Bacterial chemotaxis: biochemistry of behavior in a single cell

Living Cognition and the Nature of Organisms

There is no consensus about what cognition is. Different perspectives conceptualize it in different ways. In the same vein, there is no agreement about which systems are truly cognitive. This begs the question, what makes a process or a system cognitive? One of the most conspicuous features of cognition is that it is a set of processes. Cognition, in the end, is a collection of processes such as perception, memory, learning, decision-making, problem-solving, goal-directedness, attention, anticipation, communication, and maybe emotion. There is a debate about what they mean, and which systems possess these processes. One aspect of this problem concerns the level at which cognition and the single processes are conceptualized. To make this scenario clear, evolutionary and self-maintenance arguments are taken. Given the evolutive landscape, one sees processes shared by all organisms and their derivations in specific taxa. No matter which side of the complexity spectrum one favors, the similarities of the simple processes with the complex ones cannot be ignored, and the differences of some complex processes with their simple versions cannot be blurred. A final cognitive framework must make sense of both sides of the spectrum, their differences and similarities. Here, we discuss from an evolutionary perspective the basic elements shared by all living beings and whether these may be necessary and sufficient for understanding the cognitive process. Following these considerations, cognition can be expanded to every living being. Cognition is the set of informational and dynamic processes an organism must interact with and grasp aspects of its world. Understood at their most basic level, perception, memory, learning, problem-solving, decision-making, action, and other cognitive processes are basic features of biological functioning.

ERK signalling: a master regulator of cell behaviour, life and fate

The proteins extracellular signal-regulated kinase 1 (ERK1) and ERK2 are the downstream components of a phosphorelay pathway that conveys growth and mitogenic signals largely channelled by the small RAS GTPases. By phosphorylating widely diverse substrates, ERK proteins govern a variety of evolutionarily conserved cellular processes in metazoans, the dysregulation of which contributes to the cause of distinct human diseases. The mechanisms underlying the regulation of ERK1 and ERK2, their mode of action and their impact on the development and homeostasis of various organisms have been the focus of much attention for nearly three decades. In this Review, we discuss the current understanding of this important class of kinases. We begin with a brief overview of the structure, regulation, substrate recognition and subcellular localization of ERK1 and ERK2. We then systematically discuss how ERK signalling regulates six fundamental cellular processes in response to extracellular cues. These processes are cell proliferation, cell survival, cell growth, cell metabolism, cell migration and cell differentiation.

Initial photophysical characterization of the proteorhodopsin optical proton sensor (PROPS)

Fluorescence is not frequently used as a tool for investigating the photocycles of rhodopsins, largely because of the low quantum yield of the retinal chromophore. However, a new class of genetically encoded voltage sensors is based upon rhodopsins and their fluorescence. The first such sensor reported in the literature was the proteorhodopsin optical proton sensor (PROPS), which is capable of indicating membrane voltage changes in bacteria by means of changes in fluorescence. However, the properties of this fluorescence, such as its lifetime decay components and its origin in the protein photocycle, remain unknown. This paper reports steady-state and nanosecond time-resolved emission of this protein expressed in two strains of Escherichia coli, before and after membrane depolarization. The voltage-dependence of a particularly long lifetime component is established. Additional work to improve quantum yields and improve the general utility of PROPS is suggested.

Genes required for alleviation of uranium toxicity in sulfate reducing bacterium Desulfovibrio alaskensis G20 [corrected]

The sulfate reducing bacterium Desulfovibrio alaskensis strain G20 can grow in lactate sulfate medium with up to 4 mM uranyl acetate. In order to identify the genes that are required for the growth of strain G20 at toxic levels of uranium(VI) (U(VI)), 5,760 transposon insertion mutants were screened for U(VI) resistance defects, and 24 of them showed loss of U(VI) resistance in lactate sulfate medium with 2 mM uranyl acetate. In the 24 mutants, 23 genes were disrupted by transposon insertions, and one transposon is located in a non-coding region. In the ten mutants that were completely inhibited by 2 mM uranyl acetate, the disrupted genes are involved in DNA repair, rRNA methylation, regulation of expression and RNA polymerase renaturation. The remaining 14 mutants showed partial inhibition of growth by 2 mM U(VI), in which the disrupted genes participate in DNA repair, regulation of transcription, membrane transport, etc. In addition, none except one of these 24 mutants showed loss in its ability to reduce U(VI) to U(IV) in the washed cell test. These results altogether suggest that U(VI) toxicity mainly involves damage to nucleic acids and proteins.

