高产吡咯喹啉醌扭脱甲基杆菌的高通量选育

吡咯喹啉醌(PQQ)是一种细菌脱氢酶的辅酶,具有促进机体生长、调节机体自由基水平等功能,应用于食品、医药等领域。由于化学合成法成本较高,微生物发酵法生产PQQ受到关注。目前,发酵法生产PQQ产量较低,限制了其工业应用。然而,由于对PQQ菌株的合成与调控机制尚缺乏深入理解,以及对野生型菌株缺乏必要的基因工程改造手段,目前采用代谢工程强化PQQ合成菌株还缺乏相关基础。因此,本研究以扭脱甲基杆菌Methylobacterium extorquens I-F2为研究对象,整合常压室温等离子体诱变、流式细胞术分选和高通量筛选策略,对样品制备和流式分选过程进行优化,最终筛选出一株PQQ高产突变菌株1-C6,PQQ产量比出发菌株I-F2提高98.02%。本文所述的流式细胞术结合高通量筛选方法能简单、快速地获得高产突变菌株,相比于基因工程改造和传统筛选方法,具有提升效果明显且易于实施等优势。     

代谢物生物传感器:微生物细胞工厂构建中的合成生物学工具

代谢物生物传感器作为重要的合成生物学工具,能够感应细胞内代谢物浓度的变化,转化为特定信号输出,在微生物细胞工厂的构建中显现出巨大的应用潜力。其主要组成部分通常包括生物识别元件和信号输出元件,前者来源于自然界中丰富的调控元件,如转录因子、核糖开关等,有着不同的响应机理,后者可以为荧光信号、生长优势、特定代谢通路的开闭等,取决于应用所需。着重介绍了近年来代谢物生物传感器在微生物细胞工厂构建中的应用实例,主要包括目标化合物菌株的高通量筛选、选择、胞内代谢动态调控和非遗传异质性选择,同时也着重讨论了代谢物生物传感器的性能对于应用的影响和在实际应用中可能面临的机遇与挑战。     

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。     

基于转录和翻译调控的氨基酸高产菌株筛选及构建策略

氨基酸的工业化生产和应用有近50年的历史。除了调味料和其他食品用途外,氨基酸还被用于动物饲料、药物和化妆品等许多领域。如今大多数氨基酸通过微生物发酵生产,极低的价格对它们在工业中的应用至关重要。通常采用挑选营养缺陷型或具有类似物抗性的菌株来筛选氨基酸生产菌。然而,因部分氨基酸生产菌的生产效率低下,限制了其工业化发展。主要梳理了营养缺陷型、氨基酸类似物和富含稀有密码子标记基因3种不同筛选方法及其实际应用,旨为高产菌株的筛选与构建提供候选方案。     

微生物药物:再次站在现代科技的聚光灯下——“微生物药物创新与高效制造”专刊序言

正以青霉素、链霉素和阿维菌素为代表的微生物药物3次获得诺贝尔奖的青睐,凸显了微生物药物在治疗人类疾病、防治农业病害和修复生态环境中的重要作用。同时,病原生物抗药性的日趋严重、新型疾病的发生、节能减排高产的生产需求等呼唤新药物、新机理、新菌株、新工艺的药物创新和高效制造。旨在改变传统药物发现、研究、改造和生产模式,高通量筛选、沉默基因簇     

常规诱变结合高通量筛选选育可利霉素高产菌株

可利霉素是通过基因工程定向育种技术获得的新型大环内酯类抗生素,是国家一类新药.[目的]为满足工业化生产需要,其工程菌株的发酵水平有待提高.[方法]多种常规诱变技术交替处理和高通量筛选方法选育可利霉素高产菌株,处理方法包括原生质体紫外诱变、DES(硫酸二乙酯)诱变、紫外光复活诱变、缬氨酸抗性筛选和正突变菌株的富集.[结果]高产菌株WSJ-1-7-49-133-82-43的摇瓶生物效价比出发菌株WSJ-1-7-49提高56％,500L中试发酵罐突变菌株效价较出发株高61％.[结论]说明多轮常规诱变育种结合高通量的筛选方法可以用于工业生产菌株的高效筛选.     

