Burkholderia sp. IDO3中靛蓝合成基因的克隆表达及其合成特性

【目的】克隆和表达靛蓝合成基因,并将其用于靛蓝合成研究。【方法】对菌株Burkholderia sp.IDO3中靛蓝合成基因进行克隆和大肠杆菌异源表达,构建能合成蓝色色素的基因工程菌。利用液相色谱和质谱对产物进行分析,采用单因素法对培养温度、转速、培养基成分等进行优化,并考察优化条件下的靛蓝合成曲线。【结果】构建了一株重组大肠杆菌E.coli IND_AB,该菌株能够在LB培养基生长的过程中合成蓝色色素,产物分析表明该色素为靛蓝;菌株IND_AB在30°C和150 r/min条件下能在LB培养基中合成22.9 mg/L靛蓝,优化培养条件后产量达到25.4 mg/L;优化LB培养基各组分浓度后产量可提高到35.1 mg/L;外加50.0 mg/L吲哚或0.1 g/L色氨酸后靛蓝产量可分别提高到57.7 mg/L和64.4 mg/L,相比初始产量提高了152.0%和181.2%;靛蓝合成曲线表明在添加吲哚或色氨酸的培养基中,菌株IND_AB前6 h没有靛蓝生成,6-15 h为靛蓝合成加速期,18 h达到产量平衡。【结论】重组大肠杆菌IND_AB可用于生物合成高纯度靛蓝,为靛蓝的微生物合成提供了有效的基因资源。     

脂肪酸代谢途径影响聚酮化合物生物合成的机制及应用研究进展

聚酮化合物（PKs）作为一大类次级代谢产物，有着重要的生物活性和潜在的应用价值。链霉菌具有合成多种聚酮化合物的潜力，但野生型菌株合成聚酮化合物的产量难以满足工业化生产的需求。贮藏脂质的降解能为聚酮化合物生物合成提供大量的酰基CoA前体，因此，控制好脂肪酸与聚酮化合物生物合成通量，有利于促进目标聚酮化合物的合成。本文综述了强化脂肪酸β-氧化途径提高聚酮化合物产量的研究进展，为利用β-氧化途径促进聚酮化合物生物合成提供了新的研究策略。     

天然产物合成生物学体系的优化策略

天然产物是新药研发的重要源泉。天然产物合成生物学通过设计、重构目标化合物的高效生物合成途径,借助宿主改造,利用发酵生产目标化合物,可以有效弥补有机合成化学在复杂天然产物类药物生产方面的不足。虽然合成生物学已经取得了一些进展,但是通过合成生物学技术使目标产物的产量达到工业化生产水平依然是一项非常具有挑战性的任务。综述了天然产物合成生物学体系的优化策略,通过综合运用单个元件、外源代谢途径、底盘系统和发酵条件的优化技术,可以实现生物合成系统的最优化,最大化目标产物的产量,为来源稀缺的复杂天然产物的开发提供持续、稳定、经济的原料供给,推动天然产物类新药的研发。     

微生物核糖体工程研究进展

摘要：微生物获得特定类型的抗性突变,不仅反映了其核糖体或RNA多聚酶上相关靶位点结构的改变,也对突变菌株次级代谢产物（抗生素等）的生物合成能力产生深刻影响,因此筛选抗性突变株可作为微生物推理选育的途径之一。“核糖体工程”是利用微生物的各类抗性突变为筛选标记,高效获得次生代谢产物合成能力提高的突变株的推理育种新方法。本文综述了微生物“核糖体工程”的概念、各类突变的作用机理,并着重介绍组合抗性突变在提高出发菌株次级代谢产物产量方面的应用。     

合成微生物群落共培养研究概况

合成微生物群落的共培养是在一个培养容器中一起培养两种或多种微生物的方法,通过模拟自然生态,来构建人工的微生物群落,可导致现有天然产物积累的增加,或由于微生物串扰和化学防御而触发沉默生物合成途径的表达,产生新的化合物。本文从合成微生物群落的共培养体系及应用等方面对国内外有关合成微生物群落共培养的研究进行概述,旨在为合成微生物群落共培养的进一步深入研究及开发应用提供参考。     

