The ligand‐binding domain of a chemoreceptor from Comamonas testosteroni has a previously unknown homotrimeric structure

Transmembrane chemoreceptors are widely present in Bacteria and Archaea. They play a critical role in sensing various signals outside and transmitting to the cell interior. Here, we report the structure of the periplasmic ligand‐binding domain (LBD) of the transmembrane chemoreceptor MCP2201, which governs chemotaxis to citrate and other organic compounds in Comamonas testosteroni. The apo‐form LBD crystal revealed a typical four‐helix bundle homodimer, similar to previously well‐studied chemoreceptors such as Tar and Tsr of Escherichia coli. However, the citrate‐bound LBD revealed a four‐helix bundle homotrimer that had not been observed in bacterial chemoreceptor LBDs. This homotrimer was further confirmed with size‐exclusion chromatography, analytical ultracentrifugation and cross‐linking experiments. The physiological importance of the homotrimer for chemotaxis was demonstrated with site‐directed mutations of key amino acid residues in C. testosteroni mutants.     

Characterization of methyl-accepting chemotaxis proteins (MCPs) for amino acids in plant-growth-promoting rhizobacterium Pseudomonas protegens CHA0 and enhancement of amino acid chemotaxis by MCP genes overexpression

ABSTRACT

Pseudomonas protegens CHA0, known as plant-growth-promoting rhizobacterium, showed positive chemotactic responses toward proteinaceous L-amino acids. Genomic analysis revealed that P. protegens CHA0 possesses four putative chemoreceptors for amino acids (designated CtaA, CtaB, CtaC, and CtaD, respectively). Pseudomonas aeruginosa PCT2, a mutant defective in chemotaxis to amino acids, harboring a plasmid containing each of ctaA, ctaB, ctaC, and ctaD showed chemotactic responses to 20, 4, 4, and 11 types of amino acids, respectively. To enhance chemotaxis toward amino acids, we introduced the plasmids containing ctaA, ctaB, ctaC, or ctaD into P. protegens CHA0. By overexpression of the genes, we succeeded in enhancing chemotaxis toward more than half of the tested ligands. However, unexpectedly, the P. protegens CHA0 transformants showed unchanged or decreased responses to some amino acids when compared to wild-type CHA0. We speculate that alternation of expression of a chemoreceptor may affect the abundance of other chemoreceptors.     

Chemotaxis of Escherichia coli to pyrimidines: a new role for the signal transducer tap

Escherichia coli exhibits chemotactic responses to sugars, amino acids, and dipeptides, and the responses are mediated by methyl-accepting chemotaxis proteins (MCPs). Using capillary assays, we demonstrated that Escherichia coli RP437 is attracted to the pyrimidines thymine and uracil and the response was constitutively expressed under all tested growth conditions. All MCP mutants lacking the MCP Tap protein showed no response to pyrimidines, suggesting that Tap, which is known to mediate dipeptide chemotaxis, is required for pyrimidine chemotaxis. In order to confirm the role of Tap in pyrimidine chemotaxis, we constructed chimeric chemoreceptors (Tapsr and Tsrap), in which the periplasmic and cytoplasmic domains of Tap and Tsr were switched. When Tapsr and Tsrap were individually expressed in an E. coli strain lacking all four native MCPs, Tapsr mediated chemotaxis toward pyrimidines and dipeptides, but Tsrap did not complement the chemotaxis defect. The addition of the C-terminal 19 amino acids from Tsr to the C terminus of Tsrap resulted in a functional chemoreceptor that mediated chemotaxis to serine but not pyrimidines or dipeptides. These results indicate that the periplasmic domain of Tap is responsible for detecting pyrimidines and the Tsr signaling domain confers on Tapsr the ability to mediate efficient chemotaxis. A mutant lacking dipeptide binding protein (DBP) was wild type for pyrimidine taxis, indicating that DBP, which is the primary chemoreceptor for dipeptides, is not responsible for detecting pyrimidines. It is not yet known whether Tap detects pyrimidines directly or via an additional chemoreceptor protein.     