Effect of modeled reduced gravity conditions on bacterial morphology and physiology

BACKGROUND

Bacterial phenotypes result from responses to environmental conditions under which these organisms grow; reduced gravity has been demonstrated in many studies as an environmental condition that profoundly influences microorganisms. In this study, we focused on low-shear stress, modeled reduced gravity (MRG) conditions and examined, for Escherichia coli and Staphlyococcus aureus, a suite of bacterial responses (including total protein concentrations, biovolume, membrane potential and membrane integrity) in rich and dilute media and at exponential and stationary phases for growth. The parameters selected have not been studied in E. coli and S. aureus under MRG conditions and provide critical information about bacterial viability and potential for population growth.

RESULTS

With the exception of S. aureus in dilute Luria Bertani (LB) broth, specific growth rates (based on optical density) of the bacteria were not significantly different between normal gravity (NG) and MRG conditions. However, significantly higher bacterial yields were observed for both bacteria under MRG than NG, irrespective of the medium with the exception of E. coli grown in LB. Also, enumeration of cells after staining with 4',6-diamidino-2-phenylindole showed that significantly higher numbers were achieved under MRG conditions during stationary phase for E. coli and S. aureus grown in M9 and dilute LB, respectively. In addition, with the exception of smaller S. aureus volume under MRG conditions at exponential phase in dilute LB, biovolume and protein concentrations per cell did not significantly differ between MRG and NG treatments. Both E. coli and S. aureus had higher average membrane potential and integrity under MRG than NG conditions; however, these responses varied with growth medium and growth phase.

CONCLUSIONS

Overall, our data provides novel information about E. coli and S. aureus membrane potential and integrity and suggest that bacteria are physiologically more active and a larger percentage are viable under MRG as compared to NG conditions. In addition, these results demonstrate that bacterial physiological responses to MRG conditions vary with growth medium and growth phase demonstrating that nutrient resources are a modulator of response.

Chemotactic Behavior of Azotobacter vinelandii

Chemotaxis was exhibited by Azotobacter vinelandii motile cells. Exposure of cells to sudden increases in attractant concentration suppressed the frequency of tumbling and resulted in smooth swimming. Cells responded chemotactically to a chemical gradient produced during metabolism. Motility occurred over a temperature range of 25 to 37 degrees C with an optimum pH range of between pH 7.0 and 8.0. The average speed of motile cells was determined to be 74 mum/s or 37 body lengths per s. The speed of cells appeared to increase as a function of attractant concentration. Chemotactic systems for fructose, glucose, xylitol, and mannitol were inducible. A. vinelandii exhibited chemotaxis for a number of compounds, including hexoses, hexitols, pentitols, pentoses, disaccharides, and amino sugars. We conclude from these studies that A. vinelandii exhibits a temporal chemotactic sensing system.

Tuning chemotactic responses with synthetic multivalent ligands

BACKGROUND

Multivalent ligands have been used previously to investigate the role of ligand valency and receptor clustering in eliciting biological responses. Studies of multivalent ligand function, however, typically have employed divalent ligands or ligands of undefined valency. How cells respond to multivalent ligands of distinct valencies, which can cluster a signaling receptor to different extents, has never been examined. The chemoreceptors, which mediate chemotactic responses in bacteria, are localized, and clustering has been proposed to play a role in their function. Using multivalent ligands directed at the chemoreceptors, we hypothesized that we could exploit ligand valency to control receptor occupation and clustering and, ultimately, the cellular response.

RESULTS

To investigate the effects of ligand valency on the bacterial chemotactic response, we generated a series of linear multivalent arrays with distinct valencies by ring-opening metathesis polymerization. We report that these synthetic ligands elicit bacterial chemotaxis in both Escherichia coli and Bacillus subtilis. The chemotactic response depended on the valency of the ligand; the response of the bacteria can be altered by varying chemoattractant ligand valency. Significantly, these differences in chemotactic responses were related to the ability of the multivalent ligands to cluster chemoreceptors at the plasma membrane.

CONCLUSIONS

Our results demonstrate that ligand valency can be used to tune the chemotactic responses of bacteria. This mode of regulation may arise from changes in receptor occupation or changes in receptor clustering or both. Our data implicate changes in receptor clustering as one important mechanism for altering cellular responses. Given the diverse events modulated by changes in the spatial proximity of cell surface receptors, our results suggest a general strategy for tuning biological responses.

