Screening and development of enzymes for determination and transformation of amino acids

ABSTRACT

The high stereo- and substrate specificities of enzymes have been utilized for micro-determination of amino acids. Here, I review the discovery of l-Phe dehydrogenase and its practical use in the diagnosis of phenylketonuria in more than 5,400,000 neonates over two decades in Japan. Screening and uses of other selective enzymes for micro-determination of amino acids have also been discussed. In addition, novel enzymatic assays with the systematic use of known enzymes, including assays based on a pyrophosphate detection system using pyrophosphate dikinase for a variety of l-amino acids with amino-acyl-tRNA synthetase have been reviewed. Finally, I review the substrate specificities of a few amino acid-metabolizing enzymes that have been altered, using protein engineering techniques, mainly for production of useful chemicals, thus enabling the wider use of natural enzymes.     

2-氰基-D,L-苯丙氨酸盐酸盐的合成

合成了非天然氨基酸２－氰基－Ｄ,Ｌ－苯丙氨酸盐以及四个中间体,其结构分别通过红外光谱、核磁共振、元素分析、熔点测试等手段得到确证。     

Biotransformation of R-2-hydroxy-4-phenylbutyric acid by D-lactate dehydrogenase and Candida boidinii cells containing formate dehydrogenase coimmobilized in a fibrous bed bioreactor

R-2-hydroxy-4-phenylbutyric acid (R-HPBA) is an important intermediate in the manufacture of angiotensin converting enzyme inhibitors. In this work, a recombinant D-lactate dehydrogenase (LDH) was used to transform 2-oxo-4-phenylbutyric acid (OPBA) to R-HPBA, with concomitant oxidation of beta-nicotinamide adenine dinucleotide (NADH) to NAD(+). The cofactor NADH was regenerated by formate dehydrogenase (FDH) present in whole cells of Candida boidinii, which were pre-treated with toluene to make them permeable. The whole cells used in the process were more stable and easier to prepare as compared with the isolated FDH from the cells. Kinetic study showed that the reaction rate was dependent on the concentration of cofactor, NAD(+), and that both R-HPBA and OPBA inhibited the reaction. A novel method for co-immobilization of whole cells and LDH enzyme on cotton cloth was developed using polyethyleneimine (PEI), which induced the formation of PEI-enzyme-cell aggregates and their adsorption onto cotton cloth, leading to multilayer co-immobilization of cells and enzyme with high loading (0.5 g cell and 8 mg LDH per gram of cotton cloth) and activity yield ( > 95%). A fibrous bed bioreactor with co-immobilized cells and enzyme on the cotton cloth was then evaluated for R-HPBA production in fed-batch and repeated batch modes, which gave relatively stable reactor productivity of 9 g/L . h and product yield of 0.95 mol/mol OPBA when the concentrations of OPBA and R-HPBA were less than 10 g/L.     

深红酵母转化反式肉桂酸生成L-苯丙氨酸的研究

研究了深红酵母Ａｓ２．２７９产生Ｌ－苯丙氨酸解氨酸（ＰＡＬ）的条件、转化反式 桂酸（ｔＣａ）生成Ｌ－苯丙氨酸（Ｌ－Ｐｈｅ）的条件以及几种因素对ＰＡＬ稳定性的影响,结果表明,最佳转化条件为：１．０％ｔ－Ｃａ,８ｍｏｌ／Ｌ氨,ｐＨ１０．０,３０℃。在转化液中加入还原剂和充入Ｎ２有利于提高酶的稳定性,在此条件下可一次转化６４％的ｔ－Ｃａ,保留６０％的酶活。生成Ｌ－Ｐｈｅ浓度为５．８ｇ／Ｌ。     

Molybdenum Cofactor-Containing Oxidoreductase Family in Plants

Recent investigations on plant molybdenum-containing enzymes that include xanthine dehydrogenase (EC 1.1.1.204) and xanthine oxidase (EC 1.1.3.22), nitrate reductase (EC 1.7.1.1-3), aldehyde oxidase (EC 1.2.3.1), and sulfite oxidase (EC 1.8.3.1) are reviewed. The enzymes belong to closely related protein family and share common structural features. Special attention is being paid to the recently solved crystal structures their implications for the substrate binding and catalytic mechanism. This revised version was published online in July 2006 with corrections to the Cover Date.     

