微生物细胞工厂中多基因表达的控制策略

微生物代谢工程和合成生物学是当今微生物技术领域研究的热点,微生物的生长速度快、容易进行大规模培养;遗传背景清楚、遗传操作简便可靠等性质使其在与人类生活相关的多个领域中起到重要的作用。微生物细胞工厂是指人工设计的能够进行物质生产的微生物代谢体系。许多微生物细胞工厂的构建由于引入多个基因或整条代谢途径,而可能导致代谢失衡、部分代谢中间产物积累等问题,需要使用一定的调控策略加以控制。以下对涉及多个基因作用的微生物细胞工厂中所使用的调控策略,分为若干层次进行了总结和探讨,并对今后多基因控制策略的发展方向进行了预测与展望。     

耐受性工程调控微生物细胞工厂胁迫抗性

微生物细胞工厂的生产效率是由菌株生长性能、产品合成能力和胁迫抗性共同决定的,其中增强微生物细胞工厂的胁迫抗性是关键.耐受性工程基于微生物细胞工厂抵御胁迫压力的应激反应机制,通过巩固壁膜屏障增强胁迫防御能力,加快应激反应提高损伤修复能力,创制耐受进化工具筛选鲁棒性增强的工业微生物.文中分析归纳了耐受性工程的调控策略,并展...     

细胞工厂中的代谢传质与过程强化

细胞工厂是生物制造的重要技术平台,为生物质资源的开发和利用奠定了基础.代谢传质是细胞新陈代谢必不可少的部分,也是提高代谢产物合成的关键因素之一.胞内传质的方式和对象多样、效率不一,低效率的代谢传质严重影响了细胞工厂的生产能力.跨膜传质和无膜传质是代谢传质的两种主要形式,通过对这两种传质途径的改造和优化,可以提高细胞工厂生产初级代谢产物、次级代谢产物和生物大分子的能力.运用合成生物学和代谢工程手段,从多个角度对细胞的传质途径进行改造或从头设计、构建,可以有效提高代谢传质的效率、降低中间代谢物的损耗、提高目标产物的产量.本文从不同类型的代谢传质出发,总结了近年来利用强化代谢传质提高细胞工厂合成能力的研究,为更加深入、系统地研究代谢传质,拓宽其在细胞工厂生产中的应用提供了参考和策略.     

双载蛋白对果蝇S2细胞吞噬大肠杆菌的影响

该文研究了双载蛋白(amphiphysin,Amph)对果蝇S2细胞吞噬大肠杆菌(Escherichia coli,E.coli)的影响。在S2细胞吞入E.coli后,Amph m RNA的表达水平明显升高;但用Amph-si RNA处理后的S2细胞,其Amph蛋白质水平显著低于正常和吞噬E.coli的S2细胞。透射电镜观察发现,S2细胞可以吞噬热灭活的E.coli,且细胞内存在典型的吞噬小体,而用Amph-si RNA处理的S2细胞内则未发现吞噬小体,说明Amph可能对吞噬体形成起关键作用。Amph-si RNA处理的S2细胞对E.coli的吞噬率显著低于未用Amph-si RNA处理的S2细胞,说明敲低Amph会显著地抑制S2细胞对E.coli的吞噬率。上述结果表明,Amph在果蝇S2细胞吞噬E.coli的过程中起重要的调节作用。     

基于工业环境扰动的微生物适应性进化

合成生物学技术的快速发展极大提升了微生物细胞工厂的构建能力,为化学品的绿色高效生产提供了重要策略。然而,微生物细胞难以耐受高强度工业环境、抗逆性差,成为了限制其生产性能的关键因素。适应性进化是一种人为施加定向选择压力,使微生物经过长期或短期驯化,获得适应特定环境的表型或生理性能的重要方法。近年来,随着微流控、生物传感器、组学分析等技术的发展,适应性进化为提升微生物细胞在工业环境下的生产性能奠定了基础。本文论述了适应性进化的关键技术及在提高微生物细胞工厂环境耐受性和生产效率方面的重要应用,并展望了适应性进化实现微生物细胞工厂在工业环境下高效运行的重要前景。     

