Improvement of polyhydroxybutyrate production by deletion of csrA in Escherichia coli

BackgroundPoly-3-hydroxybutyrate (PHB) can be efficiently produced in recombinant Escherichia coli by the overexpression of an operon (NphaCAB) encoding PHB synthetase. Strain improvement is considered to be one of critical factors to lower the production cost of PHB in recombinant system. In this study, one of key regulators that affect the cell growth and PHB content was confirmed and analyzed.ResultS17-3, a mutant E. coli strain derived from S17-1, was found to be able to achieve high cell density when expressing NphaCAB with the plasmid pBhya-CAB. Whole genome sequencing of S17-3 revealed genetic alternations on the upstream regions of csrA, encoding a global regulator cross-talking between stress response, catabolite repression and other metabolic activities. Deletion of csrA or expression of mutant csrA resulted in improved cell density and PHB content.ConclusionThe impact of gene deletion of csrA was determined, dysfunction of the regulators improved the cell density of recombinant E. coli and PHB production, however, the detail mechanism needs to be further clarified.How to cite: Wu H, Li S, Ji M, et al. Improvement of polyhydroxybutyrate production by deletion of csrA in Escherichia coli. Electron J Biotechnol 2020;46. https://doi.org/10.1016/j.ejbt.2020.04.005.     

Co-production of hydrogen and ethanol by Escherichia coli SS1 and its recombinant

BackgroundThe development of a potential single culture that can co-produce hydrogen and ethanol is beneficial for industrial application. Strain improvement via molecular approach was proposed on hydrogen and ethanol co-producing bacterium, Escherichia coli SS1. Thus, the effect of additional copy of native hydrogenase gene hybC on hydrogen and ethanol co-production by E. coli SS1 was investigated.ResultsBoth E. coli SS1 and the recombinant hybC were subjected to fermentation using 10 g/L of glycerol at initial pH 7.5. Recombinant hybC had about 2-fold higher cell growth, 5.2-fold higher glycerol consumption rate and 3-fold higher ethanol productivity in comparison to wild-type SS1. Nevertheless, wild-type SS1 reported hydrogen yield of 0.57 mol/mol glycerol and ethanol yield of 0.88 mol/mol glycerol, which were 4- and 1.4-fold higher in comparison to recombinant hybC. Glucose fermentation was also conducted for comparison study. The performance of wild-type SS1 and recombinant hybC showed relatively similar results during glucose fermentation. Additional copy of hybC gene could manipulate the glycerol metabolic pathway of E. coli SS1 under slightly alkaline condition.ConclusionsHybC could improve glycerol consumption rate and ethanol productivity of E. coli despite lower hydrogen and ethanol yields. Higher glycerol consumption rate of recombinant hybC could be an advantage for bioconversion of glycerol into biofuels. This study could serve as a useful guidance for dissecting the role of hydrogenase in glycerol metabolism and future development of effective strain for biofuels production.     

大肠杆菌氨基酸转运蛋白的研究进展

总结了大肠杆菌氨基酸的原初主动转运蛋白、次级主动转运蛋白和易化扩散载体在其种类、功能、结构和转运机制方面的研究进展.详细介绍了氨基酸与势能离子相伴的同向共转运和反向共转运,并提出了大肠杆菌氨基酸转运研究中存在问题及展望.     

Metabolic engineering strategies for caffeic acid production in Escherichia coli

Caffeic acid (CA; 3,4-dihydroxycinnamic acid) is an aromatic compound obtained by the phenylpropanoid pathway. This natural product has antioxidant, antitumor, antiviral, and anti-inflammatory activities. It is also a precursor of CA phenethyl ester (CAPE), a compound with potential as an antidiabetic and liver-protective agent. CA can be found at low concentrations in plant tissues, and hence, its purification is difficult and expensive. Knowledge regarding the pathways, enzymes, and genes involved in CA biosynthesis has paved the way for enabling the design and construction of microbial strains with the capacity of synthesizing this metabolite. In this review, metabolic engineering strategies for the generation of Escherichia coli strains for the biotechnological production of CA are presented and discussed.How to cite: Hernández-Chávez G, Martinez A, Gosset G. Metabolic engineering strategies for caffeic acid production in Escherichia coli. Electron J Biotechnol 2019;38. https://doi.org/10.1016/j.ejbt.2018.12.004.     

