Genetics of methyl-accepting chemotaxis proteins in Escherichia coli: cheD mutations affect the structure and function of the Tsr transducer

Transmembrane region of bacterial chemoreceptor is capable of promoting protein clustering

Many membrane proteins are known to form higher-order oligomers, but the degree to which membrane regions could facilitate protein complex assembly remains largely unclear. Clusters of chemotaxis receptors are among the most prominent structures in the bacterial cell membrane, and they play important functions in processing of chemotactic signals. Although much work has been done to elucidate mechanisms of cluster formation, it almost exclusively focused on cytoplasmic interactions among receptors and other chemotaxis proteins, whereas involvement of membrane-mediated interactions was only hypothesized. Here we used imaging of constructs composed of only a fluorescent protein and the TM helices of Tar to demonstrate that interactions between the lipid bilayer and transmembrane (TM) helices of Escherichia coli chemoreceptors alone are sufficient to mediate clustering. We found that the ability to cluster depends on the sequence or length of the TM helices, implying that certain conformations of these helices facilitate clustering, whereas others do not. Notably, observed sequence specificity was apparently consistent with differences in clustering between native E. coli receptors, with the TM sequence of better-clustering high-abundance receptors being more efficient in promoting membrane-mediated complex formation. These results indicate that being more than just membrane anchors, TM helices could play an important role in the clustering and organization of membrane proteins in bacteria.

Methyl-accepting chemotaxis proteins: a core sensing element in prokaryotes and archaea

Chemotaxis is the directed motility by means of which microbes sense chemical cues and relocate towards more favorable environments. Methyl-accepting chemotaxis proteins (MCPs) are the most common receptors in bacteria and archaea. They are arranged as trimers of dimers that, in turn, form hexagonal arrays in the cytoplasmic membrane or in the cytoplasm. Several different classes of MCPs have been identified according to their ligand binding region and membrane topology. MCPs have been further classified based on the length and sequence conservation of their cytoplasmic domains. Clusters of membrane-embedded MCPs often localize to the poles of the cell, whereas cytoplasmic MCPs can be targeted to the poles or distributed throughout the cell body. MCPs play an important role in cell survival, pathogenesis, and biodegradation. Bacterial adaptation to diverse environmental conditions promotes diversity among the MCPs. This review summarizes structure, classification, and structure-activity relationship of the known MCP receptors, with a brief overview of the signal transduction mechanisms in bacteria and archaea.

An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli

With the wide availability of whole-genome sequencing (WGS), genetic mapping has become the rate-limiting step, inhibiting unbiased forward genetics in even the most tractable model organisms. We introduce a rapid deconvolution resource and method for untagged causative mutations after mutagenesis, screens, and WGS in Escherichia coli. We created Deconvoluter—ordered libraries with selectable insertions every 50 kb in the E. coli genome. The Deconvoluter method uses these for replacement of untagged mutations in the genome using a phage-P1-based gene-replacement strategy. We validate the Deconvoluter resource by deconvolution of 17 of 17 phenotype-altering mutations from a screen of N-ethyl-N-nitrosourea-induced mutants. The Deconvoluter resource permits rapid unbiased screens and gene/function identification and will enable exploration of functions of essential genes and undiscovered genes/sites/alleles not represented in existing deletion collections. This resource for unbiased forward-genetic screens with mapping-by-sequencing (‘forward genomics’) demonstrates a strategy that could similarly enable rapid screens in many other microbes.

Chemotaxis to the quorum-sensing signal AI-2 requires the Tsr chemoreceptor and the periplasmic LsrB AI-2-binding protein

AI-2 is an autoinducer made by many bacteria. LsrB binds AI-2 in the periplasm, and Tsr is the l-serine chemoreceptor. We show that AI-2 strongly attracts Escherichia coli. Both LsrB and Tsr are necessary for sensing AI-2, but AI-2 uptake is not, suggesting that LsrB and Tsr interact directly in the periplasm.

