Significantly enhanced production of recombinant nitrilase by optimization of culture conditions and glycerol feeding

The production of a recombinant nitrilase expressed in Escherichia coli JM109/pNLE was optimized in the present work. Various culture conditions and process parameters, including medium composition, inducer, induction condition, pH and temperature, were systematically examined. The results showed that nitrilase production in E. coli JM109/pNLE was greatly affected by the pH condition and the temperature in batch culture, and the highest nitrilase production was obtained when the fermentation was carried out at 37°C, initial pH 7.0 without control and E. coli was induced with 0.2 mM isopropyl-β-d-thiogalactoside at 4.0 h. Furthermore, enzyme production could be significantly enhanced by adopting the glycerol feeding strategy with lower flow rate. The enzyme expression was also authenticated by sodium dodecyl phosphate polyacrylamide gel electrophoresis analysis. Finally, under the optimized conditions for fed-batch culture, cell growth, specific activity and nitrilase production of the recombinant E. coli were increased by 9.0-, 5.5-, and 50-fold, respectively.     

Impact of Delftia tsuruhatensis and Achromobacter xylosoxidans on Escherichia coli dual-species biofilms treated with antibiotic agents

Recently it was demonstrated that for urinary tract infections species with a lower or unproven pathogenic potential, such as Delftia tsuruhatensis and Achromobacter xylosoxidans, might interact with conventional pathogenic agents such as Escherichia coli. Here, single- and dual-species biofilms of these microorganisms were characterized in terms of microbial composition over time, the average fitness of E. coli, the spatial organization and the biofilm antimicrobial profile. The results revealed a positive impact of these species on the fitness of E. coli and a greater tolerance to the antibiotic agents. In dual-species biofilms exposed to antibiotics, E. coli was able to dominate the microbial consortia in spite of being the most sensitive strain. This is the first study demonstrating the protective effect of less common species over E. coli under adverse conditions imposed by the use of antibiotic agents.     

Antibacterial effect of honey on the in vitro and in vivo growth of Escherichia coli

The study investigated the antibacterial effect of honey against pathogenic Escherichia coli. Honey showed inhibitory activity against the growth of E. coli (ATCC 25922) in agar plate assay. In liquid culture (48 h, 37 °C) the growth rate of bacterial cells decreased in the presence of honey (9.6 × 10⁵ c.f.u./ml) compared with sucrose (2.87 × 10⁸ c.f.u./ml). Rats fed with honey and orally inoculated with E. coli excreted significantly (P < 0.05) less bacterial cells in faeces compared to controls. Animals acclimatized to feeding of honey prior to E. coli inoculation showed a significant decrease in excreted bacterial load compared with the group provided with honey after bacterial inoculation. Consumption of honey also enhanced the concentration of short chain fatty acids in the intestine of rats (83 mM) compared with the control group (44.5 mM). The results show that honey possessed significant antibacterial activity against E. coli under in vitro and in vivo conditions, and indicate the potential benefit of consumption of honey regularly on the microbiological constitution of animals feeding on it.     

Genome‐derived minimal metabolic models for Escherichia coli MG1655 with estimated in vivo respiratory ATP stoichiometry

Metabolic network models describing growth of Escherichia coli on glucose, glycerol and acetate were derived from a genome scale model of E. coli. One of the uncertainties in the metabolic networks is the exact stoichiometry of energy generating and consuming processes. Accurate estimation of biomass and product yields requires correct information on the ATP stoichiometry. The unknown ATP stoichiometry parameters of the constructed E. coli network were estimated from experimental data of eight different aerobic chemostat experiments carried out with E. coli MG1655, grown at different dilution rates (0.025, 0.05, 0.1, and 0.3 h^?1) and on different carbon substrates (glucose, glycerol, and acetate). Proper estimation of the ATP stoichiometry requires proper information on the biomass composition of the organism as well as accurate assessment of net conversion rates under well‐defined conditions. For this purpose a growth rate dependent biomass composition was derived, based on measurements and literature data. After incorporation of the growth rate dependent biomass composition in a metabolic network model, an effective P/O ratio of 1.49 ± 0.26 mol of ATP/mol of O, K_X (growth dependent maintenance) of 0.46 ± 0.27 mol of ATP/C‐mol of biomass and m_ATP (growth independent maintenance) of 0.075 ± 0.015 mol of ATP/C‐mol of biomass/h were estimated using a newly developed Comprehensive Data Reconciliation (CDR) method, assuming that the three energetic parameters were independent of the growth rate and the used substrate. The resulting metabolic network model only requires the specific rate of growth, µ, as an input in order to accurately predict all other fluxes and yields. Biotechnol. Bioeng. 2010;107: 369–381. © 2010 Wiley Periodicals, Inc.     

