off state, the kinase-on state increased the accessibility of HAMP residues (apparently relaxing PAS-HAMP interactions), but decreased the accessibility of proximal signalling domain residues. These data are consistent with an alternating static-dynamic model in which oxidized Aer-PAS interacts directly with HAMP AS-2, enforcing a static HAMP domain that in turn promotes a dynamic proximal signalling domain, resulting in a kinase-off output. When PAS-FAD is reduced, PAS interaction with HAMP is relaxed and a dynamic HAMP and static proximal signalling domain convey a kinase-on output.

Architecture of the soluble receptor Aer2 indicates an in-line mechanism for PAS and HAMP domain signaling

Bacterial receptors typically contain modular architectures with distinct functional domains that combine to send signals in response to stimuli. Although the properties of individual components have been investigated in many contexts, there is little information about how diverse sets of modules work together in full-length receptors. Here, we investigate the architecture of Aer2, a soluble gas-sensing receptor that has emerged as a model for PAS (Per-Arnt-Sim) and poly-HAMP (histidine kinase-adenylyl cyclase-methyl-accepting chemotaxis protein-phosphatase) domain signaling. The crystal structure of the heme-binding PAS domain in the ferric, ligand-free form, in comparison to the previously determined cyanide-bound state, identifies conformational changes induced by ligand binding that are likely essential for the signaling mechanism. Heme-pocket alternations share some similarities with the heme-based PAS sensors FixL and EcDOS but propagate to the Iβ strand in a manner predicted to alter PAS-PAS associations and the downstream HAMP junction within full-length Aer2. Small-angle X-ray scattering of PAS and poly-HAMP domain fragments of increasing complexity allow unambiguous domain assignments and reveal a linear quaternary structure. The Aer2 PAS dimeric crystal structure fits well within ab initio small-angle X-ray scattering molecular envelopes, and pulsed dipolar ESR measurements of inter-PAS distances confirm the crystallographic PAS arrangement within Aer2. Spectroscopic and pull-down assays fail to detect direct interactions between the PAS and HAMP domains. Overall, the Aer2 signaling mechanism differs from the Escherichia coli Aer paradigm, where side-on PAS-HAMP contacts are key. We propose an in-line model for Aer2 signaling, where ligand binding induces alterations in PAS domain structure and subunit association that is relayed through the poly-HAMP junction to downstream domains.

HAMP domain conformers that propagate opposite signals in bacterial chemoreceptors

HAMP domains are signal relay modules in >26,000 receptors of bacteria, eukaryotes, and archaea that mediate processes involved in chemotaxis, pathogenesis, and biofilm formation. We identify two HAMP conformations distinguished by a four- to two-helix packing transition at the C-termini that send opposing signals in bacterial chemoreceptors. Crystal structures of signal-locked mutants establish the observed structure-to-function relationships. Pulsed dipolar electron spin resonance spectroscopy of spin-labeled soluble receptors active in cells verify that the crystallographically defined HAMP conformers are maintained in the receptors and influence the structure and activity of downstream domains accordingly. Mutation of HR2, a key residue for setting the HAMP conformation and generating an inhibitory signal, shifts HAMP structure and receptor output to an activating state. Another HR2 variant displays an inverted response with respect to ligand and demonstrates the fine energetic balance between "on" and "off" conformers. A DExG motif found in membrane proximal HAMP domains is shown to be critical for responses to extracellular ligand. Our findings directly correlate in vivo signaling with HAMP structure, stability, and dynamics to establish a comprehensive model for HAMP-mediated signal relay that consolidates existing views on how conformational signals propagate in receptors. Moreover, we have developed a rational means to manipulate HAMP structure and function that may prove useful in the engineering of bacterial taxis responses.