南美斑潜蝇为害对黄瓜体内4种防御酶活性的影响

植物对昆虫取食产生的防御反应,在昆虫与植物相互作用关系中起着重要的作用。为明确南美斑潜蝇Liriomyza huidobrensis(Blanchard)取食与植物防御之间的作用关系,本文分别测定了南美斑潜蝇幼虫持续为害1、3、5、7及9d后黄瓜叶片中苯丙氨酸解氨酶(PAL)、多酚氧化酶(PPO)、过氧化物酶(POD)及超氧化物歧化酶(SOD)活性的变化。结果表明：在南美斑潜蝇幼虫持续取食下,PAL、PPO、POD和SOD等4种酶活性显著上升;PAL、PPO和POD等3种酶活性随受害程度的加重而上升幅度加大,即重度受害>轻度受害>系统对照>健康对照,而SOD活性变化没有规律。在系统对照黄瓜叶片中,PAL、PPO、POD和SOD等4种酶活性最大值分别在第5、1、5和5d;在轻度受害黄瓜叶片中,PAL、PPO、POD和SOD等4种酶活性最大值分别在第5、9、5和9d;在重度受害黄瓜叶片中,PAL、PPO、POD和SOD等4种酶活性最大值分别在第7、7、5和5d。黄瓜叶片受害后,POD和PPO活性上升幅度较大,PAL和SOD活性上升幅度较小,说明POD和PPO对取食胁迫响应比PAL和SOD更灵敏。     

Fusion to a pull-down domain: a novel approach of producing Trigonopsis variabilisD-amino acid oxidase as insoluble enzyme aggregates

Insoluble protein particles showing high specific enzyme activity are potentially useful biocatalysts. The commercialized crosslinked enzyme crystals and aggregates have the disadvantage that their preparation requires isolation of the protein before the critical precipitation step. We introduce a novel concept of controlled precipitation in vivo in which the target enzyme is fused to the cellulose-binding domain (CBD) of Clostridium cellulovorans, and expression in Escherichia coli is performed under conditions that induce selective pull down of the folded chimeric protein via intermolecular self-aggregation of the CBD. The case of D-amino acid oxidase from Trigonopsis variabilis shows that upon fusion of the CBD to its N-terminus, the otherwise mainly soluble recombinant enzyme was quantitatively precipitated in protein particles, which displayed 40% of the specific activity of the highly purified oxidase. By contrast, inclusion bodies derived from an enzyme chimera, which harbored a C-terminal peptide tag, showed only little oxidase activity (相似文献   

Genetic variation of some aldehyde-oxidizing enzymes in the mouse

• 1 Twenty-six strains of mice were surveyed by starch gel electrophoresis for genetic variation of four liver enzymes; aldehyde dehydrogenase, aldehyde oxidase, xanthine oxidase and formaldehyde dehydrogenase.
• 2 A variant of aldehyde dehydrogenase was found in strains ICFW, IS/Cam, NZB, NZW, Simpson and Schneider. A variant of aldehyde oxidase was found in CE. A possible variant of xanthine oxidase was found in SF/Cam.
• 3 The gene determining the electrophoretic variant of aldehyde oxidase is either the same as, or very closely linked to, the Aox gene which determines aldehyde oxidase activity.

     

A single mutation in the NAD-specific formate dehydrogenase from Candida methylica allows the enzyme to use NADP

An homology model of Candida methylica formate dehydrogenase (cmFDH) was constructed based on the Pseudomonas sp. 101 formate dehydrogenase (psFDH) structure. An aspartic acid residue in the model was predicted to interact with the adenine ribose of the NAD cofactor, in common with many NAD-dependent oxoreductases. Replacement of this aspartic acid residue by serine in cmFDH removed the absolute requirement for NAD over NADP shown by the wild type enzyme. Taken with similar results shown by d- and l-lactate dehydrogenases, this suggests that an aspartic acid in this position is a major determinant of coenzyme specificity in NAD/NADP-dependent dehydrogenases.     

