Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli

Engineering biosynthetic pathways in microbes for the production of complex chemicals and pharmaceuticals is an attractive alternative to chemical synthesis. However, in transferring large pathways to alternate hosts and manipulating expression levels, the native regulation of carbon flux through the pathway may be lost leading to imbalances in the pathways. Previously, Escherichia coli was engineered to produce large quantities of isoprenoids by creating a mevalonate-based isopentenyl pyrophosphate biosynthetic pathway [Martin, V.J., Pitera, D.J., Withers, S.T., Newman, J.D., Keasling, J.D., 2003. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21, 796-802]. The strain produces high levels of isoprenoids, but upon further investigation we discovered that the accumulation of pathway intermediates limited flux and that high-level expression of the mevalonate pathway enzymes inhibited cell growth. Gene titration studies and metabolite profiling using liquid chromatography-mass spectrometry linked the growth inhibition phenotype with the accumulation of the pathway intermediate 3-hydroxy-3-methyl-glutaryl-coenzyme A (HMG-CoA). Such an accumulation implies that the activity of HMG-CoA reductase was insufficient to balance flux in the engineered pathway. By modulating HMG-CoA reductase production, we eliminated the pathway bottleneck and increased mevalonate production. These results demonstrate that balancing carbon flux through the heterologous pathway is a key determinant in optimizing isoprenoid biosynthesis in microbial hosts.     

大肠杆菌通过甲羟戊酸途径合成紫苏醇

紫苏醇,即[4-异丙烯基-1-环己烯]甲醇,是一种具有类似芳樟醇和松油醇特殊气味的单环单萜烯醇。在医药、食品和化妆品等行业具有广阔市场空间和研究价值。文中研究了以工程大肠杆菌通过甲羟戊酸途径合成紫苏醇的方法。首先在大肠杆菌中构建来源于粪肠球菌的MVA代谢途径合成柠檬烯,随后柠檬烯通过细胞色素P450烷烃羟化酶的羟基化转化为紫苏醇。然后将构建的紫苏醇合成菌株在摇瓶发酵条件下进行优化,研究发现工程大肠杆菌以葡萄糖为原料,通过MVA代谢途径可合成约50.12 mg/L的紫苏醇。本研究构建合成紫苏醇的MVA代谢途径也可用于其他萜类化合物的合成,为今后生物法合成萜类化合物提供了理论依据和技术支持。     

提高大肠杆菌通过MVA途径合成异戊二烯

异戊二烯是橡胶合成的重要前体物质。为了提高菌株的异戊二烯产量,本实验室在研究中构建了一株异戊二烯产气的菌株BW-01,基于蛋白质预算理论的指导,理性设计通过改变质粒拷贝数、增加稀有密码子等合成生物学手段调控关键限速酶编码基因表达,从而提高大肠杆菌外源MVA代谢途径的异戊二烯产量。摇瓶发酵实验中我们构建的新产气菌株BW-07比原有的产气菌株BW-01的产量提高了73%,达到了761.1 mg/L。为后续菌株改造及进行发酵罐实验奠定了基础。     

Coenzyme Q10 production in recombinant Escherichia coli strains engineered with a heterologous decaprenyl diphosphate synthase gene and foreign mevalonate pathway

In the present work, Escherichia coli DH5alpha was metabolically engineered for CoQ(10) production by the introduction of decaprenyl diphosphate synthase gene (ddsA) from Agrobacterium tumefaciens. Grown in 2YTG medium (1.6% tryptone, 1% yeast extract, 0.5% NaCl, and 0.5% glycerol) with an initial pH of 7, the recombinant E. coli was capable of CoQ(10) production up to 470 microg/gDCW (dry cell weight). This value could be further elevated to 900 microg/gDCW simply by increasing the initial culture pH from 7 to 9. Supplementation of 4-hydroxy benzoate did not improve the productivity any further. However, engineering of a lower mevalonate semi-pathway so as to increase the isopentenyl diphosphate (IPP) supply of the recombinant strain using exogenous mevalonate efficiently increased the CoQ(10) production. Lower mevalonate semi-pathways of Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, Enterococcus faecalis, and Saccharomyces cerevisiae were tested. Among these, the pathway of Streptococcus pneumoniae proved to be superior, yielding CoQ(10) production of 2,700+/-115 microg/gDCW when supplemented with exogenous mevalonate of 3 mM. In order to construct a complete mevalonate pathway, the upper semi-pathway of the same bacterium, Streptococcus pneumoniae, was recruited. In a recombinant E. coli DH5alpha harboring three plasmids encoding for upper and lower mevalonate semi-pathways as well as DdsA enzyme, the heterologous mevalonate pathway could convert endogenous acetyl-CoA to IPP, resulting in CoQ(10) production of up to 2,428+/-75 microg/gDCW, without mevalonate supplementation. In contrast, a whole mevalonate pathway constructed in a single operon was found to be less efficient. However, it provided CoQ(10) production of up to 1,706+/-86 microg/gDCW, which was roughly 1.9 times higher than that obtained by ddsA alone.     