Genetic evidence for interaction between the CheW and Tsr proteins during chemoreceptor signaling by Escherichia coli

This study presents two lines of genetic evidence consistent with the premise that CheW, a cytoplasmic component of the chemotactic signaling system of Escherichia coli, interacts directly with Tsr, the membrane-bound serine chemoreceptor. (i) We demonstrated phenotypic suppression between 10 missense mutant CheW proteins and six missense mutant Tsr proteins. Most of these mutant proteins had leaky chemotaxis defects and were partially dominant, implying relatively minor functional alterations. Their suppression pattern was allele specific, suggesting that the mutant proteins have compensatory conformational changes at sites of interactive contact. (ii) We isolated five partially dominant CheW mutations and found that four of them were similar or identical to the suppressible CheW mutant proteins. This implies that there are only a few ways in which CheW function can be altered to produce dominant defects and that dominance is mediated through interactions of CheW with Tsr. The amino acid replacements in these mutant proteins were inferred from their DNA sequence changes. The CheW mutations were located in five regularly spaced clusters in the first two-thirds of the protein. The Tsr mutations were located in a highly conserved region in the middle of the cytoplasmic signaling domain. The hydrophobic moments, overall hydrophobicities, and predicted secondary structures of the mutant segments were consistent with the possibility that they are located at the surface of the CheW and Tsr molecules and represent the contact sites between these two proteins.

Role of CheW protein in coupling membrane receptors to the intracellular signaling system of bacterial chemotaxis

Chemotactic behavior in Escherichia coli is mediated by membrane-associated chemoreceptors that transmit sensory signals to the flagellar motors through an intracellular signaling system, which appears to involve a protein phosphorylation cascade. This study concerns the role of CheW, a cytoplasmic protein, in coupling methyl-accepting chemotaxis proteins (MCPs), the major class of membrane receptors, to the intracellular signaling system. Steady-state flagellar rotation behavior was examined in a series of strains with different combinations and relative amounts of CheW, MCPs, and other signaling components. At normal expression levels, CheW stimulated clockwise rotation, and receptors appeared to enhance this stimulatory effect. At high expression levels, MCPs inhibited clockwise rotation, and CheW appeared to augment this inhibitory effect. Since overexpression of CheW or MCP molecules had the same behavioral effect as their absence, chemoreceptors probably use CheW to modulate two distinct signals, one that stimulates and one that inhibits the intracellular phosphorylation cascade.

Adaptational "crosstalk" and the crucial role of methylation in chemotactic migration by Escherichia coli

We investigated roles of methylation in bacterial chemotaxis by characterizing a methyl-accepting transducer protein incapable of methylation because of amino acid substitutions at the modification sites. Mutant Trg protein recognized ligand and generated excitatory signals that affected flagella but was unable to mediate efficient adaptation or net cellular migration in a relevant chemical gradient. Defects caused by lack of methyl-accepting sites on Trg were suppressed by a sufficient cellular content of other transducer molecules with functional methyl-accepting sites. These observations establish directly that methylation is crucial for transducer-mediated chemotaxis and that neither phosphotransfer reactions among the soluble Che proteins nor other interaction among those chemotactic components can effectively fulfill the functions of methylation. Suppression was correlated with adaptational "crosstalk" in which unoccupied methyl-accepting transducers acquired methyl groups, thus apparently substituting effectively for blocked methyl-accepting sites on the transducer. A plausible model for this phenomenon is that increased methylation of unstimulated transducers results from global inhibition of the demethylating enzyme in a cell with a normally active methyltransferase and no available methyl-accepting sites on the stimulated, mutant transducer. Thus methylation can perform its roles in adaptation and gradient sensing even if modification occurs on molecules different from those that recognize the stimulating compound. This observation emphasizes the central role of methylation and the modular nature of the chemosensory system.

Transmembrane signaling by bacterial chemoreceptors: E. coli transducers with locked signal output

Methyl-accepting chemotaxis proteins (MCPs) function as transmembrane signalers in bacteria. We isolated and characterized mutants of the E. coli Tsr protein that produce output signals in the absence of overt stimuli and that are refractory to sensory adaptation. The properties of these "locked" transducers indicate that MCP molecules are capable of generating signals that actively augment clockwise and counter-clockwise rotation of the flagellar motors. Transitions between MCP signaling states can be influenced by amino acid replacements in many parts of the molecule, including the methylation sites, at least one of the two membrane-spanning segments, and a linker region connecting the receptor and signaling domains. These findings suggest that transmembrane signaling may involve direct propagation of conformational changes between the periplasmic and cytoplasmic portions of the MCP molecule.