大肠杆菌突变株高密度生长的多因素分析

【背景】pBHR68是表达聚-3-羟基丁酸酯(Poly-3-Hydroxybutyrate,PHB)合成基因簇的高拷贝质粒,大肠杆菌K-12突变菌株S17-3在携带该质粒时生长密度高,耐低p H且在低pH条件下生长时高产可拉酸(Colanic Acid,CA)。【目的】系统探究与菌种(大肠杆菌S17-3)及质粒(pBHR68)相关的高密度生长现象的分子机理,提示PHB和CA合成代谢与高密度生长的偶联机制。【方法】解析质粒的构成、CA合成途径基因组成对高密度生长现象的影响;利用全基因组同比分析寻找可能的关键突变基因;开展转录组学分析,筛查大肠杆菌S17-3及其转化子在不同培养方式中的转录组数据,通过基因敲除实现基因功能及细胞生长状态的验证。【结果】大肠杆菌S17-3的高密度生长菌与PHB合成的操纵子的过表达以及rhsA的多位点突变相关,RcsA是CA合成与高密度生长中碳代谢流调控的关键调控蛋白。在低pH培养时,敲除可拉酸合成的关键糖基转移酶导致生物量提升;此外,大肠杆菌S17-3/pBHR68的高密度生长还可能与乳糖操纵子异常的转录调控相关,lacZ突变株高密度生长特性消失,而且无法合成可拉酸。【结论】研究分析了引起大肠杆菌S17-3高密度生长的多种因素,为大肠杆菌提高生长密度现象的进一步分析提供了重要线索,也为利用大肠杆菌S17-3的优异生理特性将其改造为寡糖合成的底盘细胞奠定了研究基础。     

A two‐component Kdo hydrolase in the inner membrane of Francisella novicida

Lipid A coats the outer surface of the outer membrane of Gram‐negative bacteria. In Francisella tularensis subspecies novicida lipid A is present either as the covalently attached anchor of lipopolysaccharide (LPS) or as free lipid A. The lipid A moiety of Francisella LPS is linked to the core domain by a single 2‐keto‐3‐deoxy‐D‐manno‐octulosonic acid (Kdo) residue. F. novicida KdtA is bi‐functional, but F. novicida contains a membrane‐bound Kdo hydrolase that removes the outer Kdo unit. The hydrolase consists of two proteins (KdoH1 and KdoH2), which are expressed from adjacent, co‐transcribed genes. KdoH1 (related to sialidases) has a single predicted N‐terminal transmembrane segment. KdoH2 contains 7 putative transmembrane sequences. Neither protein alone catalyses Kdo cleavage when expressed in E. coli. Activity requires simultaneous expression of both proteins or mixing of membranes from strains expressing the individual proteins under in vitro assay conditions in the presence of non‐ionic detergent. In E. coli expressing KdoH1 and KdoH2, hydrolase activity is localized in the inner membrane. WBB06, a heptose‐deficient E. coli mutant that makes Kdo₂‐lipid A as its sole LPS, accumulates Kdo‐lipid A when expressing the both hydrolase components, and 1‐dephospho‐Kdo‐lipid A when expressing both the hydrolase and the Francisella lipid A 1‐phosphatase (LpxE).     