Proteins with similar architecture exhibit similar large-scale dynamic behavior

We have investigated the similarities and differences in the computed dynamic fluctuations exhibited by six members of a protein fold family with a coarse-grained Gaussian network model. Specifically, we consider the cofactor binding fragment of CysB; the lysine/arginine/ornithine-binding protein (LAO); the enzyme porphobilinogen deaminase (PBGD); the ribose-binding protein (RBP); the N-terminal lobe of ovotransferrin in apo-form (apo-OVOT); and the leucine/isoleucine/valine-binding protein (LIVBP). All have domains that resemble a Rossmann fold, but there are also some significant differences. Results indicate that similar global dynamic behavior is preserved for the members of a fold family, and that differences usually occur in regions only where specific function is localized. The present work is a computational demonstration that the scaffold of a protein fold may be utilized for diverse purposes. LAO requires a bound ligand before it conforms to the large-scale fluctuation behavior of the three other members of the family, CysB, PBGD, and RBP, all of which contain a substrate (cofactor) at the active site cleft. The dynamics of the ligand-free enzymes LIVBP and apo-OVOT, on the other hand, concur with that of unliganded LAO. The present results suggest that it is possible to construct structure alignments based on dynamic fluctuation behavior.

Accurate flow cytometric membrane potential measurement in bacteria using diethyloxacarbocyanine and a ratiometric technique

BACKGROUND

Membrane potential (MP) plays a critical role in bacterial physiology. Existing methods for MP estimation by flow cytometry are neither accurate nor precise, due in part to the heterogeneity of size of the particles analyzed. The ratio of a size- and MP-sensitive measurement, and an MP-independent, size-sensitive measurement, should provide a better estimate of MP.

METHODS

Flow cytometry and spectrofluorometry were used to detect red (488 --> 600 nm) fluorescence associated with aggregates of diethyloxacarbocyanine (DiOC2(3)), which, in the monomeric state, is normally green (488 --> 530 nm) fluorescent.

RESULTS

In bacteria incubated with 30 microM dye, aggregate formation increases with the magnitude of the interior-negative membrane potential. Green fluorescence from stained bacteria predominantly reflects particle size, and is relatively independent of MP, whereas red fluorescence is highly dependent on both MP and size. The ratio of red to green fluorescence provides a measure of MP that is largely independent of cell size, with a low coefficient of variation (CV). Calibration with valinomycin and potassium demonstrates that the method is accurate over the range from -50 mV through -120 mV; it also accurately tracks reversible reductions in MP produced by incubation at 4 degrees C and washing in glucose-free medium.

CONCLUSIONS

The ratiometric technique for MP estimation using DiOC2(3) is substantially more accurate and precise than those previously available, and may be useful in studies of bacterial physiology and in investigations of the effects of antibiotics and other agents on microorganisms.

Determination of effective transport coefficients for bacterial migration in sand columns

A well-characterized experimental system was designed to evaluate the effect of porous media on macroscopic transport coefficients which are used to characterize the migration of bacterial populations. Bacterial density profiles of Pseudomonas putida PRS2000 were determined in the presence and absence of a chemical attractant (3-chlorobenzoate) gradient within sand columns having a narrow distribution of particle diameters. These experimental profiles were compared with theoretical predictions to evaluate the macroscopic transport coefficients. The effective random motility coefficient, used to quantify migration due to a random process in a porous medium, decreased nearly 20-fold as grain size in the columns decreased from 800 to 80 (mu)m. The effective random motility coefficient (mu)(infeff) was related to the random motility coefficient (mu), measured in a bulk aqueous system, according to (mu)(infeff) = ((epsilon)/(tau))(mu) with porosity (epsilon) and tortuosity (tau). Over the times and distances examined in these experiments, bacterial density profiles were unaffected by the presence of an attractant gradient. Theoretical profiles with the aqueous phase value of the chemotactic sensitivity coefficient (used to quantify migration due to a directed process) were consistent with this result and suggested that any chemotactic effect on bacterial migration was below the detection limits of our assay.

Relationships between C4 dicarboxylic acid transport and chemotaxis in Rhizobium meliloti

The relationship between chemotaxis and transport of C4 dicarboxylic acids was analyzed with Rhizobium meliloti dct mutants defective in one or all of the genes required for dicarboxylic acid transport. Succinate, malate, and fumarate were moderately potent chemoattractants for wild-type R. meliloti and appeared to share a common chemoreceptor. While dicarboxylate transport is inducible, taxis to succinate was shown to be constitutive. Mutations in the dctA and dctB genes both resulted in the reduction, but not elimination, of chemotactic responses to succinate, indicating that transport via DctA or chemosensing via DctB is not essential for C4 dicarboxylate taxis, although they appear to contribute to it. Mutations in dctD and rpoN genes did not affect taxis to succinate. Aspartate, which is also transported by the dicarboxylate transport system, elicited strong chemotactic responses via a chemoreceptor distinct from the succinate-malate-fumarate receptor. Taxis to aspartate was unaltered in dctA and dctB mutants but was considerably reduced in both dctD and rpoN mutants, indicating that aspartate taxis is strongly dependent on elements responsible for transcriptional activation of dctA. Methylation and methanol release experiments failed to show a significant increase in methyl esterification of R. meliloti proteins in response to any of the attractants tested.