基于辅因子调控对大肠杆菌两阶段发酵产丁二酸的影响

考察了E.coli NZN111及其重组菌株E.coli NZN111/pTrc99a-pncB发酵生产丁二酸的性能。E.coli NZN111两阶段发酵丁二酸的同时,会造成丙酮酸的大量积累。研究发现:通过过量表达烟酸转磷酸核糖激酶,两阶段发酵重组菌株E.coli NZN111/pTrc99a-pncB,减少丙酮酸的积累且无副产物乙酸生成,提高丁二酸的产量,丁二酸得率和耗糖速率分别提高了139%和20%。     

合成生物学在微生物细胞工厂构建中的应用

通过微生物发酵的方法生产大宗化学品和天然产物能够部分替代石油化工炼制和植物提取。合成生物学技术的发展极大地提高了构建微生物细胞工厂生产大宗化学品和天然产物的能力。一方面综述了合成生物学在构建细胞工厂时的关键技术,包括最优合成途径的设计、合成途径的创建与优化、细胞性能的优化;另一方面,介绍了应用这些技术构建细胞工厂生产燃料化学品、大宗化学品和天然产物的典型案例。     

酸马奶提取Kluyveromyces marxianus代谢抗菌复合物对致病性大肠杆菌的抑菌和细胞表面特性的影响

【目的】探究酸马奶提取马克斯克鲁维酵母(Kluyveromyces marxianus)代谢产生的抗菌复合物K.marxianus p H 2.0和K.marxianus p H 8.0(简称为K2和K8)对致病性大肠杆菌Escherichia coli O8的抑菌效果和细胞表面特性的影响。【方法】乙酸乙酯萃取法制备K2和K8,牛津杯法测定其对E.coli O8的抑菌圈,高效液相色谱法测定其有机酸的组成,试剂盒测定其毒素蛋白浓度,肉汤稀释法测定其对E.coli O8的最小抑菌浓度(MIC)和最小杀菌浓度(MBC),酶标比浊法测定其对E.coli O8生长曲线的影响,微生物粘附法测定其对E.coli O8细胞表面疏水性的影响,邻硝基苯β-D-半乳吡喃糖苷(ONPG)法测定其对E.coli O8细胞膜渗透性的影响。【结果】乙酸乙酯萃取法获得抗菌复合物溶液,其中p H 2.0水相与p H 8.0水相抑菌圈最大,冻干得K2和K8,主要组分为丙酸等有机酸和毒素蛋白。K2和K8对E.coli O8的MIC分别为0.025 g/m L和0.100 g/m L,MBC分别为0.100 g/m L和0.200 g/m L。K2和K8能影响E.coli O8的生长曲线,增加E.coli O8的疏水性和渗透性,且K2优于K8。【结论】酸马奶提取K.marxianus代谢抗菌复合物K2和K8能抑制致病性E.coli O8生长,影响其细胞表面特性。     

微生物细胞工厂生产大宗化学品及其产业化进展

通过微生物发酵的方法生产大宗化学品能够部分替代石油化工炼制,节能减排。合成生物学技术的发展极大地提高了构建微生物细胞工厂生产大宗化学品的能力。介绍了使用合成生物学技术构建微生物细胞工厂生产大宗化学品的研究和产业化进展,并展望了微生物细胞工厂未来的研究重点。     

微生物细胞工厂的代谢调控

代谢调控是构建微生物细胞工厂的重要技术手段。随着合成生物学技术的不断突破,挖掘和人工设计的高质量调控元件大幅度提升了对细胞代谢网络的改造能力;代谢调控研究也已从单基因的静态调控发展到系统水平上的智能精确动态调控。文中简要综述了近30年来代谢途径表达调控技术在代谢工程领域的研究进展。     

The microbial ecology of high-risk, chilled food factories; evidence for persistent Listeria spp. and Escherichia coli strains