Studies of bacterial aerotaxis in a microfluidic device

Aerotaxis, the directional motion of bacteria in gradients of oxygen, was discovered in the late 19th century and has since been reported in a variety of bacterial species. Nevertheless, quantitative studies of aerotaxis have been complicated by the lack of tools for generation of stable gradients of oxygen concentration, [O(2)]. Here we report a series of experiments on aerotaxis of Escherichia coli in a specially built experimental setup consisting of a computer-controlled gas mixer and a two-layer microfluidic device made of polydimethylsiloxane (PDMS). The setup enables generation of a variety of stable linear profiles of [O(2)] across a long gradient channel, with characteristic [O(2)] ranging from aerobic to microaerobic conditions. A suspension of E. coli cells is perfused through the gradient channel at a low speed, allowing cells enough time to explore the [O(2)] gradient, and the distribution of cells across the gradient channel is analyzed near the channel outlet at a throughput of >10(5) cells per hour. Aerotaxis experiments are performed in [O(2)] gradients with identical logarithmic slopes and varying mean concentrations, as well as in gradients with identical mean concentrations and varying slopes. Experiments in gradients with [O(2)] ranging from 0 to ~11.5% indicate that, in contrast to some previous reports, E. coli cells do not congregate at some intermediate level of [O(2)], but rather prefer the highest accessible [O(2)]. The presented technology can be applied to studies of aerotaxis of other aerobic and microaerobic bacteria.

PAS/poly-HAMP signalling in Aer-2, a soluble haem-based sensor

Poly-HAMP domains are widespread in bacterial chemoreceptors, but previous studies have focused on receptors with single HAMP domains. The Pseudomonas aeruginosa chemoreceptor, Aer-2, has an unusual domain architecture consisting of a PAS-sensing domain sandwiched between three N-terminal and two C-terminal HAMP domains, followed by a conserved kinase control module. The structure of the N-terminal HAMP domains was recently solved, making Aer-2 the first protein with resolved poly-HAMP structure. The role of Aer-2 in P. aeruginosa is unclear, but here we show that Aer-2 can interact with the chemotaxis system of Escherichia coli to mediate repellent responses to oxygen, carbon monoxide and nitric oxide. Using this model system to investigate signalling and poly-HAMP function, we determined that the Aer-2 PAS domain binds penta-co-ordinated b-type haem and that reversible signalling requires four of the five HAMP domains. Deleting HAMP 2 and/or 3 resulted in a kinase-off phenotype, whereas deleting HAMP 4 and/or 5 resulted in a kinase-on phenotype. Overall, these data support a model in which ligand-bound Aer-2 PAS and HAMP 2 and 3 act together to relieve inhibition of the kinase control module by HAMP 4 and 5, resulting in the kinase-on state of the Aer-2 receptor.

Role of the F1 region in the Escherichia coli aerotaxis receptor Aer

In Escherichia coli, the aerotaxis receptor Aer is an atypical receptor because it senses intracellular redox potential. The Aer sensor is a cytoplasmic, N-terminal PAS domain that is tethered to the membrane by a 47-residue F1 linker. Here we investigated the function, topology, and orientation of F1 by employing random mutagenesis, cysteine scanning, and disulfide cross-linking. No native residue was obligatory for function, most deleterious substitutions had radically different side chain properties, and all F1 mutants but one were functionally rescued by the chemoreceptor Tar. Cross-linking studies were consistent with the predicted α-helical structure in the N-terminal F1 region and demonstrated trigonal interactions among the F1 linkers from three Aer monomers, presumably within trimer-of-dimer units, as well as binary interactions between subunits. Using heterodimer analyses, we also demonstrated the importance of arginine residues near the membrane interface, which may properly anchor the Aer protein in the membrane. By incorporating these data into a homology model of Aer, we developed a model for the orientation of the Aer F1 and PAS regions in an Aer lattice that is compatible with the known dimensions of the chemoreceptor lattice. We propose that the F1 region facilitates the orientation of PAS and HAMP domains during folding and thereby promotes the stability of the PAS and HAMP domains in Aer.