1.7 A X-ray structure of the periplasmic ribose receptor from Escherichia coli

The X-ray structure of the periplasmic ribose receptor (binding protein) of Escherichia coli (RBP) was solved at 3 A resolution by the method of multiple isomorphous replacement. Alternating cycles of refitting and refinement have resulted in a model structure with an R-factor of 18.7% for 27,526 reflections from 7.5 to 1.7 A resolution (96% of the data). The model contains 2228 non-hydrogen atoms, including all 271 residues of the amino acid sequence, 220 solvent atoms and beta-D-ribose. The protein consists of two highly similar structural domains, each of which is composed of a core of parallel beta-sheet flanked on both sides by alpha-helices. The two domains are related to each other by an almost perfect 2-fold axis of rotation, with the C termini of the beta-strands of each sheet pointing toward the center of the molecule. Three short stretches of amino acid chain (from symmetrically related portions of the protein) link these two domains, and presumably act as a hinge to allow relative movement of the domains in functionally important conformational changes. Two water molecules are also an intrinsic part of the hinge, allowing crucial flexibility in the structure. The ligand beta-D-ribose (in the pyranose form) is bound between the domains, held by interactions with side-chains of the interior loops. The binding site is precisely tailored, with a combination of hydrogen bonding, hydrophobic and steric effects giving rise to tight binding (0.1 microM for ribose) and high specificity. Four out of seven binding-site residues are charged (2 each of aspartate and arginine) and contribute two hydrogen bonds each. The remaining hydrogen bonds are contributed by asparagine and glutamine residues. Three phenylalanine residues supply the hydrophobic component, packing against both faces of the sugar molecule. The arrangement of these hydrogen bonding and hydrophobic residues results in an enclosed binding site with the exact shape of the allowed sugar molecules; in the process of binding, the ligand loses all of its surface-accessible area. The sites of two mutations that affect the rate of folding of the ribose receptor are shown to be located near small cavities in the wild-type protein. The cavities thus allow the incorporation of the larger residues in the mutant proteins. Since these alterations would seriously affect the ability of the protein to build the first portion of the hydrophobic core in the first domain, it is proposed that this process is the rate-limiting step in folding of the ribose receptor.

A simple expression for quantifying bacterial chemotaxis using capillary assay data: application to the analysis of enhanced chemotactic responses from growth-limited cultures

An individual cell-based mathematical model of Rivero et al. provides a framework for determining values of the chemotactic sensitivity coefficient chi 0, an intrinsic cell population parameter that characterizes the chemotactic response of bacterial populations. This coefficient can theoretically relate the swimming behavior of individual cells to the resulting migration of a bacterial population. When this model is applied to the commonly used capillary assay, an approximate solution can be obtained for a particular range of chemotactic strengths yielding a very simple analytical expression for estimating the value of chi 0, [formula: see text] from measurements of cell accumulation in the capillary, N, when attractant uptake is negligible. A0 and A infinity are the dimensionless attractant concentrations initially present at the mouth of the capillary and far into the capillary, respectively, which are scaled by Kd, the effective dissociation constant for receptor-attractant binding. D is the attractant diffusivity, and mu is the cell random motility coefficient. NRM is the cell accumulation in the capillary in the absence of an attractant gradient, from which mu can be determined independently as mu = (pi/4t)(NRM/pi r2bc)2, with r the capillary tube radius and bc the bacterial density initially in the chamber. When attractant uptake is significant, a slightly more involved procedure requiring a simple numerical integration becomes necessary. As an example, we apply this approach to quantitatively characterize, in terms of the chemotactic sensitivity coefficient chi 0, data from Terracciano indicating enhanced chemotactic responses of Escherichia coli to galactose when cultured under growth-limiting galactose levels in a chemostat.

