Effect of polymyxin B on liposomal membranes derived from Escherichia coli lipids.

The specificity of the action of polymyxin B was studied using liposomes as a model membrane system. Liposomes prepared from total lipids of Gram-negative bacteria Escherichia coli, a mixture of purified E. coli phosphatidylethanolamine and cardiolipin and a mixture of phosphatidylethanolamine and phosphatidylglycerol, were extemely sensitive to polymyxin while those prepared from lipids of Gram-positive bacteria Streptococcus sanguis, lipids of sheep erythrocyte membranes, mixtures of egg lecithin and negatively charged amphiphatic molecules, were less sensitive to the action of the antibiotic. Cholesterol was shown to suppress the polymyxin-induced response in liposomes.     

Lateral phase separations in Escherichia coli membranes

Membranes from unsaturated fatty acid auxotrophs of Escherichia coli were studied by spin labeling and freeze-fracturing. From measurements of the partition of the spin label TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl) between the aqueous phase and fluid lipids in isolated membranes, temperatures, corresponding to the onset and completion of a lateral phase separation of the membrane phospholipids were determined. By freeze-fracture electron microscopy a change in the distribution of particle in the membrane was observed around the temperature of the onset of the lateral phase separation. When cells were frozen from above that temperature a netlike distribution of particles in the plasma membrane was observed for unfixed preparations. When frozen after fixing with glutaraldehyde the particle distribution was random. In membranes of cells frozen with or without fixing from a temperature below the onset of the phase separation, the particles were aggregated and large areas void of particles were present. This behavior can be understood in terms of the freezing rate with the aid of phase diagrams.     

Isolation of detergent-resistant membranes (DRMs) from Escherichia coli

Lipid rafts or membrane microdomains have been proposed to compartmentalize cellular processes by spatially organizing diverse molecules/proteins in eukaryotic cells. Such membrane microdomains were recently reported to also exist in a few bacterial species. In this work, we report the development of a procedure for membrane microdomain isolation from Escherichia coli plasma membranes as well as a method to purify the latter. The method here reported could easily be adapted to other gram-negative bacteria, wherein the isolation of this kind of sub-membrane preparation imposes special difficulties. The analysis of isolated membrane microdomains might provide important information on the nature and function of these bacterial structures and permit their comparison with the ones of eukaryotic cells.     

Isolation and identification of 5-methylthioribose from Escherichia coli B

5-Methylthioribose was isolated after incubation of Escherichia coli B in a glucose-salts medium. At least 60% of the radioactivity in absolute ethanol extracts of the residue from lyophilized medium supplemented with ³⁵SO₄²⁻ was located in two chromatographic areas that were identified as 5-methylthioribose and its sulfoxide. The sulfoxide was formed by oxidation of 5-methylthioribose during necessary processing of cultures and fractions. These compounds were characterized by functional group analysis and chromatographic comparison with authentic material. 5-Methylthioribose sulfoxide was isolated from 12 l of incubation medium of E. coli. After purification in three paper and one thin-layer chromatographic systems, 50 μg was obtained. The trimethylsilyl derivative of this compound was compared with that of authentic 5-methylthioribose sulfoxide. Gas chromatography and mass spectrometry confirmed the identity. This is the first report of 5-methylthioribose from a bacterium.     

Infrared spectra of outer and cytoplasmic membranes of Escherichia coli

Outer and cytoplasmic membranes of Escherichia coli were prepared by a method based on isopyenic centrifugation on a sucrose gradient. The infrared spectra of solid films of these membranes were studied. The cytoplasmic membrane had an amide I band at 1657 cm^?1 and an amide II band at 1548 cm^?1. The outer membrane had a broad amide I band at 1631–1657 cm^?1 and an amid II band at 1548 cm^?1 with a shoulder at 1520–1530 cm^?1. Upon deuteration, the amide I band of the cytoplasmic membrane shifted to 1648 cm^?1, whereas the band at 1631 cm^?1 of the outer membrane remained unchanged. After extraction of lipids with chloroform and methanol, the infrared spectra in the amide I and amide II regions of both membranes remained unchanged. Although the outer membrane specifically contained lipopolysaccharide, this could not account for the difference in the infrared spectra of outer and cytoplasmic membranes. It is concluded that a large portion of proteins in the outer membrane is a β-structured polypeptide, while this conformation is found less, if at all in the cytoplasmic membrane.     