Gain-of-function mutations cluster in distinct regions associated with the signalling pathway in the PAS domain of the aerotaxis receptor, Aer

The Aer receptor monitors internal energy (redox) levels in Escherichia coli with an FAD-containing PAS domain. Here, we randomly mutagenized the region encoding residues 14-119 of the PAS domain and found 72 aerotaxis-defective mutants, 24 of which were gain-of-function, signal-on mutants. The mutations were mapped onto an Aer homology model based on the structure of the PAS-FAD domain in NifL from Azotobacter vinlandii. Signal-on lesions clustered in the FAD binding pocket, the beta-scaffolding and in the N-cap loop. We suggest that the signal-on lesions mimic the 'signal-on' state of the PAS domain, and therefore may be markers for the signal-in and signal-out regions of this domain. We propose that the reduction of FAD rearranges the FAD binding pocket in a way that repositions the beta-scaffolding and the N-cap loop. The resulting conformational changes are likely to be conveyed directly to the HAMP domain, and on to the kinase control module. In support of this hypothesis, we demonstrated disulphide band formation between cysteines substituted at residues N98C or I114C in the PAS beta-scaffold and residue Q248C in the HAMP AS-2 helix.

Polypeptide-mediated switchable microarray of bacteria

This paper describes a feasible solution for the bacterial cell death and contamination from cell division that occurs in microfluidic applications. The method adopts a smart thermoresponsive surface, highly resolved micropatterns, and surface-functionalized bacteria tagged with thermoresponsive molecules. We developed a method for controllable bacterial attachment and detachment using an elastin-like polypeptide (ELP). To create a smart surface with switchable properties, the surface of a glass substrate was conjugated with thermoresponsive ELP molecules. The attachment of bacterial cells to the ELP surface was induced by the hydrophobic affinity of the ELPs on the glass surface to tagged ELPs on the bacterial surface. A cell-repellent polymer was micropatterned to create a highly resolved space for specific bacterial adhesion. Reversible bacterial attachment and detachment was achieved by controlling the thermoresponsive phase transition of ELP molecules. Five different types of bacteria were successfully conjugated with ELPs and arrayed on the surface. The viability of the bacteria that had attached to the surface was evaluated by determining colony forming units of released bacteria on an agar plate.

Unexpected chemoreceptors mediate energy taxis towards electron acceptors in Shewanella oneidensis

Shewanella oneidensis uses a wide range of terminal electron acceptors for respiration. In this study, we show that the chemotactic response of S. oneidensis to anaerobic electron acceptors requires functional electron transport systems. Deletion of the genes encoding dimethyl sulphoxide and trimethylamine N-oxide reductases, or inactivation of these molybdoenzymes as well as nitrate reductase by addition of tungstate, abolished electron acceptor taxis. Moreover, addition of nigericin prevented taxis towards trimethylamine N-oxide, dimethyl sulphoxide, nitrite, nitrate and fumarate, showing that this process depends on the DeltapH component of the proton motive force. These data, together with those concerning response to metals (Bencharit and Ward, 2005), support the idea that, in S. oneidensis, taxis towards electron acceptors is governed by an energy taxis mechanism. Surprisingly, energy taxis in S. oneidensis is not mediated by the PAS-containing chemoreceptors but rather by a chemoreceptor (SO2240) containing a Cache domain. Four other chemoreceptors also play a minor role in this process. These results indicate that energy taxis can be mediated by new types of chemoreceptors.

Cryophotolysis of a caged oxygen compound for use in low temperature biological studies

Mechanistic investigations of biological enzymatic processes require controlled initiation and monitoring of catalytic reactions. A well-known technique to trap and observe reaction intermediates building up along a reaction pathway is the use of low temperature conditions. Here, we report a kinetically competent system for the release of molecular oxygen at cryogenic temperature, using a cobalt-based caged oxygen molecule, (micro-peroxo)(micro-hydroxo)bis[bis(bipyridyl)cobalt(III)] nitrate. Cryophotolysis of this compound was induced using 266 nm laser light and monitored by absorption microspectrophotometry. Furthermore, to verify that photo-fragmentation was accompanied by release of the active caged molecule, the production of dioxygen during cryophotolysis was directly visualized. This work lays the foundations for the use of low temperature reaction triggering as a tool to prolong the lifetime of normally unstable intermediate states in oxygen-dependent enzymes.