红霉素链霉菌突变株的生化互补和红霉素生物合成途径的研究

红霉素链霉菌经不同诱变因素处理后,采用琼脂块法大量筛选得到26株无活性菌株,再用琼脂条共合成方法测定了这些无活性菌株351对互补菌株对,其中85对有共合成能力的生化互补菌株。根据供体菌与受体菌(或转化菌)生化互补共合成红霉素的特性,26株无活性菌株可分为4个类群:这4个类群液体培养共合成试验结果,有的互补对红霉素产量在1,500微克/毫升以上,这为提取和研究红霉素生物合成的中间产物提供了方便。根据固体和液体生化互补顺序,初步绘制了26株无活性突变株的红霉素生物合成途径。     

基因工程微生物合成鼠李糖脂表面活性剂的研究进展

鼠李糖脂是一类重要的生物表面活性剂。相比于化学合成的表面活性剂,其具有更优秀的理化性质及环境友好等特点,被广泛应用于微生物采油、环境污染修复等工程中。目前,鼠李糖脂的工业生产主要采用铜绿假单胞菌这一具有致病性的天然合成菌株,与此同时,受菌株遗传背景的限制,优化发酵过程等方法在产量提升方面遇到了一些瓶颈问题。利用基因工程方法对菌株进行改良有望进一步提高鼠李糖脂生产的安全性、产量、产物性能等多项指标,因此受到了越来越广泛的关注。本文综述了近年来利用基因工程方法优化鼠李糖脂生物合成的最新进展,讨论了异源合成、代谢通路改造、基因表达优化、蛋白质工程、底盘工程等多种策略的应用,并展望了一系列可行的研究方向。     

代谢工程改造酿酒酵母合成柠檬烯及其衍生物

柠檬烯及其衍生物紫苏酸作为重要的生物活性天然产物，广泛应用于食品、化妆品、保健品和医药等行业。然而，低效率的植物提取与高能耗的化工合成限制了柠檬烯和紫苏酸的工业合成。本研究在酿酒酵母中通过过氧化物酶体区室化表达绿薄荷来源的柠檬烯合酶，构建获得重组菌株，柠檬烯产量为0.038 mg/L。采用模块化工程分步表达参与柠檬烯合成的基因ERG10、ERG13、tHMGR、ERG12、ERG8、IDI1、MVD1、ERG20ww以及tLS，以研究其对柠檬烯产量的影响。通过增加前体模块，柠檬烯产量增加至1.14 mg/L。采用高拷贝数的质粒表达上述关键基因，柠檬烯的产量显著提高，达到86.74 mg/L，提高至初始菌株产量的4 337倍。以构建的柠檬烯生产菌株为出发菌株，通过表达丹参来源的细胞色素P450酶基因，实现了紫苏酸的生成，其产量达4.42 mg/L，为利用酿酒酵母构建高产单萜类天然产物的细胞工厂奠定了基础。     

卡西霉素生物合成基因簇中调控基因calR1的功能

【背景】卡西霉素(calcimycin)是重要的离子载体抗生素,其生物合成基因簇已从教酒链霉菌NRRL3882的基因组DNA中成功克隆,但基因簇内的部分生物合成基因及调控基因的功能有待研究。【目的】研究卡西霉素产生菌教酒链霉菌NRRL3882中编码TylR家族同源转录调控蛋白的calR1基因的功能。【方法】通过PCR-targeting的方法,构建calR1基因敲除突变株及回补菌株,对突变菌株及回补菌株进行发酵,通过HPLC分析其代谢产物。利用荧光定量PCR检测ΔcalR1突变菌株和野生菌株的生物合成基因转录水平。【结果】calR1基因敲除突变株丧失产生卡西霉素的能力,但仍有中间产物噻唑霉素的积累,回补菌株中卡西霉素的产量有一定程度的恢复。RT-qPCR结果表明,卡西霉素合成相关的一些重要基因calC、calG、calU3等基因的表达量明显改变。【结论】TylR家族转录调控基因calR1是卡西霉素生物合成的调控基因。     