高产洛蒙真菌素洛蒙德链霉菌高通量筛选方法的建立与复合育种

[背景]洛蒙德链霉菌S015能生物合成具有广谱抗菌活性的吩嗪类化合物洛蒙真菌素。[目的]因S015菌株的洛蒙真菌素产量较低,将S015菌株经复合诱变育种和基因工程改造,提高洛蒙真菌素产量。[方法]建立洛蒙真菌素产生菌的高通量筛选方法,对出发菌株S0 15进行常压室温等离子体(atmospheric and room temperature plasma,ARTP)技术和紫外复合诱变,筛选得到高产菌株;并在高产菌株上敲除洛蒙真菌素的前体分支酸竟争途径中的关键基因trpE1、trpE2,再过表达全局调控基因afsR。[结果]利用洛蒙真菌素在紫外波长375 nm处的特征吸收峰,以及洛蒙真菌素浓度和375 nm处吸光度值的正相关关系,建立了基于24孔深孔板发酵和酶标仪快速检测的高通量筛选方法。经过6轮ARTP和紫外复合诱变及高通量筛选,从4 320株突变株中筛选得到遗传稳定的高产菌株M6,其洛蒙真菌素的产量为61.33 mg/L,是S015菌株的7.35倍;M6菌株的分支途径基因trpE1、trpE2双敲株的洛蒙真菌素产量为81.89 mg/L,是S015菌株的9.82倍;在该基因工程菌株中过表达全局调控基因afsR,产量为109.53 mg/L,是S015菌株的13.13倍。[结论]建立的高通量筛选方法可以有效筛选高产洛蒙真菌素的突变株,并且操作简单快速。通过ARTP和紫外复合诱变,结合高产株M6的基因工程改造,能进一步提升洛蒙真菌素的产量。     

大肠杆菌芳香族氨基酸代谢工程研究进展

芳香族氨基酸包括L-苯丙氨酸(L-Phe)、L-酪氨酸(L-Tyr)和L-色氨酸(L-Trp),是生物体内非常重要的必需氨基酸,具有重要的生物学功能,广泛应用于医药、食品和饲料等领域。本文中,笔者介绍了芳香族氨基酸的生物合成途径以及代谢调控,综述了构建大肠杆菌芳香族氨基酸生产菌株的代谢工程策略。针对现阶段工业化生产芳香族氨基酸存在的问题,笔者对进一步应用代谢工程策略改造芳香族氨基酸菌株进行了展望。     

谷氨酸棒杆菌生产异亮氨酸辅因子策略及其基因组整合研究进展

L?异亮氨酸属于三大支链氨基酸,是人体8种必需氨基酸之一,广泛应用于食品、药品、保健品、化妆品等领域。目前,微生物发酵法是工业生产L?异亮氨酸的主要方法,其中谷氨酸棒杆菌（Corynebacterium glutamicum）是发酵生产L?异亮氨酸的优势菌株,然而随机诱变会使产量的提高能力达到饱和,难以得到更加高产的菌株,因此针对诱变菌株进行理性改造已成为进一步提高产量的主要方式;且随着遗传操作技术在谷氨酸棒杆菌中的应用与优化,代谢工程育种已逐渐取代传统的诱变育种。综述了谷氨酸棒杆菌中L?异亮氨酸的生物合成途径、代谢调控机制和理性改造L?异亮氨酸生产菌株的策略,并对辅助因子工程应用于理性改造及对谷氨酸棒杆菌基因组整合策略进行了系统阐述,以期为工业水平稳定生产L?异亮氨酸高产菌株的基因组整合策略提供参考依据。     