Recognition of dominant attractants by key chemoreceptors mediates recruitment of plant growth-promoting rhizobacteria

Chemotaxis to plant root exudates is supposed to be a prerequisite for efficient root colonization by rhizobacteria. This is a highly multifactorial process since root exudates are complex compound mixtures of which components are recognized by different chemoreceptors. Little information is available as to the key components in root exudates and their receptors that drive colonization related chemotaxis. We present here the first global assessment of this issue using the plant growth-promoting rhizobacterium (PGPR) Bacillus velezensis SQR9 (formerly B. amyloliquefaciens). This strain efficiently colonizes cucumber roots, and here, we show that chemotaxis to cucumber root exudates was essential in this process. We conducted chemotaxis assays using cucumber root exudates at different concentrations, individual exudate components as well as recomposed exudates, taking into account their concentrations detected in root exudates. Results indicated that two key chemoreceptors, McpA and McpC, were essential for root exudate chemotaxis and root colonization. Both receptors possess a broad ligand range and recognize most of the exudate key components identified (malic, fumaric, gluconic and glyceric acids, Lys, Ser, Ala and mannose). The remaining six chemoreceptors did not contribute to exudate chemotaxis. This study provides novel insight into the evolution of the chemotaxis system in rhizobacteria.     

Molecular Cloning, Sequencing, and Expression of a Chemoreceptor Gene from Leptospirillum ferrooxidans

We have cloned and sequenced a 2,262-bp chromosomal DNA fragment from the chemolithoautotrophic acidophilic bacterium Leptospirillum ferrooxidans. This DNA contained an open reading frame for a 577-amino-acid protein showing several characteristics of the bacterial chemoreceptors and, therefore, we named this gene lcrI for Leptospirillum chemotaxis receptor I. This is the first sequence reported for a gene from L. ferrooxidans encoding a protein. The lcrI gene showed both ς²⁸-like and ς⁷⁰-like putative promoters. The LcrI deduced protein contained two hydrophobic regions most likely corresponding to the two transmembrane regions present in all of the methyl-accepting chemotaxis proteins (MCPs) which make them fold with both periplasmic and cytoplasmic domains. We have proposed a cytoplasmic domain for LcrI, which also contains the highly conserved domain (HCD region), present in all of the chemotactic receptors, and two probable methylation sites. The in vitro expression of a DNA plasmid containing the 2,262-bp fragment showed the synthesis of a 58-kDa protein which was immunoprecipitated by antibodies against the Tar protein (an MCP from Escherichia coli), confirming some degree of antigenic conservation. In addition, this 58-kDa protein was expressed in E. coli, being associated with its cytoplasmic membrane fraction. It was not possible to determine a chemotactic receptor function for LcrI expressed in E. coli. This was most likely due to the fact that the periplasmic pH of E. coli, which differs by 3 to 4 pH units from that of acidophilic chemolithotrophs, does not allow the right conformation for the LcrI periplasmic domain.     

Chemoreceptor Gene Loss and Acquisition via Horizontal Gene Transfer in Escherichia coli

Chemotaxis allows bacteria to more efficiently colonize optimal microhabitats within their larger environment. Chemotaxis in Escherichia coli is the best-studied model system, and a large number of E. coli strains have been sequenced. The Escherichia/Shigella genus encompasses a great variety of commensal and pathogenic strains, but the role of chemotaxis in their association with the host remains poorly understood. Here we show that the core chemotaxis genes are lost in many, but not all, nonmotile strains but are well preserved in all motile strains. The genes encoding the Tar, Tsr, and Aer chemoreceptors, which mediate chemotaxis to a broad spectrum of chemical and physical cues, are also nearly uniformly conserved in motile strains. In contrast, the clade of extraintestinal pathogenic E. coli strains apparently underwent an ancestral loss of Trg and Tap chemoreceptors, which sense sugars, dipeptides, and pyrimidines. The broad range of time estimated for the loss of these genes (1 to 3 million years ago) corresponds to the appearance of the genus Homo.     