On-line monitoring of enzymes in downstream processing by flow injection analysis (FIA)

Flow injection analysis (FIA) has been employed to automate enzyme assays for formate dehydrogenase (FDH) and l-leucine dehydrogenase (l-LeuDH). Coupled to a special sampling device the FIA assays were used to monitor on-line downstream processes, e.g. disintegration of microbial cells and cross-flow filtration of cell homogenates.     

Fusion protein of Vitreoscilla hemoglobin with D-amino acid oxidase enhances activity and stability of biocatalyst in the bioconversion process of cephalosporin C

In this study we constructed an artificial flavohemoprotein by fusing Vitreoscilla hemoglobin (VHb) with D-amino acid oxidase (DAO) of Rhodotorula gracilis to determine whether bacterial hemoglobin can be used as an oxygen donor to immobilized flavoenzyme. This chimeric enzyme significantly enhanced DAO activity and stability in the bioconversion process of cephalosporin C. In a 200-mL bioreactor, the catalytic efficiency of immobilized VHb-DAO against cephalosporin C was 12.5-fold higher than that of immobilized DAO, and the operational stability of the immobilized VHb-DAO was approximately threefold better than that of the immobilized DAO. In the scaled-up bioprocess with a 5-L bioreactor, immobilized VHb-DAO (2500 U/L) resulted in 99% bioconversion of 120 mM cephalosporin C within 60 min at an oxygen flow rate of 0.2 (v/v) x min. Ninety percent of the initial activity of immobilized VHb-DAO could be maintained at up to 50 cycles of the enzymatic reaction without exogenous addition of H(2)O(2) and flavin adenine dinucleotide (FAD). The purity of the final product, glutaryl-7-aminocephalosporanic acid, was confirmed to be 99.77% by high-performance liquid chromatography (HPLC) analysis. Relative specificity of immobilized VHb-DAO on D-alpha-aminoadipic acid, a precursor in cephalosporin C biosynthesis, increased twofold, compared with that of immobilized DAO, suggesting that conformational modification of the VHb-DAO fusion protein may be altered in favor of cephalosporin C.     

酸性和碱性酶稳定性机制及其识别

了解酸性和碱性酶稳定性机制并对其进行识别具有重要理论和实践意义。通过分析105条酸性酶和111条碱性酶序列的氨基酸组成, 结果表明: 酸性酶中Trp、Tyr、Thr和Ser的含量明显高于平均值, 而Glu、Lys、Met和Arg的含量则明显低于平均值; 碱性酶中Trp、Ala和Cys的含量略高于平均值, 而Lys、Arg和Glu的含量则略低于平均值; 酸性和碱性酶中Ala、Glu、Leu、Asn、Arg、Ser和Thr的含量存在较大差异。在此基础上, 发展了一种加权氨基酸组成的方法对两种酶进行识别, 其自一致性检验的识别精度可达86.1%, 5倍交叉验证的精度为83.3%。建立了一种基于序列识别酸性和碱性酶的新方法。     

Biotransformation of tea catechins into theaflavins with immobilized polyphenol oxidase

Theaflavins, an active antioxidant, a natural pigment and pharmacologically active molecule obtained from black tea were bioprocessed on an immobilized tea polyphenol oxidase (PPO) system by the conversion of tea catechins extracted from green tea leaves with an overall conversion efficiency of 85% about 14-fold increase over maximum achievable in normal black teas. The immobilized enzyme (IE) system consists of activated cellulose matrix on to which the freshly extracted tea leaf polyphenol oxidase was covalently linked. Cellulose as a matrix of choice was considered primarily for its non-toxic nature, natural origin, low cost and easy availability. The kinetic parameters of the IE system were; protein loading capacity 11.8 mg/g; pH optimum 5.9; temperature optimum 37.5 °C; K_m 4.76 ± 0.08 mM; V_max 20 ± 1.80 nmol/min; enzyme activity retention (83.58%) and number of batches per turnover without loss of activity was 14. The product from IE system was identified by HPLC and ESI-QTOF-MS spectrometry.     

