Discrimination between different methylation states of chemotaxis receptor Tar by receptor methyltransferase CheR

Tethered particle motion of the adaptation enzyme CheR in bacterial chemotaxis

Bacteria perform chemotactic adaptation by sequential modification of multiple modifiable sites on chemoreceptors through stochastic action of tethered adaptation enzymes (CheR and CheB). To study the molecular kinetics of this process, we measured the response to different concentrations of MeAsp for the Tar-only Escherichia coli strain. We found a strong dependence of the methylation rate on the methylation level and established a new mechanism of adaptation kinetics due to tethered particle motion of the methylation enzyme CheR. Experiments with various lengths of the C-terminal flexible chain in the Tar receptor further validated this mechanism. The tethered particle motion resulted in a CheR concentration gradient that ensures encounter-rate matching of the sequential modifiable sites. An analytical model of multisite catalytic reaction showed that this enables robustness of methylation to fluctuations in receptor activity or cell-to-cell variations in the expression of adaptation enzymes and reduces the variation in methylation level among individual receptors.

Methylation-Independent Chemotaxis Systems Are the Norm for Gastric-Colonizing Helicobacter Species

Many bacteria and archaea rely on chemotaxis signal transduction systems for optimal fitness. These complex, multiprotein signaling systems have core components found in all chemotactic microbes, as well as variable proteins found in only some species. We do not yet understand why these variations exist or whether there are specific niches that favor particular chemotaxis signaling organization. One variation is in the presence/absence of the chemotaxis methylation adaptation enzymes CheB and CheR. Genes for CheB and CheR are missing in the gastric pathogen Helicobacter pylori but present in related Helicobacter that colonize the liver or intestine. In this work, we asked whether there was a general pattern of CheB/CheR across multiple Helicobacter species. Helicobacter spp. all possess chemotactic behavior, based on the presence of genes for core signaling proteins CheA, CheW, and chemoreceptors. Genes for the CheB and CheR proteins, in contrast, were variably present. Niche mapping supported the idea that these genes were present in enterohepatic Helicobacter species and absent in gastric ones. We then analyzed whether there were differences between gastric and enterohepatic species in the CheB/CheR chemoreceptor target methylation sites. Indeed, these sites were less conserved in gastric species that lack CheB/CheR. Lastly, we determined that cheB and cheR could serve as markers to indicate whether an unknown Helicobacter species was of enterohepatic or gastric origin. Overall, these findings suggest the interesting idea that methylation-based adaptation is not required in specific environments, particularly the stomach. IMPORTANCE Chemotaxis signal transduction systems are common in the archaeal and bacterial world, but not all systems contain the same components. The rationale for this system variation remains unknown. In this report, comparative genomics analysis showed that the presence/absence of CheR and CheB is one main variation within the Helicobacter genus, and it is strongly associated with the niche of Helicobacter species: gastric Helicobacter species, which infect animal stomachs, have lost their CheB and CheR, while enterohepatic Helicobacter species, which infect the liver and intestine, retain them. This study not only provides an example that a chemotaxis system variant is associated with particular niches but also proposes that CheB and CheR are new markers distinguishing gastric from enterohepatic Helicobacter species.

Sequential modification of bacterial chemoreceptors is key for achieving both accurate adaptation and high gain

Many regulatory and signaling proteins have multiple modification sites. In bacterial chemotaxis, each chemoreceptor has multiple methylation sites that are responsible for adaptation. However, whether the ordering of the multisite methylation process affects adaptation remains unclear. Furthermore, the benefit of having multiple modification sites is also unclear. Here, we show that sequentially ordered methylation/demethylation is critical for perfect adaptation; adaptation accuracy decreases as randomness in the multisite methylation process increases. A tradeoff between adaptation accuracy and response gain is discovered. We find that this accuracy-gain tradeoff is lifted significantly by having more methylation sites, but only when the multisite modification process is sequential. Our study suggests that having multiple modification sites and a sequential modification process constitute a general strategy to achieve both accurate adaptation and high response gain simultaneously. Our theory agrees with existing data and predictions are made to help identify the molecular mechanism underlying ordered covalent modifications.

