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Exploring linker's sequence diversity to fuse carotene cyclase and hydroxylase for zeaxanthin biosynthesis 利用连接子序列多样性融合胡萝卜素环化酶和羟化酶合成玉米黄质
IF 5.2 Q1 Engineering Pub Date : 2023-06-01 DOI: 10.1016/j.mec.2023.e00222
Aurélie Bouin , Congqiang Zhang , Nic D. Lindley , Gilles Truan , Thomas Lautier

Fusion of catalytic domains can accelerate cascade reactions by bringing enzymes in close proximity. However, the design of a protein fusion and the choice of a linker are often challenging and lack of guidance. To determine the impact of linker parameters on fusion proteins, a library of linkers featuring various lengths, secondary structures, extensions and hydrophobicities was designed. Linkers were used to fuse the lycopene cyclase (crtY) and β-carotene hydroxylase (crtZ) from Pantoea ananatis to create fusion proteins to produce zeaxanthin. The fusion efficiency was assessed by comparing the carotenoids content in a carotenoid-producer Escherichia coli strain. It was shown that in addition to the orientation of the enzymes and the size of the linker, the first amino acid of the linker is also a key factor in determining the efficiency of a protein fusion. The wide range of sequence diversity in our linker library enables the fine tuning of protein fusion and this approach can be easily transferred to other enzyme couples.

催化结构域的融合可以通过使酶接近来加速级联反应。然而,蛋白质融合体的设计和连接体的选择往往具有挑战性,并且缺乏指导。为了确定连接体参数对融合蛋白的影响,设计了一个具有不同长度、二级结构、延伸和疏水性的连接体库。连接子用于融合来自Pantea ananatis的番茄红素环化酶(crtY)和β-胡萝卜素羟化酶(crtZ),以产生融合蛋白来生产玉米黄质。通过比较类胡萝卜素产生菌大肠杆菌菌株中的类胡萝卜素含量来评估融合效率。研究表明,除了酶的取向和连接体的大小外,连接体的第一个氨基酸也是决定蛋白质融合效率的关键因素。我们的接头库中广泛的序列多样性使得能够对蛋白质融合进行微调,并且这种方法可以很容易地转移到其他酶对中。
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引用次数: 1
Adaptive laboratory evolution of Bacillus subtilis to overcome toxicity of lignocellulosic hydrolysate derived from Distiller's dried grains with solubles (DDGS) 枯草芽孢杆菌的适应性实验室进化以克服蒸馏器干燥谷物中木质纤维素水解物的毒性(DDGS)
IF 5.2 Q1 Engineering Pub Date : 2023-06-01 DOI: 10.1016/j.mec.2023.e00223
Jasper L.S.P. Driessen , Josefin Johnsen , Ivan Pogrebnyakov , Elsayed T.T. Mohamed , Solange I. Mussatto , Adam M. Feist , Sheila I. Jensen , Alex T. Nielsen

Microbial tolerance to toxic compounds formed during biomass pretreatment is a significant challenge to produce bio-based products from lignocellulose cost effectively. Rational engineering can be problematic due to insufficient prerequisite knowledge of tolerance mechanisms. Therefore, adaptive laboratory evolution was applied to obtain 20 tolerant lineages of Bacillus subtilis strains able to utilize Distiller's Dried Grains with Solubles-derived (DDGS) hydrolysate. Evolved strains showed both improved growth performance and retained heterologous enzyme production using 100% hydrolysate-based medium, whereas growth of the starting strains was essentially absent. Whole-genome resequencing revealed that evolved isolates acquired mutations in the global regulator codY in 15 of the 19 sequenced isolates. Furthermore, mutations in genes related to oxidative stress (katA, perR) and flagella function appeared in both tolerance and control evolution experiments without toxic compounds. Overall, tolerance adaptive laboratory evolution yielded strains able to utilize DDGS-hydrolysate to produce enzymes and hence proved to be a valuable tool for the valorization of lignocellulose.

