Rapid identification of Escherichia coli safety and laboratory strain lineages based on Multiplex-PCR

Escherichia coli K-12, B, C and W strains are the most frequently used bacterial safety and laboratory strains. Lineage-specific DNA fragments were detected by microplate subtractive hybridization and utilized to create a fast differentiation method using a single PCR reaction to differentiate clearly the four lineages and separate them from pathogenic variants. The method has been evaluated on a comprehensive selection of widely used laboratory strains and a variety of pathogenic E. coli representatives. In addition, in silico analysis on all available E. coli genomes and the genomes of the close relatives Shigella and Salmonella confirmed the reliability of the proposed method. A fast identification and differentiation of E. coli safety strains by Multiplex-PCR is a useful tool for researchers and companies to check and monitor their reference stocks.     

Escherichia coli W as a new platform strain for the enhanced production of L-valine by systems metabolic engineering

A less frequently employed Escherichia coli strain W, yet possessing useful metabolic characteristics such as less acetic acid production and high L ‐valine tolerance, was metabolically engineered for the production of L ‐valine. The ilvA gene was deleted to make more pyruvate, a key precursor for L ‐valine, available for enhanced L ‐valine biosynthesis. The lacI gene was deleted to allow constitutive expression of genes under the tac or trc promoter. The ilvBN^mut genes encoding feedback‐resistant acetohydroxy acid synthase (AHAS) I and the L ‐valine biosynthetic ilvCED genes encoding acetohydroxy acid isomeroreductase, dihydroxy acid dehydratase, and branched chain amino acid aminotransferase, respectively, were amplified by plasmid‐based overexpression. The global regulator Lrp and L ‐valine exporter YgaZH were also amplified by plasmid‐based overexpression. The engineered E. coli W (ΔlacI ΔilvA) strain overexpressing the ilvBN^mut, ilvCED, ygaZH, and lrp genes was able to produce an impressively high concentration of 60.7 g/L L ‐valine by fed‐batch culture in 29.5 h, resulting in a high volumetric productivity of 2.06 g/L/h. The most notable finding is that there was no other byproduct produced during L ‐valine production. The results obtained in this study suggest that E. coli W can be a good alternative to Corynebacterium glutamicum and E. coli K‐12, which have so far been the most efficient L ‐valine producer. Furthermore, it is expected that various bioproducts including other amino acids might be more efficiently produced by this revisited platform strain of E. coli. Bioeng. 2011; 108:1140–1147. © 2010 Wiley Periodicals, Inc.     

General transducing phages like Salmonella phage P22 isolated using a smooth strain of Escherichia coli as host

A smooth colony strain, resistant to phages λ and P22, was isolated from sewage and identified as Escherichia coli (strain H). Four temperate phages plaquing on strain H were isolated from sewage. The archetype, HK620, does not plaque on strains C and K12 of E. coli nor on the LT2 strain of Salmonella enterica. Bacterial mutants resistant to a clear plaque mutant of HK620 produce rough colonies. Some are also galactose-negative, a few are histidine auxotrophs, and most show sensitivity to λ. HK620 can transduce a wide variety of auxotrophic mutants of E. coli H to prototrophy. It can recombine with λ but its virions resemble those of P22.     

L(-)-carnitine production using a recombinant Escherichia coli strain

The L(-)-carnitine production by biotransformation using the recombinant strain Escherichia coli pT7-5KE32 has been studied and optimized with crotonobetaine and D(+)-carnitine as substrates. A resting rather than a growing cells system for L(-)-carnitine production was chosen, crotonobetaine being the best substrate. High biocatalytic activity was obtained after growing the cells under anaerobic conditions at 37°C and with crotonobetaine or L(-)-carnitine as inducer. The growth incubation temperature (37°C) was high enough as to activate the heat-inducible λp_L promoter inserted in the plasmid pGP1-2. The best biotransformation conditions were with resting cells, under aerobiosis, with 4 g l⁻¹ and 100 mM biomass and substrate concentrations respectively. Under these conditions the biotransformation time (1 h) was shorter and the L(-)-carnitine yield (70%) higher than previously reported. Consequently productivity value (11.3 g l⁻¹h⁻¹) was highly improved when comparing with other published works. The resting cells could be reused until eight times maintaining product yield levels well over 50% that meant to increase ten times the L(-)-carnitine obtained per gram of biomass.     

