嗜热毁丝霉高通量培养技术及其应用

【背景】丝状真菌是一类重要的工业发酵生产宿主菌,如何进行高通量纯菌培养和高效检测筛选性能优异的菌株是工业丝状真菌研究的重要方向。【目的】研究建立丝状真菌的高通量培养技术并测试应用效果。【方法】通过对丝状真菌培养过程中的制种、接种、培养和检测研究,建立基于孔板的高通量培养技术,并以嗜热毁丝霉为例对该技术进行验证。【结果】与传统的平板制种和摇瓶接种培养方式相比,高通量孔板的培养方式将制种通量提高24倍,单位面积产孢子能力提高350%,液体培养转接效率提高10-40倍,并建立96孔板测定乙醇含量的高通量检测技术。【结论】将丝状真菌的培养和检测通量提高1-2个数量级,为快速检测丝状真菌改造过程产生的大量性状不同菌株并获得目标菌株奠定基础,为丝状真菌高通量筛选研究提供应用指导价值。     

FACSAria流式细胞仪96孔微孔板单个细胞分选方法的优化和应用

对FACSAria流式细胞仪96孔微孔板单个细胞分选方法进行优化和应用。通过对液流的调节,获得较稳定的分选设定值;在96孔微孔板盖上分选肉眼可见液滴,确定分选液滴在96孔微孔板每孔相对应的盖上的位置;分选结束后,计数单个细胞存在的细胞孔数;分选细胞培养7d后,记录单个细胞存在孔数及单克隆形成的数量。结果5个细胞形成的液滴即肉眼清晰可见;96微孔板有单个细胞的孔数为80～90个,单个细胞获得率为83.3%～93.7%,培养7d后,有活细胞存在的孔数为5～38孔,即单克隆形成率为6.3%～42.2%。分选前在96孔微孔板板盖上分选肉眼可见液滴的简单方法使得对液流位置的判断直观可见;流式细胞仪96孔微孔板单细胞分选是一种简单易行,准确有效地获得单个细胞和单克隆的方法。     

毕赤酵母液滴微流控高通量筛选方法的建立与应用

巴斯德毕赤酵母是当前应用最为方便和广泛的外源蛋白表达系统之一,为了进一步提高其表达外源蛋白的能力,文中建立了基于液滴微流控的毕赤酵母高通量筛选方法,并以木聚糖酶融合荧光蛋白为例,筛选获得木聚糖酶表达和分泌能力提高的突变株。通过PCR扩增得到木聚糖酶xyn5基因和绿色荧光蛋白gfp基因融合片段,并克隆到毕赤酵母表达载体pPIC9K中构建出木聚糖酶融合绿色荧光蛋白的质粒pPIC9K-xyn5-gfp,电转化至毕赤酵母GS115中得到表达木聚糖酶和绿色荧光蛋白的毕赤酵母SG菌株。该菌株经过常压室温等离子体诱变后进行单细胞液滴包埋,液滴培养24h后进行微流控筛选,获得高表达木聚糖酶的突变菌株,进而用于下一轮的诱变突变库构建和筛选。以此类推,经过5轮液滴微流控筛选,获得一株高产菌株SG-m5,其木聚糖酶活为149.17U/mg,较出发菌株提升300%,分泌外源蛋白的能力较出发菌株提高160%。文中建立的毕赤酵母单细胞液滴微流控高通量筛选方法能达到每小时10万菌株的筛选通量,筛选百万级别的菌株库仅需10h,消耗荧光试剂体积100μL,对比传统的微孔板筛选方法降低试剂成本近百万倍,为高效、低成本筛选获得表达和分泌外源蛋白能力提高的毕赤酵母提供了一条新途径。     

发酵液中色氨酸含量高通量快速测定

为了高通量筛选色氨酸工程菌,利用色氨酸与MAA在酸性条件下产生荧光物质(激发波长253 nm,发射波长450nm),荧光强度与色氨酸含量在一定范围内成正比的原理,建立了96孔微孔板中高通量测定发酵液色氨酸含量的方法。反应液80℃反应15 min后,测量荧光强度。线性范围为1 mg.L-1~100 mg.L-1,为大规模筛选色氨酸基因工程菌打下了基础。     