Bacterial chemoreceptors have multiple methylation sites, but whether the order of methylation matters is unclear. Here, the authors show that sequentially ordered methylation is critical for perfect adaptation and for attenuating the trade-off between accurate adaptation and high response gain.

Methyltransferase CheR binds to its chemoreceptor substrates independent of their signaling conformation yet modifies them differentially

Methylation of specific chemoreceptor glutamyl residues by methyltransferase CheR mediates sensory adaptation and gradient sensing in bacterial chemotaxis. Enzyme action is a function of chemoreceptor signaling conformation: kinase-off receptors are more readily methylated than kinase-on, a feature central to adaptational and gradient-sensing mechanisms. Differential enzyme action could reflect differential binding, catalysis or both. We investigated by measuring CheR binding to kinase-off and kinase-on forms of Escherichia coli aspartate receptor Tar deleted of its CheR-tethering, carboxyl terminus pentapeptide. This allowed characterization of the low-affinity binding of enzyme to the substrate receptor body, otherwise masked by high-affinity interaction with pentapeptide. We quantified the low-affinity protein-protein interactions by determining kinetic rate constants of association and dissociation using bio-layer interferometry and from those values calculating equilibrium constants. Whether Tar signaling conformations were shifted by ligand occupancy or adaptational modification, there was little or no difference between the two signaling conformations in kinetic or equilibrium parameters of enzyme-receptor binding. Thus, differential methyltransferase action does not reflect differential binding. Instead, the predominant determinants of binding must be common to different signaling conformations. Characterization of the dependence of association rate constants on Deybe length, a measure of the influence of electrostatics, implicated electrostatic interactions as a common binding determinant. Taken together, our observations indicate that differential action of methyltransferase on kinase-off and kinase-on chemoreceptors is not the result of differential binding and suggest it reflects differential catalytic propensity. Differential catalysis rather than binding could well be central to other enzymes distinguishing alternative conformations of protein substrates.

Behavioral Variability and Phenotypic Diversity in Bacterial Chemotaxis

Living cells detect and process external signals using signaling pathways that are affected by random fluctuations. These variations cause the behavior of individual cells to fluctuate over time (behavioral variability) and generate phenotypic differences between genetically identical individuals (phenotypic diversity). These two noise sources reduce our ability to predict biological behavior because they diversify cellular responses to identical signals. Here, we review recent experimental and theoretical advances in understanding the mechanistic origin and functional consequences of such variation in Escherichia coli chemotaxis-a well-understood model of signal transduction and behavior. After briefly summarizing the architecture and logic of the chemotaxis system, we discuss determinants of behavior and chemotactic performance of individual cells. Then, we review how cell-to-cell differences in protein abundance map onto differences in individual chemotactic abilities and how phenotypic variability affects the performance of the population. We conclude with open questions to be addressed by future research.

Paradoxical enhancement of chemoreceptor detection sensitivity by a sensory adaptation enzyme

A sensory adaptation system that tunes chemoreceptor sensitivity enables motile Escherichia coli cells to track chemical gradients with high sensitivity over a wide dynamic range. Sensory adaptation involves feedback control of covalent receptor modifications by two enzymes: CheR, a methyltransferase, and CheB, a methylesterase. This study describes a CheR function that opposes the signaling consequences of its catalytic activity. In the presence of CheR, a variety of mutant serine chemoreceptors displayed up to 40-fold enhanced detection sensitivity to chemoeffector stimuli. This response enhancement effect did not require the known catalytic activity of CheR, but did involve a binding interaction between CheR and receptor molecules. Response enhancement was maximal at low CheR:receptor stoichiometry and quantitative analyses argued against a reversible binding interaction that simply shifts the ON-OFF equilibrium of receptor signaling complexes. Rather, a short-lived CheR binding interaction appears to promote a long-lasting change in receptor molecules, either a covalent modification or conformation that enhances their response to attractant ligands.