Caged molecules: principles and practical considerations

A caged molecule is an inert but photosensitive molecule that is transformed by photolysis into a biologically active molecule at high speed (typically 1 msec). The process is referred to as photorelease. The spatial resolution of photorelease is limited by the properties of light; submicrometer resolution is potentially achievable. Therefore, focal photorelease of caged molecules enables one to control biological processes with high spatio-temporal precision. The principles underlying caged molecules as well as practical considerations for their use are discussed in this unit.

Structure-function relationships in the HAMP and proximal signaling domains of the aerotaxis receptor Aer

Aer, the Escherichia coli aerotaxis receptor, faces the cytoplasm, where the PAS (Per-ARNT-Sim)-flavin adenine dinucleotide (FAD) domain senses redox changes in the electron transport system or cytoplasm. PAS-FAD interacts with a HAMP (histidine kinase, adenylyl cyclase, methyl-accepting protein, and phosphatase) domain to form an input-output module for Aer signaling. In this study, the structure of the Aer HAMP and proximal signaling domains was probed to elucidate structure-function relationships important for signaling. Aer residues 210 to 290 were individually replaced with cysteine and then cross-linked in vivo. The results confirmed that the Aer HAMP domain is composed of two alpha-helices separated by a structured loop. The proximal signaling domain consisted of two alpha-helices separated by a short undetermined structure. The Af1503 HAMP domain from Archaeoglobus fulgidus was recently shown to be a four-helix bundle. To test whether the Af1503 HAMP domain is a prototype for the Aer HAMP domain, the latter was modeled using coordinates from Af1503. Several findings supported the hypothesis that Aer has a four-helix HAMP structure: (i) cross-linking independently identified the same residues at the dimer interface that were predicted by the model, (ii) the rate of cross-linking for residue pairs was inversely proportional to the beta-carbon distances measured on the model, and (iii) clockwise lesions that were not contiguous in the linear Aer sequence were clustered in one region in the folded HAMP model, defining a potential site of PAS-HAMP interaction during signaling. In silico modeling of mutant Aer proteins indicated that the four-helix HAMP structure was important for Aer stability or maturation. The significance of the HAMP and proximal signaling domain structure for signal transduction is discussed.

Evidence for fast conformational change upon ligand dissociation in the HemAT class of bacterial oxygen sensors

Here we report the results of transient absorption and photoacoustic calorimetry studies of CO photodissociation from the heme domain of the bacterial oxygen sensor HemAT-Bs. The results indicate that CO photolysis is accompanied by an overall DeltaH of -19 kcal mol(-1) and DeltaV of +4 ml mol(-1) as well as a red-shifted kinetic difference spectrum all occurring in <50 ns. Analysis of the DeltaH/DeltaV reveals that a conformational change takes place with a DeltaH(conf) of -40 kcal mol(-1) and DeltaV(conf) of -22 ml mol(-1). These thermodynamic changes are consistent with an increase in the solvent accessible surface area of the protein upon ligand dissociation, as observed in the X-ray structure of the ferric CN-bound and CN free forms of HemAT-Bs.

Organization of the aerotaxis receptor aer in the membrane of Escherichia coli

The Aer receptor guides Escherichia coli to specific oxygen and energy-generating niches. The input sensor in Aer is a flavin adenine dinucleotide-binding PAS domain, which is separated from a HAMP/signaling output domain by two membrane-spanning segments that flank a short (four-amino-acid) periplasmic loop. In this study, we determined the overall membrane organization of Aer by introducing combinations of residues that allowed us to differentiate intradimeric collisions from interdimeric collisions. Collisions between proximal residues in the membrane anchor were exclusively intra- or interdimeric but, with one exception, not both. Cross-linking profiles were consistent, with a rigid rather than flexible periplasmic loop and a tilted TM2 helix that crossed TM2' at residue V197C, near the center of the lipid bilayer. The periplasmic loop formed a stable neighborhood that (i) included a maximum of three Aer dimers, (ii) did not swap neighbors over time, and (iii) appeared to be constrained by interactions in the cytosolic signaling domain.