Quantitative studies of bacterial chemotaxis and microbial population dynamics

Although there is a long history of conjecture regarding the role and significance of bacterial chemotaxis in microbial ecology, only recently has a significant body of work appeared attempting to address this issue. The purpose of this paper is to provide a concise overview of this work, which combined mathematical modeling of bacterial population migration and experimental measurement of the model parameters with modeling of competitive microbial population dynamics in a nonmixed environment. Predictions from the population dynamics models, based on experimental estimates of the various motility and growth parameter values, are related to the small number of experimental observations available to date dealing with the effects of bacterial motility on competition in a nonmixed environment. Current results indicate that cell motility and chemotaxis properties can be as important to population dynamics as cell growth kinetic properties, so that greater attention to this aspect of microbial behavior is warranted in future studies of microbial ecology.

Bacterial chemotaxis signaling complexes: formation of a CheA/CheW complex enhances autophosphorylation and affinity for CheY

We have demonstrated that a complex of the proteins CheA (CheAL and CheAS) and CheW can be isolated and constitutes a functional unit that responds to the signaling state of the chemoreceptors. The autophosphorylation rate of CheAL is much greater when CheAL and CheAS are complexed with CheW. Moreover, the presence of mutant chemoreceptors that cause cells to tumble increases this rate. At wild-type levels of expression, the isolated CheAL/CheAS/CheW complex accounts for about 10% of the total number of CheAL, CheAS, and CheW molecules and exists in a 1:1:1 stoichiometry. This complex is also required for CheAL/CheAS and CheW binding to the phosphorylation substrate, CheY. A separate interaction between CheY and another chemotaxis component, CheZ, was also detected. The CheY-CheZ interaction does not require participation of the CheAL/CheAS/CheW complex.

Isolation of behavioral mutants of Azospirillum brasilense by using Tn5 lacZ

Tn5 lacZ mutants were generated with Azospirillum brasilense 7030 by mating that strain with Escherichia coli strains carrying suicide plasmid pCIB100 or pCIB110. Kanamycin-resistant Azospirillum colonies were obtained with a maximum frequency of 10(-6) per recipient cell. The potential of Tn5 lacZ for random transposon mutagenesis coupled to transcription analysis in A. brasilense 7030 was demonstrated. Sixty percent of all Kmr A. brasilense 7030 mutants expressed beta-galactosidase activity. Mutants affected in motility (Fla-) and general chemotaxis (Che-) were identified. Chromosomal insertions of Tn5 lacZ are involved, except for two Che- mutants. The latter che loci reside on a 90-megadalton plasmid. Expression of an acidic protein (Mr, 110,000) was abolished in these mutants.

Nucleotide sequence and expression of cheF, an essential gene for chemotaxis in Bacillus subtilis

The cheF gene, which is involved in chemotaxis in Bacillus subtilis, has been cloned, expressed, and sequenced. This gene is contained in a 0.7-kilobase PstI DNA fragment that was isolated from a lambda Charon 4A B. subtilis chromosomal DNA library. This fragment was subcloned into the expression vector pSI-1 and shown to complement the cheF mutation both for chemotaxis and for methanol production in response to the addition of attractants. Plasmid-encoded DNA expression in B. subtilis maxicells indicated that a membrane-associated polypeptide of 20-kilodaltons was expressed from this 0.7-kilobase DNA. The nucleotide sequence of this DNA fragment was determined, and an open reading frame capable of encoding a putative 175-amino-acid protein (Mr 20,002) was identified. In an effort to understand the function of the cheF protein, the dosage of the cheF gene product was varied by altering the concentration of IPTG (isopropyl-beta-D-thiogalactopyranoside) during growth. In the presence of high concentrations of IPTG, chemotaxis was inhibited and methanol production was impaired.

"Frizzy" aggregation genes of the gliding bacterium Myxococcus xanthus show sequence similarities to the chemotaxis genes of enteric bacteria

The frz genes of Myxococcus xanthus are necessary for proper aggregation of cells to form fruiting bodies. Mutations in the frz genes affect the frequency with which individual cells reverse their direction of movement. We have subcloned and determined the nucleotide sequence of three of the frz genes. From the sequence we predict three open reading frames corresponding to frzA, frzB, and frzCD. The putative FrzA protein (17,094 Da) exhibits 28.1% amino acid identity with the CheW protein of Salmonella typhimurium. The putative FrzCD protein (43,571 Da) contains a region of about 250 amino acids which is similar to the C-terminal portions of the methyl-accepting chemotaxis receptor proteins of the enteric bacteria. FrzCD also contains a region with potentially significant similarity to the DNA-binding region of the Bacillus subtilis sigma 43. The putative FrzB protein (12,066 Da) shares no significant identity with known chemotaxis proteins. The sequence similarities between the putative Frz proteins and the chemotaxis proteins of the enteric bacteria strongly support the hypothesis that the frz genes define a system of signal transduction analogous to the enterobacterial chemotaxis systems.