微生物对生物质预处理过程中形成的有毒化合物的耐受性是从木质纤维素生产生物基产品的一个重大挑战。由于对公差机制的先决条件知识不足,理性工程可能会出现问题。因此,应用适应性实验室进化获得了20个枯草芽孢杆菌菌株的耐受谱系,这些菌株能够利用具有可溶物衍生(DDGS)水解物的Distiller’s Dried Grains。使用100%基于水解产物的培养基,进化菌株显示出提高的生长性能和保留的异源酶产量,而起始菌株基本上没有生长。全基因组重测序显示,进化的分离株在19个测序的分离株中的15个中获得了全球调节因子codY的突变。此外,在没有有毒化合物的耐受和控制进化实验中,都出现了与氧化应激(katA、perR)和鞭毛功能相关的基因突变。总体而言,耐受性适应性实验室进化产生了能够利用DDGS水解物生产酶的菌株,因此被证明是木质纤维素增值的有价值工具。
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引用次数: 0
Engineering sorghum for higher 4-hydroxybenzoic acid content 工程高粱具有较高的4-羟基苯甲酸含量
IF 5.2 Q1 Engineering Pub Date : 2022-12-01 DOI: 10.1016/j.mec.2022.e00207
Chien-Yuan Lin , Yang Tian , Kimberly Nelson-Vasilchik , Joel Hague , Ramu Kakumanu , Mi Yeon Lee , Venkataramana R. Pidatala , Jessica Trinh , Christopher M. De Ben , Jutta Dalton , Trent R. Northen , Edward E.K. Baidoo , Blake A. Simmons , John M. Gladden , Corinne D. Scown , Daniel H. Putnam , Albert P. Kausch , Henrik V. Scheller , Aymerick Eudes

Engineering bioenergy crops to accumulate coproducts in planta can increase the value of lignocellulosic biomass and enable a sustainable bioeconomy. In this study, we engineered sorghum with a bacterial gene encoding a chorismate pyruvate-lyase (ubiC) to reroute the plastidial pool of chorismate from the shikimate pathway into the valuable compound 4-hydroxybenzoic acid (4-HBA). A gene encoding a feedback-resistant version of 3-deoxy-d-arabino-heptulonate-7-phosphate synthase (aroG) was also introduced in an attempt to increase the carbon flux through the shikimate pathway. At the full maturity and senesced stage, two independent lines that co-express ubiC and aroG produced 1.5 and 1.7 dw% of 4-HBA in biomass, which represents 36- and 40-fold increases compared to the titer measured in wildtype. The two transgenic lines showed no obvious phenotypes, growth defects, nor alteration of cell wall polysaccharide content when cultivated under controlled conditions. In the field, when harvested before grain maturity, transgenic lines contained 0.8 and 1.2 dw% of 4-HBA, which represent economically relevant titers based on recent technoeconomic analysis. Only a slight reduction (11–15%) in biomass yield was observed in transgenics grown under natural environment. This work provides the first metabolic engineering steps toward 4-HBA overproduction in the bioenergy crop sorghum to improve the economics of biorefineries by accumulating a value-added coproduct that can be recovered from biomass and provide an additional revenue stream.

改造生物能源作物,在植物中积累副产品,可以增加木质纤维素生物质的价值,实现可持续的生物经济。在这项研究中,我们用一种编码choris酸丙酮酸裂解酶(ubiC)的细菌基因改造高粱,将choris酸的质体池从莽草酸途径转变为有价值的化合物4-羟基苯甲酸(4-HBA)。一个编码3-脱氧-d-阿拉伯-庚二酸-7-磷酸合成酶(aroG)的抗反馈基因也被引入,试图通过莽草酸途径增加碳通量。在完全成熟和衰老阶段,两个共同表达ubiC和aroG的独立品系在生物量中产生了1.5和1.7 dw%的4-HBA,与野生型相比,分别增加了36倍和40倍。在控制条件下培养时,两种转基因系均无明显表型、生长缺陷和细胞壁多糖含量变化。在田间,当在籽粒成熟前收获时,转基因品系含有0.8和1.2 dw%的4-HBA,根据最近的技术经济分析,这代表了经济上相关的滴度。在自然环境下生长的转基因作物的生物量产量仅略有下降(11-15%)。这项工作为生物能源作物高粱中4-HBA过量生产提供了第一个代谢工程步骤,通过积累可从生物质中回收的增值副产品来提高生物精炼厂的经济效益,并提供额外的收入来源。
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引用次数: 1
Engineering of Yarrowia lipolytica for terpenoid production 产萜类化合物的聚脂耶氏菌工程
IF 5.2 Q1 Engineering Pub Date : 2022-12-01 DOI: 10.1016/j.mec.2022.e00213
Jonathan Asmund Arnesen, Irina Borodina