A model of globin evolution

Putative globins have been identified in 426 bacterial, 32 Archaeal and 67 eukaryote genomes. Among these sequences are the hitherto unsuspected presence of single domain sensor globins within Bacteria, Fungi, and a Euryarchaeote. Bayesian phylogenetic trees suggest that their occurrence in the latter two groups could be the result of lateral gene transfer from Bacteria. Iterated psiblast searches based on groups of globin sequences indicate that bacterial flavohemoglobins are closer to metazoan globins than to the other two lineages, the 2-over-2 globins and the globin-coupled sensors. Since Bacteria is the only kingdom to have all the subgroups of the three globin lineages, we propose a working model of globin evolution based on the assumption that all three lineages originated and evolved only in Bacteria. Although the 2-over-2 globins and the globin-coupled sensors recognize flavohemoglobins, there is little recognition between them. Thus, in the first stage of globin evolution, we favor a flavohemoglobin-like single domain protein as the ancestral globin. The next stage comprised the splitting off to single domain 2-over-2 and sensor-like globins, followed by the covalent addition of C-terminal domains resulting in the chimeric flavohemoglobins and globin-coupled sensors. The last stage encompassed the lateral gene transfers of some members of the three globin lineages to specific groups of Archaea and Eukaryotes.

The plant pathogen Ralstonia solanacearum needs aerotaxis for normal biofilm formation and interactions with its tomato host

Ralstonia solanacearum is a soilborne pathogen that causes bacterial wilt of diverse plant species. To locate and infect host plant roots R. solanacearum needs taxis, the ability to move toward more favorable conditions. However, the specific signals that attract this pathogen were unknown. One candidate is aerotaxis, or energy taxis, which guides bacteria toward optimal intracellular energy levels. The R. solanacearum genome encodes two putative aerotaxis transducers. Cloned R. solanacearum aer1 and aer2 genes restored aerotaxis to an Escherichia coli aer mutant, demonstrating that both genes encode heterologously functional aerotaxis transducers. Site-directed mutants lacking aer1, aer2, or both aer1 and aer2 were significantly less able to move up an oxygen gradient than the wild-type parent strain; in fact, the aerotaxis of the aer mutants was indistinguishable from that of a completely nonmotile strain. Tomato plants inoculated with either the aer2 or the aer1/aer2 mutant had slightly delayed wilt disease development. Furthermore, the aer1/aer2 double mutant was significantly impaired in the ability to rapidly localize on tomato roots compared to its wild-type parent. Unexpectedly, all nonaerotactic mutants formed thicker biofilms on abiotic surfaces than the wild type. These results indicate that energy taxis contributes significantly to the ability of R. solanacearum to locate and effectively interact with its host plants.

Oxygen and Redox Sensing by Two‐Component Systems That Regulate Behavioral Responses: Behavioral Assays and Structural Studies of Aer Using In Vivo Disulfide Cross‐Linking