N-terminal half of CheB is involved in methylesterase response to negative chemotactic stimuli in Escherichia coli

The chemotactic receptor-transducer proteins of Escherichia coli are responsible for directing the swimming behavior of cells by signaling for either straight swimming or tumbling in response to chemostimuli. The signaling states of these proteins are affected not only by the concentrations of various stimuli but also by the extent to which they have been methylated at specific glutamyl residues. The activities of a chemotaxis-specific methyltransferase (CheR) and a chemotaxis-specific methylesterase (CheB) are regulated in response to chemotactic stimuli to enable sensory adaptation to unchanging levels of stimuli by appropriately shifting the signaling states of the transducer proteins. For CheB this regulation involves a feedback loop that requires some of the components making up the chemotactic signal transduction machinery of the cell. This feedback loop causes the methylesterase activity of CheB to decrease transiently in response to attractant stimuli and to increase transiently in response to negative stimuli (repellent addition or attractant removal). In this report we demonstrate that the methylesterase response to negative stimuli involves the N-terminal half of the CheB protein, whereas the response to positive stimuli does not require this segment of the protein. Both aspects of the methylesterase response to positive stimuli does not require this segment of the protein. Both aspects of the methylesterase response require CheA. In addition, we demonstrate that mutant forms of CheB lacking methylesterase activity can adversely affect the swimming behavior and chemotactic ability of cells and can markedly diminish modulation of the wild-type methylesterase activity in response to negative stimuli. The significance of these results is discussed in relation to the recent demonstration of phosphoryl transfer from CheA to CheB (J. F. Hess, K. Oosawa, N. Kaplan, and M. I. Simon, Cell 53:79-87, 1988) and the discovery of sequence homology between the N-terminal half of CheB and CheY (A. Stock, D. E. Koshland, Jr., and J. Stock, Proc. Natl. Acad. Sci. USA 82:7989-7993, 1985).

Receptor interactions through phosphorylation and methylation pathways in bacterial chemotaxis

The effects of messages initiated by one receptor on the covalent modification of a second receptor were studied by use of a technique for rapidly separating the receptors. Methylation of the bacterial-chemotactic serine receptor increases as a result of aspartate binding to the aspartate receptor. The aspartate-induced methylation on the serine receptor is absent in a strain that lacks cheA and cheW genes and is not the result of physical interaction, such as the formation of heterodimers between the aspartate and serine receptors, or of alterations in the affinity of the serine receptor for the methyltransferase and the methylesterase. Serine-induced methylation of the serine receptor did not require cheA and cheW. A model is presented in which the receptor methylation level depends on the combination of (i) a ligand-induced conformational change on the receptor substrate of the methylation enzymes and (ii) an indirect cytoplasmic signal that operates through the methylesterase.

Aspartate taxis mutants of the Escherichia coli tar chemoreceptor

The Tar protein of Escherichia coli belongs to a family of methyl-accepting inner membrane proteins that mediate chemotactic responses to a variety of compounds. These transmembrane signalers monitor the chemical environment by means of specific ligand-binding sites arrayed on the periplasmic side of the membrane, and in turn control cytoplasmic signals that modulate the flagellar rotational machinery. The periplasmic receptor domain of Tar senses two quite different chemoeffectors, aspartate and maltose. Aspartate is detected through direct binding to Tar molecules, whereas maltose is detected indirectly when complexed with the periplasmic maltose-binding protein. Saturating levels of either aspartate or maltose do not block behavioral responses to the other compound, indicating that the detection sites for these two attractants are not identical. We initiated structure-function studies of these chemoreceptor sites by isolating tar mutants which eliminate aspartate or maltose taxis, while retaining the ability to respond to the other chemoeffector. Mutants with greatly reduced aspartate taxis are described and characterized in this report. When present in single copy in the chromosome, these tar mutations generally eliminated chemotactic responses to aspartate and structurally related compounds, such as glutamate and methionine. Residual responses to these compounds were shifted to higher concentrations, indicating a reduced affinity of the aspartate-binding site in the mutant receptors. Maltose responses in the mutants ranged from 10 to 80% of normal, but had no detectable threshold shifts, indicating that these receptor alterations may have little effect on maltose detection sensitivity. The mutational changes in 17 mutants were determined by DNA sequence analysis. Each mutant exhibited a single amino acid replacement at residue 64, 69, or 73 in the Tar molecule. The wild-type Tar transducer contains arginines at all three of these positions, implying that electrostatic forces may play an important role in aspartate detection.

