Chemotaxis toward sugars in Escherichia coli

Using a quantitative assay for measuring chemotaxis, we tested a variety of sugars and sugar derivatives for their ability to attract Escherichia coli bacteria. The most effective attractants, i.e., those that have thresholds near 10(-5) M or below, are N-acetyl-d-glucosamine, 6-deoxy-d-glucose, d-fructose, d-fucose, 1-d-glycerol-beta-d-galactoside, galactitol, d-galactose, d-glucosamine, d-glucose, alpha-d-glucose-1-phosphate, lactose, maltose, d-mannitol, d-mannose, methyl-beta-d-galactoside, methyl-beta-d-glucoside, d-ribose, d-sorbitol, and trehalose. Lactose, and probably d-glucose-1-phosphate, are attractive only after conversion to the free monosaccharide, while the other attractants do not require breakdown for taxis. Nine different chemoreceptors are involved in detecting these various attractants. They are called the N-acetyl-glucosamine, fructose, galactose, glucose, maltose, mannitol, ribose, sorbitol, and trehalose chemoreceptors; the specificity of each was studied. The chemoreceptors, with the exception of the one for d-glucose, are inducible. The galactose-binding protein serves as the recognition component of the galactose chemoreceptor. E. coli also has osmotically shockable binding activities for maltose and d-ribose, and these appear to serve as the recognition components for the corresponding chemoreceptors.     

Chemotaxis for methamphetamine in Escherichia coli

Escherichia coli showed the chemotactic response for methamphetamine, a biogenic stimulative amine. The response was qualitatively detected by using a paper disk filter. The quantitative assay showed that E. coli responded to methamphetamine at 10(-5) M or more.     

Imprecision of Adaptation in Escherichia coli Chemotaxis

Adaptability is an essential property of many sensory systems, enabling maintenance of a sensitive response over a range of background stimulus levels. In bacterial chemotaxis, adaptation to the preset level of pathway activity is achieved through an integral feedback mechanism based on activity-dependent methylation of chemoreceptors. It has been argued that this architecture ensures precise and robust adaptation regardless of the ambient ligand concentration, making perfect adaptation a celebrated property of the chemotaxis system. However, possible deviations from such ideal adaptive behavior and its consequences for chemotaxis have not been explored in detail. Here we show that the chemotaxis pathway in Escherichia coli shows increasingly imprecise adaptation to higher concentrations of attractants, with a clear correlation between the time of adaptation to a step-like stimulus and the extent of imprecision. Our analysis suggests that this imprecision results from a gradual saturation of receptor methylation sites at high levels of stimulation, which prevents full recovery of the pathway activity by violating the conditions required for precise adaptation. We further use computer simulations to show that limited imprecision of adaptation has little effect on the rate of chemotactic drift of a bacterial population in gradients, but hinders precise accumulation at the peak of the gradient. Finally, we show that for two major chemoeffectors, serine and cysteine, failure of adaptation at concentrations above 1 mM might prevent bacteria from accumulating at toxic concentrations of these amino acids.     

Chemotaxis toward amino acids in Escherichia coli

Escherichia coli cells are shown to be attracted to the l-amino acids alanine, asparagine, aspartate, cysteine, glutamate, glycine, methionine, serine, and threonine, but not to arginine, cystine, glutamine, histidine, isoleucine, leucine, lysine, phenylalanine, tryptophan, tyrosine, or valine. Bacteria grown in a proline-containing medium were, in addition, attracted to proline. Chemotaxis toward amino acids is shown to be mediated by at least two detection systems, the aspartate and serine chemoreceptors. The aspartate chemoreceptor was nonfunctional in the aspartate taxis mutant, which showed virtually no chemotaxis toward aspartate, glutamate, or methionine, and reduced taxis toward alanine, asparagine, cysteine, glycine, and serine. The serine chemoreceptor was nonfunctional in the serine taxis mutant, which was defective in taxis toward alanine, asparagine, cysteine, glycine, and serine, and which showed no chemotaxis toward threonine. Additional data concerning the specificities of the amino acid chemoreceptors with regard to amino acid analogues are also presented. Finally, two essentially nonoxidizable amino acid analogues, alpha-aminoisobutyrate and alpha-methylaspartate, are shown to be attractants for E. coli, demonstrating that extensive metabolism of attractants is not required for amino acid taxis.     