A remarkable increase in the number of annotated aerotaxis (oxygen-seeking) and redox taxis sensors can be attributed to recent advances in bacterial genomics. However, in silico predictions should be supported by behavioral assays and genetic analyses that confirm an aerotaxis or redox taxis function. This chapter presents a collection of procedures that have been highly successful in characterizing aerotaxis and redox taxis in Escherichia coli. The methods are described in enough detail to enable investigators of other species to adapt the procedures for their use. A gas flow cell is used to quantitate the temporal responses of bacteria to a step increase or decrease in oxygen partial pressure or redox potential. Bacterial behavior in spatial gradients is analyzed using optically flat capillaries and soft agar plates (succinate agar or tryptone agar). We describe two approaches to estimate the preferred partial pressure of oxygen that attracts a bacterial species; this concentration is important for understanding microbial ecology. At the molecular level, we describe procedures used to determine the structure and topology of Aer, a membrane receptor for aerotaxis. Cysteine-scanning mutagenesis and in vivo disulfide cross-linking procedures utilize the oxidant Cu(II)-(1,10-phenanthroline)(3) and bifunctional sulfhydryl-reactive probes. Finally, we describe methods used to determine the boundaries of transmembrane segments of receptors such as Aer. These include 5-iodoacetamidofluorescein, 4-acetamido-4-disulfonic acid, disodium salt (AMS), and methoxy polyethylene glycol maleimide, a 5-kDa molecular mass probe that alters the mobility of Aer on SDS-PAGE.

Differentiation between electron transport sensing and proton motive force sensing by the Aer and Tsr receptors for aerotaxis

Aerotaxis (oxygen-seeking) behaviour in Escherichia coli is a response to changes in the electron transport system and not oxygen per se. Because changes in proton motive force (PMF) are coupled to respiratory electron transport, it is difficult to differentiate between PMF, electron transport or redox, all primary candidates for the signal sensed by the aerotaxis receptors, Aer and Tsr. We constructed electron transport mutants that produced different respiratory H+/e- stoichiometries. These strains expressed binary combinations of one NADH dehydrogenase and one quinol oxidase. We then introduced either an aer or tsr mutation into each mutant to create two sets of electron transport mutants. In vivo H+/e- ratios for strains grown in glycerol medium ranged from 1.46+/-0.18-3.04+/-0.47, but rates of respiration and growth were similar. The PMF jump in response to oxygen was proportional to the H+/e- ratio in each set of mutants (r2=0.986-0.996). The length of Tsr-mediated aerotaxis responses increased with the PMF jump (r2=0.988), but Aer-mediated responses did not correlate with either PMF changes (r2=0.297) or the rate of electron transport (r2=0.066). Aer-mediated responses were linked to NADH dehydrogenase I, although there was no absolute requirement. The data indicate that Tsr responds to changes in PMF, but strong Aer responses to oxygen are associated with redox changes in NADH dehydrogenase I.

Differential activation of Escherichia coli chemoreceptors by blue-light stimuli

Enteric bacteria tumble, swim slowly, and are then paralyzed upon exposure to 390- to 530-nm light. Here, we analyze this complex response in Escherichia coli using standard fluorescence microscope optics for excitation at 440 +/- 5 nm. The slow swimming and paralysis occurred only in dye-containing growth media or buffers. Excitation elicited complete paralysis within a second in 1 muM proflavine dye, implying specific motor damage, but prolonged tumbling in buffer alone. The tumbling half-response times were subsecond for onset but more than a minute for recovery. The response required the chemotaxis signal protein CheY and receptor-dependent activation of its kinase CheA. The study of deletion mutants revealed a specific requirement for either the aerotaxis receptor Aer or the chemoreceptor Tar but not the Tar homolog Tsr. The action spectrum of the wild-type response was consistent with a flavin, but the chromophores remain to be identified. The motile response processed via Aer was sustained, with recovery to either step-up or -down taking more than a minute. The response processed via Tar was transient, recovering on second time scales comparable to chemotactic responses. The response duration and amplitude were dependent on relative expression of Aer, Tar, and Tsr. The main response features were reproduced when each receptor was expressed singly from a plasmid in a receptorless host strain. However, time-resolved motion analysis revealed subtle kinetic differences that reflect the role of receptor cluster interactions in kinase activation-deactivation dynamics.