抗菌活性放线菌的界面微滴移液互作分离筛选方法

【背景】放线菌是天然产物的宝库,目前应用于临床的天然抗生素有70%来源于放线菌的次级代谢产物。随着细菌对传统抗生素耐药问题的日趋严重,如何从自然生境中高效筛选新型活性放线菌资源并发现新型抗生素成为当前微生物学者面临的重要挑战。通过传统方法筛选活性放线菌不仅费时费力、试剂耗材消耗量大,并且筛选通量非常有限,难以对自然样品中的复杂微生物群落进行整体全面的解析。【目的】提出一种基于多孔板液滴阵列培养的新策略,可高通量筛选抗菌活性放线菌。分析模式放线菌在微液滴中的培养特征与筛选条件,为进一步建立基于液滴阵列技术的超高通量活性放线菌筛选平台奠定基础。【方法】采用界面移液技术,将传统的多孔板高通量筛选体系微缩至1μL水平,在油相填充的多孔板(96孔板)中生成微升培养液滴阵列,每个微孔液滴中封装一个放线菌孢子或菌丝团。经过短期培养,放线菌在微滴中完成菌丝分化与次级代谢产物的分泌。这时,通过第二步界面移液技术与液滴融合加入带有荧光标记的指示菌,通过全菌拮抗筛选定位活性目标菌株,并将活性谱转化为量化的荧光数值。【结果】通过对模式放线菌的测试发现,放线菌菌丝可以在微液滴中达到最佳培养状态,并积累足够的生物质与代谢物,对荧光指示菌有明显的抑制作用。【结论】通过建立上述基于微孔板液滴阵列的高通量筛选技术,能从单细胞水平快速筛选出具有抑菌活性的菌株,显著节约了筛选成本并提高了筛选通量,为新型活性天然产物的发现提供了一种新的简单有效的筛选方法。     

一种产邻苯二酚菌株高通量筛选方法

目的：对产邻苯二酚菌株进行筛选。方法：采用前期筛得的产邻苯二酚菌为出发菌株,通过硫酸二乙酯诱变的方法使该菌株突变,同时建立96孔板培养和酶标仪检测方法对产邻苯二酚菌株进行高通量筛选。结果：硫酸二乙酯的终浓度为0.1%,诱变时间为8 min的条件下,突变菌致死率为84.5%,突变效果最好。筛选培养基中吸光值（495nm）和富集培养基中菌液浊度值（OD630）的加和值较大的突变菌株产邻苯二酚能力高。通过诱变和筛选得到的菌株,产邻苯二酚浓度可达0.87mg/ml,比出发菌株的提高了262.5%。经过形态学和生理生化反应,初步鉴定该菌株属于假单胞菌属（Pseudomonas sp.）。结论：硫酸二乙酯诱变和96孔板筛选的方法能以高通量方式快速筛选出产邻苯二酚菌株。     

Nisin高产菌株的高通量筛选

【目的】乳酸链球菌素(nisin)是一种天然生物活性抗菌肽,对包括食品腐败菌和致病菌在内的许多革兰氏阳性菌具有强烈的抑制作用,而用作食品的防腐剂。本研究通过建立高通量筛选方法,实现高效快速省力的高产菌株筛选,为工业上筛选高产菌株提供研究方案。【方法】通过对Lactococcus lactis ATCC11454菌株进行紫外诱变,获得2511株突变株。利用Biomek FXP自动工作站建立96微孔板的高通量筛选方法,突变株经高通量挑选、菌种培养及菌液稀释后,加入到生长至对数中期的藤黄微球菌中,采用改进后的比浊法快速检测nisin生物活性。用此方法对突变株进行初筛、复筛后可得到nisin高产菌株,并通过摇瓶发酵评估高通量筛选方法。【结果】确定比浊法检测的条件为:nisin活性稀释在10–25 IU/m L范围内,与藤黄微球菌反应2 h后检测藤黄微球菌的菌体量(OD600)。2511株突变株经过2轮高通量筛选,最终获得约50株产量提升的菌株,对其中8株进行摇瓶精确测量,显示产量均有提高,并且其中一株产量提升了30%,成功建立了高通量筛选nisin高产菌株的方法。【结论】利用比浊检测法,在其基础上成功建立高通量筛选高产nisin菌的方法,经过初筛复筛,整个周期由1人耗时5 d即可完成2511株突变株的筛选工作。相较于传统的选育方法,高通量筛选具有快速、稳定、高效的特点,提高了筛选效率,缩短了选育周期,是工业上筛选高产nisin菌的有效手段。     

高通量自动化微生物微液滴进化培养与筛选技术及其装备化

液滴微流控由于可以快速生成大量微液滴,并实现单个液滴独立的控制,每个液滴都可以作为独立的单元进行微生物培养,因此在微生物的高通量培养方面具有独特的应用优势。然而现有研究多停留在实验室搭建和使用阶段,存在操作要求高、影响因素多、缺乏自动化集成技术等关键问题,制约了液滴微流控技术在微生物研究中的应用。文中以解决液滴微流控技术用于微生物培养的装备化问题为目标,系统研究了微流控各单元模块的结构与功能,通过对液滴的发生、培养、检测、分割、融合、分选等多种操作的开发与集成,成功研制出了小型一体化、全自动高通量的微生物微液滴培养(Microbial Microdroplet Culture system,MMC)装备系统,可用于微生物的生长曲线测定、适应性进化、单因素多水平分析及代谢物检测等,为面向微生物菌种高效选育的进化培养和筛选提供了高通量仪器平台。     