Escherichia coli heme oxygenase modulates host innate immune responses

Induction of mammalian heme oxygenase (HO)‐1 and exposure of animals to carbon monoxide (CO) ameliorates experimental colitis. When enteric bacteria, including Escherichia coli, are exposed to low iron conditions, they express an HO‐like enzyme, chuS, and metabolize heme into iron, biliverdin and CO. Given the abundance of enteric bacteria residing in the intestinal lumen, our postulate was that commensal intestinal bacteria may be a significant source of CO and those that express chuS and other Ho‐like molecules suppress inflammatory immune responses through release of CO. According to real‐time PCR, exposure of mice to CO results in changes in enteric bacterial composition and increases E. coli 16S and chuS DNA. Moreover, the severity of experimental colitis correlates positively with E. coli chuS expression in IL‐10 deficient mice. To explore functional roles, E. coli were genetically modified to overexpress chuS or the chuS gene was deleted. Co‐culture of chuS‐overexpressing E. coli with bone marrow‐derived macrophages resulted in less IL‐12p40 and greater IL‐10 secretion than in wild‐type or chuS‐deficient E. coli. Mice infected with chuS‐overexpressing E. coli have more hepatic CO and less serum IL‐12 p40 than mice infected with chuS‐deficient E. coli. Thus, CO alters the composition of the commensal intestinal microbiota and expands populations of E. coli that harbor the chuS gene. These bacteria are capable of attenuating innate immune responses through expression of chuS. Bacterial HO‐like molecules and bacteria‐derived CO may represent novel targets for therapeutic intervention in inflammatory conditions.     

Kinetic processes in Escherichia coli membranes and cells: A laser photolysis study using derivatives of pyrene

Pyrene and several derivatives of pyrene are used to investigate photo-induced kinetic processes in whole cells and membranes extracted from Escherichia coli. A mutant of E. coli was used which, under appropriate growth conditions, produced a complete or incomplete lipopolysaccharide in the outer membrane. The pyrene derivatives used were: pyrene sulfonic acid, pyrene butyric acid and the ester of pyrene butyric acid and 10-hydroxydecanoic acid. The pyrene chromophore was excited by the ultraviolet pulse from a Q switch, frequency-doubled, ruby laser. The lifetimes of the pyrene fluorescence in the presence of the quenchers O₂, thallous ion (TI⁺), I-and CH₃NO₂ were measured and tabulated as second order rate constants. For the most part the quenching rate constants were much lower than the corresponding values observed in simple nonviscous solution, e.g. ethanol. This is interpreted as being due to the location of the probe within the membrane. The membrane inhibits the movement of the quenchers to the excited state. Cell membranes containing complete lipopolysaccharide showed significantly lower quenching rates for the probes pyrene and pyrene sulfonic acid than cell membranes with incomplete lipopolysaccharide. From an analysis of the kinetic data it is suggested that pyrene and pyrene sulfonic acid are located near and under lipopolysaccharide and close to membrane proteins. On the other hand, no effect of lipopolysaccharide composition was observed for the probes pyrene butyric acid and pyrene butyroyl decanoic acid. This may suggest that these probes are located primarily in the lipid part of the membrane. A simple model for the outer membrane of E. coli is suggested that accounts for the observed laser-induced kinetic processes.     

Bacterial growth properties at low optical densities

A method for accurate quantification of growth rate and yield of bacterial populations at low densities was developed with a modified version of a stepwise linear model for fitting growth curves based on optical density measurements, and adapted to measurements at low optical densities in 96-well microtiter plates. The method can be used for rapid and precise estimates of growth rate and yield, based on optical density measurements of large numbers of cultures of Escherichia coli. E. coli B lines were serially propagated at low glucose concentration during a long-term evolution experiment. Growth rate and yield of populations sampled from each of 12 lines that evolved for 20,000 generations under these conditions and two ancestral clones was measured. Populations were grown at three different glucose concentrations. Consistent with earlier findings, statistical analysis showed that both exponential growth rate and yield per unit of glucose differed significantly between the three glucose concentrations tested. Significant adaptation of the evolved populations to the nutrient conditions in which they evolved for 20,000 generations was observed. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Analysis of functioning ribosome content in Escherichia coli at different growth rates

Summary The amount of functioning ribosome in E. coli was measured using gel filtration chromatography. Cells were grown in a continuous fermentor to provide the same growth conditions at different growth rates. The functioning ribosome content and the fraction of functioning ribosome in the cell increased with growth rates. However, the nonfunctioning ribosome content was almost constant, regardless of the growth rate.     