Function of the N-terminal cap of the PAS domain in signaling by the aerotaxis receptor Aer

Aer, the Escherichia coli receptor for behavioral responses to oxygen (aerotaxis), energy, and redox potential, contains a PAS sensory-input domain. Within the PAS superfamily, the N-terminal segment (N-cap) is poorly conserved and its role is not well understood. We investigated the role of the N-cap (residues 1 to 19) in the Aer PAS domain by missense and truncation mutagenesis. Aer-PAS N-cap truncations and an Aer-M21P substitution resulted in low cellular levels of the mutant proteins, suggesting that the N-terminal region was important for stabilizing the structure of the PAS domain. The junction of the N-cap and PAS core was critical for signaling in Aer. Mutations and truncations in the sequence encoding residues 15 to 21 introduced a range of phenotypes, including defects in FAD binding, constant tumbling motility, and an inverse response in which E. coli cells migrated away from oxygen concentrations to which they are normally attracted. The proximity of two N-cap regions in an Aer dimer was assessed in vivo by oxidatively cross-linking serial cysteine substitutions. Cross-linking of several cysteine replacements at 23 degrees C was attenuated at 10 degrees C, indicating contact was not at a stable dimer interface but required lateral mobility. We observed large multimers of Aer when we combined cross-linking of N-cap residues with a cysteine replacement that cross-links exclusively at the Aer dimer interface. This suggests that the PAS N-cap faces outwards in a dimer and that PAS-PAS contacts can occur between adjacent dimers.

A phylogenomic profile of globins

Background

Globins occur in all three kingdoms of life: they can be classified into single-domain globins and chimeric globins. The latter comprise the flavohemoglobins with a C-terminal FAD-binding domain and the gene-regulating globin coupled sensors, with variable C-terminal domains. The single-domain globins encompass sequences related to chimeric globins and «truncated» hemoglobins with a 2-over-2 instead of the canonical 3-over-3 α-helical fold.

Results

A census of globins in 26 archaeal, 245 bacterial and 49 eukaryote genomes was carried out. Only ~25% of archaea have globins, including globin coupled sensors, related single domain globins and 2-over-2 globins. From one to seven globins per genome were found in ~65% of the bacterial genomes: the presence and number of globins are positively correlated with genome size. Globins appear to be mostly absent in Bacteroidetes/Chlorobi, Chlamydia, Lactobacillales, Mollicutes, Rickettsiales, Pastorellales and Spirochaetes. Single domain globins occur in metazoans and flavohemoglobins are found in fungi, diplomonads and mycetozoans. Although red algae have single domain globins, including 2-over-2 globins, the green algae and ciliates have only 2-over-2 globins. Plants have symbiotic and nonsymbiotic single domain hemoglobins and 2-over-2 hemoglobins. Over 90% of eukaryotes have globins: the nematode Caenorhabditis has the most putative globins, ~33. No globins occur in the parasitic, unicellular eukaryotes such as Encephalitozoon, Entamoeba, Plasmodium and Trypanosoma.

Conclusion

Although Bacteria have all three types of globins, Archaeado not have flavohemoglobins and Eukaryotes lack globin coupled sensors. Since the hemoglobins in organisms other than animals are enzymes or sensors, it is likely that the evolution of an oxygen transport function accompanied the emergence of multicellular animals.

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.

Interactions between the PAS and HAMP domains of the Escherichia coli aerotaxis receptor Aer

The Escherichia coli energy-sensing Aer protein initiates aerotaxis towards environments supporting optimal cellular energy. The Aer sensor is an N-terminal, FAD-binding, PAS domain. The PAS domain is linked by an F1 region to a membrane anchor, and in the C-terminal half of Aer, a HAMP domain links the membrane anchor to the signaling domain. The F1 region, membrane anchor, and HAMP domain are required for FAD binding. Presumably, alterations in the redox potential of FAD induce conformational changes in the PAS domain that are transmitted to the HAMP and C-terminal signaling domains. In this study we used random mutagenesis and intragenic pseudoreversion analysis to examine functional interactions between the HAMP domain and the N-terminal half of Aer. Missense mutations in the HAMP domain clustered in the AS-2 alpha-helix and abolished FAD binding to Aer, as previously reported. Three amino acid replacements in the Aer-PAS domain, S28G, A65V, and A99V, restored FAD binding and aerotaxis to the HAMP mutants. These suppressors are predicted to surround a cleft in the PAS domain that may bind FAD. On the other hand, suppression of an Aer-C253R HAMP mutant was specific to an N34D substitution with a predicted location on the PAS surface, suggesting that residues C253 and N34 interact or are in close proximity. No suppressor mutations were identified in the F1 region or membrane anchor. We propose that functional interactions between the PAS domain and the HAMP AS-2 helix are required for FAD binding and aerotactic signaling by Aer.