HAPLOFREQ--estimating haplotype frequencies efficiently.

A commonly used tool in disease association studies is the search for discrepancies between the haplotype distribution in the case and control populations. In order to find this discrepancy, the haplotypes frequency in each of the populations is estimated from the genotypes. We present a new method HAPLOFREQ to estimate haplotype frequencies over a short genomic region given the genotypes or haplotypes with missing data or sequencing errors. Our approach incorporates a maximum likelihood model based on a simple random generative model which assumes that the genotypes are independently sampled from the population. We first show that if the phased haplotypes are given, possibly with missing data, we can estimate the frequency of the haplotypes in the population by finding the global optimum of the likelihood function in polynomial time. If the haplotypes are not phased, finding the maximum value of the likelihood function is NP-hard. In this case, we define an alternative likelihood function which can be thought of as a relaxed likelihood function. We show that the maximum relaxed likelihood can be found in polynomial time and that the optimal solution of the relaxed likelihood approaches asymptotically to the haplotype frequencies in the population. In contrast to previous approaches, our algorithms are guaranteed to converge in polynomial time to a global maximum of the different likelihood functions. We compared the performance of our algorithm to the widely used program PHASE, and we found that our estimates are at least 10% more accurate than PHASE and about ten times faster than PHASE. Our techniques involve new algorithms in convex optimization. These algorithms may be of independent interest. Particularly, they may be helpful in other maximum likelihood problems arising from survey sampling.     

Chemotaxis in Escherichia coli: associations of protein components

Interactions between protein components of the chemotaxis mechanism in Escherichia coli were investigated by using the cleavable cross-linking reagent, dithiobis(succinimidyl propionate). Two methods were used to allow detection of chemotaxis-specific proteins in intact cells. The first method was to program their synthesis in the presence of [35S]methionine using lambda E. coli hybrid phages which carry the chemotaxis genes. The second method was to label endogenous methyl-accepting chemotaxis proteins (MCP's), with the methyl donor S-adenosyl-L-[methyl-3H]methionine, after permeabilizing the cells with EGTA. Physical associations between proteins were analyzed, after cross-linking, by two dimensional NaDodSO4-polyacrylamide gel electrophoresis. Both labeling methods demonstrate that MCP I and MCP II exist as functional tetramers. Other proteins involved with chemotaxis were found to form dimers and higher polymers. Phage-directed products of cheW, cheX, motA, and cheA formed dimers. CheB and hag products formed multimers. A number of apparent interactions between different gene products were detected as well. Products of cheB, cheW, cheZ, motA, and motB were found to form complexes with other gene products. Included are results consistent with interactions between the products of cheB and cheZ.     

Importance of Multiple Methylation Sites in Escherichia coli Chemotaxis

Bacteria navigate within inhomogeneous environments by temporally comparing concentrations of chemoeffectors over the course of a few seconds and biasing their rate of reorientations accordingly, thereby drifting towards more favorable conditions. This navigation requires a short-term memory achieved through the sequential methylations and demethylations of several specific glutamate residues on the chemotaxis receptors, which progressively adjusts the receptors’ activity to track the levels of stimulation encountered by the cell with a delay. Such adaptation also tunes the receptors’ sensitivity according to the background ligand concentration, enabling the cells to respond to fractional rather than absolute concentration changes, i.e. to perform logarithmic sensing. Despite the adaptation system being principally well understood, the need for a specific number of methylation sites remains relatively unclear. Here we systematically substituted the four glutamate residues of the Tar receptor of Escherichia coli by non-methylated alanine, creating a set of 16 modified receptors with a varying number of available methylation sites and explored the effect of these substitutions on the performance of the chemotaxis system. Alanine substitutions were found to desensitize the receptors, similarly but to a lesser extent than glutamate methylation, and to affect the methylation and demethylation rates of the remaining sites in a site-specific manner. Each substitution reduces the dynamic range of chemotaxis, by one order of magnitude on average. The substitution of up to two sites could be partly compensated by the adaptation system, but the full set of methylation sites was necessary to achieve efficient logarithmic sensing.     