Combined fluorescent antibody assay and viability staining for the assessment of the physiological states of Escherichia coli in seawaters

AIMS: A comparison of methods that combine the use of immune sera with specific fluorescent probes for testing viability at single cell level was performed in order to estimate different living attributes of Escherichia coli in natural seawater samples. METHODS AND RESULTS: Cell culturability was assayed by plate method, respiratory activity and membrane integrity were determined by an indirect fluorescent antibody assay, combined with 5-cyano-2, 3 ditolyl tetrazolium chloride and propidium iodide, respectively. Results showed the coexistence of different physiological states within the E. coli population, of which a large fraction (46%) of cells was actively respiring. CONCLUSIONS: The methodological approach used offer interesting perspectives in water pollution monitoring, particularly when the differentiation between dead and living E. coli cells is required for a more precise assessment of the bacteriological quality of seawaters. SIGNIFICANCE AND IMPACT OF THE STUDY: The study suggests the importance of knowledge of the viability status of faecal bacteria in aquatic environments as a fundamental issue for the preservation of public health; the availability of rapid analytical procedures for this purpose may find significant applications in the evaluation of the sanitary risk consequent to water use.     

An improved Escherichia coli donor strain for diparental mating

We present a new method for diparental mating with the outstanding advantage that counterselection of the Escherichia coli donor strain is not required. This improved method uses a new donor strain, E. coli ST18, a hemA deletion mutant defective in tetrapyrrole biosynthesis. The hemA mutation can be complemented by addition of 5-aminolevulinic acid. Therefore, counterselection is carried out only using standard media and growth conditions optimal for the recipient strain. Consequently, recipient strains are isolated in a significantly shorter period.     

一株产L-天冬氨酸酶大肠埃希氏菌的噬菌体分离和生物学特性

【目的】从大肠埃希氏菌CICC 11021S发酵液中分离一株噬菌体,对其生物学特性进行研究。【方法】采用双层平板法分离噬菌体CICC 80003;利用透射电镜观察噬菌体形态;提取噬菌体基因组,核酸内切酶处理并进行凝胶电泳;分析噬菌体最佳感染复数、一步生长曲线、p H和温度稳定性、宿主谱。考察CICC 80003对CICC 11021S生长和L-天冬氨酸酶活力的影响。【结果】CICC 80003噬菌斑圆形透明,有明显晕环;头部规则,直径约50-60 nm,尾部长约120-130 nm;基因组能被核酸内切酶Bam H I和Mlu I切开;最佳感染复数0.1,潜伏期5 min,裂解期25 min,平均裂解量约86个;最适p H值8.0;90°C温育15 min,噬菌体全部失活;能裂解大肠埃希氏菌和沙门氏菌的部分菌株。发生噬菌体污染时,CICC 11021S无法正常生长,基本检测不到L-天冬氨酸酶活力。【结论】CICC 80003属于长尾噬菌体科ds DNA噬菌体,液体环境中能够彻底裂解大肠埃希氏菌CICC 11021S。     

Metabolic engineering of Escherichia coli for the production of fumaric acid

Fumaric acid is a naturally occurring organic acid that is an intermediate of the tricarboxylic acid cycle. Fungal species belonging to Rhizopus have traditionally been employed for the production of fumaric acid. In this study, Escherichia coli was metabolically engineered for the production of fumaric acid under aerobic condition. For the aerobic production of fumaric acid, the iclR gene was deleted to redirect the carbon flux through the glyoxylate shunt. In addition, the fumA, fumB, and fumC genes were also deleted to enhance fumaric acid formation. The resulting strain was able to produce 1.45 g/L of fumaric acid from 15 g/L of glucose in flask culture. Based on in silico flux response analysis, this base strain was further engineered by plasmid‐based overexpression of the native ppc gene, encoding phosphoenolpyruvate carboxylase (PPC), from the strong tac promoter, which resulted in the production of 4.09 g/L of fumaric acid. Additionally, the arcA and ptsG genes were deleted to reinforce the oxidative TCA cycle flux, and the aspA gene was deleted to block the conversion of fumaric acid into L ‐aspartic acid. Since it is desirable to avoid the use of inducer, the lacI gene was also deleted. To increase glucose uptake rate and fumaric acid productivity, the native promoter of the galP gene was replaced with the strong trc promoter. Fed‐batch culture of the final strain CWF812 allowed production of 28.2 g/L fumaric acid in 63 h with the overall yield and productivity of 0.389 g fumaric acid/g glucose and 0.448 g/L/h, respectively. This study demonstrates the possibility for the efficient production of fumaric acid by metabolically engineered E. coli. Biotechnol. Bioeng. 2013; 110: 2025–2034. © 2013 Wiley Periodicals, Inc.     