Characterization and reactivity of broiler chicken sera to selected recombinant Campylobacter jejuni chemotactic proteins

Campylobacter jejuni, a Gram-negative rod bacterium, is the leading causative agent of human acute bacterial gastroenteritis worldwide. Consumption and handling of raw or undercooked poultry are regarded as a major source for human infection. Because bacterial chemotaxis guides microorganisms to colonization and invasion in the host cells, proteins involved in chemotactic processes can be novel targets for vaccine development. In this communication, we report amplification, cloning and expression of the C. jejuni chemotactic proteins in an Escherichia coli expression system. A total of 15 chemotactic protein genes were successfully expressed. These recombinant proteins were confirmed by nucleotide sequencing, SDS-PAGE analysis and immunoblot analysis of six-His and hemagglutinin tags. Twelve recombinant chemotactic proteins were further tested whether they were antigenic using sera from broiler chickens older than 4 weeks. The immunoblot results show that each chicken serum reacted to a variety of the recombinant proteins, but all sera reacted to the Cjj0473 gene product (annotated as a methyl-accepting chemotaxis protein), suggesting that anti-Campylobacter antibodies may be prevalent in the poultry population. These antibody screening results provide a rationale for further evaluation of the Cjj0473 protein as a potential vaccine for broilers to improve human food safety.     

Ensifer alkalisoli YIC4027趋化受体基因的比较及相关蛋白序列分析

[目的] 田菁共生根瘤菌Ensifer alkalisoli YIC4027是从宿主植物田菁的根瘤中分离出来的一株新型高效的固氮菌。本研究对E.alkalisoli的趋化受体基因与其他研究透彻的物种进行比较以及相关蛋白分析。[方法] 利用NCBI的BLAST对E.alkalisoli趋化受体基因进行序列相似性搜索。以Pfam数据库为基础,用HMMR3对甲基化趋化受体蛋白（MCP）进行比较分析。[结果] E.alkalisoli有2个趋化基因簇,共有13个MCP,含有不同的信号传感结构。此外,这些MCPs的胞质结构域除了一个是由40个七肽重复序列组成,其余都是由36个七肽重复序列组成。[结论] 尽管E.alkalisoli的趋化受体与已被广泛研究的物种的趋化受体具有较高的相似性,但仍显示出其特性。通过基因的比对以及相关蛋白的分析,我们能够更好地理解E.alkalisoli是如何通过趋化系统来响应外界变化的。     

Correlation between signal input and output in PctA and PctB amino acid chemoreceptor of Pseudomonas aeruginosa

The PctA and PctB chemoreceptors of Pseudomonas aeruginosa mediate chemotaxis toward amino acids. A general feature of signal transduction processes is that a signal input is converted into an output. We have generated chimeras combining the Tar signaling domain with either the PctA or PctB ligand binding domain (LBD). Escherichia coli harboring either PctA‐Tar or PctB‐Tar mediated chemotaxis toward amino acids. The responses of both chimeras were determined using fluorescence resonance energy transfer, and the derived EC₅₀ values are a measure of output. PctA‐Tar and PctB‐Tar responded to 19 and 11 L‐amino acids respectively. The EC₅₀ values of PctA‐Tar responses differed by more than three orders of magnitude, whereas PctB‐Tar responded preferentially to L‐Gln. The comparison of amino acid binding constants and the corresponding EC₅₀ values for both receptors revealed statistically significant correlations between inputs and outputs. PctA and PctB possess a double PDC (PhoQ‐DcuS‐CitA) LBD – a family of binding domain found in various other amino acid chemoreceptors. Similarly, various chemoreceptors share the preferential response to certain amino acids (e.g. L‐Cys, L‐Ser and L‐Thr) that we observed for PctA. Defining the specific inputs and outputs of these chemoreceptors is an important step toward better understanding of their physiological role.     

Opposite responses by different chemoreceptors set a tunable preference point in Escherichia coli pH taxis

In bacterial habitats, the ability to follow spatial gradients of environmental factors that affect growth and survival can be largely advantageous. The bacterial strategy for unidirectional chemotactic movement in gradients of typical attractants or repellents, such as nutrients or toxins, is well understood. Optimal levels of other factors, however, may be found at intermediate points of a gradient and thus require a bidirectional tactic movement towards the optimum. Here we investigate the chemotactic response of Escherichia coli to pH as an example of such bidirectional taxis. We confirm that E. coli uses chemotaxis to avoid both extremes of low and high pH and demonstrate that the sign of the response is inverted from base‐seeking to acid‐seeking at a well‐defined value of pH. Such inversion is enabled by opposing pH sensing by the two major chemoreceptors, Tar and Tsr, such that the relative strength of the response is modulated by adaptive receptor methylation. We further demonstrate that the inversion point of the pH response can be adjusted in response to changes in the cell density.     