Effects of p-Fluorophenylalanine and Chloramphenicol on Chemotaxis in Escherichia coli

The effects of chloramphenicol and p-fluorophenylalanine (p-FPA) on growth, proportion of motile cells, average rate of motility, and the chemotactic response of a methionine auxotroph of Escherichia coli K-12 were studied. Kinetic studies revealed that the inhibition of chemotaxis by p-FPA can be explained by the effect on growth, proportion of motile cells, and average rate of motility rather than a selective inhibition of chemotaxis per se. The effect of chloramphenicol on chemotaxis could not be explained in terms of these characteristics. It is concluded that low concentrations of chloramphenicol, unlike p-FPA, selectively inhibit chemotaxis.     

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.     

Chemotaxis and cyclic-di-GMP signalling control surface attachment of Escherichia coli

Attachment to surfaces is an important early step during bacterial infection and during formation of submerged biofilms. Although flagella-mediated motility is known to be important for attachment of Escherichia coli and other bacteria, implications of motility regulation by cellular signalling remain to be understood. Here, we show that motility largely promotes attachment of E. coli, including that mediated by type 1 fimbriae, by allowing cells to reach, get hydrodynamically trapped at and explore the surface. Inactivation or inhibition of the chemotaxis signalling pathway improves attachment by suppressing cell reorientations and thereby increasing surface residence times. The attachment is further enhanced by deletion of genes encoding the cyclic diguanosine monophosphate (c-di-GMP)-dependent flagellar brake YcgR or the diguanylate cyclase DgcE. Such increased attachment in absence of c-di-GMP signalling is in contrast to its commonly accepted function as a positive regulator of the sessile state. It is apparently due to the increased swimming speed of E. coli in absence of YcgR-mediated motor control, which strengthens adhesion mediated by the type 1 fimbriae. Thus, both signalling networks that regulate motility of E. coli also control its engagement with both biotic and abiotic surfaces, which has likely implications for infection and biofilm formation.     

R-plasmid transfer frequencies from environmental isolates of Escherichia coli to laboratory and fecal strains.

Multiple-drug-resistant strains of Escherichia coli were isolated from the water at an estuarine site. They represented about 8.3% of the total E. coli population. Fifty-five strains, representing each of the 32 resistance patterns identified, were mated with an E. coli K-12 F- strain. Matings were performed on membrane filters, and the cells were washed to remove any colicins produced by the donors. Thirty-one strains, about 5% of the mean E. coli density in the samples, transferred drug resistance and, hence, posessed conjugative R plasmids. Of these, 80% transferred drug resistance at a frequency of about 10(-4) or less. Nine environmental R+ strains were mated with three fecal recipients. The R-plasmid transfer frequencies to the fecal strains from the environmental donors correlated well with those from a derepressed K-12 R+ laboratory donor. The R+ X K-12 F- lac- transconjugants from 16 environmental strains were "backcrossed" to a lac+ K-12 F- strain. All transfer frequencies were higher in the backcrosses than in the original matings from the environmental donor. Furthermore, 7 of 13 different transconjugants, which accepted plasmids at repressed frequencies of less than 10(-3), donated them at frequencies greater than 10(-2). This suggests that these were derepressed plasmids in a repressed host.     

Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation

The chemotaxis system in the bacterium Escherichia coli is remarkably sensitive to small relative changes in the concentrations of multiple chemical signals over a broad range of ambient concentrations. Interactions among receptors are crucial to this sensitivity as is precise adaptation, the return of chemoreceptor activity to prestimulus levels in a constant chemoeffector environment. Precise adaptation relies on methylation and demethylation of chemoreceptors by the enzymes CheR and CheB, respectively. Experiments indicate that when transiently bound to one receptor, these enzymes act on small assistance neighborhoods (AN) of five to seven receptor homodimers. In this paper, we model a strongly coupled complex of receptors including dynamic CheR and CheB acting on ANs. The model yields sensitive response and precise adaptation over several orders of magnitude of attractant concentrations and accounts for different responses to aspartate and serine. Within the model, we explore how the precision of adaptation is limited by small AN size as well as by CheR and CheB kinetics (including dwell times, saturation, and kinetic differences among modification sites) and how these kinetics contribute to noise in complex activity. The robustness of our dynamic model for precise adaptation is demonstrated by randomly varying biochemical parameters.     