Crystal structure of pentapeptide-independent chemotaxis receptor methyltransferase (CheR) reveals idiosyncratic structural determinants for receptor recognition

Chemotactic methyltransferase, CheR catalyse methylation of specific glutamate residues in the cytoplasmic domain of methyl-accepting chemotactic protein receptors (MCPRs). The methylation of MCPRs is essential for the chemical sensing and chemotactic bacterial mobility towards favorable chemicals or away from unfavorable ones. In this study, crystal structure of B. subtilis CheR (BsCheR) in complex with S-adenosyl-l-homocysteine (SAH) has been determined to 1.8Å resolution. This is the first report of crystal structure belonging to the pentapeptide-independent CheR (PICheR) class. Till date, only one crystal structure of CheR from S. typhimurium (StCheR) belonging to pentapeptide-dependent CheR (PDCheR) class is available. Structural analysis of BsCheR reveals a helix-X-helix motif (HXH) with Asp53 as the linker residue in the N-terminal domain. The key structural features of the PDCheR β-subdomain involved in the formation of a tight complex with the pentapeptide binding motif in MCPRs were found to be absent in the structure of BsCheR. Additionally, isothermal titration calorimetry (ITC) experiments were performed to investigate S-adenosyl-(l)-methionine (SAM) binding affinity and K_D was determined to be 0.32mM. The structure of BsCheR reveals that mostly residues of the large C-terminal domain contribute to SAH binding, with contributions of few residues from the linker region and the N-terminal domain. Structural investigations and sequence analysis carried out in this study provide critical insights into the distinct receptor recognition mechanism of the PDCheR and PICheR methyltransferase classes.

In silico and proteomic analysis of protein methyltransferase CheR from Bacillus subtilis

Protein methyltransferase (CheR) catalyzes the methylation of the cytosolic domain of the membrane bound chemotaxis receptors, and plays a pivotal role in the chemotactic signal transduction pathway in bacteria. Crystal structure of CheR is available only from the gram-negative bacterium Salmonella typhimurium (StCheR), which contain a catalytic C-terminal domain, encompassing a β-subdomain, connected via a linker to the N-terminal domain. The structural-functional similitude between CheR of the gram-negative and the gram-positive bacteria remains obscure. We investigated CheR, from a gram-positive bacterium, Bacillus subtilis (BsCheR), and have identified the functional roles of its N-terminal domain, by using the in silico molecular modeling and docking approach along with mass spectrophotometry and sequence analysis. The structural studies established that the N-terminal domain directly bound to S-Adenosyl-l-homocysteine (SAH). Structural and sequence analyses revealed that the α2 helix of the N-terminal domain was involved in the recognition of the methylation site of the chemotactic receptor. Additionally, immunoblot analysis showed that the purified BsCheR was phosphorylated. Further, mass spectrometry studies detected the phosphorylation at Thr3 position in the N-terminal domain of BsCheR. Phosphorylation of BsCheR suggested a regulatory role of the N-terminal domain, analogous to its antagonistic enzyme, the chemotaxis-specific methylesterase (CheB).

Universal response-adaptation relation in bacterial chemotaxis

The bacterial strategy of chemotaxis relies on temporal comparisons of chemical concentrations, where the probability of maintaining the current direction of swimming is modulated by changes in stimulation experienced during the recent past. A short-term memory required for such comparisons is provided by the adaptation system, which operates through the activity-dependent methylation of chemotaxis receptors. Previous theoretical studies have suggested that efficient navigation in gradients requires a well-defined adaptation rate, because the memory time scale needs to match the duration of straight runs made by bacteria. Here we demonstrate that the chemotaxis pathway of Escherichia coli does indeed exhibit a universal relation between the response magnitude and adaptation time which does not depend on the type of chemical ligand. Our results suggest that this alignment of adaptation rates for different ligands is achieved through cooperative interactions among chemoreceptors rather than through fine-tuning of methylation rates for individual receptors. This observation illustrates a yet-unrecognized function of receptor clustering in bacterial chemotaxis.