Changes of Escherichia coli cell cycle parameters during fast growth and throughout growth with limiting amounts of thymine

It is generally accepted that during fast growth of Escherichia coli, the time (D) between the end of a round of DNA replication and cell division is constant. This concept is not consistent with the fact that average cell mass of a culture is an exponential function of the growth rate, if it is also accepted that average cell mass per origin of DNA replication (M_i) changes with growth rate and negative exponential cell age distribution is taken into account. Data obtained from cell composition analysis of E. coli OV-2 have shown that not only (M_i) but also D varied with growth rate at generation times () between 54 and 30 min. E. coli OV-2 is a thymine auxotroph in which the replication time (C) can be lengthened, without inducing changes in , by growth with limiting amounts of thymine. This property has been used to study the relationship between cell size and division from cell composition measurements during growth with different amounts of thymine. When C increased, average cell mass at the end of a round of DNA replication also increased while D decreased, but only the time lapse (d) between the end of a replication round and cell constriction initiation appeared to be affected because the constriction period remained fairly constant. We propose that the rate at which cells proceed to constriction initiation from the end of replication is regulated by cell mass at this event, big cells having shorter d times than small cells.Abbreviations OD₄₅₀ and OD₆₃₀ Optical density at a given wavelength in nm Dedicated to Dr. John Ingraham to honor him for his many contributions to Science     

Influence of cultural conditions and mutations on the composition of the outer membrane proteins ofEscherichia coli

Summary VariousEscherichia coli strains differ in the composition of their major outer membrane proteins. However, allE. coli K12 strains tested possess the same major outer membrane proteinsa, b, c andd although quantitative differences were detected.The influence of growth conditions on the composition of the major outer membrane proteins ofE. coli was analyzed. It was found that neither the growth phase at which the cells are harvested, nor the fatty acid composition of the phospholipids has a considerable influence on the composition of these proteins. However, the composition of the growth medium, and, to a less extent, the growth temperature, have a pronounced influence.Certain mutants, changed in the composition of their lipopolysaccharide, are deficient in proteinb. Also mutants deficient in proteinc andd respectively, are described.Proteinsb andc ofE. coli K12 were found to be associated with peptidoglycan. Protein bands, corresponding with flagellin and pilin respectively, were identified.     

Escherichia coli K12 relA strains as safe hosts for expression of recombinant DNA

Most Escherichia coli K12 strains survive for a relatively long time outside the laboratory. Under the same conditions the isoallelic E. coli K12 relA mutants die faster because they lack the stringent response. The killing rate is increased by using a plasmid-encoded suicide system consisting of the phage T7 lysozyme gene driven by the E. coli alkaline phosphatase gene promoter (phoA). Cells containing this system were rapidly and effectively killed as soon as phosphate was made limiting. The combination of the chromosomal relA mutation and a conditional suicide system of this type provides an effective means of biological containment for recombinant E. coli strains.     

Construction of an Escherichia coli mutant producing monophosphoryl lipid A

Lipid A is a major component in the outer membrane of most Gram-negative bacteria. Monophosphoryl lipid A contains no phosphate group at 1-position and can be used as an adjuvant. We constructed an Escherichia coli mutant CW001 by integrating a gene lpxE into the chromosome of E. coli W3110. The gene lpxE encodes an enzyme LpxE which removes the 1-phosphate group of lipid A. CW001 predominantly produces 1-dephosphorylated lipid A in vivo, as adjudged by thin layer chromatography and electro-spray ionization mass spectrometry. This study not only is important for the development of lipid A adjuvants but also provides a novel method for integration of heterologous genes into the chromosome of E. coli.     

Effect of vitamin A pretreatment on Escherichia coli-induced lipid peroxidation and level of 3-nitrotyrosine in kidney of guinea pig

In the present study, we report the effect of vitamin A (Vit A, retinol palpitate) on kidney lipid peroxidation and 3-nitrotyrosine (3-NT) levels induced after Escherichia coli administration to guinea pigs. Vit A was administrated intraperitoneally (i.p.) to guinea pigs at a dose 15,000 IU/kg per day for 7 days prior to E. coli injection. On day 8, the animals were injected i.p. with E. coli dosed at 12 ×10⁹ colony forming units per kilogram. Kidneys were collected 6 h after administration of E. coli. Malondialdehyde (MDA) as a lipid peroxidation product, and 3-NT levels were measured by reverse phase high-performance liquid chromatography. There was a significant increase in MDA and 3-NT levels in lipopolysaccaharide-induced group (p<0.001). 3-NT was not detectable in kidney of normal control animals. However, Vit A administration prior to E. coli injection prevented 3-NT formation but did not prevent the rice in MDA level of kidney (p<0.001). Vit A alone did not alter the MDA level in the kidney of the control group. (Mol Cell Biochem 278: 33–37, 2005)     