Evolutionary Genomics Suggests That CheV Is an Additional Adaptor for Accommodating Specific Chemoreceptors within the Chemotaxis Signaling Complex

Escherichia coli and Salmonella enterica are models for many experiments in molecular biology including chemotaxis, and most of the results obtained with one organism have been generalized to another. While most components of the chemotaxis pathway are strongly conserved between the two species, Salmonella genomes contain some chemoreceptors and an additional protein, CheV, that are not found in E. coli. The role of CheV was examined in distantly related species Bacillus subtilis and Helicobacter pylori, but its role in bacterial chemotaxis is still not well understood. We tested a hypothesis that in enterobacteria CheV functions as an additional adaptor linking the CheA kinase to certain types of chemoreceptors that cannot be effectively accommodated by the universal adaptor CheW. Phylogenetic profiling, genomic context and comparative protein sequence analyses suggested that CheV interacts with specific domains of CheA and chemoreceptors from an orthologous group exemplified by the Salmonella McpC protein. Structural consideration of the conservation patterns suggests that CheV and CheW share the same binding spot on the chemoreceptor structure, but have some affinity bias towards chemoreceptors from different orthologous groups. Finally, published experimental results and data newly obtained via comparative genomics support the idea that CheV functions as a “phosphate sink” possibly to off-set the over-stimulation of the kinase by certain types of chemoreceptors. Overall, our results strongly suggest that CheV is an additional adaptor for accommodating specific chemoreceptors within the chemotaxis signaling complex.     

Chemotactic responses of Rhodobacter sphaeroides in the absence of apparent adaptation

Rhodobacter sphaeroides, which lacks methyl accepting chemotaxis proteins, showed a strong response to gradients of either pyruvate or propionate. If cells were placed in a saturating background of pyruvate they no longer responded to a gradient of propionate but they still responded to potassium or ammonia. This demonstrates that pyruvate saturated the response to another carbon source, but not to other classes of compound. The total movement of cells in a pyruvate background was maintained at a high level relative to a buffer control, indicating an apparent lack of adaptation to saturating pyruvate. The response of R. sphaeroides to a saturating background of pyruvate was weak in cells grown on limiting ammonia although these cells showed a strong response to ammonia. These data suggest that cells show a strong response to the class of compound that currently limits motility. Two hypotheses to explain these results are presented. Firstly, cells show a chemotactic response to a gradient of the limiting compound until saturated by it, they then respond to a gradient of the new compound that has then become limiting. The chemotactic response is the result of a decrease in stopping frequency as cells move up a gradient and an increase as they move down. Secondly, the behavioural response may have two components, a short term chemotactic response and a long term excitation of motility.Abbreviations MCP methyl accepting chemotaxis protein     

Elucidation of the multiple roles of CheD in Bacillus subtilis chemotaxis

Chemotaxis by Bacillus subtilis requires the CheD protein for proper function. In a cheD mutant when McpB was the sole chemoreceptor in B. subtilis, chemotaxis to asparagine was quite good. When McpC was the sole chemoreceptor in a cheD mutant, chemotaxis to proline was very poor. The reason for the difference between the chemoreceptors is because CheD deamidates Q609 in McpC and does not deamidate McpB. When mcpC‐Q609E is expressed as the sole chemoreceptor in a cheD background, chemotaxis is almost fully restored. Concomitantly, in vitro McpC activates the CheA kinase poorly, whereas McpC‐Q609E activates it much more. Moreover, CheD, which activates chemoreceptors, binds better to McpC‐Q609E compared with unmodified McpC. Using hydroxyl radical susceptibility in the presence or absence of CheD, the most likely sites of CheD binding were the modification sites where CheD, CheB and CheR carry out their catalytic activities. Thus, CheD appears to have two separate roles in B. subtilis chemotaxis – to bind to chemoreceptors to activate them as part of the CheC/CheD/CheYp adaptation system and to deamidate selected residues to activate the chemoreceptors and enable them to mediate amino acid chemotaxis.     