植酸酶菌种筛选方法的研究

通过微板培养法对植酸酶产生菌菌种筛选方法进行了研究,建立了一种快速、有效的高通量植酸酶菌种筛选方法。利用该方法结合菌种诱变技术已选育出植酸酶酶活高达297u／mL的A,niger 496-1菌株。     

常压室温等离子体(ARTP)诱变及高通量筛选那西肽高产菌株

采用新型常压室温等离子体(ARTP)诱变活跃链霉菌(Streptomyces actuosu),并应用抑菌圈和48孔板培养方法高通量筛选高产那西肽菌株。研究表明抑菌圈径的大小与48孔板效价之间以及48孔板效价与摇瓶效价之间均有较好的相关性,系数R分别达到0.534和0.896。通过多轮ARTP诱变及高通量筛选最终获得了3株相对效价提高50%以上的遗传性能稳定的突变株。ARTP诱变技术作为获得那西肽高产菌株的有效途径,与传统摇瓶发酵筛选相比,48孔板及抑菌圈法能显著提高那西肽高产菌株的筛选效率。     

基于ARTP诱变和高通量筛选的绿针假单胞菌GP72育种方法

【目的】绿针假单胞菌GP72是一种植物根围促生细菌,其分泌的次级代谢产物2-羟基-吩嗪(2-OH-PHZ)具有广谱抗真菌活性,但其产量较低,不能满足农业生产的应用需求,因此需对GP72进行改造,从而提高产量。【方法】从GP72的野生株出发,首次将2-OH-PHZ合成途径的限制性因子Phz O用绿色荧光蛋白(GFP)替换,以一种新型的常压室温等离子体技术(Atmospheric and room temperature plasma,ARTP)进行诱变,通过酶标仪测定96孔板中突变株的荧光强度进行高通量筛选;最后将荧光强度高的菌株中绿色荧光蛋白(Green fluorescent protein,GFP)替换为Phz O以获得2-OH-PHZ高产突变株。【结果】经过五轮诱变后,获得一株荧光强度增加1.62倍的突变株,用phz O基因回替后,该突变株在KB培养基中摇瓶培养时2-OH-PHZ的产量为野生型的4.62倍。【结论】基于安全、高效ARTP诱变技术,并以GFP替换限制性因子作为标记进行高通量筛选,可以快速获得高产2-OH-PHZ的GP72突变株,克服了传统诱变育种方法筛选难度大、费时费力的不足,为其它微生物的育种提供了参考。     

Fluorinert, an oxygen carrier, improves cell culture performance in deep square 96-well plates by facilitating oxygen transfer

In bioprocess development, the 96-well plate format has been widely used for high-throughput screening of production cell line or culture conditions. However, suspension cell cultures in conventional 96-well plates often fail to reach high cell density under normal agitation presumably due to constraints in oxygen transfer. Although more vigorous agitation can improve gas transfer in 96-well plate format, it often requires specialized instruments. In this report, we employed Fluorinert, a biologically inert perfluorocarbon, to improve oxygen transfer in 96-well plate and to enable the growth of a Chinese Hamster Ovary cell line expressing a recombinant monoclonal antibody. When different amounts of Fluorinert were added to the cell culture medium, a dose-dependent improvement in cell growth was observed in both conventional and deep square 96-well plates. When sufficient Fluorinert was present in the culture, the cell growth rate, the peak cell density, and recombinant protein production levels achieved in deep square 96-wells were comparable to cultures in ventilated shake flasks. Although Fluorinert is known to dissolve gases such as oxygen and CO(2), it does not dissolve nor extract medium components, such as glucose, lactate, or amino acids. We conclude that mixing Fluorinert with culture media is a suitable model for miniaturization of cell line development and process optimization. Proper cell growth and cellular productivity can be obtained with a standard shaker without the need for any additional aeration or vigorous agitation.     