An insight into the interaction mode between CheB and chemoreceptor from two crystal structures of CheB methylesterase catalytic domain

We have determined 2.2 Å resolution crystal structure of Thermotoga maritima CheB methylesterase domain to provide insight into the interaction mode between CheB and chemoreceptors. T. maritima CheB methylesterase domain has identical topology of a modified doubly-wound α/β fold that was observed from the previously reported Salmonella typhimurium counterpart, but the analysis of the electrostatic potential surface near the catalytic triad indicated considerable charge distribution difference. As the CheB demethylation consensus sites of the chemoreceptors, the CheB substrate, are not uniquely conserved between T. maritima and S. typhimurium, such surfaces with differing electrostatic properties may reflect CheB regions that mediate protein-protein interaction. Via the computational docking of the two T. maritima and S. typhimurium CheB structures to the respective T. maritima and Escherichia coli chemoreceptors, we propose a CheB:chemoreceptor interaction mode.

The Pseudomonas aeruginosa chemotaxis methyltransferase CheR1 impacts on bacterial surface sampling

The characterization of factors contributing to the formation and development of surface-associated bacterial communities known as biofilms has become an area of intense interest since biofilms have a major impact on human health, the environment and industry. Various studies have demonstrated that motility, including swimming, swarming and twitching, seems to play an important role in the surface colonization and establishment of structured biofilms. Thereby, the impact of chemotaxis on biofilm formation has been less intensively studied. Pseudomonas aeruginosa has a very complex chemosensory system with two Che systems implicated in flagella-mediated motility. In this study, we demonstrate that the chemotaxis protein CheR1 is a methyltransferase that binds S-adenosylmethionine and transfers a methyl group from this methyl donor to the chemoreceptor PctA, an activity which can be stimulated by the attractant serine but not by glutamine. We furthermore demonstrate that CheR1 does not only play a role in flagella-mediated chemotaxis but that its activity is essential for the formation and maintenance of bacterial biofilm structures. We propose a model in which motility and chemotaxis impact on initial attachment processes, dispersion and reattachment and increase the efficiency and frequency of surface sampling in P. aeruginosa.

Molecular modeling of flexible arm-mediated interactions between bacterial chemoreceptors and their modification enzyme

Sensory adaptation in bacterial chemotaxis is mediated by methylation and demethylation of specific glutamyl residues in the cytoplasmic domain of chemoreceptors. Methylation is catalyzed by methyltransferase CheR. In E. coli and related organisms, methylation sufficiently rapid to be physiologically effective requires a carboxyl terminal pentapeptide sequence on the receptor being modified or, via adaptational assistance, on a neighboring homodimer in a receptor cluster. Pentapeptide-enhanced methylation is thought to be mediated by a approximately 30 residue, potentially disordered sequence that serves as a flexible arm connecting the receptor body and pentapeptide-bound methyltransferase, thus allowing diffusionally restricted enzyme to reach methyl-accepting sites. However, it was not known how many or which sites on the same or neighboring receptors were accessible to the tethered enzyme. We investigated using molecular modeling and found that, in a hexagonal array of trimers of receptor dimers, CheR tethered to a dimer of chemoreceptor Tar by its native 30-residue flexible-arm sequence could reach all methyl-accepting sites on the dimer to which it was tethered plus 48 methyl-accepting sites distributed among nine neighboring dimers, equivalent to the total sites carried by six receptors. This modeling-determined methylation neighborhood of one enzyme-binding dimer and six neighbors corresponds precisely with the experimentally identified neighborhood of seven. Thus, the experimentally observed adaptational assistance can occur by docking of pentapeptide-bound, diffusionally restricted enzyme to methyl-accepting sites on neighboring receptors. Our analysis introduces the notion that physiologically relevant adaptational assistance could occur even if only a subset of sites on a particular receptor are within reach.

Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors

As an important model for transmembrane signaling, methyl-accepting chemotaxis proteins (MCPs) have been extensively studied by using genetic, biochemical, and structural techniques. However, details of the molecular mechanism of signaling are still not well understood. The availability of genomic information for hundreds of species enables the identification of features in protein sequences that are conserved over long evolutionary distances and thus are critically important for function. We carried out a large-scale comparative genomic analysis of the MCP signaling and adaptation domain family and identified features that appear to be critical for receptor structure and function. Based on domain length and sequence conservation, we identified seven major MCP classes and three distinct structural regions within the cytoplasmic domain: signaling, methylation, and flexible bundle subdomains. The flexible bundle subdomain, not previously recognized in MCPs, is a conserved element that appears to be important for signal transduction. Remarkably, the N- and C-terminal helical arms of the cytoplasmic domain maintain symmetry in length and register despite dramatic variation, from 24 to 64 7-aa heptads in overall domain length. Loss of symmetry is observed in some MCPs, where it is concomitant with specific changes in the sensory module. Each major MCP class has a distinct pattern of predicted methylation sites that is well supported by experimental data. Our findings indicate that signaling and adaptation functions within the MCP cytoplasmic domain are tightly coupled, and that their coevolution has contributed to the significant diversity in chemotaxis mechanisms among different organisms.

Characterization of the Thermotoga maritima chemotaxis methylation system that lacks pentapeptide-dependent methyltransferase CheR:MCP tethering

Sensory adaptation in bacterial chemotaxis is mediated by covalent modifications of specific glutamate and glutamine residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins (MCPs). In Escherichia coli and Salmonella enterica, efficient methylation of MCPs depends on the localization of methyltransferase CheR to MCP clusters through an interaction between the CheR beta-subdomain and a pentapeptide sequence (NWETF or NWESF) at the C-terminus of the MCP. In vitro methylation analyses utilizing S. enterica and Thermotoga maritima CheR proteins and MCPs indicate that MCP methylation in T. maritima occurs independently of a pentapeptide-binding motif. Kinetic and binding measurements demonstrate that despite efficient methylation, the interaction between T. maritima CheR and T. maritima MCPs is of relatively low affinity. Comparative protein sequence analyses of CheR beta-subdomains from organisms having MCPs that contain and/or lack pentapeptide-binding motifs identified key similarities and differences in residue conservation, suggesting the existence of two distinct classes of CheR proteins: pentapeptide-dependent and pentapeptide-independent methyltransferases. Analysis of MCP C-terminal ends showed that only approximately 10% of MCPs contain a putative C-terminal binding motif, the majority of which are restricted to the different proteobacteria classes (alpha, beta, gamma, delta). These findings suggest that tethering of CheR to MCPs is a relatively recent event in evolution and that the pentapeptide-independent methylation system is more common than the well-characterized pentapeptide-dependent methylation system.

Identification of methylation sites in Thermotoga maritima chemotaxis receptors

Adaptation in bacterial chemotaxis involves reversible methylation of specific glutamate residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins. The specific sites of methylation in Salmonella enterica and Escherichia coli chemoreceptors, identified 2 decades ago, established a consensus sequence for methylation by methyltransferase CheR. Here we report the in vitro methylation of chemoreceptors from Thermotoga maritima, a hyperthermophile that has served as a useful source of chemotaxis proteins for structural analysis. Sites of methylation have been identified by liquid chromatography-mass spectrometry/mass spectrometry. Fifteen sites of methylation were identified within the cytoplasmic domains of four different T. maritima chemoreceptors. The results establish a consensus sequence for chemoreceptor methylation sites in T. maritima that is distinct from the previously identified consensus sequence for E. coli and S. enterica. These findings suggest that consensus sequences for posttranslational modifications in one organism may not be directly extrapolated to analogous modifications in other bacteria.