代谢工程改造大肠杆菌合成羟基酪醇

羟基酪醇是重要精细化学品,作为天然抗氧化剂被广泛应用于食品、医药领域.利用合成生物学技术生产羟基酪醇具有重要意义.本文克隆并功能鉴定了来源于大肠杆菌Escherichia coli BL21的羟化酶编码基因HpaBC,结果表明该酶的两个亚基均能成功表达并能催化酪醇生成羟基酪醇.通过CRISPR-Cas9技术将由tac启...     

Predictive tool for recombinant protein production in Escherichia coli shake-flask cultures using an on-line monitoring system

As Escherichia coli (E. coli) is well defined with respect to its genome and metabolism, it is a favored host organism for recombinant protein production. However, many processes for recombinant protein production run under suboptimal conditions caused by wrong or incomplete information from an improper screening procedure, because appropriate on-line monitoring systems are still lacking. In this study, the oxygen transfer rate (OTR), determined on-line in shake flasks by applying a respiration activity monitoring system (RAMOS) device, was used to characterize the metabolic state of the recombinant organisms. Sixteen clones of E. coli SCS1 with foreign gene sequences, encoding for different target proteins, were cultivated in an autoinduction medium, containing glucose, lactose, and glycerol, to identify relationships between respiration activity and target protein production. All 16 clones showed a remarkably different respiration activity, biomass, and protein formation under induced conditions. However, the clones could be classified into three distinct types, and correlations could be made between OTR patterns and target protein production. For two of the three types, a decrease of the target protein was observed, after the optimal harvest time had passed. The acquired knowledge was used to modify the autoinduction medium to increase the product yield. Additional 1.5 g/L glucose accelerated the production process for one clone, shifting the time point of the maximal product yield from 24 to 17 h. For another clone, lactose addition led to higher volumetric product yields, in fact 25 and 38% more recombinant protein for 2 and 6 g/L additional lactose, respectively.     

构建一种检测水中As3+的敏感型大肠杆菌

为构建一种敏感性强、特异性好的检测砷离子的大肠杆菌荧光报告菌株,本研究利用基因敲除技术,敲除了大肠杆菌中负责向胞外转运砷离子的ars B基因,构建对As~(3+)敏感的菌株;利用egfp基因作为报告基因,构建融合检测载体p ET28b-Pars-ars R-egfp。然后将检测载体p ET28b-Pars-ars R-egfp转化至ars B基因敲除菌中完成敏感型As~(3+)检测菌株的构建。接着对此微生物传感器进行了检测条件的优化,以及线性检测范围、最低检出限、特异性等性能的确定。研究结果表明,与利用野生大肠杆菌作为检测宿主相比,此敏感型砷检测菌株对检测As~(3+)的灵敏度有显著提高,最适检测As~(3+)浓度范围为0.013-42.71μmol/L,最低检出下限为5.13 nmol/L。因此,本研究利用基因敲除技术对大肠杆菌进行改造,成功地提高了砷检测微生物传感器的灵敏度,为重金属微生物传感器的优化研究工作提供了有用方案。     

A method of enhancing verocytotoxin production by Escherichia coli

The number of verocytotoxin producing Escherichia coli (VTEC) present in the faeces during an infection may be very low, making their detection difficult. We report a method for enhancing toxin production by VTEC using mitomycin C as an inducing agent with the aim of improving the detection of VTEC. In pure culture, mitomycin C enhanced toxin production up to 100-fold. When applied to mixed faecal culture, toxin could be detected in mitomycin C treated samples when standard cultures were negative and when substantially fewer verocytotoxin-producing bacteria were present. Use of this method may aid in the detection of VTEC and is appropriate for use in the routine diagnostic laboratory.     