Hybrid Escherichia coli sensory transducers with altered stimulus detection and signaling properties

The tar and tap loci of Escherichia coli encode methyl-accepting inner membrane proteins that mediate chemotactic responses to aspartate and maltose or to dipeptides. These genes lie adjacent to each other in the same orientation on the chromosome and have extensive sequence homology throughout the C-terminal portions of their coding regions. Many spontaneous deletions in the tar-tap region appear to be generated by recombination between these regions of homology, leading to gene fusions that produce hybrid transducer molecules in which the N terminus of Tar is joined to the C terminus of Tap. The properties of two such hybrids are described in this report. Although Tar and Tap molecules have homologous domain structures, these Tar-Tap hybrids exhibited defects in stimulus detection and flagellar signaling. Both hybrid transducers retained Tar receptor specificity, but had reduced detection sensitivity. This defect was correlated with the presence of the C-terminal methyl-accepting segment of Tap, which may have more methylation sites than its Tar counterpart, leading to elevated steady-state methylation levels in the hybrid molecules. One of the hybrids, which carried a more extensive segment from Tap, appeared to generate constitutive signals that locked the flagellar motors in a counterclockwise rotational mode. Changes in the methylation state of this transducer were ineffective in cancelling this aberrant signal. These findings implicate the conserved C-terminal domain of bacterial transducers in the generation or regulation of flagellar signals.

Reconstitution of signaling in bacterial chemotaxis

Strains missing several genes required for chemotaxis toward amino acids, peptides, and certain sugars were tethered and their rotational behavior was analyzed. Null strains (called gutted) were deleted for genes that code for the transducers Tsr, Tar, Tap, and Trg and for the cytoplasmic proteins CheA, CheW, CheR, CheB, CheY, and CheZ. Motor switch components were wild type, flaAII(cheC), or flaBII(cheV). Gutted cells with wild-type motors spun exclusively counterclockwise, while those with mutant motors changed their directions of rotation. CheY reduced the bias (the fraction of time that cells spun counterclockwise) in either case. CheZ offset the effect of CheY to an extent that varied with switch allele but did not change the bias when tested alone. Transducers also increased the bias in the presence of CheY but not when tested alone. However, cells containing transducers and CheY failed to respond to attractants or repellents normally detected in the periplasm. This sensitivity was restored by addition of CheA and CheW. Thus, CheY both enhances clockwise rotation and couples the transducers to the flagella. CheZ acts, at the level of the motor, as a CheY antagonist. CheA or CheW or both are required to complete the signal pathway. A model is presented that explains these results and is consistent with other data found in the literature.

Chemotaxis in Escherichia coli: construction and properties of lambda tsr transducing phage

The tsr gene of Escherichia coli, located at approximately 99 min on the chromosomal map, encodes a methyl-accepting protein that serves as the chemoreceptor and signal transducer for chemotactic responses to serine and several repellents. To determine whether any other chemotaxis or motility genes were located in the tsr region, we constructed and characterized two lambda tsr transducing phages that each contain about 12 kilobases of chromosomal material adjacent to tsr. lambda tsr70 carries sequences from the promoter-proximal side of tsr; lambda tsr72 carries sequences from the promoter-distal side of tsr. Restriction maps of the bacterial inserts in these phages and Southern hybridization analyses of the bacterial chromosome indicated that the tsr gene is transcribed in the counterclockwise direction on the genetic map. Insert deletions were isolated in lambda tsr70 and transferred into the host chromosome to examine the null phenotype of tsr. All such strains exhibited wild-type swimming patterns and chemotactic responses to a variety of stimuli, but were specifically defective in serine taxis and other Tsr-mediated responses. In addition, UV programming experiments demonstrated that Tsr and several of its presumptive degradation products were the only bacterial proteins encoded by lambda tsr70 and lambda tsr72 that required host FlbB/FlaI function for expression. These findings indicate that there are probably no other chemotaxis-related genes in the tsr region. A series of tsr point mutations were isolated by propagating lambda tsr70 on a mutD host and used to construct a fine-structure map of the tsr locus. These mutations should prove valuable in exploring structure-function relationships in the Tsr transducer.