Lipid phase transitions in cytoplasmic and outer membranes of Escherichia coli

The cytoplasmic and outer membranes containing either trans-Δ⁹-octadecenoate, trans-Δ⁹-hexadecenoate or cis-Δ⁹-octadecenoate as predominant unsaturated fatty acid residues in the phospholipids were prepared from a fatty acid auxotroph, Escherichia coli strain K1062. Order-disorder transitions of the phospholipids were revealed in both fractions of the cell envelope by fluorescent probing or wide angle X-ray diffraction. The mid-transition temperatures, $\text{T}\text{t}$, and the range of the transition, $\text{ΔT}$, are similar in the outer and cytoplasmic membrane. Relative to the corresponding extracted lipids, 60–80% of the hydrocarbon chains take part in the transition in the cytoplasmic membrane whereas in the outer membrane only 25–40% of the chains become ordered. The results suggest that in the outer membrane part of the lipids form fluid domains in the form of mono- and/or bilayers.     

Effect of procaine hydrochloride on DNA repair in Escherichia coli

Liquid-holding recovery and rejoining of γ-radiation-induced DNA singlestrand scissions in Escherichia coli could be effectively inhibited by procaine hydrochloride at the concentration of 20 m M. At this concentration, the drug also reversibly altered cellular permeability barrier as evidenced from the uptake of acriflavin by bacterial cells.     

Nucleotide regulation of phosphoenolpyruvate carboxylase from Escherichia coli

Adenine, cytosine, guanine, and uracil nucleotides were surveyed as possible modulators of Escherichia coli phosphoenolpyruvate carboxylase. CMP, CDP, CTP, GDP, and GTP activate, ATP and GMP inhibit. The other nucleotides are without effect. Nucleotide activation is synergistic with acetyl-CoA or laurate. Cytosine nucleotide activation is also synergistic with fructose 1,6-diphosphate, whereas guanine nucleotide activation is not. The pH profiles for CMP and GDP activation, studied individually between pH 7.0 and 9.0, are similar to those for activation by fructose 1,6-diphosphate. ATP inhibits activation by acetyl-CoA, laurate, or fructose 1,6-diphosphate. Pairs of activators synergistically relieve the inhibition. Acetyl-CoA with laurate is most effective. Energy charge profiles suggest little sensitivity to charge fluctuation near 0.8. Ribose 5-phosphate also inhibits activation by acetyl-CoA, laurate, or fructose 1,6-diphosphate. GMP selectively inhibits fructose 1,6-diphosphate activation.     

Crystal structure of D-serine dehydratase from Escherichia coli

D-Serine dehydratase from Escherichia coli is a member of the β-family (fold-type II) of the pyridoxal 5′-phosphate-dependent enzymes, catalyzing the conversion of D-serine to pyruvate and ammonia. The crystal structure of monomeric D-serine dehydratase has been solved to 1.97 Å-resolution for an orthorhombic data set by molecular replacement. In addition, the structure was refined in a monoclinic data set to 1.55 Å resolution. The structure of DSD reveals a larger pyridoxal 5′-phosphate-binding domain and a smaller domain. The active site of DSD is very similar to those of the other members of the β-family. Lys118 forms the Schiff base to PLP, the cofactor phosphate group is liganded to a tetraglycine cluster Gly279-Gly283, and the 3-hydroxyl group of PLP is liganded to Asn170 and N1 to Thr424, respectively. In the closed conformation the movement of the small domain blocks the entrance to active site of DSD. The domain movement plays an important role in the formation of the substrate recognition site and the catalysis of the enzyme. Modeling of D-serine into the active site of DSD suggests that the hydroxyl group of D-serine is coordinated to the carboxyl group of Asp238. The carboxyl oxygen of D-serine is coordinated to the hydroxyl group of Ser167 and the amide group of Leu171 (O1), whereas the O2 of the carboxyl group of D-serine is hydrogen-bonded to the hydroxyl group of Ser167 and the amide group of Thr168. A catalytic mechanism very similar to that proposed for L-serine dehydratase is discussed.     