Terpenoids are a group of chemicals of great importance for human health and prosperity. Terpenoids can be used for human and animal nutrition, treating diseases, enhancing agricultural output, biofuels, fragrances, cosmetics, and flavouring. However, due to the rapid depletion of global natural resources and manufacturing practices relying on unsustainable petrochemical synthesis, there is a need for economic alternatives to supply the world's demand for these essential chemicals. Microbial biosynthesis offers the means to develop scalable and sustainable bioprocesses for terpenoid production. In particular, the non-conventional yeast Yarrowia lipolytica demonstrates excellent potential as a chassis for terpenoid production due to its amenability to industrial production scale-up, genetic engineering, and high accumulation of terpenoid precursors. This review aims to illustrate the scientific progress in developing Y. lipolytica terpenoid cell factories, focusing on metabolic engineering approaches for strain improvement and cultivation optimization.

萜类化合物是一组对人类健康和繁荣非常重要的化学物质。萜类化合物可用于人类和动物营养、治疗疾病、提高农业产量、生物燃料、香料、化妆品和调味剂。然而,由于全球自然资源的迅速枯竭和依赖于不可持续的石化合成的制造实践,需要经济的替代品来满足世界对这些基本化学品的需求。微生物生物合成为开发可扩展和可持续的萜类化合物生产生物工艺提供了手段。特别是,由于其易于工业化生产规模扩大、基因工程和萜类前体的高积累,非常规酵母解脂耶氏酵母表现出作为萜类生产的良好潜力。本文综述了脂肪瘤萜类细胞工厂的科学进展,重点介绍了代谢工程方法在菌株改良和培养优化方面的应用。
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引用次数: 6
A targeted metabolomics method for extra- and intracellular metabolite quantification covering the complete monolignol and lignan synthesis pathway 一种用于细胞外和细胞内代谢物定量的靶向代谢组学方法,涵盖了完整的单脂素和木脂素合成途径
IF 5.2 Q1 Engineering Pub Date : 2022-12-01 DOI: 10.1016/j.mec.2022.e00205
Andrea Steinmann , Katrin Schullehner , Anna Kohl , Christina Dickmeis , Maurice Finger , Georg Hubmann , Guido Jach , Ulrich Commandeur , Marco Girhard , Vlada B. Urlacher , Stephan Lütz

Microbial synthesis of monolignols and lignans from simple substrates is a promising alternative to plant extraction. Bottlenecks and byproduct formation during heterologous production require targeted metabolomics tools for pathway optimization.

In contrast to available fractional methods, we established a comprehensive targeted metabolomics method. It enables the quantification of 17 extra- and intracellular metabolites of the monolignol and lignan pathway, ranging from amino acids to pluviatolide. Several cell disruption methods were compared. Hot water extraction was best suited regarding monolignol and lignan stability as well as extraction efficacy. The method was applied to compare enzymes for alleviating bottlenecks during heterologous monolignol and lignan production in E. coli. Variants of tyrosine ammonia-lyase had a considerable influence on titers of subsequent metabolites. The choice of multicopper oxidase greatly affected the accumulation of lignans. Metabolite titers were monitored during batch fermentation of either monolignol or lignan-producing recombinant E. coli strains, demonstrating the dynamic accumulation of metabolites.

The new method enables efficient time-resolved targeted metabolomics of monolignol- and lignan-producing E. coli. It facilitates bottleneck identification and byproduct quantification, making it a valuable tool for further pathway engineering studies. This method will benefit the bioprocess development of biotransformation or fermentation approaches for microbial lignan production.