AIMS: The intention of this study was to provide evidence of any Listeria spp. or Escherichia coli strain persistence, and to identify whether strains of these organisms adapt to specific environmental or product niches in food factories. METHODS AND RESULTS: A 3-year assessment of the microbial ecology of four, ready-to-eat food-processing factories was undertaken in which approx. 196 000 and 75 000 product and environmental samples were examined for Escherichia coli and Listeria spp. respectively. A total of 152 E. coli isolates (44 environmental and 108 product in 62 ribogroups) and 260 Listeria spp. isolates (174 environmental and 86 product in 30 ribogroups) were identified and ribotyped. The overall prevalence of E. coli (0.08%), all Listeria spp. (0.35%) and L. monocytogenes (0.23%) was very low. Some 10 E. coli ribogroups and 14 Listeria spp. ribogroups showed evidence for persistence, defined as the isolation of the same strain, from the same site, over a prolonged time period. The majority of E. coli strains were product niche oriented whilst the majority of Listeria spp. strains were environmental niche oriented. CONCLUSION: Current UK high-risk food factory designs, personnel hygiene and cleaning and disinfection regimes are sufficient to control Listeria spp. and E. coli to very low levels. SIGNIFICANCE AND IMPACT OF THE STUDY: Persistent strains of these organisms, however, can remain within factory high-risk production areas over considerable time periods, warranting an examination of the strain persistence mechanisms and alternative hygiene controls.     

大肠杆菌细胞工厂的创建技术

大肠杆菌作为一种重要的模式工业微生物,在医药、化工、农业等方面具有广泛的应用。近30年来,多种代谢工程改造的新策略和新技术,被用于设计、构建和优化大肠杆菌化学品细胞工厂,极大地提高了生物法合成化学品的生产速率和产量。文中将从大肠杆菌途径设计、合成途径创建与优化和细胞全局优化三个方面,对大肠杆菌代谢改造起重要推动作用的技术进行综述,并对大肠杆菌代谢工程中关键技术的应用进行了展望。     

Cell chromatography: separation of different microbial cells using IMAC supermacroporous monolithic columns

Supermacroporous monolithic columns with Cu(2+)-IDA ligands have been successfully used for chromatographic separation of different types of microbial cells. The bed of monolithic matrix is formed by a cryogel of poly(acrylamide) cross-linked with methylenebis(acrylamide) and has a network of large (10-100 microm) interconnected pores allowing unhindered passage of whole cells through the plain cryogel column containing no ligands. Two model systems have been studied: the mixtures of wild-type Escherichia coli (w.t. E. coli) and recombinant E. coli cells displaying poly-His peptides (His-tagged E. coli) and of w.t. E. coli and Bacillus halodurans cells. Wild-type E. coli and His-tagged E. coli were quantitatively captured from the feedstock containing equal amounts of both cell types and recovered by selective elution with imidazole and EDTA, with yields of 80% and 77%, respectively. The peak obtained after EDTA elution was 8-fold enriched with His-tagged E. coli cells as compared with the peak from imidazole elution, which contained mainly weakly bound w.t. E. coli cells. Haloalkalophilic B. halodurans cells had low affinity to the Cu(2+)-IDA cryogel column and could be efficiently separated from a mixture with w.t. E. coli cells, which were retained and recovered in high yields from the column with imidazole gradient. All the cells maintained their viability after the chromatographic procedure. The results show that chromatography on affinity supermacroporous monolithic columns is a promising approach to efficient separations of individual cell types.     

Mechanism of enhancement of microbial cell hydrophobicity by cationic polymers.