大肠杆菌的mRNA的翻译效率决定于Shine-Dalgarno的局部结构

在大肠杆菌中,多胺对mRNA翻译的影响程度决定于Shine-Dalgarno (SD)序列局部结构。与信使RNA其它区域松散配对的SD序列的局部结构受多胺的扰动较大,其局部解链的概率也较大,因而SD序列结合到核糖体RNA上并启动蛋白质翻译的概率也较大,相反,则启动mRNA翻译的概率就会较小。基于此,建立一个简单数学模型来描述这一现象,即蛋白质的表达水平是与由多胺刺激而引起mRNA的SD序列局部暴露的概率相关的。结果显示,模型与实验结果相符的很好。     

Vif基因体外表达载体构建及其在无细胞系统中的表达

随着-omics（组学）时代的到来,无细胞蛋白质合成系统以具有快速、方便、易于高通量等优点,正在被广泛地研究和应用。本文选取HIV病毒感染因子Vif作为目标蛋白,构建了适宜体外表达的Vif表达载体pIVEX2.4c-Vif,并将其在大肠杆菌无细胞蛋白质合成系统中进行表达,为下一步进行高通量药物筛选奠定了一定的基础。     

西藏牦牛大肠埃希氏菌黏附素及胞外蛋白酶的测定

本文通过对牦牛致病性大肠埃希氏菌(西藏-9903)和大肠埃希氏菌标准菌种(C83907)黏附素的测定,红细胞凝集谱测定试验表明,西藏-9903只能凝集家兔红细胞,血凝谱窄,凝集价为29,C83907能凝集家兔、鸡、鸭、猪红细胞,血凝谱广,凝集价分别为29、211、28、28;通过对西藏-9903菌株和C83907进行菌毛小肠上皮细胞刷状缘黏附试验,结果表明,每一个乳兔小肠上皮刷状缘细胞至少能吸附7个菌细胞,二者均能较强或强黏附于刷状缘细胞上。胞外蛋白酶活性试验检测结果为西藏-9903菌株和C83907检测均为阳性,说明黏附素及胞外蛋白酶是牦牛大肠埃希氏菌重要的毒力因子,此研究为该病的防制提供一定科学依据。     

Improvement of anther cultures conditions using the Taguchi method in three cereal crops

BackgroundPlant tissue cultures have the potential to reprogram the development of microspores from normal gametophytic to sporophytic pathway resulting in the formation of androgenic embryos. The efficiency of this process depends on the genotype, media composition and external conditions. However, this process frequently results in the regeneration of albino instead of green plants. Successful regeneration of green plants is affected by the concentration of copper sulfate (CuSO₄) and silver nitrate (AgNO₃) and the length of induction step. In this study, we aimed at concurrent optimization of these three factors in barley (Hordeum vulgare L.), wheat (Triticum aestivum L.), and triticale (x Triticosecale spp. Wittmack ex A. Camus 1927) using the Taguchi method. We evaluated uniform donor plants under varying experimental conditions of in vitro anther culture using the Taguchi approach, and verified the optimized conditions.ResultsOptimization of the regeneration conditions resulted in an increase in the number of green regenerants compared with the control. Statistic Taguchi method for optimization of the in vitro tissue culture plant regeneration via anther cultures allowed reduction of the number of experimental designs from 27 needed if full factorial analysis is used to 9. With the increase in the number of green regenerants, the number of spontaneous doubled haploids decreased. Moreover, in barley and triticale, the number of albino regenerants was reduced.ConclusionThe statistic Taguchi approach could be successfully used for various factors (here components of induction media, time of incubation on induction media) at a one time, that may impact on cereals anther cultures to improve the regeneration efficiency.How to cite: Orłowska R, Pachota KA, Machczyńska J, et al. Improvement of anther cultures conditions using the Taguchi method in three cereal crops. Electron J Biotechnol 2020;43. https://doi.org/10.1016/j.ejbt.2019.11.001.     

Escherichia coli GutM4 produces 2,5-diketopiperazines and inhibits human pathogens in vitro

BackgroundIt has been a very common practice to use probiotics or their metabolites as alternative antimicrobial strategies for the treatment and prevention of infections as rampant and indiscriminate use of antibiotics causes the development of antibiotic-resistant pathogens. The objective of this study was to select a potential antimicrobial probiotic strain of Escherichia coli from the human gastrointestinal tract and investigate the production of diketopiperazines that contribute to the antimicrobial activity.ResultsE. coli GutM4 was isolated from the feces of a healthy adult. E. coli GutM4 showed significant antagonistic activity against 10 indicator pathogens, and this activity was no less than that of the reference strain E. coli Nissle 1917 against eight of the indicator pathogens. Moreover, E. coli GutM4 produced antagonistic substances containing trypsin-targeted peptide bonds because the inhibitory effects of E. coli GutM4 supernatant significantly decreased upon treatment with trypsin. Consistent with the antagonistic activity and peptide compounds of E. coli GutM4, 14 2,5-diketopiperazines were isolated from the fermented broth of E. coli GutM4, including 12 cyclo(Pro-Phe), 3 cyclo(Pro-Tyr), and 5 cyclo(4-hydroxyl-Pro-Leu), which are reported to have antipathogenic activity.ConclusionE. coli GutM4 produces 2,5-diketopiperazines that are partly involved in antagonistic action against human pathogens in vitro.     