利用CRISPR-Cas9系统与核糖体工程获得新型可利霉素产生菌

可利霉素 (Carrimycin,CAM) 是将异戊酰基转移酶基因 (Isovaleryltransferase gene,ist) 导入到螺旋链霉菌中产生的以异戊酰螺旋霉素 (Isovalerylspiramycin,ISP) 为主组分的抗生素。原工程菌中的ist基因与螺旋霉素 (Spiramycin,SP) 生物合成基因簇相距较远,且具有两种抗性基因,难以对其进行基因改造,因此需要构建新型CAM工程菌株。文中通过CRISPR-Cas9基因编辑系统靶向切割2个位点,将ist和其正调控基因acyB2通过同源重组插入到SP生物合成基因簇附近且不参与SP合成的orf54基因下游,获得2种无外源抗性基因插入的CAM产生菌54IA-1和54IA-2,经发酵产物检测发现54IA-2菌株中的ISP产量明显高于54IA-1菌株。通过实时定量PCR (Quantitative real-time PCR,qPCR) 检测证实54IA-2菌株中ist和acyB2基因以及部分SP生物合成基因的表达量均高于54IA-1菌株。为进一步获得高产菌株,以54IA-2为出发菌株,利用核糖体工程的方法筛选利福平 (Rifampicin,RFP) 抗性菌株,在RFP浓度为40 μg/mL的抗性菌株中,ISP的产量明显提高,最高可达842.9 μg/mL,比原始菌株提高约6倍。对其中7株菌的rpoB基因进行测序分析,每株菌的第576位丝氨酸都突变为丙氨酸,在其他错义突变中产量最高的菌株RFP40-6-8在第424位的谷氨酰胺突变为亮氨酸。综上所述,本研究应用CRISPR-Cas9系统成功构建了无任何抗性标记的新型CAM工程菌株54IA-1和54IA-2,并通过核糖体工程技术筛选获得了新型CAM高产菌株RFP40-6-8,为CAM工程菌株的进一步优化改造奠定了基础。     

Modular co-culture engineering,a new approach for metabolic engineering

With the development of metabolic engineering, employment of a selected microbial host for accommodation of a designed biosynthetic pathway to produce a target compound has achieved tremendous success in the past several decades. Yet, increasing requirements for sophisticated microbial biosynthesis call for establishment and application of more advanced metabolic engineering methodologies. Recently, important progress has been made towards employing more than one engineered microbial strains to constitute synthetic co-cultures and modularizing the biosynthetic labor between the co-culture members in order to improve bioproduction performance. This emerging approach, referred to as modular co-culture engineering in this review, presents a valuable opportunity for expanding the scope of the broad field of metabolic engineering. We highlight representative research accomplishments using this approach, especially those utilizing metabolic engineering tools for microbial co-culture manipulation. Key benefits and major challenges associated with modular co-culture engineering are also presented and discussed.     

Reliable online measurement of population dynamics for filamentous co-cultures

Understanding population dynamics is a key factor for optimizing co-culture processes to produce valuable compounds. However, the measurement of independent population dynamics is difficult, especially for filamentous organisms and in presence of insoluble substrates like cellulose. We propose a workflow for fluorescence-based online monitoring of individual population dynamics of two filamentous microorganisms. The fluorescent tagged target co-culture is composed of the cellulolytic fungus Trichoderma reesei RUT-C30—mCherry and the pigment-producing bacterium Streptomyces coelicolor A3(2)—mNeonGreen (mNG) growing on insoluble cellulose as a substrate. To validate the system, the fluorescence-to-biomass and fluorescence-to-scattered-light correlation of the two strains was characterized in depth under various conditions. Thereby, especially for complex filamentous microorganisms, microbial morphologies have to be considered. Another bias can arise from autofluorescence or pigments that can spectrally interfere with the fluorescence measurement. Green autofluorescence of both strains was uncoupled from different green fluorescent protein signals through a spectral unmixing approach, resulting in a specific signal only linked to the abundance of S. coelicolor A3(2)—mNG. As proof of principle, the population dynamics of the target co-culture were measured at varying inoculation ratios in presence of insoluble cellulose particles. Thereby, the respective fluorescence signals reliably described the abundance of each partner, according to the variations in the inocula. With this method, conditions can be fine-tuned for optimal growth of both partners along with natural product formation by the bacterium.     