Purification and characterization of the wild-type and mutant carboxy-terminal domains of the Escherichia coli Tar chemoreceptor

The carboxy-terminal half of the Escherichia coli Tar chemoreceptor protein was cloned into an overproducing plasmid with the transcription of the insert under the control of the strong hybrid tac promoter. Two dominant mutations in the tar gene, which result in "tumble-only" (tar-526) or "swim-only" (tar-529) phenotypes and which are postulated to produce proteins locked in specific signalling modes, were introduced separately onto the overproducing plasmid. After induction with isopropyl-beta-D-thiogalactopyranoside, cells containing the plasmids produced about 10% of their soluble cellular protein as the carboxy-terminal fragments. A scheme to purify the overproduced fragments was developed. Typical yields of pure fragment were 5, 30, and 20 mg per liter of induced culture for the wild type, 526 mutant, and 529 mutant, respectively. Fast-protein liquid chromatography-gel filtration analysis of the pure fragments showed that they all existed as oligomers (ca. 103,000 daltons), possibly trimers or tetramers (monomer size is 31,000 daltons). However, the 529 mutant fragment showed an additional oligomeric form (240,000 daltons) corresponding approximately to an octamer. When chromatographed in the presence of 1% octylglucoside, all three fragments showed an identical single oligomeric size of about 135,000 daltons. Further differences between the fragments such as ion-exchange behavior and susceptibility to degradation were found. Taken together, these results suggest that conformational differences between the 529 mutant fragment and the other fragments exist and that these differences may correlate with the phenotypic effects of the tar-529 mutation.

Cloning of the C-terminal cytoplasmic fragment of the tar protein and effects of the fragment on chemotaxis of Escherichia coli

A gene encoding only the C-terminal portion of the receptor-transducer protein Tar of Escherichia coli was constructed. The gene product was detected and localized in the cytoplasmic fraction of the cell by immunoblotting with anti-Tar antibodies. The C-terminal fragments from wild-type and mutant tar genes were characterized in vivo. The C-terminal fragment generated from tar-526, a mutation that results in a dominant "tumble" phenotype, was found to be deamidated and methylated by the CheB and CheR proteins, respectively. The C-terminal fragment derived from a wild-type gene was poorly deamidated, and the C-terminal fragment derived from tar-529, a dominant mutant with a "smooth swimming" phenotype, was not apparently modified. Cells carrying the C-terminal fragment with the tar-526 mutation as the sole receptor-transducer protein showed a high frequency of tumbling and chemotaxis responses to changes in intracellular pH. These results suggest that the cytoplasmic C-terminal fragment of Tar retains some of the functions of the whole protein in vivo.

Phosphorylation of three proteins in the signaling pathway of bacterial chemotaxis

Six cytoplasmic che gene products are required for signal transduction in bacterial chemotaxis, but the nature of their biochemical interactions is not known. We show that in vitro the CheA protein becomes autophosphorylated in the presence of ATP. In addition, the phosphate group on CheA can be rapidly transferred to CheB, a protein involved in adaptation to stimuli, or to CheY, a protein involved in the excitation response. The phosphorylation of CheB and CheY is transient; they readily dephosphorylate. We have also found that CheZ, a protein that appears to antagonize CheY function in vivo, accelerates the hydrolysis of the phosphate on CheY. These results suggest that signal transduction in bacterial chemotaxis may involve the flow of phosphate through a cascade of phosphorylated protein intermediates.

The evolutionary origin of eukaryotic transmembrane signal transduction

1. A comparison was made of transmembrane signal transduction mechanisms in different eukaryotes and prokaryotes. 2. Much attention was given to eukaryotic microbes and their signal transduction mechanisms, since these organisms are intermediate in complexity between animals, plants and bacteria. 3. Signal transduction mechanisms in eukaryotic microbes, however, do not appear to be intermediate between those in animals, plants and bacteria, but show features characteristic of the higher eukaryotes. 4. These similarities include the regulation of receptor function, adenylate cyclase activity, the presence of a phosphatidylinositol cycle and of GTP-binding regulatory proteins. 5. It is proposed that the signal transduction systems known to operate in present-day eukaryotes evolved in the earliest eukaryotic cells.