微生物从简单底物中合成单脂醇和木脂素是一种很有前途的植物提取替代方法。异种生产过程中的瓶颈和副产物形成需要靶向代谢组学工具进行途径优化。与现有的分数方法相比,我们建立了一种全面的靶向代谢组学方法。它能够定量17个单脂素和木脂素途径的细胞外和细胞内代谢物,范围从氨基酸到pluviatolide。比较了几种细胞破坏方法。单脂素和木脂素的稳定性和提取效果最好的是热水提取。该方法用于比较缓解大肠杆菌中异源单脂素和木脂素生产瓶颈的酶。酪氨酸解氨酶的变异对随后代谢产物的滴度有相当大的影响。多铜氧化酶的选择对木脂素的积累有很大影响。在分批发酵过程中,对产生单脂素或木脂素的重组大肠杆菌菌株的代谢物滴度进行监测,显示代谢物的动态积累。新方法能够有效的时间分辨靶向代谢组学的单脂素和木脂素生产大肠杆菌。它有助于瓶颈识别和副产物量化,使其成为进一步途径工程研究的有价值的工具。该方法将有利于微生物木脂素生产的生物转化或发酵方法的生物工艺发展。
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引用次数: 0
Tuning a high performing multiplexed-CRISPRi Pseudomonas putida strain to further enhance indigoidine production 调整一个高性能的多重crispri恶臭假单胞菌菌株,进一步提高靛蓝苷的产量
IF 5.2 Q1 Engineering Pub Date : 2022-12-01 DOI: 10.1016/j.mec.2022.e00206
Jeffrey J. Czajka , Deepanwita Banerjee , Thomas Eng , Javier Menasalvas , Chunsheng Yan , Nathalie Munoz Munoz , Brenton C. Poirier , Young-Mo Kim , Scott E. Baker , Yinjie J. Tang , Aindrila Mukhopadhyay

In this study, a 14-gene edited Pseudomonas putida KT2440 strain for heterologous indigoidine production was examined using three distinct omic datasets. Transcriptomic data indicated that CRISPR/dCpf1-interference (CRISPRi) mediated multiplex repression caused global gene expression changes, implying potential undesirable changes in metabolic flux. 13C-metabolic flux analysis (13C-MFA) revealed that the core P. putida flux network after CRISPRi repression was conserved, with moderate reduction of TCA cycle and pyruvate shunt activity along with glyoxylate shunt activation during glucose catabolism. Metabolomic results identified a change in intracellular TCA metabolites and extracellular metabolite secretion profiles (sugars and succinate overflow) in the engineered strains. These omic analyses guided further strain engineering, with a random mutagenesis screen first identifying an optimal ribosome binding site (RBS) for Cpf1 that enabled stronger product-substrate pairing (1.6–fold increase). Then, deletion strains were constructed with excision of the PHA operon (ΔphaAZC-IID) resulting in a 2.2–fold increase in indigoidine titer over the optimized Cpf1-RBS construct at the end of the growth phase (∼6 h). The maximum indigoidine titer (at 72 h) in the ΔphaAZC-IID strain had a 1.5–fold and 1.8–fold increase compared to the optimized Cpf1-RBS construct and the original strain, respectively. Overall, this study demonstrated that integration of omic data types is essential for understanding responses to complex metabolic engineering designs and directly quantified the effect of such modifications on central metabolism.

在这项研究中,使用三个不同的组学数据集对一株14个基因编辑的恶臭假单胞菌KT2440菌株进行了异种靛蓝素生产的检测。转录组学数据表明,CRISPR/ dcpf1干扰(CRISPRi)介导的多重抑制导致了全球基因表达的变化,这意味着代谢通量可能发生不良变化。13c -代谢通量分析(13C-MFA)显示,CRISPRi抑制后的核心P. putida通量网络是保守的,在葡萄糖分解代谢过程中,TCA循环和丙酮酸分流活性以及glyoxylate分流活性适度降低。代谢组学结果确定了工程菌株细胞内TCA代谢物和细胞外代谢物分泌谱(糖和琥珀酸溢出)的变化。这些组学分析指导了进一步的菌株工程,随机突变筛选首先确定Cpf1的最佳核糖体结合位点(RBS),使产物-底物配对更强(增加1.6倍)。然后,通过去除PHA操纵子(ΔphaAZC-IID)构建缺失菌株,在生长阶段结束时(~ 6 h),其靛蓝素滴度比优化的Cpf1-RBS结构提高了2.2倍。与优化的Cpf1-RBS结构和原始菌株相比,ΔphaAZC-IID菌株的最大靛蓝素滴度(72 h)分别提高了1.5倍和1.8倍。总体而言,本研究表明,整合组学数据类型对于理解对复杂代谢工程设计的反应至关重要,并可直接量化此类修饰对中枢代谢的影响。
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引用次数: 6
Dynamic and single cell characterization of a CRISPR-interference toolset in Pseudomonas putida KT2440 for β-ketoadipate production from p-coumarate 对香豆酸酯生产β-酮己二酸假单胞菌KT2440的crispr干扰工具集的动态和单细胞特性
IF 5.2 Q1 Engineering Pub Date : 2022-12-01 DOI: 10.1016/j.mec.2022.e00204
Jacob A. Fenster , Allison Z. Werner , Jian Wei Tay , Matthew Gillen , Leo Schirokauer , Nicholas C. Hill , Audrey Watson , Kelsey J. Ramirez , Christopher W. Johnson , Gregg T. Beckham , Jeffrey C. Cameron , Carrie A. Eckert

