Characterization of dihydroflavonol 4-reductases for recombinant plant pigment biosynthesis applications

Anthocyanins are colorful plant pigments with promising applications as pharmaceuticals and colorants. In order to engineer efficient pigment biosynthesis in Escherichia coli, the activities of various dihydroflavonol 4-reductases (DFRs) were characterized for the three primary dihydroflavonol substrates. The biochemical assays demonstrated variable DFR activities for dihydroflavonol with one B-ring hydroxyl group, the precursor of pelargonidin derivatives. In contrast, dihydroflavonols with two and three B-ring hydroxylation were metabolized with comparable efficiency. Furthermore, the catalysis of DFR for the secondary substrates, flavanones, also depended on the number of B-ring hydroxyl groups. Engineering the expression of the DFR clones together with plant-specific 4-coumaroyl:CoA ligase, chalcone synthase, chalcone isomerase, and flavanone 3-hydroxylase in E. coli resulted in the synthesis of pelargonidin at various levels, from p-coumaric acids. The identification of a robust DFR from this study can also be used for engineering recombinant synthesis of other bioactive flavonoids, such as flavan-3-ols.     

Alteration of a single amino acid changes the substrate specificity of dihydroflavonol 4-reductase

Many plant species exhibit a reduced range of flower colors due to the lack of an essential gene or to the substrate specificity of a biosynthetic enzyme. Petunia does not produce orange flowers because dihydroflavonol 4-reductase (DFR) from this species, an enzyme involved in anthocyanin biosynthesis, inefficiently reduces dihydrokaempferol, the precursor to orange pelargonidin-type anthocyanins. The substrate specificity of DFR, however, has not been investigated at the molecular level. By analyzing chimeric DFRs of Petunia and Gerbera, we identified a region that determines the substrate specificity of DFR. Furthermore, by changing a single amino acid in this presumed substrate-binding region, we developed a DFR enzyme that preferentially reduces dihydrokaempferol. Our results imply that the substrate specificity of DFR can be altered by minor changes in DFR.     

Structure prediction of dihydroflavonol 4- reductase and anthocyanidin synthase from spinach

Spinach is an important dietary vegetable associated with beneficial health effects. Flavonoids have various biological activities such as antioxidant, antibacterial, and anticancer effect Flavonoid including anthocyanin provides brilliant and colored pigments in different plant tissues. Anthocyanidin synthase and dihydroflavonol 4-reductase are responsible for anthocyanin biosynthesis. They contributed in plant protection against UV-B radiation, microbial and herbivore pathogens. A 3D structures of anthocyanidin synthase and dihydroflavonol 4-reductase from spinach are constructed in this study through homology modeling. The homology modeling is done by using the MODELLER 9v7 software. The energy of models was minimized by applying molecular mechanics method. The root mean square deviation (RMSD) for C atoms between the template and the homology-modeled structures was estimated by CE program. The final models were assessed by PROCHECK and WHATCHECK which showed that the final refined models are reliable.     

Heterologous expression of dihydroflavonol 4-reductases from various plants

Dihydroflavonol 4-reductases (DFR) catalyze the stereospecific reduction of dihydroflavonols to the respective flavan 3,4-diols (leucoanthocyanidins) and might also be involved in the reduction of flavanones to flavan-4-ols, which are important intermediates in the 3-deoxyflavonoid pathway. Several cDNA clones encoding DFR have been isolated from different plant species. Despite the important function of these enzymes in the flavonoid pathway, attempts at heterologous expression of cDNA clones in Escherichia coli have failed so far. Here, three well known heterologous expression systems for plant-derived genes were tested to obtain the functional protein of DFR from Gerbera hybrids. Successful synthesis of an active DFR enzyme was achieved in eukaryotic cells, using either baker's yeast (Saccharomyces cerevisiae) or tobacco protoplasts (Nicotiana tabacum), transformed with expression vectors containing the open reading frame of Gerbera DFR. These expression systems provide useful and powerful tools for rapid biochemical characterization, in particular the substrate specificity, of the increasing number of cloned DFR sequences. Furthermore, this tool allows the stereospecific synthesis of (14)C-labeled leucoanthocyanidins in high quality and quantity, which is a prerequisite for detailed biochemical investigation of the less understood enzymatic reactions located downstream of DFR in anthocyanin, catechin and proanthocyanidin biosynthesis.     