High-level soluble expression of phospholipase D from Streptomyces chromofuscus in Escherichia coli by combinatorial optimization

BackgroundPhospholipase D (PLD) is used as the biocatalyst for phosphatidylserine (PS) production. In general, PLD was expressed in insoluble form in Escherichia coli. High-level soluble expression of PLD with high activity in E. coli is very important for industrial production of PLD.ResultsStreptomyces chromofuscus PLD coding gene was codon-optimized, cloned without signal peptide, and expressed in E. coli. The optimal recombinant E. coli pET-28a+PLD/BL21(DE3) was constructed with pET-28a without His-tag. The highest PLD activity reached 104.28 ± 2.67 U/mL in a 250-mL shake flask after systematical optimization. The highest PLD activity elevated to 122.94 ± 1.49 U/mL by feeding lactose and inducing at 20°C after scaling up to a 5.0-L fermenter. Substituting the mixed carbon source with 1.0 % (w/v) of cheap dextrin and adding a feeding medium could still attain a PLD activity of 105.81 ± 2.72 U/mL in a 5.0-L fermenter. Fish peptone from the waste of fish processing and dextrin from the starch are both very cheap, which were found to benefit the soluble PLD expression.ConclusionsAfter combinatorial optimization, the high-level soluble expression of PLD was fulfilled in E. coli. The high PLD activity along with cheap medium obtained at the fermenter level can completely meet the requirements of industrial production of PLD.How to cite: Wu R, Cao J, Liu F, et al. High-level soluble expression of phospholipase D from Streptomyces chromofuscus in Escherichia coli by combinatorial optimization. Electron J Biotechnol 2021;50.https://doi.org/10.1016/j.ejbt.2020.12.002     

Dielectrophoretic microfluidic device for the continuous sorting of Escherichia coli from blood cells

Microfluidic diagnostic devices promise faster disease identification by purifying and concentrating low-abundance analytes from a flowing sample. The diagnosis of sepsis, a whole body inflammatory response often caused by microbial infections of the blood, is a model system for pursuing the advantages of microfluidic devices over traditional diagnostic protocols. Traditional sepsis diagnoses require large blood samples and several days to culture and identify the low concentration microbial agent. During these long delays while culturing, the physician has little or no actionable information to treat this acute illness. We designed a microfluidic chip using dielectrophoresis to sort and concentrate the target microbe from a flowing blood sample. This design was optimized using the applicable electrokinetic and hydrodynamic theories. We quantify the sorting efficiency of this device using growth-based assays which show 30% of injected microbes are recovered viable, consistent with the electroporation of target cells by the dielectrophoretic cell sorters. Finally, the results illustrate the device is capable of a five-fold larger microbe concentration in the target analyte stream compared to the waste stream at a continuous sample flow rate of 35 μl∕h.     

Expression,purification and thermal stability evaluation of an engineered amaranth protein expressed in Escherichia coli

BackgroundThe acidic subunit of amarantin (AAC)—the predominant amaranth seed storage protein—has functional potential and its third variable region (VR) has been modified with antihypertensive peptides to improve this potential. Here, we modified the C-terminal in the fourth VR of AAC by inserting four VY antihypertensive peptides. This modified protein (AACM.4) was expressed in Escherichia coli. In addition, we also recombinantly expressed other derivatives of the amarantin protein. These include: unmodified amarantin acidic subunit (AAC); amarantin acidic subunit modified at the third VR with four VY peptides (AACM.3); and amarantin acidic subunit doubly modified, in the third VR with four VY peptides and in the fourth VR with the RIPP peptide (AACM.3.4).ResultsE. coli BL21-CodonPlus (DE3)-RIL was the most favorable strain for the expression of proteins. After 6 h of induction, it showed the best recombinant protein titer. The AAC and AACM.4 were obtained at higher titers (0.56 g/L) while proteins modified in the third VR showed lower titers: 0.44 g/L and 0.33 g/L for AACM.3 and AACM.3.4, respectively. As these AAC variants were mostly expressed in an insoluble form, we applied a refolding protocol. This made it possible to obtain all proteins in soluble form. Modification of the VR 4 improves the thermal stability of amarantin acidic subunit; AAC manifested melting temperature (T_m) at 34°C and AACM.4 at 37.2°C. The AACM.3 and AACM.3.4 did not show transition curves.ConclusionsModifications to the third VR affect the thermal stability of amarantin acidic subunit.     