Pseudomonas putida KT2440 is a well-studied bacterium for the conversion of lignin-derived aromatic compounds to bioproducts. The development of advanced genetic tools in P. putida has reduced the turnaround time for hypothesis testing and enabled the construction of strains capable of producing various products of interest. Here, we evaluate an inducible CRISPR-interference (CRISPRi) toolset on fluorescent, essential, and metabolic targets. Nuclease-deficient Cas9 (dCas9) expressed with the arabinose (8K)-inducible promoter was shown to be tightly regulated across various media conditions and when targeting essential genes. In addition to bulk growth data, single cell time lapse microscopy was conducted, which revealed intrinsic heterogeneity in knockdown rate within an isoclonal population. The dynamics of knockdown were studied across genomic targets in exponentially-growing cells, revealing a universal 1.75 ± 0.38 h quiescent phase after induction where 1.5 ± 0.35 doublings occur before a phenotypic response is observed. To demonstrate application of this CRISPRi toolset, β-ketoadipate, a monomer for performance-advantaged nylon, was produced at a 4.39 ± 0.5 g/L and yield of 0.76 ± 0.10 mol/mol from p-coumarate, a hydroxycinnamic acid that can be derived from grasses. These cultivation metrics were achieved by using the higher strength IPTG (1K)-inducible promoter to knockdown the pcaIJ operon in the βKA pathway during early exponential phase. This allowed the majority of the carbon to be shunted into the desired product while eliminating the need for a supplemental carbon and energy source to support growth and maintenance.

恶臭假单胞菌KT2440是一种被充分研究的细菌,用于将木质素衍生的芳香族化合物转化为生物制品。恶臭杆菌先进遗传工具的发展减少了假设检验的周转时间,并使菌株的构建能够产生各种感兴趣的产品。在这里,我们评估了一种可诱导的crispr干扰(CRISPRi)工具集,用于荧光、必需和代谢靶标。用阿拉伯糖(8K)诱导启动子表达的核酸酶缺陷Cas9 (dCas9)在各种培养基条件下和靶向必需基因时受到严格调控。除了大量生长数据外,还进行了单细胞延时显微镜观察,结果显示了在同克隆群体中敲除率的内在异质性。在指数生长的细胞中,研究了基因组靶点的敲低动力学,揭示了诱导后普遍存在1.75±0.38 h的静止期,在观察到表型应答之前发生1.5±0.35倍。为了演示该CRISPRi工具集的应用,我们以4.39±0.5 g/L的产率和0.76±0.10 mol/mol的产率从可从草中提取的羟基肉桂酸对香豆酸中制备了性能优越的尼龙单体β-酮己二酸。这些培养指标是通过在早期指数阶段使用更高强度的IPTG (1K)诱导启动子敲除βKA通路中的pcaIJ操纵子来实现的。这使得大部分碳被分流到所需的产品中,同时消除了补充碳和能源来支持生长和维持的需要。
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引用次数: 4
Itaconic acid production is regulated by LaeA in Aspergillus pseudoterreus 假地曲霉衣康酸的产生受LaeA调控
IF 5.2 Q1 Engineering Pub Date : 2022-12-01 DOI: 10.1016/j.mec.2022.e00203
Kyle R. Pomraning , Ziyu Dai , Nathalie Munoz , Young-Mo Kim , Yuqian Gao , Shuang Deng , Teresa Lemmon , Marie S. Swita , Jeremy D. Zucker , Joonhoon Kim , Stephen J. Mondo , Ellen Panisko , Meagan C. Burnet , Bobbie-Jo M. Webb-Robertson , Beth Hofstad , Scott E. Baker , Kristin E. Burnum-Johnson , Jon K. Magnuson , for the Agile BioFoundry