Mutation plus amplification of a transducer gene disrupts general chemotactic behavior in Escherichia coli

Transducers are transmembrane receptor proteins that generate intracellular signals on stimulation and participate in adaptation by appropriate changes in the level of methylation. The transducer mutation trg-21 conferred a Trg- phenotype and defective taxis to galactose and ribose but a normal response to other attractants when present in a single chromosomal copy. Amplification of trg-21 by a multicopy plasmid made host cells generally nonchemotactic. The dominant phenotype resulted from a strong counterclockwise rotational bias of flagellar motors in Che- cells. Apparently, the Trg21 transducer sends a continuous counterclockwise signal to flagella independent of tactic stimulation. It appears that the cell has a homeostatic capacity that is sufficient to compensate for the effect of mutant transducers produced from a single chromosomal copy of trg-21, but the capacity is exceeded in cells that have multiple copies of the gene. The Trg21 protein did not have a significant effect on methylesterase activity, indicating that the two global effects of a stimulated transducer, that is, on flagellar rotation and on modification enzymes, can occur independently. The mutant protein exhibited essentially normal turnover of methyl groups but had a drastic defect in deamidation which thus reduced the number of methyl-accepting sites. The trg-21 mutation substitutes a threonine for Ala-419. This alanine is a conserved residue in all sequenced transducers and is in a region of the carboxy-terminal domain in which homology among the transducers is very high. The Trg21 phenotype implicates this conserved region in the generation of the excitatory signal which is directed at the flagella.

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.

Peptide chemotaxis in E. coli involves the Tap signal transducer and the dipeptide permease

Bacterial chemotaxis provides a simple model system for the more complex sensory responses of multicellular eukaryotic organisms. In Escherichia coli, methylation and demethylation of four related membrane proteins, the methyl-accepting chemotaxis proteins (or MCPs), is central to chemotactic sensing and signal transduction. Three of these proteins, Tar, Tsr and Trg, have been assigned specific roles in chemotaxis. However, the role of the fourth MCP, Tap, has remained obscure. We demonstrate here that Tap functions as a conventional signal transducer, enabling the cell to respond chemotactically to dipeptides. This provides the first evidence of specific bacterial chemotaxis towards peptides. Peptide taxis requires the function of a periplasmic component of the dipeptide permease. This protein represents the first example of a periplasmic chemoreceptor that does not have a sugar substrate.

Transfer of chromosomal mutations to plasmids via Hfr-mediated conduction

Nonconjugative plasmids can be transferred from an Hfr donor to a recipient by Hfr-mediated conduction. We found that this phenomenon can be employed to obtain a plasmid in which a mutation in a chromosomal gene has been transferred to the copy of that gene contained in the hybrid plasmid.

Aberrant regulation of methylesterase activity in cheD chemotaxis mutants of Escherichia coli

The adaptation process in several cheD chemotaxis mutants, which carry defects in tsr, the serine transducer gene, was examined. cheD mutants are smooth swimming and generally nonchemotactic; the defect is dominant to the wild-type tsr gene (J. S. Parkinson, J. Bacteriol. 142:953-961, 1980). All classes of methyl-accepting chemotaxis proteins synthesized in unstimulated cheD strains are overmethylated relative to the wild type. We found that the steady-state rate of demethylation in cheD mutants was low; this may explain their overmethylated phenotype. In addition, all cheD mutants showed diminished responsiveness of methylesterase activity to attractant and repellent stimuli transduced by either the Tsr or Tar protein, and they did not adapt. These results suggest that the dominant nature of the cheD mutations is manifested as a general defect in the regulation of demethylation. Some of these altered properties of methylesterase activity in cheD mutants were exhibited in wild-type cells that were treated with saturating concentrations of serine. The mutant Tsr protein thus seems to be locked into a signaling mode that suppresses tumbling and inhibits methylesterase activity in a global fashion. We found that the Tar and mutant Tsr proteins synthesized in cheD strains were methylated and deamidated at the correct sites and that the mutations were not located in the methylated peptides. Thus, the signaling properties of the transducers may be controlled at sites distinct from the methyl-accepting sites.