基于PTP转运蛋白的瓜氨酸利用菌株高通量筛选策略及其应用评估

【目的】为降低发酵体系中氨基甲酸乙酯前体物瓜氨酸的浓度,建立基于PTP (putative transport protein)转运蛋白的瓜氨酸利用菌株高通量筛选策略,对不同样品中的瓜氨酸利用菌株进行分离、筛选和鉴定,并对其胞外瓜氨酸利用能力进行比较和分析。【方法】通过对瓜氨酸转运蛋白PTP的氨基酸序列进行比对分析,确定其保守区域,并通过设计获得简并引物,结合溴甲酚紫变色圈法、简并引物菌落PCR和二乙酰一肟显色法,建立瓜氨酸利用菌株的高通量筛选策略。【结果】设计出一对可用于筛选瓜氨酸利用菌株的简并引物,利用建立的高通量筛选策略从环境中分离获得65株具有瓜氨酸利用能力的菌株,其中Levilactobacillus brevis PC4可在4 h内消耗体系中91.08%的瓜氨酸。对分离菌株PTP编码基因在基因组中的位置进行分析发现,Latilactobacillussakei等4株菌的PTP编码基因都位于arc基因簇内,表明PTP蛋白的功能与分离菌株的瓜氨酸代谢途径密切相关。【结论】PTP蛋白是菌株胞外瓜氨酸利用的重要功能蛋白,基于PTP编码基因设计的高通量筛选策略可用于高效地从环境中分离...     

Design and characterization of auxotrophy-based amino acid biosensors

Efficient and inexpensive methods are required for the high-throughput quantification of amino acids in physiological fluids or microbial cell cultures. Here we develop an array of Escherichia coli biosensors to sensitively quantify eleven different amino acids. By using online databases, genes involved in amino acid biosynthesis were identified that - upon deletion - should render the corresponding mutant auxotrophic for one particular amino acid. This rational design strategy suggested genes involved in the biosynthesis of arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, threonine, tryptophan, and tyrosine as potential genetic targets. A detailed phenotypic characterization of the corresponding single-gene deletion mutants indeed confirmed that these strains could neither grow on a minimal medium lacking amino acids nor transform any other proteinogenic amino acid into the focal one. Site-specific integration of the egfp gene into the chromosome of each biosensor decreased the detection limit of the GFP-labeled cells by 30% relative to turbidometric measurements. Finally, using the biosensors to determine the amino acid concentration in the supernatants of two amino acid overproducing E. coli strains (i.e. ΔhisL and ΔtdcC) both turbidometrically and via GFP fluorescence emission and comparing the results to conventional HPLC measurements confirmed the utility of the developed biosensor system. Taken together, our study provides not only a genotypically and phenotypically well-characterized set of publicly available amino acid biosensors, but also demonstrates the feasibility of the rational design strategy used.     

Computational design of auxotrophy-dependent microbial biosensors for combinatorial metabolic engineering experiments

Combinatorial approaches in metabolic engineering work by generating genetic diversity in a microbial population followed by screening for strains with improved phenotypes. One of the most common goals in this field is the generation of a high rate chemical producing strain. A major hurdle with this approach is that many chemicals do not have easy to recognize attributes, making their screening expensive and time consuming. To address this problem, it was previously suggested to use microbial biosensors to facilitate the detection and quantification of chemicals of interest. Here, we present novel computational methods to: (i) rationally design microbial biosensors for chemicals of interest based on substrate auxotrophy that would enable their high-throughput screening; (ii) predict engineering strategies for coupling the synthesis of a chemical of interest with the production of a proxy metabolite for which high-throughput screening is possible via a designed bio-sensor. The biosensor design method is validated based on known genetic modifications in an array of E. coli strains auxotrophic to various amino-acids. Predicted chemical production rates achievable via the biosensor-based approach are shown to potentially improve upon those predicted by current rational strain design approaches. (A Matlab implementation of the biosensor design method is available via http://www.cs.technion.ac.il/~tomersh/tools).     

Amino acid transport in taxonomically diverse cyanobacteria and identification of two genes encoding elements of a neutral amino acid permease putatively involved in recapture of leaked hydrophobic amino acids.