Engineered isoprenoid pathway enhances astaxanthin production in Escherichia coli

The isoprenoid pathway is a versatile biosynthetic network leading to over 23,000 compounds. Similar to other biosynthetic pathways, the production of isoprenoids in microorganisms is controlled by the supply of precursors, among other factors. To engineer a host that has the capability to supply geranylgeranyl diphosphate (GGPP), a common precursor of isoprenoids, we cloned and overexpressed isopentenyl diphosphate (IPP) isomerase (encoded by idi) from Escherichia coli and GGPP synthase (encoded by gps) from the archaebacterium Archaeoglobus fulgidus. The latter was shown to be a multifunctional enzyme converting dimethylallyl diphosphate (DMAPP) to GGPP. These two genes and the gene cluster (crtBIYZW) of the marine bacterium Agrobacterium aurantiacum were introduced into E. coli to produce astaxanthin, an orange pigment and antioxidant. This metabolically engineered strain produces astaxanthin 50 times higher than values reported before. To determine the rate-controlling steps in GGPP production, the IDI-GPS pathway was compared with another construct containing idi, ispA (encoding farnesyl diphosphate (FPP) synthase in E. coli), and crtE (encoding GGPP synthase from Erwinia uredovora). Results show that the conversion from FPP to GGPP is the first bottleneck, followed sequentially by IPP isomerization and FPP synthesis. Removal of these bottlenecks results in an E. coli strain providing sufficient precursors for in vivo synthesis of isoprenoids.     

Engineering a mevalonate pathway in Escherichia coli for production of terpenoids

Isoprenoids are the most numerous and structurally diverse family of natural products. Terpenoids, a class of isoprenoids often isolated from plants, are used as commercial flavor and fragrance compounds and antimalarial or anticancer drugs. Because plant tissue extractions typically yield low terpenoid concentrations, we sought an alternative method to produce high-value terpenoid compounds, such as the antimalarial drug artemisinin, in a microbial host. We engineered the expression of a synthetic amorpha-4,11-diene synthase gene and the mevalonate isoprenoid pathway from Saccharomyces cerevisiae in Escherichia coli. Concentrations of amorphadiene, the sesquiterpene olefin precursor to artemisinin, reached 24 microg caryophyllene equivalent/ml. Because isopentenyl and dimethylallyl pyrophosphates are the universal precursors to all isoprenoids, the strains developed in this study can serve as platform hosts for the production of any terpenoid compound for which a terpene synthase gene is available.     

重组大肠杆菌高密度发酵产甲羟戊酸动力学

为提高甲羟戊酸产量,探究其发酵生产规律,以重组大肠杆菌YJM16为供试菌株,进行5 L发酵罐匀速补料的高密度发酵实验,最终细胞产量达到54.48 g/L,甲羟戊酸产量达到40.43 g/L,产率为20.2%。然后根据Logistic方程、Luedeking-Piret方程和类似Luedeking-Piret方程,拟合出重组大肠杆菌高密度发酵过程中菌体生长、甲羟戊酸合成、基质消耗的动力学模型及模型参数。结果表明,甲羟戊酸的合成与重组大肠杆菌的生长速率及菌体积累量均有关。菌体生长、底物消耗模型和产物形成模型拟合度R2分别达到了0.931 9、0.957 8和0.975 1,可用于描述利用重组大肠杆菌高密度发酵生产甲羟戊酸过程。     

Synergy between methylerythritol phosphate pathway and mevalonate pathway for isoprene production in Escherichia coli