植物类胡萝卜素代谢工程与应用

类胡萝卜素是人类所需要的重要营养成分之一,不仅具有抗氧化、预防肿瘤和心血管等疾病的作用,而且还是人体合成维生素A的前体。全球大约有280万～330万学龄前儿童出现维生素缺乏（vitaminAdeficiency,VAD）的临床症状;近2亿儿童处于半缺乏状态。通过对植物类胡萝卜素生物合成途径的解析,以及对参与这一代谢过程的酶及其调控机制的深入了解,目前已经可以通过基因工程在主要农作物中组织特异性地促进类胡萝卜素的合成与积累。从理论上已经可以利用转基因植物来减少VAD的出现。该文简要回顾近年来这一领域的研究进展。     

大肠杆菌苏氨酸合成途径动力学模型的构建与分析

动力学模型分析有利于理解生物系统的调控机制,从而为高效细胞工厂的理性设计提供指导。基于以往发表的相关途径动力学模型和测量的酶动力学数据,开发了大肠杆菌苏氨酸合成途径的动力学模型。模型包含从天冬氨酸至苏氨酸的合成途径及葡萄糖开始的为合成途径提供前体以及能量的代谢途径。与以往模型不同的是新模型中考虑了能量和还原力的平衡,从而使模型模拟的系统自身成为一个不需要从外界提供能量和还原力的自洽系统。模型稳态分析的结果表明PTS、G6PDH和HDH等反应对苏氨酸合成反应的通量控制系数较大,通过过表达这些反应的酶可以有效增加苏氨酸合成反应的通量。     

大肠杆菌生产异戊二烯的代谢工程研究进展

异戊二烯作为一种重要的化工原料,主要用于合成橡胶。此外,还广泛应用于医药或化工中间体、食品、粘合剂及航空燃料等领域。利用微生物法生产异戊二烯因具有环境友好、利用廉价的可再生原料、可持续发展等优势而成为当今研究的热点。这里介绍了大肠杆菌生产异戊二烯的代谢途径及关键酶,从代谢工程的角度出发综述了目前为提高大肠杆菌异戊二烯产量所应用到的方法和策略,并对今后的发展方向进行了展望。     

Extreme promiscuity of a bacterial and a plant diterpene synthase enables combinatorial biosynthesis

Diterpenes are widely distributed across many biological kingdoms, where they serve a diverse range of physiological functions, and some have significant industrial utility. Their biosynthesis involves class I diterpene synthases (DTSs), whose activity can be preceded by that of class II diterpene cyclases (DTCs). Here, a modular metabolic engineering system was used to examine the promiscuity of DTSs. Strikingly, both a bacterial and plant DTS were found to exhibit extreme promiscuity, reacting with all available precursors with orthogonal activity, producing an olefin or hydroxyl group, respectively. Such DTS promiscuity enables combinatorial biosynthesis, with remarkably high yields for these unoptimized non-native enzymatic combinations (up to 15 mg/L). Indeed, it was possible to readily characterize the 13 unknown products. Notably, 16 of the observed diterpenes were previously inaccessible, and these results provide biosynthetic routes that are further expected to enable assembly of more extended pathways to produce additionally elaborated ‘non-natural’ diterpenoids.     