Chemoreceptors of Escherichia coli CFT073 Play Redundant Roles in Chemotaxis toward Urine

Community-acquired urinary tract infections (UTIs) are commonly caused by uropathogenic Escherichia coli (UPEC). We hypothesize that chemotaxis toward ligands present in urine could direct UPEC into and up the urinary tract. Wild-type E. coli CFT073 and chemoreceptor mutants with tsr, tar, or aer deletions were tested for chemotaxis toward human urine in the capillary tube assay. Wild-type CFT073 was attracted toward urine, and Tsr and Tar were the chemoreceptors mainly responsible for mediating this response. The individual components of urine including L-amino acids, D-amino acids and various organic compounds were also tested in the capillary assay with wild-type CFT073. Our results indicate that CFT073 is attracted toward some L- amino acids and possibly toward some D-amino acids but not other common compounds found in urine such as urea, creatinine and glucuronic acid. In the murine model of UTI, the loss of any two chemoreceptors did not affect the ability of the bacteria to compete with the wild-type strain. Our data suggest that the presence of any strong attractant and its associated chemoreceptor might be sufficient for colonization of the urinary tract and that amino acids are the main chemoattractants for E. coli strain CFT073 in this niche.     

L‐fucose influences chemotaxis and biofilm formation in Campylobacter jejuni

Campylobacter jejuni and Campylobacter coli are zoonotic pathogens once considered asaccharolytic, but are now known to encode pathways for glucose and fucose uptake/metabolism. For C. jejuni, strains with the fuc locus possess a competitive advantage in animal colonization models. We demonstrate that this locus is present in > 50% of genome‐sequenced strains and is prevalent in livestock‐associated isolates of both species. To better understand how these campylobacters sense nutrient availability, we examined biofilm formation and chemotaxis to fucose. C. jejuni NCTC11168 forms less biofilms in the presence of fucose, although its fucose permease mutant (fucP) shows no change. In a newly developed chemotaxis assay, both wild‐type and the fucP mutant are chemotactic towards fucose. C. jejuni 81‐176 naturally lacks the fuc locus and is unable to swim towards fucose. Transfer of the NCTC11168 locus into 81‐176 activated fucose uptake and chemotaxis. Fucose chemotaxis also correlated with possession of the pathway for C. jejuni RM1221 (fuc+) and 81116 (fuc‐). Systematic mutation of the NCTC11168 locus revealed that Cj0485 is necessary for fucose metabolism and chemotaxis. This study suggests that components for fucose chemotaxis are encoded within the fuc locus, but downstream signals only in fuc + strains, are involved in coordinating fucose availability with biofilm development.     

Analysis of a chemotaxis operon in Rhizobium meliloti*

Genes controlling chemotaxis towards L-amino acids and d -mannitol in Rhizobium meliloti have been identified by Tn5 insertions that lead to chemotaxis-deficient mutants. The tagged genes span an 8.7 kbp region that has been sequenced. These genes are part of a large operon containing three novel open reading frames, orf1, orf2 and orf9, and six familiar chemotaxis (che) genes, cheY1-cheA-cheW-cheR-cheB-cheY2, that have been assigned by their similarity to known Escherichia coli genes. The second copy of cheY may be part of a second signalling chain; orf1 and orf2 encode sequence motifs that resemble the signalling domain of E. coli MCPs (methyl-accepting chemotaxis proteins), while the product of orf9 may contain a transmembrane domain. No protein methylation has been observed in Rhizobium meliloti in response to l -amino acids. However, the presence of cheR (methyltransferase gene) and cheB (methyl-esterase gene) suggested that MCPs are likely components of the chemotactic response in R. meliloti. Therefore, it is postulated that two chemotaxis pathways are functional in R meliloti: one responds to l -amino acids via ORF1-ORF2, whereas the other (probably responding to specific plant exudates) acts via MCP-like receptors, and both interact with the central components CheW-CheA-CheY1 and/or CheY2.     