Isoprene, a key building block of synthetic rubber, is currently produced entirely from petrochemical sources. In this work, we engineered both the methylerythritol phosphate (MEP) pathway and the mevalonate (MVA) pathway for isoprene production in E. coli. The synergy between the MEP pathway and the MVA pathway was demonstrated by the production experiment, in which overexpression of both pathways improved the isoprene yield about 20-fold and 3-fold, respectively, compared to overexpression of the MEP pathway or the MVA pathway alone. The ¹³C metabolic flux analysis revealed that simultaneous utilization of the two pathways resulted in a 4.8-fold increase in the MEP pathway flux and a 1.5-fold increase in the MVA pathway flux. The synergy of the dual pathway was further verified by quantifying intracellular flux responses of the MEP pathway and the MVA pathway to fosmidomycin treatment and mevalonate supplementation. Our results strongly suggest that coupling of the complementary reducing equivalent demand and ATP requirement plays an important role in the synergy of the dual pathway. Fed-batch cultivation of the engineered strain overexpressing the dual pathway resulted in production of 24.0 g/L isoprene with a yield of 0.267 g/g of glucose. The synergy of the MEP pathway and the MVA pathway also successfully increased the lycopene productivity in E. coli, which demonstrates that it can be used to improve the production of a broad range of terpenoids in microorganisms.     

Farnesol production from Escherichia coli by harnessing the exogenous mevalonate pathway

Farnesol (FOH) production has been carried out in metabolically engineered Escherichia coli. FOH is formed through the depyrophosphorylation of farnesyl pyrophosphate (FPP), which is synthesized from isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) by FPP synthase. In order to increase FPP synthesis, E. coli was metabolically engineered to overexpress ispA and to utilize the foreign mevalonate (MVA) pathway for the efficient synthesis of IPP and DMAPP. Two‐phase culture using a decane overlay of the culture broth was applied to reduce volatile loss of FOH produced during culture and to extract FOH from the culture broth. A FOH production of 135.5 mg/L was obtained from the recombinant E. coli harboring the pTispA and pSNA plasmids for ispA overexpression and MVA pathway utilization, respectively. It is interesting to observe that a large amount of FOH could be produced from E. coli without FOH synthase by the augmentation of FPP synthesis. Introduction of the exogenous MVA pathway enabled the dramatic production of FOH by E. coli while no detectable FOH production was observed in the endogenous MEP pathway‐only control. Biotechnol. Bioeng. 2010;107: 421–429. © 2010 Wiley Periodicals, Inc.     

Stability of Escherichia coli strains harboring recombinant plasmids for L-threonine production

Escherichia coli recombinant strains bearing the thr operon have been previously selected for threonine production and phenotypically classified according to antibiotic resistance properties (Nudel et al. 1987).Further analysis of those strains permitted the isolation and restriction mapping of two different plasmids of 13 kb and 18.6 kb. The smaller one, which expressed tetracycline resistance gave better results on threonine accumulation but it was rather unstable when grown without antibiotic pressure. Therefore, other hosts were transformed with those plasmids to improve stability.A threonine-auxotrophic strain was a better host for plasmid maintenance and expression of thr operon. Host influence in plasmid-mediated threonine production was studied in terms of specific yields (the ratios of threonine accumulated to biomass values) and of plasmid maintenance (percent of Ap^rTc^r clones after cultivation in non selective media).We also determined that semisynthetic media of defined composition were better than rich media for threonine expression, due to feed-back controls exerted by undesired catabolites accumulated in complex media.     

稳定表达MVA途径基因提高番茄红素产量

萜类化合物的直接前体物质异戊烯焦磷酸(IPP)和二甲基烯丙基焦磷酸酯(DMAPP)可以由2-甲基-D-赤藻糖醇-4-磷酸途径(MEP途径)和甲羟戊酸途径(MVA途径)合成。在已经优化MEP合成途径、番茄红素合成途径关键基因表达的重组大肠杆菌LYC101中,引入MVA途径基因,进一步提高重组大肠杆菌合成萜类化合物的能力。质粒pALV23和pALV145是本实验室在研究MVA途径基因协调表达时,用核糖体结合位点(RBS)文库连接MVA途径各基因构建质粒文库,而筛选到的有效提高β-胡萝卜素产量的质粒。首先比较了两个质粒分别在低产和高产番茄红素的菌株中对番茄红素合成的影响。结果表明,两个质粒在高、低产番茄红素的菌株中都可以有效提高番茄红素产量。在高产菌LYC101中pALV23比pALV145使番茄红素产量更高。然后,用CRISPR-Cas9系统辅助同源重组的方法,将MVA途经基因和启动子一共6.7kb的条带整合到LYC101菌株的染色体上,得到遗传稳定的菌株LYC102。LYC102的番茄红素产率达40.9mg/g,是出发菌株LYC101产率的2.19倍,比用质粒表达MVA途径基因的菌株提高了20%。在重组大肠杆菌中同时表达MVA途径和MEP途径,可以有效提高萜类化合物产率;文中构建了不含质粒的、遗传稳定的高产番茄红素菌株,为产业化合成番茄红素提供基础;同时构建平台菌株,可以用于其他萜类化合物合成。     

Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the anti-malarial drug precursor amorpha-4,11-diene

The introduction or creation of metabolic pathways in microbial hosts has allowed for the production of complex chemicals of therapeutic and industrial importance. However, these pathways rarely function optimally when first introduced into the host organism and can often deleteriously affect host growth, resulting in suboptimal yields of the desired product. Common methods used to improve production from engineered biosynthetic pathways include optimizing codon usage, enhancing production of rate-limiting enzymes, and eliminating the accumulation of toxic intermediates or byproducts to improve cell growth. We have employed these techniques to improve production of amorpha-4,11-diene (amorphadiene), a precursor to the anti-malarial compound artemisinin, by an engineered strain of Escherichia coli. First we developed a simple cloning system for expression of the amorphadiene biosynthetic pathway in E. coli, which enabled the identification of two rate-limiting enzymes (mevalonate kinase (MK) and amorphadiene synthase (ADS)). By optimizing promoter strength to balance expression of the encoding genes we alleviated two pathway bottlenecks and improved production five fold. When expression of these genes was further increased by modifying plasmid copy numbers, a seven-fold increase in amorphadiene production over that from the original strain was observed. The methods demonstrated here are applicable for identifying and eliminating rate-limiting steps in other constructed biosynthetic pathways.     

甲羟戊酸途径限速步骤研究及其在产番茄红素重组大肠杆菌中的应用

甲羟戊酸途径(MVA途径)被引入重组大肠杆菌中,能够提高重组大肠杆菌中萜类化合物的合成能力。但因重组大肠杆菌中萜类化合物合成途径中间产物积累,导致细胞生长和萜类化合物合成受到限制。本研究在稳定表达MVA途径以及优化2-甲基-D-赤藻糖醇-4-磷酸途径(MEP途径)、番茄红素合成途径关键基因表达的重组大肠杆菌LYC103中,用质粒高表达MVA途径和番茄红素合成途径关键基因,挖掘该途径的限速步骤。结果表明,ispA、crtE、mvaK1、idi和mvaD基因过表达后,细胞生长没有明显变化,番茄红素产量依次提高了13.5%、16.5%、17.95%、33.7%和61.1%,说明这几个基因可能是合成番茄红素的限速步骤。mvaK1、mvaK2、mvaD三个基因在同一操纵子上,用mRNA稳定区(RNA stabilizing region)进行启动子文库(mRSL)调控mvaK1,相当于对3个基因同时调控。用高效基因组编辑技术(CAGO)对mvaK1基因的mRNA稳定区进行启动子文库的调控,得到菌株LYC104。番茄红素产量与对照菌株LYC103相比增加了2倍,细胞生长提高了32%。然后,利用CR...     

Enhanced lycopene production in Escherichia coli engineered to synthesize isopentenyl diphosphate and dimethylallyl diphosphate from mevalonate

To increase expression of lycopene synthetic genes crtE, crtB, crtI, and ipiHP1, the four exogenous genes were cloned into a high copy pTrc99A vector with a strong trc promoter. Recombinant Escherichia coli harboring pT-LYCm4 produced 17 mg/L of lycopene. The mevalonate lower pathway, composed of mvaK1, mvaK2, mvaD, and idi, was engineered to produce pSSN12Didi for an efficient supply of the lycopene building blocks, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Mevalonate was supplied as a substrate for the mevalonate lower pathway. Lycopene production in E. coli harboring pT-LYCm4 and pSSN12Didi with supplementation of 3.3 mM mevalonate was more than threefold greater than bacteria with pT-LYCm4 only. Lycopene production was dependent on mevalonate concentration supplied in the culture. Clump formation was observed as cells accumulated more lycopene. Further clumping was prevented by adding the surfactant Tween 80 0.5% (w/v), which also increased lycopene production and cell growth. When recombinant E. coli harboring pT-LYCm4 and pSSN12Didi was cultivated in 2YT medium containing 2% (w/v) glycerol as a carbon source, 6.6 mM mevalonate for the mevalonate lower pathway, and 0.5% (w/v) Tween 80 to prevent clump formation, lycopene production was 102 mg/L and 22 mg/g dry cell weight, and cell growth had an OD(600) value of 15 for 72 h.     