Crystal structure of grape dihydroflavonol 4-reductase, a key enzyme in flavonoid biosynthesis

The nicotinamide adenine dinucleotide phosphate (NADPH)-dependent enzyme dihydroflavonol 4-reductase (DFR) catalyzes a late step in the biosynthesis of anthocyanins and condensed tannins, two flavonoid classes of importance to plant survival and human nutrition. This enzyme has been widely investigated in many plant species, but little is known about its structural and biochemical properties. To provide a basis for detailed structure-function studies, the crystal structure of Vitis vinifera DFR, heterologously expressed in Escherichia coli, has been determined at 1.8 Å resolution. The 3D structure of the ternary complex obtained with the oxidized form of nicotinamide adenine dinucleotide phosphate and dihydroquercetin, one of the DFR substrates, presents common features with the short-chain dehydrogenase/reductase family, i.e., an N-terminal domain adopting a Rossmann fold and a variable C-terminal domain, which participates in substrate binding. The structure confirms the importance of the 131-156 region, which lines the substrate binding site and enlightens the role of a specific residue at position 133 (Asn or Asp), assumed to control substrate recognition. The activity of the wild-type enzyme and its variant N133D has been quantified in vitro, using dihydroquercetin or dihydrokaempferol. Our results demonstrate that position 133 cannot be solely responsible for the recognition of the B-ring hydroxylation pattern of dihydroflavonols.     

Molecular cloning,substrate specificity of the functionally expressed dihydroflavonol 4-reductases from Malus domestica and Pyrus communis cultivars and the consequences for flavonoid metabolism

Treatment with the dioxygenase inhibitor prohexadione-Ca leads to major changes in the flavonoid metabolism of apple (Malus domestica) and pear (Pyrus communis) leaves. Accumulation of unusual 3-deoxyflavonoids is observed, which have been linked to an enhanced resistance toward fire blight. The committed step in this pathway is the reduction of flavanones. Crude extracts from leaves are able to perform this reaction. There was previous evidence that DFR enzymes of certain plants possess additional flavanone 4-reductase (FNR) activity. Such an FNR activity of DFR enzymes is proved here by heterologous expression of the enzymes. The heterologously expressed DFR/FNR enzymes of Malus and Pyrus possess distinct differences in substrate specificities despite only minor differences of the amino acid sequences. Kinetic studies showed that dihydroflavonols generally are the preferred substrates. However, with the observed substrate specificities the occurrence of 3-deoxyflavonoids in vivo after application of prohexadione-Ca can be explained.     

Improved E. coli erythromycin A production through the application of metabolic and bioprocess engineering

In this report, small-scale culture and bioreactor experiments were used to compare and improve the heterologous production of the antibiotic erythromycin A across a series of engineered prototype Escherichia coli strains. The original strain, termed BAP1(pBPJW130, pBPJW144, pHZT1, pHZT2, pHZT4, pGro7), was designed to allow full erythromycin A biosynthesis from the exogenous addition of propionate. This strain was then compared against two alternatives hypothesized to increase final product titer. Strain TB3(pBPJW130, pBPJW144, pHZT1, pHZT2, pHZT4, pGro7) is a derivative of BAP1 designed to increase biosynthetic pathway carbon flow as a result of a ygfH deletion; whereas, strain TB3(pBPJW130, pBPJW144, pHZT1, pHZT2, pHZT4-2, pGro7) provided an extra copy of a key deoxysugar glycosyltransferase gene. Production was compared across the three strains with TB3(pBPJW130, pBPJW144, pHZT1, pHZT2, pHZT4, pGro7) showing significant improvement in erythronolide B (EB), 3-mycarosylerythronolide B (MEB), and erythromycin A titers. This strain was further tested in the context of batch bioreactor production experiments with time-course titers leveling at 4 mg/L, representing an approximately sevenfold increase in final erythromycin A titer.     