Monitoring growth of Escherichia coli using a two-channel optical sensor

Summary The growth of Escherichia coli strain TG 1 was monitored, measuring simultaneously the culture fluorescence and the 360° reflection at 578 nm with a two-channel optical sensor. It was observed that the culture fluorescence at 366 nm excitation was approximately three times higher than the NADH fluorescence of washed E. coli cells whereas the 360° reflection at 578 nm was comparable. The reason for this effect was found to be the accumulation of riboflavin in the cultivation liquid of the E. coli cells being equal to approximately 0.05 mg/g biomass. In shaken batch cultivations of the same strain the amount of riboflavin in the cell-free cultivation liquid correlated with the biomass being a very sensitive indicator of E. coli growth.Correspondence to: W. S. Kunz     

Drug-induced changes in lipid composition of E. coli and of mammalian cells in culture: ethanol, pentobarbital, and chlorpromazine.

Both Chinese hamster ovary cells in culture and $\text{E.}$$\text{coli}$ cells change their lipid composition when grown in the presence of ethanol, pentobarbital, and chlorpromazine. The effects of ethanol and the cross-tolerant drug, pentobarbital, are similar. Both cause a shift from 18:0 fatty acid to 16:0 fatty acids in CHO cells and a decrease in the proportion of saturated fatty acids in $\text{E.}$$\text{coli}$. Chlorpromazine, a non-cross-tolerant drug, causes the opposite effect in $\text{E.}$$\text{coli}$, a decrease in the proportion of unsaturated fatty acids. Chlorpromazine has little effect on the fatty acid composition of CHO cells. These changes in lipid composition are proposed as an adaptive response and a part of the mechanism for the development of drug tolerance.     

Role of nutrient limitation in the competition between uropathogenic strains of Klebsiella pneumoniae and Escherichia coli in mixed biofilms

Klebsiella pneumoniae and Escherichia coli form mixed species biofilms in catheter-associated urinary tract infections. Recently, a detrimental effect of K. pneumoniae over E. coli was observed in mixed species biofilms grown in an artificial urine medium. The mechanism behind this competitive interaction was studied. K. pneumoniae partially outcompeted E. coli in early-stage batch-fed biofilms, whereas both microorganisms co-exist at longer times (K. pneumoniae:E. coli ratio, 55:1), as shown by cell counts and confocal microscopy. E. coli cells were scattered along the K. pneumoniae biofilm. Biofilm supernatants did not appear to contain either antimicrobial or anti-biofilm activities against E. coli. Biofilms grown under continuous flow prevented interspecies competition. K. pneumoniae showed both increased siderophore production and better growth in iron-limited media compared to E. coli. In summary, these results indicate the importance of nutrient (particularly iron) competition in the modulation of the bacterial composition of mixed species biofilms formed by uropathogenic K. pneumoniae and E. coli.     

The development and characterization of an E. coli O25B bioconjugate vaccine

Extraintestinal pathogenic Escherichia coli (ExPEC) cause a wide range of clinical diseases such as bacteremia and urinary tract infections. The increase of multidrug resistant ExPEC strains is becoming a major concern for the treatment of these infections and E. coli has been identified as a critical priority pathogen by the WHO. Therefore, the development of vaccines has become increasingly important, with the surface lipopolysaccharide constituting a promising vaccine target. This study presents genetic and structural analysis of clinical urine isolates from Switzerland belonging to the serotype O25. Approximately 75% of these isolates were shown to correspond to the substructure O25B only recently described in an emerging clone of E. coli sequence type 131. To address the high occurrence of O25B in clinical isolates, an O25B glycoconjugate vaccine was prepared using an E. coli glycosylation system. The O antigen cluster was integrated into the genome of E. coli W3110, thereby generating an E. coli strain able to synthesize the O25B polysaccharide on a carrier lipid. The polysaccharide was enzymatically conjugated to specific asparagine side chains of the carrier protein exotoxin A (EPA) of Pseudomonas aeruginosa by the PglB oligosaccharyltransferase from Campylobacter jejuni. Detailed characterization of the O25B-EPA conjugate by use of physicochemical methods including NMR and GC-MS confirmed the O25B polysaccharide structure in the conjugate, opening up the possibility to develop a multivalent E. coli conjugate vaccine containing O25B-EPA.