The global regulator LaeA controls secondary metabolism in diverse Aspergillus species. Here we explored its role in regulation of itaconic acid production in Aspergillus pseudoterreus. To understand its role in regulating metabolism, we deleted and overexpressed laeA, and assessed the transcriptome, proteome, and secreted metabolome prior to and during initiation of phosphate limitation induced itaconic acid production. We found that secondary metabolite clusters, including the itaconic acid biosynthetic gene cluster, are regulated by laeA and that laeA is required for high yield production of itaconic acid. Overexpression of LaeA improves itaconic acid yield at the expense of biomass by increasing the expression of key biosynthetic pathway enzymes and attenuating the expression of genes involved in phosphate acquisition and scavenging. Increased yield was observed in optimized conditions as well as conditions containing excess nutrients that may be present in inexpensive sugar containing feedstocks such as excess phosphate or complex nutrient sources. This suggests that global regulators of metabolism may be useful targets for engineering metabolic flux that is robust to environmental heterogeneity.

全球调节剂LaeA控制着多种曲霉种的次级代谢。本文探讨了其在假地曲霉衣康酸生产调控中的作用。为了了解其在调节代谢中的作用,我们删除和过表达laeA,并在磷酸盐限制诱导衣康酸产生之前和开始期间评估转录组、蛋白质组和分泌代谢组。我们发现二级代谢产物簇,包括衣康酸生物合成基因簇,受laeA调控,laeA是衣康酸高产生产所必需的。LaeA的过表达增加了关键生物合成途径酶的表达,减弱了参与磷酸盐获取和清除的基因的表达,从而以牺牲生物量为代价提高衣康酸的产量。在优化条件下,以及在含有过量磷酸盐或复杂营养源等廉价糖原料中可能存在的过量营养条件下,观察到产量增加。这表明,代谢的全局调节因子可能是工程代谢通量的有用靶点,对环境异质性具有鲁棒性。
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引用次数: 7
Development of a dedicated Golden Gate Assembly Platform (RtGGA) for Rhodotorula toruloides 专用金门组装平台(RtGGA)的开发
IF 5.2 Q1 Engineering Pub Date : 2022-12-01 DOI: 10.1016/j.mec.2022.e00200
Nemailla Bonturi , Marina Julio Pinheiro , Paola Monteiro de Oliveira , Eka Rusadze , Tobias Eichinger , Gintare Liudžiūtė , Juliano Sabedotti De Biaggi , Age Brauer , Maido Remm , Everson Alves Miranda , Rodrigo Ledesma-Amaro , Petri-Jaan Lahtvee

Rhodotorula toruloides is a potential chassis for microbial cell factories as this yeast can metabolise different substrates into a diverse range of natural products, but the lack of efficient synthetic biology tools hinders its applicability. In this study, the modular, versatile and efficient Golden Gate DNA assembly system (RtGGA) was adapted to the first basidiomycete, an oleaginous yeast R. toruloides. R. toruloides CCT 0783 was sequenced, and used for the GGA design. The DNA fragments were assembled with predesigned 4-nt overhangs and a library of standardized parts was created containing promoters, genes, terminators, insertional regions, and resistance genes. The library was combined to create cassettes for the characterization of promoters strength and to overexpress the carotenoid production pathway. A variety of reagents, plasmids, and strategies were used and the RtGGA proved to be robust. The RtGGA was used to build three versions of the carotenoid overexpression cassette by using different promoter combinations. The cassettes were transformed into R. toruloides and the three new strains were characterized. Total carotenoid concentration increased by 41%. The dedicated GGA platform fills a gap in the advanced genome engineering toolkit for R. toruloides, enabling the efficient design of complex metabolic pathways.