Metabolic flux analysis for succinic acid production by recombinant Escherichia coli with amplified malic enzyme activity

A pfl ldhA double mutant Escherichia coli strain NZN111 was used to produce succinic acid by overexpressing the E. coli malic enzyme. Escherichia coli strain NZN111 harboring pTrcML produced 6 and 8 g/L of succinic acid from 20 g/L of glucose in flask culture at 37 degrees C and 30 degrees C, respectively. When NZN111(pTrcML) was cultured at 30 degrees C with intermittent glucose feeding the final succinic acid concentration obtained was 9.5 g/L and the ratio of succinic acid to acetic acid was 13:1. This system could not be analyzed by conventional metabolic flux analysis techniques, since some pyruvate and succinic acid were accumulated intracellularly. Therefore, a new flux analysis method was proposed by introducing intracellular pyruvate and succinic acid pools. By this new method the concentrations of intracellular metabolites were successfully predicted and the differences between the measured and calculated reaction rates could be considerably reduced.     

高等植物二氢黄酮醇4-还原酶基因研究进展

花青素苷是影响植物花瓣呈色的重要色素,而花色是决定花卉观赏价值和商业价值的一个重要因素。在花青素苷的生物合成过程中,二氢黄酮醇4-还原酶（DFR）是花青素苷生物合成下游途径中的第一个关键的酶。因此,DFR在高等植物花色的形成过程中发挥极其重要的作用,是形成花青素苷的一个非常重要的调控点。DFR对3种二氢黄酮醇底物具有选择特异性,但决定DFR底物特异性的分子机制目前仍不十分清楚。该文简单概述了花青素苷生物合成途径及其转录调控机制,并结合作者的工作重点综述了DFR的底物特异性以及克隆的DFR基因在植物基因工程中的应用。     

好氧发酵生产琥珀酸工程菌株的构建

通过分析大肠杆菌的碳源代谢途径, 利用基因敲除手段, 以Escherichia coli MG1655为出发菌株, 成功构建了琥珀酸好氧发酵生产工程菌E. coli QZ1111 (MG1655?ptsG?poxB?pta?iclR?sdhA)。检测结果表明该菌株能以葡萄糖为碳源, 在好氧发酵且不表达任何异源基因的条件下大量积累琥珀酸。摇瓶试验证明, 琥珀酸发酵产量达到26.4 g/L, 乙酸盐作为唯一检测到的副产物产量为2.3 g/L。二者浓度比达到11.5:1。     

Metabolic engineering of Escherichia coli for the production of fumaric acid

Fumaric acid is a naturally occurring organic acid that is an intermediate of the tricarboxylic acid cycle. Fungal species belonging to Rhizopus have traditionally been employed for the production of fumaric acid. In this study, Escherichia coli was metabolically engineered for the production of fumaric acid under aerobic condition. For the aerobic production of fumaric acid, the iclR gene was deleted to redirect the carbon flux through the glyoxylate shunt. In addition, the fumA, fumB, and fumC genes were also deleted to enhance fumaric acid formation. The resulting strain was able to produce 1.45 g/L of fumaric acid from 15 g/L of glucose in flask culture. Based on in silico flux response analysis, this base strain was further engineered by plasmid‐based overexpression of the native ppc gene, encoding phosphoenolpyruvate carboxylase (PPC), from the strong tac promoter, which resulted in the production of 4.09 g/L of fumaric acid. Additionally, the arcA and ptsG genes were deleted to reinforce the oxidative TCA cycle flux, and the aspA gene was deleted to block the conversion of fumaric acid into L ‐aspartic acid. Since it is desirable to avoid the use of inducer, the lacI gene was also deleted. To increase glucose uptake rate and fumaric acid productivity, the native promoter of the galP gene was replaced with the strong trc promoter. Fed‐batch culture of the final strain CWF812 allowed production of 28.2 g/L fumaric acid in 63 h with the overall yield and productivity of 0.389 g fumaric acid/g glucose and 0.448 g/L/h, respectively. This study demonstrates the possibility for the efficient production of fumaric acid by metabolically engineered E. coli. Biotechnol. Bioeng. 2013; 110: 2025–2034. © 2013 Wiley Periodicals, Inc.