Methylation-independent aerotaxis mediated by the Escherichia coli Aer protein

Aer is a membrane-associated protein that mediates aerotactic responses in Escherichia coli. Its C-terminal half closely resembles the signaling domains of methyl-accepting chemotaxis proteins (MCPs), which undergo reversible methylation at specific glutamic acid residues to adapt their signaling outputs to homogeneous chemical environments. MCP-mediated behaviors are dependent on two specific enzymes, CheR (methyltransferase) and CheB (methylesterase). The Aer signaling domain contains unorthodox methylation sites that do not conform to the consensus motif for CheR or CheB substrates, suggesting that Aer, unlike conventional MCPs, might be a methylation-independent transducer. Several lines of evidence supported this possibility. (i) The Aer protein was not detectably modified by either CheR or CheB. (ii) Amino acid replacements at the putative Aer methylation sites generally had no deleterious effect on Aer function. (iii) Aer promoted aerotactic migrations on semisolid media in strains that lacked all four of the E. coli MCPs. CheR and CheB function had no influence on the rate of aerotactic movements in those strains. Thus, Aer senses and signals efficiently in the absence of deamidation or methylation, methylation changes, methylation enzymes, and methyl-accepting chemotaxis proteins. We also found that chimeric transducers containing the PAS-HAMP sensing domain of Aer joined to the signaling domain and methylation sites of Tar, an orthodox MCP, exhibited both methylation-dependent and methylation-independent aerotactic behavior. The hybrid Aear transducers demonstrate that methylation independence does not emanate from the Aer signaling domain but rather may be due to transience of the cellular redox changes that are thought to trigger Aer-mediated behavioral responses.

Aer and Tsr guide Escherichia coli in spatial gradients of oxidizable substrates

The Aer and Tsr chemoreceptors in Escherichia coli govern tactic responses to oxygen and redox potential that are parts of an overall behaviour known as energy taxis. They are also proposed to mediate responses to rapidly utilized carbon sources, glycerol and succinate, via the energy taxis mechanism. In this study, the Aer and Tsr proteins were individually expressed in an 'all-transducer-knockout' strain of E. coli and taxis was analysed in gradients of various oxidizable carbon sources. In addition to the known response to glycerol and succinate, it was found that Aer directed taxis towards ribose, galactose, maltose, malate, proline and alanine as well as the phosphotransferase system (PTS) carbohydrates glucose, mannitol, mannose, sorbitol and fructose, but not to aspartate, glutamate, glycine and arabinose. Tsr directed taxis towards sugars (including those transported by the PTS), but not to organic acids or amino acids. When a mutated Aer protein unable to bind the FAD cofactor was expressed in the receptor-less strain, chemotaxis was not restored to any substrate. Aer appears to mediate responses to rapidly oxidizable substrates, whether or not they are effective growth substrates, whereas Tsr appears to mediate taxis to substrates that support maximal growth, whether or not they are rapidly oxidizable. This correlates with the hypothesis that Aer and Tsr sense redox and proton motive force, respectively. Taken together, the results demonstrate that Aer and Tsr mediate responses to a broad range of chemicals and their attractant repertoires overlap with those of specialized chemoreceptors, namely Trg (ribose, galactose) and Tar (maltose).