Crystal Structure of Metal-Dependent Allantoinase from Escherichia coli

Allantoinase acts as a key enzyme for the biogenesis and degradation of ureides by catalyzing the conversion of (S)-allantoin into allantoate, the final step in the ureide pathway. Despite limited sequence similarity, biochemical studies of the enzyme suggested that allantoinase belongs to the amidohydrolase family. In this study, the crystal structure of allantoinase from Escherichia coli was determined at 2.1 Å resolution. The enzyme consists of a homotetramer in which each monomer contains two domains: a pseudo-triosephosphate-isomerase barrel and a β-sheet. Analogous to other enzymes in the amidohydrolase family, allantoinase retains a binuclear metal center in the active site, embedded within the barrel fold. Structural analyses demonstrated that the metal ions in the active site ligate one hydroxide and six residues that are conserved among allantoinases from other organisms. Functional analyses showed that the presence of zinc in the metal center is essential for catalysis and enantioselectivity of substrate. Both the metal center and active site residues Asn94 and Ser317 play crucial roles in dictating enzyme activity. These structural and functional features are distinctively different from those of the metal-independent allantoinase, which was very recently identified.     

Phosphate transport in membrane vesicles from Escherichia coli

Escherichia coli strain AN710 possesses only the PIT system for phosphate transport. Membrane vesicles from this strain, which contain phosphate internally, perform exchange and active transport of phosphate. The energy for active transport is supplied by the respiratory chain with ascorbate-phenazine methosulphate as electron donor. To a lesser extent also the oxidation of d-lactate energizes phosphate transport; the oxidation of succinate is only marginally effective. Phosphate transport is driven by the proton-motive force and in particular by the pH gradient across the membrane. This view is supported by the observation that phosphate transport is stimulated by valinomycin, inhibited by nigericin and abolished by the uncoupler carbonyl cyanide m-chlorophenylhydrazone. Neither inhibitor affects phosphate exchange. The phosphate analogue arsenate inhibits both the exchange reaction and active transport. Both processes are stimulated by K⁺ and Mg²⁺, the highest activities being observed with both ions present.Membrane vesicles have also been isolated from Escherichia coli K10, a strain which possesses only a functional PST phosphate transport system. These vesicles perform neither exchange nor active transport of phosphate, although active transport of amino acids is observed in the presence of ascorbate-phenazine methosulphate or d-lactate.     

The binding of lipopolysaccharide from Escherichia coli to mammalian cell membranes and its effect on liposomes

The kinetics of the absorption of ³²P- or ¹⁴C-labelled lipopolysaccharide from Escherichia coli NCTC 8623, serotype 0 125, chemotype XII, to erythrocytes, leukocytes, peritoneal macrophages and peritoneal lymphocytes was examined. Under variable conditions maximal levels of binding were found due to saturation of receptor sites on the cell membrane or steric hindrance by bound lipopolysaccharide. During adsorption slight leakage of haemoglobin was found but complete lysis of erythrocytes was ruled out after noting the effect of lipopolysaccharide on artificial lipid bilayers.The affinity of lipopolysaccharide to cell membranes revealed a consistent pattern of cyclic fluctuation between adsorption and desorption. A model was proposed to explain this cyclic fluctuation in binding based on membrane reorganization. It was significant that the cycle of lipopolysaccharide adsorption-desorption proceeded to completion even if the process was interrupted. The indication was that, once triggered, membrane reorganization occurred independently without influence from the test environment.     

The purification of methionine sulfoxide reductase from Escherichia coli

A sensitive assay, based on the acylation of tRNA^Met, has been developed to measure the enzymatic reduction of methionine sulfoxide to methionine. Using this assay, methionine sulfoxide reductase has been purified to near homogeneity from extracts of Escherichia coli.     

Crystal structure of non-redox regulated SSADH from Escherichia coli

SSADH is involved in the final step of GABA degradation, converting SSA to succinic acid in the human mitochondrial matrix, and its activity is known to be regulated via ‘redox-switch modulation’ of the catalytic loop. We present the crystal structure of EcSSADH, revealing that the catalytic loop of EcSSADH, unlike that of human SSADH, does not undergo disulfide bond-mediated structural changes upon changes of environmental redox status. Subsequent redox change experiments using recombinant proteins confirm the non-redox regulation of this protein. Detailed structural analysis shows that a difference in the conformation of the connecting loop (β15-β16) causes the formation of a water molecule-mediated hydrogen bond network between the connecting loop and the catalytic loop in EcSSADH, making the catalytic loop of EcSSADH more rigid compared to that of human SSADH. The cytosolic localization of EcSSADH and the cellular function of the GABA shunt in E. coli might result in the non-redox mediated regulatory mechanisms of the protein.     