Engineering co-culture system for production of apigetrin in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Microbial cells have extensively been utilized to produce value-added bioactive compounds. Based on advancement in protein engineering, DNA recombinant technology, genome engineering, and metabolic remodeling, the microbes can be re-engineered to produce industrially and medicinally important platform chemicals. The emergence of co-culture system which reduces the metabolic burden and allows parallel optimization of the engineered pathway in a modular fashion restricting the formation of undesired byproducts has become an alternative way to synthesize and produce bioactive compounds. In this study, we present genetically engineered E. coli-based co-culture system to the de novo synthesis of apigetrin (APG), an apigenin-7-O-β-d-glucopyranoside of apigenin. The culture system consists of an upstream module including 4-coumarate: CoA ligase (4CL), chalcone synthase, chalcone flavanone isomerase (CHS, CHI), and flavone synthase I (FNSI) to synthesize apigenin (API) from p-coumaric acid (PCA). Whereas, the downstream system contains a metabolizing module to enhance the production of UDP-glucose and expression of glycosyltransferase (PaGT3) to convert API into APG. To accomplish this improvement in titer, the initial inoculum ratio of strains for making the co-culture system, temperature, and media component was optimized. Following large-scale production, a yield of 38.5 µM (16.6 mg/L) of APG was achieved. In overall, this study provided an efficient tool to synthesize bioactive compounds in microbial cells.     

Increasing diterpene yield with a modular metabolic engineering system in E. coli: comparison of MEV and MEP isoprenoid precursor pathway engineering

Engineering biosynthetic pathways in heterologous microbial host organisms offers an elegant approach to pathway elucidation via the incorporation of putative biosynthetic enzymes and characterization of resulting novel metabolites. Our previous work in Escherichia coli demonstrated the feasibility of a facile modular approach to engineering the production of labdane-related diterpene (20 carbon) natural products. However, yield was limited (<0.1 mg/L), presumably due to reliance on endogenous production of the isoprenoid precursors dimethylallyl diphosphate and isopentenyl diphosphate. Here, we report incorporation of either a heterologous mevalonate pathway (MEV) or enhancement of the endogenous methyl erythritol phosphate pathway (MEP) with our modular metabolic engineering system. With MEP pathway enhancement, it was found that pyruvate supplementation of rich media and simultaneous overexpression of three genes (idi, dxs, and dxr) resulted in the greatest increase in diterpene yield, indicating distributed metabolic control within this pathway. Incorporation of a heterologous MEV pathway in bioreactor grown cultures resulted in significantly higher yields than MEP pathway enhancement. We have established suitable growth conditions for diterpene production levels ranging from 10 to >100 mg/L of E. coli culture. These amounts are sufficient for nuclear magnetic resonance analyses, enabling characterization of enzymatic products and hence, pathway elucidation. Furthermore, these results represent an up to >1,000-fold improvement in diterpene production from our facile, modular platform, with MEP pathway enhancement offering a cost effective alternative with reasonable yield. Finally, we reiterate here that this modular approach is expandable and should be easily adaptable to the production of any terpenoid natural product.     

Energy coupling in Saccharomyces cerevisiae: selected opportunities for metabolic engineering

Free-energy (ATP) conservation during product formation is crucial for the maximum product yield that can be obtained, but often overlooked in metabolic engineering strategies. Product pathways that do not yield ATP or even demand input of free energy (ATP) require an additional pathway to supply the ATP needed for product formation, cellular maintenance, and/or growth. On the other hand, product pathways with a high ATP yield may result in excess biomass formation at the expense of the product yield. This mini-review discusses the importance of the ATP yield for product formation and presents several opportunities for engineering free-energy (ATP) conservation, with a focus on sugar-based product formation by Saccharomyces cerevisiae. These engineering opportunities are not limited to the metabolic flexibility within S.?cerevisiae itself, but also expression of heterologous reactions will be taken into account. As such, the diversity in microbial sugar uptake and phosphorylation mechanisms, carboxylation reactions, product export, and the flexibility of oxidative phosphorylation via the respiratory chain and H(+) -ATP synthase can be used to increase or decrease free-energy (ATP) conservation. For product pathways with a negative, zero or too high ATP yield, analysis and metabolic engineering of the ATP yield of product formation will provide a promising strategy to increase the product yield and simplify process conditions.     