Increased a-lytic protease production from recombinant Escherichia coli grown with oxygen limitation

Production of a mutant of the enzyme a-lytic protease from recombinant E. coli JM109 increased from 50 units/l to 750 units/l as the dissolved oxygen was decreased from above 30% saturation to near zero during batch growth on a complex medium. This represents a 60-fold increase in specific protease production (units/g cell dry wt.). Limiting the oxygen supply decreased the maximum growth rate from 0.55 h -1 to 0.066 h -1 which may in turn regulate the synthesis of recombinant protease in this system so that increased levels of product are obtained.     

L-Fucose production by engineered Escherichia coli

L -Fucose (6-deoxy-L -galactose) is a major constituent of glycans and glycolipids in mammals. Fucosylation of glycans can confer unique functional properties and may be an economical way to manufacture L -fucose. Research can extract L -fucose directly from brown algae, or by enzymatic hydrolysis of L -fucose-rich microbial exopolysaccharides. However, these L -fucose production methods are not economical or scalable for various applications. We engineered an Escherichia coli strain to produce L -fucose. Specifically, we modified the strain genome to eliminate endogenous L -fucose and lactose metabolism, produce 2′-fucosyllactose (2′-FL), and to liberate L -fucose from 2′-FL. This E. coli strain produced 16.7 g/L of L -fucose with productivity of 0.1 g·L⁻¹·h⁻¹ in a fed-batch fermentation. This study presents an efficient one-pot biosynthesis strategy to produce a monomeric form of L -fucose by microbial fermentation, making large-scale industrial production of L -fucose feasible.     

Enhancing GDP-fucose production in recombinant Escherichia coli by metabolic pathway engineering

Guanosine 5′-diphosphate (GDP)-fucose is the indispensible donor substrate for fucosyltransferase-catalyzed synthesis of fucose-containing biomolecules, which have been found involving in various biological functions. In this work, the salvage pathway for GDP-fucose biosynthesis from Bacterioides fragilis was introduced into Escherichia coli. Besides, the biosynthesis of guanosine 5′-triphosphate (GTP), an essential substrate for GDP-fucose biosynthesis, was enhanced via overexpression of enzymes involved in the salvage pathway of GTP biosynthesis. The production capacities of metabolically engineered strains bearing different combinations of recombinant enzymes were compared. The shake flask fermentation of the strain expressing Fkp, Gpt, Gmk and Ndk obtained the maximum GDP-fucose content of 4.6 ± 0.22 μmol/g (dry cell mass), which is 4.2 fold that of the strain only expressing Fkp. Through fed-batch fermentation, the GDP-fucose content further rose to 6.6 ± 0.14 μmol/g (dry cell mass). In addition to a better productivity than previous fermentation processes based on the de novo pathway for GDP-fucose biosynthesis, the established schemes in this work also have the advantage to be a potential avenue to GDP-fucose analogs encompassing chemical modification on the fucose residue.     

High-yield resveratrol production in engineered Escherichia coli

Plant polyphenols have been the subject of several recent scientific investigations since many of the molecules in this class have been found to be highly active in the human body, with a plethora of health-promoting activities against a variety of diseases, including heart disease, diabetes, and cancer, and with even the potential to slow aging. Further development of these potent natural therapeutics hinges on the formation of robust industrial production platforms designed using specifically selected as well as engineered protein sources along with the construction of optimal expression platforms. In this work, we first report the investigation of various stilbene synthases from an array of plant species considering structure-activity relationships, their expression efficiency in microorganisms, and their ability to synthesize resveratrol. Second, we looked into the construct environment of recombinantly expressed stilbene synthases, including different promoters, construct designs, and host strains, to create an Escherichia coli strain capable of producing superior resveratrol titers sufficient for commercial usage. Further improvement of metabolic capabilities of the recombinant strain aimed at improving the intracellular malonyl-coenzyme A pool, a resveratrol precursor, resulted in a final improved titer of 2.3 g/liter resveratrol.