阿拉伯海假交替单胞菌N1230-9两个甲基受体趋化蛋白的功能鉴定

【目的】作为海洋中的特有及优势种群,假交替单胞菌(Pseudoalteromonas)普遍拥有多个甲基受体趋化蛋白(methyl-accepting chemotaxis protein, MCP),探究这些趋化受体的功能。【方法】以太平洋表层海水来源的一株阿拉伯海假交替单胞菌(Pseudoalteromonas arabiensis) N1230-9为研究对象,利用软琼脂平板法测试该菌株对23种碳源的趋化能力,继而利用同源重组策略构建2个含sCache结构域MCP编码基因(woc28264和woc27036)缺失突变体,并分析突变体对10种碳源的趋化能力。【结果】菌株N1230-9对海藻糖、麦芽糖、蔗糖、N-乙酰氨基葡萄糖、l-苹果酸、乙酸钠、丙酸钠、丙酮酸钠、柠檬酸和琥珀酸10种碳源具有趋化能力。WOC28264是l-苹果酸和蔗糖的特异性趋化受体,WOC27036则是柠檬酸和琥珀酸的特异性趋化受体。此外,WOC28264和WOC27036还均是N-乙酰氨基葡萄糖和海藻糖的趋化受体。【结论】WOC28264和WOC27036存在重叠的碳源效应物。     

Polar localization of Escherichia coli chemoreceptors requires an intact Tol–Pal complex

Subcellular biomolecular localization is critical for the metabolic and structural properties of the cell. The functional implications of the spatiotemporal distribution of protein complexes during the bacterial cell cycle have long been acknowledged; however, the molecular mechanisms for generating and maintaining their dynamic localization in bacteria are not completely understood. Here we demonstrate that the trans‐envelope Tol–Pal complex, a widely conserved component of the cell envelope of Gram‐negative bacteria, is required to maintain the polar positioning of chemoreceptor clusters in Escherichia coli. Localization of the chemoreceptors was independent of phospholipid composition of the membrane and the curvature of the cell wall. Instead, our data indicate that chemoreceptors interact with components of the Tol–Pal complex and that this interaction is required to polarly localize chemoreceptor clusters. We found that disruption of the Tol–Pal complex perturbs the polar localization of chemoreceptors, alters cell motility, and affects chemotaxis. We propose that the E. coli Tol–Pal complex restricts mobility of the chemoreceptor clusters at the cell poles and may be involved in regulatory mechanisms that co‐ordinate cell division and segregation of the chemosensory machinery.     

Two CheW coupling proteins are essential in a chemosensory pathway of Borrelia burgdorferi

In the model organism Escherichia coli, the coupling protein CheW, which bridges the chemoreceptors and histidine kinase CheA, is essential for chemotaxis. Unlike the situation in E. coli, Borrelia burgdorferi, the causative agent of Lyme disease, has three cheW homologues (cheW₁, cheW₂ and cheW₃). Here, a comprehensive approach is utilized to investigate the roles of the three cheWs in chemotaxis of B. burgdorferi. First, genetic studies indicated that both the cheW₁ and cheW₃ genes are essential for chemotaxis, as the mutants had altered swimming behaviours and were non‐chemotactic. Second, immunofluorescence and cryo‐electron tomography studies suggested that both CheW₁ and CheW₃ are involved in the assembly of chemoreceptor arrays at the cell poles. In contrast to cheW₁ and cheW₃, cheW₂ is dispensable for chemotaxis and assembly of the chemoreceptor arrays. Finally, immunoprecipitation studies demonstrated that the three CheWs interact with different CheAs: CheW₁ and CheW₃ interact with CheA₂ whereas CheW₂ binds to CheA₁. Collectively, our results indicate that CheW₁ and CheW₃ are incorporated into one chemosensory pathway that is essential for B. burgdorferi chemotaxis. Although many bacteria have more than one homologue of CheW, to our knowledge, this report provides the first experimental evidence that two CheW proteins coexist in one chemosensory pathway and that both are essential for chemotaxis.