Disruption of MIR396e and MIR396f improves rice yield under nitrogen-deficient conditions

The microRNA miR396 directly represses GROWTH-REGULATING FACTORs (OsGRFs) and has been implicated in regulating rice yield and in nitrogen assimilation. Overexpressing the miR396 targets OsGRF4 and OsGRF6 improves rice yield via increased grain size and panicle branching, respectively. Here, we used CRISPR/Cas9 to assess the function of miR396 genes in rice. Knockout of MIR396ef (MIR396e and MIR396f), but not other isoforms, enhanced both grain size and panicle branching, resulting in increased grain yield. Importantly, under nitrogen-deficient conditions, mir396ef mutants showed an even higher relative increase in grain yield as well as elevated above-ground biomass. Furthermore, we identified OsGRF8 as a new target of miR396, in addition to the known targets OsGRF4 and OsGRF6. Disruption of the miR396-targeting site in OsGRF8 was sufficient to both enlarge grain size and elongate panicles. Our results suggest that rice-seed and panicle development are regulated by miR396ef-GRF4/6/8-GIF1/2/3 modules and that miR396ef are promising targets of genome editing for breeding environmentally friendly rice varieties that require less nitrogen fertilization.     

抗人B7-2单链抗体基因的构建及其在大肠杆菌中的表达

在成功建立稳定分泌鼠抗人B7-2杂交瘤细胞株基础上,扩增并克隆出该单克隆抗体的重链(VH)和轻链(VL)可变区基因。通过重叠延伸PCR(SOE-PCR)方法,在VH和VL可变区基因之间引入连接肽(Gly4Ser)3,体外构建抗人B7-2单链抗体(B7-2 ScFv)基因。为便于表达产物的纯化,在抗人B7-2 ScFv的C端增加了6×His tag序列。将其克隆至表达载体pET32a并在大肠杆菌中进行原核表达。SDS-PAGE和Western-blot分析结果表明,抗人B7-2 ScFv在大肠杆菌BL21(DE3)菌中获得表达,重组融合蛋白的相对分子量约为43 kD,表达产物以不溶性包涵体形式存在,经溶解包涵体,体外复性和Ni-NTA亲和柱纯化,获得了高纯度的抗人B7-2 ScFv,纯化蛋白得率约16.2%。成果为抗人B7-2单链抗体的生物学活性研究和抗肿瘤药物开发奠定了基础。     

Antibiotic susceptibility test based on the dielectrophoretic behavior of elongated Escherichia coli with cephalexin treatment

This study reports the use of dielectrophoresis (DEP), which determined the crossover frequency (cof) of antibiotic-induced elongation of Escherichia coli (E. coli) with regard to the rapid antibiotic susceptibility test (AST). Different dielectric properties and elongation rates of E. coli are caused by various concentrations of cephalexin treatment. According to the authors' results, significant changes in the cof of bacteria treated with 32 μg∕ml antibiotic for 60 min can be found by using a quadruple electrode array, and the results of DEP-based AST correspond with that of agar dilution method. Utilizing this approach could greatly reduce the period of bacteria growth, and obtain the minimum inhibition concentration of E. coli to cephalexin.     

Media development and process parameter optimization using statistical experimental designs for the production of nonribosomal peptides in Escherichia coli

BackgroundNonribosomal peptide synthases (NRPS) can synthesize functionally diverse bioactive peptides by incorporating nonproteinogenic amino acids, offering a rich source of new drug leads. The bacterium Escherichia coli is a well-characterized production host and a promising candidate for the synthesis of nonribosomal peptides, but only limited bioprocess engineering has been reported for such molecules. We therefore developed a medium and optimized process parameters using the design of experiments (DoE) approach.ResultsWe found that glycerol is not suitable as a carbon source for rhabdopeptide production, at least for the NRPS used for this study. Alternative carbon sources from the tricarboxylic acid cycle achieved much higher yields. DoE was used to optimize the pH and temperature in a stirred-tank reactor, revealing that optimal growth and optimal production required substantially different conditions.ConclusionsWe developed a chemically defined adapted M9 medium matching the performance of complex medium (lysogeny broth) in terms of product concentration. The maximum yield in the reactor under optimized conditions was 126 mg L^-1, representing a 31-fold increase compared to the first shaking-flask experiments with M9 medium and glycerol as the carbon source. Conditions that promoted cell growth tended to inhibit NRPS productivity. The challenge was therefore to find a compromise between these factors as the basis for further process development.How to cite: Oestreich AM, Suli LI, Gerlach D. et al. Media development and process parameter optimization using statistical experimental designs for the production of nonribosomal peptides in Escherichia coli. Electron J Biotechnol 2021;52. https://doi.org/10.1016/j.ejbt.2021.05.001