Evidence for methyl group transfer between the methyl-accepting chemotaxis proteins in Bacillus subtilis

We present evidence for methyl (as methyl or methoxy) transfer from the methyl-accepting chemotaxis proteins H1 and possibly H3 of Bacillus subtilis to the methyl-accepting chemotaxis protein H2. This methyl transfer, which has been observed in vitro (D. J. Goldman and G. W. Ordal, Biochemistry 23:2600-2606, 1984), was strongly stimulated by the chemoattractant aspartate and thus may play an important role in the sensory processing system of this organism. Although radiolabeling of H1 and H3 began at once after the addition of [3H]methionine, radiolabeling of H2 showed a lag. Furthermore, the addition of excess nonradioactive methionine caused immediate exponential delabeling of H1 and H3 while labeling of H2 continued to increase. Methylation of H2 required the chemotactic methyltransferase, probably to first methylate H1 and H3. Aspartate caused increased labeling of H2 and strongly decreased labeling of H1 and H3 after the addition of nonradioactive methionine. Without the addition of nonradioactive methionine, aspartate caused demethylation of H1 and to a lesser extent H3, with an approximately equal increase of methylation of H2.

Methylation-independent and methylation-dependent chemotaxis in Rhodobacter sphaeroides and Rhodospirillum rubrum

In vivo and in vitro methylation, methanol production assays, and the use of specific antibodies raised against the sensory transducing protein Tar in Escherichia coli all failed to demonstrate the presence of methyl-accepting chemotaxis proteins (MCPs) in the photosynthetic bacterium Rhodobacter sphaeroides, although such proteins did exist in another photosynthetic bacterium, Rhodospirillum rubrum. The range of chemicals to which Rhodobacter sphaeroides responds, the lack of an all-or-none response, and the lack of true repellents indicate an alternative chemosensory pathway. The existence of MCPs in Rhodospirillum rubrum means that the lack of MCPs is not the result of a phototrophic metabolism, but may be connected to the unidirectional flagellar motor of Rhodobacter sphaeroides.

Bacterial chemotaxis. Cell flux model, parameter measurement, population dynamics, and genetic manipulation

In this paper, we summarized our recent efforts toward accomplishing four key goals important for control of microbial population dynamics in nonmixed systems: (1) derivation of a cell population flux model based on individual cell properties; (2) measurement of the population random motility and chemotaxis parameters appearing in this model using a simple experimental assay; (3) quantitative understanding of the effects of cell motility and chemotaxis properties on microbial population dynamics; and (4) manipulation of chemotactic responses by genetic modification.

Protein phosphorylation is involved in bacterial chemotaxis

The nature of the biochemical signal that is involved in the excitation response in bacterial chemotaxis is not known. However, ATP is required for chemotaxis. We have purified all of the proteins involved in signal transduction and show that the product of the cheA gene is rapidly autophosphorylated, while some mutant CheA proteins cannot be phosphorylated. The presence of stoichiometric levels of two other purified components in the chemotaxis system, the CheY and CheZ proteins, induces dephosphorylation. We suggest that the phosphorylation of CheA by ATP plays a central role in signal transduction in chemotaxis.

Consequences of detailed balance in a model for sensory adaptation based on ligand-induced receptor modification

A model for exact sensory adaptation has been published by Segel and co-workers in several papers [e.g., Knox, B. E., Devreotes, P. N., Goldbeter, A. & Segel, L. A. (1986) Proc. Natl. Acad. Sci. USA 83, 2345-2349]. The model comprises a pair of states whose relative probabilities are determined by the binding of a ligand. A second pair of states related by the same ligand binding is accessible as a consequence of either a conformational change or a "covalent modification." By taking proper account of detailed balance, we show that the notion of covalent modification in this context includes three cases, two of which involve dissipation of metabolic energy. The condition for exact adaptation is dependent on metabolite concentrations in all cases of covalent modification. The performance of the model is critically examined on thermodynamic and kinetic grounds.

Expert systems in psychiatry. A review

Existing computer-based decision aids in the areas of psychiatric diagnosis and consultation are reviewed, and the prospects for expert system development within the mental health field are discussed. Emphasis is placed upon the decision-making models used in these systems rather than on their particular application area. The decision-making paradigms discussed are (1) data bank analysis, (2) statistical pattern recognition, (3) Bayesian analysis, (4) logical flow chart method, and (5) knowledge-based (expert system) approaches. For each paradigm, its essential features, its strengths and weaknesses, and some example applications are presented.