Polycationic polymers have been noted for their effects in promoting cell adhesion to various surfaces, but previous studies have failed to describe a mechanism dealing with this type of adhesion. In the present study, three polycationic polymers (chitosan, poly-L-lysine, and lysozyme) were tested for their effects on microbial hydrophobicity, as determined by adhesion to hydrocarbon and polystyrene. Test strains (Escherichia coli, Candida albicans, and a nonhydrophobic mutant, MR-481, derived from Acinetobacter calcoaceticus RAG-1) were vortexed with hexadecane in the presence of the various polycations, and the extent of adhesion was measured turbidimetrically. Adhesion of all three test strains rose from near zero values to over 90% in the presence of low concentrations of chitosan (125 to 250 micrograms/ml). Adhesion occurred by adsorption of chitosan directly to the cell surface, since E. coli cells preincubated in the presence of the polymer were highly adherent, whereas hexadecane droplets pretreated with chitosan were subsequently unable to bind untreated cells. Inorganic cations (Na+, Mg2+) inhibited the chitosan-mediated adhesion of E. coli to hexadecane, presumably by interfering with the electrostatic interactions responsible for adsorption of the polymer to the bacterial surface. Chitosan similarly promoted E. coli adhesion to polystyrene at concentrations slightly higher than those which mediated adhesion to hexadecane. Poly-L-lysine also promoted microbial adhesion to hexadecane, although at concentrations somewhat higher than those observed for chitosan. In order to study the effect of the cationic protein lysozyme, adhesion was studied at 0 degree C (to prevent enzymatic activity), using n-octane as the test hydrocarbon. Adhesion of E. coli increased by 70% in the presence of 80 micrograms of lysozyme per ml. When the negatively charged carboxylate residues on the E. coli cell surface were substituted for positively charged ammonium groups, the resulting cells became highly hydrophobic, even in the absence of polycations. The observed "hydrophobicity" of the microbial cells in the presence of polycations is thus probably due to a loss of surface electronegativity. The data suggest that enhancement of hydrophobicity by polycationic polymers is a general phenomenon.     

Independent and Additive Effects of Glutamic Acid and Methionine on Yeast Longevity

It is established that glucose restriction extends yeast chronological and replicative lifespan, but little is known about the influence of amino acids on yeast lifespan, although some amino acids were reported to delay aging in rodents. Here we show that amino acid composition greatly alters yeast chronological lifespan. We found that non-essential amino acids (to yeast) methionine and glutamic acid had the most significant impact on yeast chronological lifespan extension, restriction of methionine and/or increase of glutamic acid led to longevity that was not the result of low acetic acid production and acidification in aging media. Remarkably, low methionine, high glutamic acid and glucose restriction additively and independently extended yeast lifespan, which could not be further extended by buffering the medium (pH 6.0). Our preliminary findings using yeasts with gene deletion demonstrate that glutamic acid addition, methionine and glucose restriction prompt yeast longevity through distinct mechanisms. This study may help to fill a gap in yeast model for the fast developing view that nutrient balance is a critical factor to extend lifespan.     

Isolation and functional analysis of a 24-residue linear alpha-helical antimicrobial peptide from Korean blackish cicada, Cryptotympana dubia (Homoptera)

A new antimicrobial peptide, cryptonin, was isolated and characterized from the adult Korean blackish cicada, Cryptotympana dubia. It consists of 24 amino acid residues and has a molecular weight of 2,704 Da on mass spectroscopy. The predicted alpha-helical structure analysis and increased helix percent in 40% trifloroethanol of cryptonin suggests that it belongs to the typical linear alpha-helix forming peptide. Binding of the biotin-labeled cryptonin at the surface of E. coli cells and increased influx of propidium iodide in E. coli after cryptonin treatment indicates that it kills microbial cells by binding bacterial cell surfaces and disrupting the cell permeability. Cryptonin showed strong antibacterial (MIC 1.56-25 microg/ml) and antifungal (MIC 3.12-50 microg/ml) activities against tested bacteria and fungi including two antibiotic-resistant bacterial strains; methicilin-resistant S. aureus and vancomycin-resistant Enterococci (MIC 25 microg/ml, each).     

Lonidamine extends lifespan of adult Caenorhabditis elegans by increasing the formation of mitochondrial reactive oxygen species