Process control for enhanced L-phenylalanine production using different recombinant Escherichia coli strains

A novel fed-batch approach for the production of L-phenylalanine (L-Phe) with recombinant E. coli is presented concerning the on-line control of the key fermentation parameters glucose and tyrosine. Two different production strains possessing either the tyrosine feedback resistant aroF(fbr) (encoding tyrosine feedback resistant DAHP-synthase (3-desoxy-D-arabino-heptusonate-7-phosphate)) or the wild-type aroF(wt) were used as model systems to elucidate the necessity of finding an individual process optimum for each genotype. With the aid of tyrosine control, wild-type aroF(wt) could be used for L-Phe production achieving higher final L-Phe titers (34 g/L) than the aroF(fbr) strain (28 g/L) and providing higher DAHP-synthase activities. With on-line glucose control, an optimum glucose concentration of 5 g/L could be identified that allowed a sufficient carbon supply for L-Phe production while at the same time an overflow metabolism leading to acetate by-product formation was avoided. The process approach is suitable for other production strains not only in lab-scale but also in pilot-scale bioreactors.     

重组大肠杆菌生产谷胱甘肽发酵条件的研究

研究了重组Ｅ．Ｃｏｌｉ产ＧＳＨ的发酵条件,重点考察了添加酵母膏、前体氨基酸和ＡＴＰ的影响。结果发现,前体氨基酸和ＡＴＰ均能促进胞内ＧＳＨ的积累,若在发酵０ｈ和１２ｈ分别加入２０ｇ／ＬＡＴＰ和９ｍｍｏｌ／Ｌ前体氨基酸,则细胞干重和胞内ＧＳＨ含量可分别比对照提高２４％和１４倍。应用正交试验得出的针对细胞干重和ＧＳＨ总量的最佳组合,最大细胞干重和ＧＳＨ总量比原试验中的最好结果分别提高了１０％和２６％。在分析了该菌对葡萄糖利用情况的基础上,对该菌进行了指数流加培养,２５ｈ细胞干重与发酵液内ＧＳＨ总量分别达到８０ｇ／Ｌ和８８０ｍｇ／Ｌ,比摇瓶最好结果分别提高了８３和４６倍。     

Analysis of NADPH supply during xylitol production by engineered Escherichia coli

Escherichia coli strain PC09 (DeltaxylB, cAMP-independent CRP (crp*) mutant) expressing an NADPH-dependent xylose reductase from Candida boidinii (CbXR) was previously reported to produce xylitol from xylose while metabolizing glucose [Cirino et al. (2006) Biotechnol Bioeng 95(6): 1167-1176]. This study aims to understand the role of NADPH supply in xylitol yield and the contribution of key central carbon metabolism enzymes toward xylitol production. Studies in which the expression of CbXR or a xylose transporter was increased suggest that enzyme activity and xylose transport are not limiting xylitol production in PC09. A constraints-based stoichiometric metabolic network model was used to understand the roles of central carbon metabolism reactions and xylose transport energetics on the theoretical maximum molar xylitol yield (xylitol produced per glucose consumed), and xylitol yields (Y(RPG)) were measured from resting cell biotransformations with various PC09 derivative strains. For the case of xylose-proton symport, omitting the Zwf (glucose-6-phosphate dehydrogenase) or PntAB (membrane-bound transhydrogenase) reactions or TCA cycle activity from the model reduces the theoretical maximum yield from 9.2 to 8.8, 3.6, and 8.0 mol xylitol (mol glucose)(-1), respectively. Experimentally, deleting pgi (encoding phosphoglucose isomerase) from strain PC09 improves the yield from 3.4 to 4.0 mol xylitol (mol glucose)(-1), while deleting either or both E. coli transhydrogenases (sthA and pntA) has no significant effect on the measured yield. Deleting either zwf or sucC (TCA cycle) significantly reduces the yield from 3.4 to 2.0 and 2.3 mol xylitol (mol glucose)(-1), respectively. Expression of a xylose reductase with relaxed cofactor specificity increases the yield to 4.0. The large discrepancy between theoretical maximum and experimentally determined yield values suggests that biocatalysis is compromised by pathways competing for reducing equivalents and dissipating energy. The metabolic role of transhydrogenases during E. coli biocatalysis has remained largely unspecified. Our results demonstrate the importance of direct NADPH supply by NADP+-utilizing enzymes in central metabolism for driving heterologous NADPH-dependent reactions, and suggest that the pool of reduced cofactors available for biotransformation is not readily interchangeable via transhydrogenase.     