Chemoreception in Paramecium tetraurelia: acetate and folate-induced membrane hyperpolarization

Acetic and folic acids hyperpolarize the membrane potential of Paramecium tetraurelia in a concentration-dependent manner. The membrane responses are accompanied by small changes in cell resistance, and are significantly reduced by increasing extracellular cation concentrations, suggesting that the attractants bring about the membrane potential change by increasing cell permeability to cations. The inability to show a reversal potential for the hyperpolarization to attractants suggests that the effects of cations on the response are non-specific, however. The possible roles of Ca++, K+, and Na+ in the attractant-induced responses were further investigated by applying acetate and folate to cells with genetic defects in specific ion conductances, by collapsing the driving forces for these ions, and by testing the effects of ion channel blockers on the responses. These studies suggest that the membrane responses to attractants are not due to the direct effects of increased or decreased membrane permeability to cations. Attempts to block the acetate and folate-induced hyperpolarization by collapsing surface potential or using a mutant with reduced surface charge were inconclusive, as were studies on the possible role of attractant transport in the membrane responses. We hypothesize that the membrane hyperpolarization may be due to either the indirect effects of increased calcium permeability, to extrusion of calcium through activation of a calcium pump, or to a proton efflux.

Restoration of flagellar clockwise rotation in bacterial envelopes by insertion of the chemotaxis protein CheY

When cells of the bacterium Salmonella typhimurium are incubated with penicillin and lysed in a dilute buffer, flagellated cytoplasm-free envelopes are formed. When the envelopes are tethered to glass by their flagella and then energized, some of them spin. The direction of rotation of wild-type envelopes is exclusively counterclockwise (CCW). We perturbed this system by including in the lysis medium (and hence in the envelopes) the chemotaxis protein CheY. As a result, some of the envelopes rotated exclusively clockwise (CW). The fraction of envelopes that did so increased with the concentration of CheY; at a concentration of 48 microM (pH 8), all functional envelopes spun CW. The fraction also increased with the pH of the lysis medium in the range of 6.6-8.4. The results were the same in the presence or absence of intracellular Ca2+. Reconstituted envelopes failed to respond to chemotactic stimuli. None of them changed the direction of their rotation. However, when the intracellular pH was lowered to 6.6 or below, envelopes that spun CW stopped rotating, while envelopes that spun CCW continued to rotate. This phenomenon was reversible. We conclude that CheY per se, without any additional free cytoplasmic mediators, interacts with a switch at the base of the flagellum to cause CW rotation.

Characterization of Escherichia coli chemotaxis receptor mutants with null phenotypes

Hydroxylamine mutagenesis was used to alter the tar gene that encodes the transmembrane Tar protein required for chemotaxis. Mutants defective in chemotaxis were selected, and the mutation was characterized by DNA sequencing. Two classes of mutations were found: nonsense and missense. The nonsense mutations were distributed throughout the gene, while the missense mutations were found to cluster in a region that includes 185 amino acids at the C-terminal end of the Tar protein. Partial characterization of mutant phenotypes suggested that some are completely defective in signaling while responding to attractants and repellents by differential methylation. Other mutants are undermethylated and constantly tumble, while yet another class of mutants is overmethylated and biased toward constant swimming with little or no tumbling. These mutants will be useful in experiments designed to understand the mechanism of chemotaxis.

Subdivision of flagellar genes of Salmonella typhimurium into regions responsible for assembly, rotation, and switching

Three flagellar genes of Salmonella typhimurium (flaAII.2, flaQ, and flaN) were found to be multifunctional, each being associated with four distinct mutant phenotypes: nonflagellate (Fla-), paralyzed (Mot-), nonchemotactic (Che-) with clockwise motor bias, and nonchemotactic (Che-) with counterclockwise motor bias. The distribution of Fla, Mot, and Che mutational sites within each gene was examined. Fla sites were fairly broadly distributed, whereas Mot and Che sites were more narrowly defined. Local subregions rich in sites of one type were not generally rich in sites of another type. Among Che sites, there was little overlap between those corresponding to a clockwise bias and those corresponding to a counterclockwise bias. Our results suggest that within the corresponding gene products there are specialized subregions for flagellar structure, motor rotation, and control of the sense of rotation.

Complementation and characterization of chemotaxis mutants of Bacillus subtilis

A set of chemotaxis mutants of Bacillus subtilis was complemented by using SP beta c2 transducing bacteriophage either containing cloned segments of DNA or derived from abnormal excision of SP beta c2 dl2::Tn917 inserted into the chemotaxis region. Representative mutants were characterized in capillary assays for chemotaxis toward four amino acids and mannitol and in tethered-cell experiments for addition and removal of two attractants and two repellents. Twenty complementation groups were identified, in addition to the cheR previously characterized. All were found to be defective in chemotaxis toward all chemoeffectors. They were assigned the names cheA through cheU. The large number of general chemotaxis genes in B. subtilis, in contrast to the six in Escherichia coli, suggests fundamental differences in the mechanism of chemotaxis in the two species.