The activities of uptake of thirteen 14C-labeled amino acids were determined in nine cyanobacteria, including the unicellular strains Synechococcus sp. strain PCC 7942 and Synechocystis sp. strain PCC 6803; the filamentous strain Pseudanabaena sp. strain PCC 6903, and the filamentous, heterocyst-forming strains Anabaena sp. strains PCC 7120 and PCC 7937; Nostoc sp. strains PCC 7413 and PCC 7107; Calothrix sp. strain PCC 7601 (which is a mutant unable to develop heterocysts); and Fischerella muscicola UTEX 1829. Amino acid transport mutants, selected as mutants resistant to some amino acid analogs, were isolated from the Anabaena, Nostoc, Calothrix, and Pseudanabaena strains. All of the tested cyanobacteria bear at least a neutral amino acid transport system, and some strains also bear transport systems specific for basic or acidic amino acids. Two genes, natA and natB, encoding elements (conserved component, NatA, and periplasmic binding protein, NatB) of an ABC-type permease for neutral amino acids were identified by insertional mutagenesis of strain PCC 6803 open reading frames from the recently published genomic DNA sequence of this cyanobacterium. DNA sequences homologous to natA and natB from strain PCC 6803 were detected by hybridization in eight cyanobacterial strains tested. Mutants unable to transport neutral amino acids, including natA and natB insertional mutants, accumulated in the extracellular medium a set of amino acids that always included Ala, Val, Phe, Ile, and Leu. A general role for a cyanobacterial neutral amino acid permease in recapture of hydrophobic amino acids leaked from the cells is suggested.     

氨基酸发酵生产的研究进展

由于氨基酸在食品、饲料、医药、农业和日用化工等方面有极其广泛的用途,尤其随着抗癌药物制剂、氨基酸输液制剂及甜味二肽生产的飞速发展,对原料氨基酸的需求量日益增长。传统的发酵工业越来越不能满足需求,势必被以基因工程为基础的新兴发酵工业所代替。通过对发酵法生产氨基酸的历史进行回顾,及对未来前景作出展望,指出了运用ＤＮＡ 重组、定向突变等手段,对代谢途径及关键酶进行了深入系统的研究的必要性。     

RAG GTPases in nutrient-mediated TOR signaling pathway

Amino acids are key nutrients for protein synthesis and many metabolic processes. There is compelling evidence that amino acids themselves regulate protein synthesis, degradation, and cell growth. Mammalian target of rapamycin complex 1 (mTORC1) plays a central role in cellular growth regulation. Amino acids potently activate mTORC1, however, the mechanism of amino acid signaling is largely unknown. Recent studies have identified Rag small GTPases as key components mediating amino acid signals to mTORC1 activation.     

蜡状芽胞杆菌群代谢途径的分析和比较

微生物基因组测序和高通量分析方法获得了大量的数据和信息,利用这些信息研究代谢网络成为当前的一个新热点。文章在比较和分析重构代谢网络不同方法的基础上,利用蜡状芽胞杆菌群中已测序的9株蜡状芽胞杆菌、6株炭疽芽胞杆菌、6株苏云金芽胞杆菌基因组,对它们的碳水化合物代谢途径、氨基酸代谢途径和能量代谢途径进行比较与分析,找出它们的共性和特性。这3种菌都存在必需的糖酵解、三羧酸循环、丙氨酸代谢、组氨酸代谢及能量代谢等途径;同时它们还存在特殊的代谢途径,蜡状芽胞杆菌对单糖的利用率较高;炭疽芽胞杆菌的氨基酸降解和转运途径较丰富;苏云金芽胞杆菌中存在催化谷氨酸转化的代谢旁路等。代谢途径的分析为深入研究它们的食物毒素、炭疽毒素和杀虫毒素提供了新思路。     

Metabolite profiles and the risk of developing diabetes

Emerging technologies allow the high-throughput profiling of metabolic status from a blood specimen (metabolomics). We investigated whether metabolite profiles could predict the development of diabetes. Among 2,422 normoglycemic individuals followed for 12 years, 201 developed diabetes. Amino acids, amines and other polar metabolites were profiled in baseline specimens by liquid chromatography-tandem mass spectrometry (LC-MS). Cases and controls were matched for age, body mass index and fasting glucose. Five branched-chain and aromatic amino acids had highly significant associations with future diabetes: isoleucine, leucine, valine, tyrosine and phenylalanine. A combination of three amino acids predicted future diabetes (with a more than fivefold higher risk for individuals in top quartile). The results were replicated in an independent, prospective cohort. These findings underscore the potential key role of amino acid metabolism early in the pathogenesis of diabetes and suggest that amino acid profiles could aid in diabetes risk assessment.