Rapid purification of highly active ribosomes from Escherichia coli

Highly active salt-washed ribosomes from Escherichia coli are isolated by gel filtration on Sephacryl S-200 in a buffer containing 1 m ammonium chloride and putrescine, spermidine, calcium, and magnesium ions. Up to several hundred grams of cells can be processed in less than 24 h. The ribosome solution made 30% (v/v) in methanol is best stored as a liquid at ?20°C. An improved poly(U)-dependent peptide synthesis assay is described in which phenylalanine polymerization is greatly enhanced while the misincorporation of leucine is kept at in vivo levels.     

ATP-binding cassette transporters in Escherichia coli

ATP-binding cassette (ABC) transporters are integral membrane proteins that actively transport molecules across cell membranes. In Escherichia coli they consist primarily of import systems that involve in addition to the ABC transporter itself a substrate binding protein and outer membrane receptors or porins, and a number of transporters with varied functions. Recent crystal structures of a number of ATPase domains, substrate binding proteins, and full-length transporters have given new insight in the molecular basis of transport. Bioinformatics approaches allow an approximate identification of all ABC transporters in E. coli and their relation to other known transporters. Computational approaches involving modeling and simulation are beginning to yield insight into the dynamics of the transporters. We summarize the function of the known ABC transporters in E. coli and mechanistic insights from structural and computational studies.     

Unidirectional replication in Escherichia coli of three small plasmids derived from R factor R12

Replicating molecules of three small plasmids, pSM1, pSM2, and pSM3, were isolated from a CsCl density gradient containing ethidium bromide. These plasmids are all derived from R12, a mutant of NR1 (same as R100). By means of pulse-labeling experiments, the replicating forms were located at buoyant densities intermediate between those of the closed circular and open circular DNA bands. These molecules were analyzed by electron microscopy following digestion with restriction endonucleases. Digestion of pSM2 with EcoR1 and with HindIII revealed the presence of a single origin of replication located 1.72 kilobases (kb) from the EcoR1 cutting site (2.04 kb from the HindIII cutting site). These experiments also demonstrated that replication occurs in a unidirectional mode from the origin. Analysis of EcoR1-cleaved replicating molecules of pSM1 and pSM3, which carry common sequences completely or partly homologous to pSM2, provides further evidence for the unidirectional replication of these plasmids from a common origin. The site of the origin of replication was fixed at 85.5 on the kilobase map of R100. This origin, which is located in the RTF region, probably corresponds to one of the replication origins of R100.     

Genome-scale genetic engineering in Escherichia coli

Genome engineering has been developed to create useful strains for biological studies and industrial uses. However, a continuous challenge remained in the field: technical limitations in high-throughput screening and precise manipulation of strains. Today, technical improvements have made genome engineering more rapid and efficient. This review introduces recent advances in genome engineering technologies applied to Escherichia coli as well as multiplex automated genome engineering (MAGE), a recent technique proposed as a powerful toolkit due to its straightforward process, rapid experimental procedures, and highly efficient properties.     

Regulation of the intracellular potassium concentration in Escherichia coli B 525

The mutant Escherichia coli B 525 requires histidine, leucine and methionine and an elevated extracellular K⁺ concentration for growth, and is unable to retain K⁺ tightly inside the cells when incubated in media supplemented with glucose, arabinose, galactose or lactose as the sole energy and carbon source. The loss of K⁺ from the cells of B 525 can be prevented by adding histidine and leucine, which react specifically and only in combination. In media supplemented with glycerol as the substrate, with glucose and NH₄⁺, or with glucose under anaerobic conditions, a stationary level of K⁺ inside the cells can be obtained without the addition of histidine-leucine.On the addition of ribose to glycerol-adapted cells of B 525 preincubated in glycerol media, the intracellular K⁺ decreased immediately and markedly. This decrease can be overcome by the addition of histidine-leucine.