Post-prenylation-processing enzymes as new targets in oncogenesis

RAS and many other oncogenic proteins undergo a complex series of post-translational modifications that are initiated by the addition of an isoprenoid lipid through a process known as prenylation. Following prenylation, these proteins usually undergo endoproteolytic processing by the RCE1 protease and then carboxyl methylation by a unique methyltransferase known as isoprenylcysteine carboxyl methyltransferase (ICMT). Although inhibitors that have been designed to target the prenylation step are now in advanced-stage clinical trials, their utility and efficacy seem to be limited. Recent findings, however, indicate that the inhibition of these post-prenylation-processing steps--particularly that of ICMT-catalysed methylation--might provide a better approach to the control of cancer-cell proliferation.

Site-specific and synergistic stimulation of methylation on the bacterial chemotaxis receptor Tsr by serine and CheW

Background

Specific glutamates in the methyl-accepting chemotaxis proteins (MCPs) of Escherichia coli are modified during sensory adaptation. Attractants that bind to MCPs are known to increase the rate of receptor modification, as with serine and the serine receptor (Tsr), which contributes to an increase in the steady-state (adapted) methylation level. However, MCPs form ternary complexes with two cytoplasmic signaling proteins, the kinase (CheA) and an adaptor protein (CheW), but their influences on receptor methylation are unknown. Here, the influence of CheW on the rate of Tsr methylation has been studied to identify contributions to the process of adaptation.

Results

Methyl group incorporation was measured in a series of membrane samples in which the Tsr molecules were engineered to have one available methyl-accepting glutamate residue (297, 304, 311 or 493). The relative rates at these sites (0.14, 0.05, 0.05 and 1, respectively) differed from those found previously for the aspartate receptor (Tar), which was in part due to sequence differences between Tar and Tsr near site four. The addition of CheW generated unexpectedly large and site-specific rate increases, equal to or larger than the increases produced by serine. The increases produced by serine and CheW (added separately) were the largest at site one, ~3 and 6-fold, respectively, and the least at site four, no change and ~2-fold, respectively. The rate increases were even larger when serine and CheW were added together, larger than the sums of the increases produced by serine and CheW added separately (except site four). This resulted in substantially larger serine-stimulated increases when CheW was present. Also, CheW enhanced methylation rates when either two or all four sites were available.

Conclusion

The increase in the rate of receptor methylation upon CheW binding contributes significantly to the ligand specificity and kinetics of sensory adaptation. The synergistic effect of serine and CheW binding to Tsr is attributed to distinct influences on receptor structure; changes in the conformation of the Tsr dimer induced by serine binding improve methylation efficiency, and CheW binding changes the arrangement among Tsr dimers, which increases access to methylation sites.

A new type of protein methylation activated by tyrphostin A25 and vanadate

It has been reported that S-adenosylmethionine-dependent protein methylation in rat kidney extracts can be greatly stimulated by tyrphostin A25, a tyrosine kinase inhibitor. We have investigated the nature of this stimulation. We find that addition of tyrphostin A25, in combination with the protein phosphatase inhibitor vanadate, leads to the stimulation of methylation of polypeptides of 64, 42, 40, 36, 31, and 15 kDa in cytosolic extracts of mouse kidney. The effect of tyrphostin appears to be relatively specific for the A25 species. The enhanced methylation does not represent the activity of the families of protein histidine, lysine or arginine methyltransferases, nor that of the l-isoaspartyl/d-aspartyl methyltransferase, enzymes responsible for the bulk of protein methylation in most cell types. Chemical and enzymatic analyses of the methylated polypeptides suggest that the methyl group is in an ester linkage to the protein. In heart extracts, we find a similar situation but here the stimulation of methylation is not dependent upon vanadate and an additional 18 kDa methylated species is found. In contrast, little or no stimulation of methylation is found in brain or testis extracts. This work provides evidence for a novel type of protein carboxyl methylation reaction that may play a role in signaling reactions in certain mammalian tissues.