An Enzymatic Assay for High-Throughput Screening of Cytidine-Producing Microbial Strains

Cytidine is an industrially useful precursor for the production of antiviral compounds and a variety of industrial compounds. Interest in the microbial production of cytidine has grown recently and high-throughput screening of cytidine over-producers is an important approach in large-scale industrial production using microorganisms. An enzymatic assay for cytidine was developed combining cytidine deaminase (CDA) and indophenol method. CDA catalyzes the cleavage of cytidine to uridine and NH₃, the latter of which can be accurately determined using the indophenol method. The assay was performed in 96-well plates and had a linear detection range of cytidine of 0.058 - 10 mM. This assay was used to determine the amount of cytidine in fermentation flasks and the results were compared with that of High Perfomance Liquid Chromatography (HPLC) method. The detection range of the CDA method is not as wide as that of the HPLC, furthermore the correlation factor of CDA method is not as high as that of HPLC. However, it was suitable for the detection of large numbers of crude samples and was applied to high-throughput screening for high cytidine-producing strains using 96-well deep-hole culture plates. This assay was proved to be simple, accurate, specific and suitable for cytidine detection and high-throughput screening of cytidine-producing strains in large numbers of samples (96 well or more).     

High-throughput colorimetric assays optimized for detection of ketones and aldehydes produced by microbial cell factories

Randomized strain and pathway engineering are critical to improving microbial cell factory performance, calling for the development of high-throughput screening and selection systems. To facilitate this effort, we have developed two 96-well plate format colorimetric assays for reliable quantification of various ketones and aldehydes from culture supernatants, based on either a vanillin-acetone reaction or the 2,4-dinitrophenylhydrazine (2,4-DNPH) reagent. The vanillin-acetone assay enabled accurate and selective measurement of acetone titers up to 2 g l⁻¹ in a minimal culture medium. The 2,4-DNPH-based assay can be used for a wide range of aldehydes and ketones, shown here through the optimization of conditions for 15 different compounds. Both assays were implemented to improve acetone production from different substrates by an engineered Escherichia coli strain. The fast and user-friendly colorimetric assays proposed here open the potential for iterative rounds of (automated) strain and pathway engineering and screening, facilitating the efforts towards further boosting production titers of industrially relevant ketones and aldehydes.     

An integrated high throughput strategy to screen mutants of Paenibacillus polymyxa with high polymyxin E-productivity

An integrated high-throughput screening (HTS) strategy was developed to screen large numbers of polymyxin E-producing mutants of Paenibacillus polymyxa. Various types of mutants were transferred onto the surfaces of solidified agar in 96-well microtiter plates, and then inoculated to 96-deep-well microtiter plates for micro-cultivation. The culture conditions were optimized for the production of polymyxin E. The supernatants from the micro-culture plates were transferred to 96-well bioassay microtiter plates containing Escherichia coli JM109 for high-throughput bioassay. By using this high-throughput screening (HTS) procedure, one best producer P. polymyxa PE 5.808 was identified from a large NTG mutated library with about 5,000 isolates. The volumetric productivity of polymyxin E of P. polymyxa PE 5.808 was 1,200 μg/ml in shake flasks, about 140% improvement compared with that of the wild type strain.     

A live-cell high-throughput screening assay for identification of fatty acid uptake inhibitors

We developed a live-cell high-throughput assay system using the baker's yeast Saccharomyces cerevisiae to screen for chemical compounds that will inhibit fatty acid uptake. The target for the inhibitors is a mammalian fatty acid transport protein (mmFATP2), which is involved in the fatty acid transport and activation pathway. The mmFATP2 was expressed in a S. cerevisiae mutant strain deficient in Fat1p-dependent fatty acid uptake and reduced in long-chain fatty acid activation, fat1Deltafaa1Delta. To detect fatty acid import, a fluorescent fatty acid analog, 4,4-difluoro-5-methyl-4-bora-3a,4a-diaza-s-indacene-3-dodecanoic acid (C1-BODIPY-C12), was incubated with cells expressing FATP2 in a 96-well plate. The mmFATP2-dependent C1-BODIPY-C12 uptake was monitored by measuring intracellular C1-BODIPY-C12 fluorescence on a microtiter plate reader, whereas extracellular fluorescence was quenched by a cell viability dye, trypan blue. Using this high-throughput screening method, we demonstrate that the uptake of the fluorescent fatty acid ligand was effectively competed by the natural fatty acid oleate. Inhibition of uptake was also demonstrated to occur when cells were pretreated with sodium azide or Triacsin C. This yeast live-cell-based assay is rapid to execute, inexpensive to implement, and has adequate sensitivity for high-throughput screening. The assay basis and limitations are discussed.     

Product-driven high-throughput screening of industrial filamentous actinomycetes

Traditional strain breeding of industrial filamentous actinomycetes has long been hampered by insufficient screening throughput. From microtiter plate based methods to droplet-based microfluidic screening, various novel product-driven high-throughput screening (HTS) methods have pushed the screening speed limit towards a minimum of hundreds of strains per second with single cell resolution.