Compounds that delay aging in model organisms may be of significant interest to antiaging medicine, since these substances potentially provide pharmaceutical approaches to promote healthy lifespan in humans. The aim of the study was to test whether pharmaceutical concentrations of the glycolytic inhibitor lonidamine are capable of extending lifespan in a nematodal model organism for aging processes, the roundworm Caenorhabditis elegans. Several hundreds of adult C. elegans roundworms were maintained on agar plates and fed E. coli strain OP50 bacteria. Lonidamine was applied to test whether it may promote longevity by quantifying survival in the presence and absence of the compound. In addition, several biochemical and metabolic assays were performed with nematodes exposed to lonidamine. Lonidamine significantly extends both median and maximum lifespan of C. elegans when applied at a concentration of 5 micromolar by 8% each. Moreover, the compound increases paraquat stress resistance, and promotes mitochondrial respiration, culminating in increased formation of reactive oxygen species (ROS). Extension of lifespan requires activation of pmk-1, an orthologue of p38 MAP kinase, and is abolished by co-application of an antioxidant, indicating that increased ROS formation is required for the extension of lifespan by lonidamine. Consistent with the concept of mitohormesis, lonidamine is capable of promoting longevity in a pmk-1 sensitive manner by increasing formation of ROS.     

pH neutralization protects against reduction in replicative lifespan following chronological aging in yeast

Chronological and replicative aging have been studied in yeast as alternative paradigms for post-mitotic and mitotic aging, respectively. It has been known for more than a decade that cells of the S288C background aged chronologically in rich medium have reduced replicative lifespan relative to chronologically young cells. Here we report replication of this observation in the diploid BY4743 strain background. We further show that the reduction in replicative lifespan from chronological aging is accelerated when cells are chronologically aged under standard conditions in synthetic complete medium rather than rich medium. The loss of replicative potential with chronological age is attenuated by buffering the pH of the chronological aging medium to 6.0, an intervention that we have previously shown can extend chronological lifespan. These data demonstrate that extracellular acidification of the culture medium can cause intracellular damage in the chronologically aging population that is asymmetrically segregated by the mother cell to limit subsequent replicative lifespan.     

Calorie restriction extends the chronological lifespan of Saccharomyces cerevisiae independently of the Sirtuins

Calorie restriction (CR) extends the mean and maximum lifespan of a wide variety of organisms ranging from yeast to mammals, although the molecular mechanisms of action remain unclear. For the budding yeast Saccharomyces cerevisiae reducing glucose in the growth medium extends both the replicative and chronological lifespans (CLS). The conserved NAD(+)-dependent histone deacetylase, Sir2p, promotes replicative longevity in S. cerevisiae by suppressing recombination within the ribosomal DNA locus and has been proposed to mediate the effects of CR on aging. In this study, we investigated the functional relationships of the yeast Sirtuins (Sir2p, Hst1p, Hst2p, Hst3p and Hst4p) with CLS and CR. SIR2, HST2, and HST4 were not major regulators of CLS and were not required for the lifespan extension caused by shifting the glucose concentration from 2 to 0.5% (CR). Deleting HST1 or HST3 moderately shortened CLS, but did not prevent CR from extending lifespan. CR therefore works through a Sirtuin-independent mechanism in the chronological aging system. We also show that low temperature or high osmolarity additively extends CLS when combined with CR, suggesting that these stresses and CR act through separate pathways. The CR effect on CLS was not specific to glucose. Restricting other simple sugars such as galactose or fructose also extended lifespan. Importantly, growth on nonfermentable carbon sources that force yeast to exclusively utilize respiration extended lifespan at nonrestricted concentrations and provided no additional benefit when restricted, suggesting that elevated respiration capacity is an important determinant of chronological longevity.     

pH neutralization protects against reduction in replicative lifespan following chronological aging in yeast

Chronological and replicative aging have been studied in yeast as alternative paradigms for post-mitotic and mitotic aging, respectively. It has been known for more than a decade that cells of the S288C background aged chronologically in rich medium have reduced replicative lifespan relative to chronologically young cells. Here we report replication of this observation in the diploid BY4743 strain background. We further show that the reduction in replicative lifespan from chronological aging is accelerated when cells are chronologically aged under standard conditions in synthetic complete medium rather than rich medium. The loss of replicative potential with chronological age is attenuated by buffering the pH of the chronological aging medium to 6.0, an intervention that we have previously shown can extend chronological lifespan. These data demonstrate that extracellular acidification of the culture medium can cause intracellular damage in the chronologically aging population that is asymmetrically segregated by the mother cell to limit subsequent replicative lifespan.