Experimental and computational optimization of an Escherichia coli co-culture for the efficient production of flavonoids

Metabolic engineering and synthetic biology have enabled the use of microbial production platforms for the renewable production of many high-value natural products. Titers and yields, however, are often too low to result in commercially viable processes. Microbial co-cultures have the ability to distribute metabolic burden and allow for modular specific optimization in a way that is not possible through traditional monoculture fermentation methods. Here, we present an Escherichia coli co-culture for the efficient production of flavonoids in vivo, resulting in a 970-fold improvement in titer of flavan-3-ols over previously published monoculture production. To accomplish this improvement in titer, factors such as strain compatibility, carbon source, temperature, induction point, and inoculation ratio were initially optimized. The development of an empirical scaled-Gaussian model based on the initial optimization data was then implemented to predict the optimum point for the system. Experimental verification of the model predictions resulted in a 65% improvement in titer, to 40.7±0.1 mg/L flavan-3-ols, over the previous optimum. Overall, this study demonstrates the first application of the co-culture production of flavonoids, the most in-depth co-culture optimization to date, and the first application of empirical systems modeling for improvement of titers from a co-culture system.     

Engineering of In Vitro 3D Capillary Beds by Self-Directed Angiogenic Sprouting

In recent years, microfluidic systems have been used to study fundamental aspects of angiogenesis through the patterning of single-layered, linear or geometric vascular channels. In vivo, however, capillaries exist in complex, three-dimensional (3D) networks, and angiogenic sprouting occurs with a degree of unpredictability in all x,y,z planes. The ability to generate capillary beds in vitro that can support thick, biological tissues remains a key challenge to the regeneration of vital organs. Here, we report the engineering of 3D capillary beds in an in vitro microfluidic platform that is comprised of a biocompatible collagen I gel supported by a mechanical framework of alginate beads. The engineered vessels have patent lumens, form robust ∼1.5 mm capillary networks across the devices, and support the perfusion of 1 µm fluorescent beads through them. In addition, the alginate beads offer a modular method to encapsulate and co-culture cells that either promote angiogenesis or require perfusion for cell viability in engineered tissue constructs. This laboratory-constructed vascular supply may be clinically significant for the engineering of capillary beds and higher order biological tissues in a scalable and modular manner.     

Microbial transformation of tannin-rich substrate to gallic acid through co-culture method

Modified solid-state fermentation (MSSF) of tannin-rich substrate yielding tannase and gallic acid was carried out using a co-culture of the filamentous fungi, Rhizopus oryzae (RO IIT RB-13, NRRL 21498) and Aspergillus foetidus (GMRB013 MTCC 3557). Powdered fruits of Terminalia chebula and powdered pod cover of Caesalpinia digyna was used in the process and the different process parameters for maximum production of tannase and gallic acid by co-culture method were optimized through media engineering. MSSF was carried out at the optimum conditions of 30 degrees C and 80% relative humidity. The optimal pH and incubation period was 5.0 and 48 h respectively. Through the co-culture technique the maximum yield of tannase and gallic acid was found to be 41.3 U/ml and 94.8% respectively.     

Protein design for pathway engineering

Design and construction of biochemical pathways has increased the complexity of biosynthetically-produced compounds when compared to single enzyme biocatalysis. However, the coordination of multiple enzymes can introduce a complicated set of obstacles to overcome in order to achieve a high titer and yield of the desired compound. Metabolic engineering has made great strides in developing tools to optimize the flux through a target pathway, but the inherent characteristics of a particular enzyme within the pathway can still limit the productivity. Thus, judicious protein design is critical for metabolic and pathway engineering. This review will describe various strategies and examples of applying protein design to pathway engineering to optimize the flux through the pathway. The proteins can be engineered for altered substrate specificity/selectivity, increased catalytic activity, reduced mass transfer limitations through specific protein localization, and reduced substrate/product inhibition. Protein engineering can also be expanded to design biosensors to enable high through-put screening and to customize cell signaling networks. These strategies have successfully engineered pathways for significantly increased productivity of the desired product or in the production of novel compounds.