产琥珀酸工程菌株的发酵工艺条件优化

对实验室构建的产琥珀酸大肠杆菌工程菌株(E.coliQZ1111)进行发酵工艺条件研究。以AM1低盐培养基为基础,研究不同C、N源及其质量浓度,培养基初始pH和发酵温度等因素对琥珀酸的影响,并在5L发酵罐中进行了补料-分批发酵实验。优化后的发酵条件为葡萄糖20g/L,玉米浆10g/L,pH6.4,发酵温度37℃。在5L发酵罐中培养,琥珀酸产量达到47.9g/L。     

Dissecting the roles of Escherichia coli hydrogenases in biohydrogen production.

Escherichia coli can perform at least two modes of anaerobic hydrogen metabolism and expresses at least two types of hydrogenase activity. Respiratory hydrogen oxidation is catalysed by two 'uptake' hydrogenase isoenzymes, hydrogenase -1 and -2 (Hyd-1 and -2), and fermentative hydrogen production is catalysed by Hyd-3. Harnessing and enhancing the metabolic capability of E. coli to perform anaerobic mixed-acid fermentation is therefore an attractive approach for bio-hydrogen production from sugars. In this work, the effects of genetic modification of the genes encoding the uptake hydrogenases, as well as the importance of preculture conditions, on hydrogen production and fermentation balance were examined. In suspensions of resting cells pregrown aerobically with formate, deletions in Hyd-3 abolished hydrogen production, whereas the deletion of both uptake hydrogenases improved hydrogen production by 37% over the parent strain. Under fermentative conditions, respiratory H2 uptake activity was absent in strains lacking Hyd-2. The effect of a deletion in hycA on H2 production was found to be dependent upon environmental conditions, but H2 uptake was not significantly affected by this mutation.     

Secretion of an Aeromonas hydrophila aerolysin by a mutant strain of Escherichia coli

Abstract Expression of the Aeromonas hydrophila AH2 aerolysin was analysed in 2 mutant derivatives of Escherichia coli 5K that overproduce E. coli haemolysin, encoded by the multicopy plasmid pANN202–312. When plasmid pHPC3–700 carrying the A. hydrophila aerolysin genes was transformed into one of the mutants, Hha-2T, the transformants produced external aerolysin. Neither the parental 5K strain or the other mutant, Hha-1T, showed extracellular aerolysin activity. For strain Hha-2T, the kinetics of external aerolysin production was similar to that previously reported for A. hydrophila AH2. No cell lysis or release of other proteins to the culture medium could be detected for the period of time that strain Hha-2T exported aerolysin into the external medium.     

CTX-M-producing Escherichia coli in pigs from a Czech farm during production cycle

We evaluated the prevalence and epidemiology of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates in pigs during production cycle on a Czech farm with the history of previous use of ceftiofur. ESBL-producing E. coli isolates were obtained from rectal swabs from pigs of different age groups (suckling piglets, weaned piglets, growers and sows). Collected samples were directly cultivated on MacConkey agar with cefotaxime (2 mg l⁻¹), whereas intestinal swabs of slaughtered pigs and surface swabs from pig carcasses were also pre-enriched in buffered peptone water without antimicrobials before the cultivation. Clonal relationship of selected isolates was determined by XbaI pulse-field gel electrophoresis and multi-locus sequence typing. The transferability of plasmids carrying bla_CTX-M genes was tested by conjugation experiments. From all examined samples, 141 (43·7%, n = 323) were positive for ESBL-producing E. coli. All ESBL-producing isolates showed resistance to multiple antimicrobials and were positive for bla_CTX-M genes. The bla_CTX-M-1 was carried by conjugative IncN/ST1 plasmids (c. 40–45 kb) while the bla_CTX-M-15 was located on conjugative F plasmids with F:18:A5:B1 formula (c. 165 kb). This study demonstrated the persistence of CTX-M-positive E. coli isolates 2 months after banner of ceftiofur usage and indicated possible risk of transmission of these isolates to humans via the food chain.