toruloides红酵母是微生物细胞工厂的潜在基础,因为这种酵母可以将不同的底物代谢成多种天然产物,但缺乏有效的合成生物学工具阻碍了其适用性。本研究将模块化、多用途和高效的金门DNA组装系统(Golden Gate DNA assembly system, RtGGA)应用于第一担子菌——产油酵母toruloides。对toruloides CCT 0783进行测序,并用于GGA设计。将DNA片段与预先设计的4-nt悬垂进行组装,并创建一个包含启动子、基因、终止子、插入区和抗性基因的标准化部分文库。该文库被组合成盒式磁带,用于表征启动子强度和过表达类胡萝卜素的产生途径。使用了各种试剂、质粒和策略,RtGGA被证明是健壮的。RtGGA通过使用不同的启动子组合构建了三个版本的类胡萝卜素过表达盒。将这些盒式菌转化为toruloides,并对3个新菌株进行了鉴定。总类胡萝卜素浓度增加41%。专用的GGA平台填补了toruloides先进基因组工程工具包的空白,使复杂代谢途径的有效设计成为可能。
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引用次数: 8
RNA polymerase II-driven CRISPR-Cas9 system for efficient non-growth-biased metabolic engineering of Kluyveromyces marxianus RNA聚合酶ii驱动的CRISPR-Cas9系统高效非生长偏倚克卢维酵母代谢工程
IF 5.2 Q1 Engineering Pub Date : 2022-12-01 DOI: 10.1016/j.mec.2022.e00208
Danielle Bever , Ian Wheeldon , Nancy Da Silva

The thermotolerant yeast Kluyveromyces marxianus has gained significant attention in recent years as a promising microbial candidate for industrial biomanufacturing. Despite several contributions to the expanding molecular toolbox for gene expression and metabolic engineering of K. marxianus, there remains a need for a more efficient and versatile genome editing platform. To address this, we developed a CRISPR-based editing system that enables high efficiency marker-less gene disruptions and integrations using only 40 bp homology arms in NHEJ functional and non-functional K. marxianus strains. The use of a strong RNA polymerase II promoter allows efficient expression of gRNAs flanked by the self-cleaving RNA structures, tRNA and HDV ribozyme, from a single plasmid co-expressing a codon optimized Cas9. Implementing this system resulted in nearly 100% efficiency of gene disruptions in both NHEJ-functional and NHEJ-deficient K. marxianus strains, with donor integration efficiencies reaching 50% and 100% in the two strains, respectively. The high gRNA targeting performance also proved instrumental for selection of engineered strains with lower growth rate but improved polyketide biosynthesis by avoiding an extended outgrowth period, a common method used to enrich for edited cells but that fails to recover advantageous mutants with even slightly impaired fitness. Finally, we provide the first demonstration of simultaneous, markerless integrations at multiple loci in K. marxianus using a 2.6 kb and a 7.6 kb donor, achieving a dual integration efficiency of 25.5% in a NHEJ-deficient strain. These results highlight both the ease of use and general robustness of this system for rapid and flexible metabolic engineering in this non-conventional yeast.

近年来,耐热酵母菌马氏克鲁维菌(Kluyveromyces marxianus)作为一种有前景的工业生物制造微生物候选者受到了极大的关注。尽管对K. marxianus的基因表达和代谢工程的分子工具箱有了一些贡献,但仍然需要一个更高效、更通用的基因组编辑平台。为了解决这个问题,我们开发了一种基于crispr的编辑系统,该系统可以在NHEJ功能性和非功能性马氏k.m arxianus菌株中使用仅40 bp的同源臂进行高效的无标记基因破坏和整合。使用强大的RNA聚合酶II启动子,可以从一个共表达密码子优化的Cas9的质粒上有效地表达带有自切割RNA结构、tRNA和HDV核酶的gRNAs。该系统对nhej功能菌株和nhej缺陷菌株的基因破坏效率均接近100%,两株菌株的供体整合效率分别达到50%和100%。高gRNA靶向性能也被证明有助于选择生长速度较低但通过避免延长生长周期而改善聚酮生物合成的工程菌株,这是一种用于富集编辑细胞的常用方法,但无法恢复适应性略有受损的有利突变体。最后,我们首次展示了利用2.6 kb和7.6 kb的供体在马氏K. marxianus的多个位点上同时进行无标记整合,在缺乏nhej的菌株中实现了25.5%的双整合效率。这些结果突出了该系统的易用性和总体稳健性,可用于这种非常规酵母的快速和灵活的代谢工程。
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引用次数: 2
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Metabolic Engineering Communications
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