Novel Mutations Affecting a Signaling Component for Chemotaxis of Escherichia coli

The genetic relationship between tsr and cheD mutations, which affect chemotactic ability and map at approximately 99 min on the Escherichia coli chromosome, was investigated. Mutants defective in tsr function typically exhibited wild-type swimming patterns, but were unable to carry out chemotactic responses to a number of attractant and repellent chemicals. In contrast, cheD mutants swam smoothly, with few spontaneous directional changes, and were generally nonchemotactic. In complementation tests, cheD mutations, unlike tsr, proved to be dominant to wild type, suggesting that the cheD defect might be due to an active inhibitor of chemotaxis. Mutations that inactivated the putative inhibitor were obtained by selecting for restoration of chemotactic ability or for loss of cheD dominance. The resultant double mutants were shown to carry the original cheD mutation and a second tightly linked mutation, some of which exhibited nonsense or temperature-sensitive phenotypes, implying that they had occurred in a structural gene for a protein. All such double mutants behaved like typical tsr mutants in all other respects, including complementation pattern, swimming behavior, and chemotactic ability. These findings implied that either overproduction of tsr product or synthesis of an aberrant tsr product was responsible for the chemotaxis defect of cheD strains. Such mutants should be useful in analyzing the role of the tsr product in chemotactic responses.     

不同来源标本中大肠埃希菌耐药率的比较分析

目的研究不同标本来源中大肠埃希菌的耐药谱,为临床用药提供治疗参考。方法对温州医学院附属第二医院2010年1月到12月患者送检的体液标本进行培养,用microcsan walkaway 96S微生物自动鉴定仪对菌种鉴定及药敏分析,结果用2分割法进行统计分析。结果分离出大肠埃希菌597株,其中痰液、脓液、血液、分泌物、引流液中分别分离出295、148、102、37、15株。所有分离株均对亚胺培南敏感,对氨苄西林、哌拉西林的耐药率最高。痰液分离株对氨曲南、氨苄西林、氨苄西林/舒巴坦、哌拉西林、妥布霉素及所有头孢类的耐药率显著高于血液分离株的耐药率(P<0.05);痰液分离株对氨曲南、氨苄西林/舒巴坦、除头孢他啶外的所有头孢类的耐药率显著高于脓液分离株的耐药率(P<0.05);脓液分离株对氨苄西林、哌拉西林、妥布霉素的耐药率明显高于血液分离株的耐药率(P<0.05)。痰液中ESBLs阳性率显著高于血液和脓液中ESBLs阳性率。产ESBLs的大肠埃希菌共316株,所占的比例为52.9%;痰液分离的ESBLs阳性株对四环素、环丙沙星、加替沙星、左氧氟沙星、甲氧苄啶/磺胺呷恶唑、阿米卡星的耐药率显著低于脓液分离株的耐药率(P<0.05)。结论痰液分离的大肠埃希菌对β-内酰胺类抗生素的耐药率普遍高于脓液和血液分离株的耐药率,同时认识到该院抗生素的耐药现象很严重,临床上更加合理的使用抗菌药物。     

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.     

Comparison of the flagellins from different flagellar morphotypes of Escherichia coli.

The molecular weights of the flagellins of 13 strains of Escherichia coli, each with a different H antigen, were estimated using polyacrylamide gel electrophoresis. In each case only one major polypeptide was demonstrated, although some strains possessed apparently sheathed flagella. Considerable differences in the molecular weight of flagellin accompanied the previously described structural differences between flagella from strains with different H antigens. The relationship between flagellar diameter and the molecular weight of the corresponding flagellins was similar for both unsheathed and apparently sheathed flagella. Crosss-polymerization occurred between seed consisting of fragment of unsheathed flagella and flagellin solution from apparently sheathed flagella and vice versa. Co-polymerization of flagellin from unsheathed flagella and flagellin from apparently sheathed flagella was also demonstrated. These polymerization experiments indicate that the assembly pattern of flagellin molecules is probably the same in all E. coli flagella. The above and other evidence suggests that there is no true sheath, but that the differences in flagellar surface structure between different E. coli flagella are the result of differences in the superficial parts of the flagellin molecules.