Site-specific incorporation of unnatural amino acids into urate oxidase in Escherichia coli

Urate oxidase catalyzes the oxidation of uric acid with poor solubility to produce 5-hydroxyisourate and allantoin. Since allantoin is excreted in vivo, urate oxidase has the potential to be a therapeutic target for the treatment of gout. However, its severe immunogenicity limits its clinical application. Furthermore, studies on the structure-function relationships of urate oxidase have proven difficult. We developed a method for genetically incorporating p-azido-L-phenylalanine into target protein in Escherichia coli in a site-specific manner utilizing a tyrosyl suppressor tRNA/aminoacyl-tRNA synthetase system. We substituted p-azido-L-phenylalanine for Phe(170) or Phe(281) in urate oxidase. The products were purified and their enzyme activities were analyzed. In addition, we optimized the system by adding a "Shine-Dalgarno (SD) sequence" and tandem suppressor tRNA. This method has the benefit of site-specifically modifying urate oxidase with homogeneous glycosyl and PEG derivates, which can provide new insights into structure-function relationships and improve pharmacological properties of urate oxidase.     

Biosilicification of dual-fusion enzyme immobilized on magnetic nanoparticle

Rapid recovery, immobilization, and silica encapsulation of a dual-fusion enzyme was achieved by using iminodiacetic acid (IDA) modified magnetic nanoparticle as a carrier. D-amino acid oxidase (DAAO) of Rhodosporidium toruloides was used as a model enzyme in which a silica-precipitating peptide R5 and a metal ion complexing peptide (His)(6) were fused to its N- and C-terminal, respectively. After charging the magnetic particle with Cu(2+), the dual-fusion DAAO of 0.43 g could be directly recovered from the recombinant E. coli crude extract and immobilized on 1 g of the magnetic particle. Once in contact with hydrolyzed tetramethoxysilane (TMOS), the homogeneously dispersed immobilized dual-fusion DAAO was biosilicificated to form aggregates with size about 50 microm. The silica-encapsulated immobilized DAAO demonstrated a pyruvic acid production rate comparable with that of the naked immobilized DAAO in five repeated batch reactions when D-alanine was used as substrate. Furthermore, 85% of its activity remained after incubation at 60 degrees C for 1 h while the naked immobilized DAAO lost all its activity. This process provides the advantages that recombinant fusion enzyme can be directly recovered from crude extract, silica encapsulation protects the enzyme from leakage and denaturation, and the enzyme activity can be easily retrieved by applying a magnetic field.     

Production of D-amino acid oxidase (DAO) of Trigonopsis variabilis in Schizosaccharomyces pombe and the characterization of biocatalysts prepared with recombinant cells

The cDNA of D-amino acid oxidase (DAO) gene isolated from Trigonopsis variabilis was expressed in Schizosaccharomyces pombe. A clone, ASP327-10, transformed with plasmid vector, pTL2M5DAO, expressed catalytically active DAO in the presence of G418, and converted Cephalosprin C to alpha-ketoadipyl-7-cephalosporanic acid (KA-7-ACA) and glutaryl-7-aminocephalosporanic acid (GL-7-ACA). Biocatalysts were prepared using ASP327-10 and T. variabilis, and evaluated to demonstrate the feasibility of recombinant S. pombe for industrial application. The cells were immobilized by crosslinking polyethylene imine after glutardialdehyde (GDA) fixation and permeabilization by alkaline treatment. Although the biocatalyst prepared from ASP327-10 exhibited DAO activity, catalase activity still remained fully even after permeabilization, under which condition, the catalase activity of T. variabilis decreased to 20-30%. Heat treatment was required before cell fixation by GDA to inactivate the catalase in S. pombe. This improved the efficiency of bioconversion to GL-7-ACA, but caused poor mechanical strength in the biocatalyst of S. pombe. To overcome this weakness, a catalase-deficient host strain was obtained by ethylmethansulfate mutagenesis. Moreover, taking economics into consideration, the integrative vector, pTL2M5DAO-8XL, with multi-copies of expression cassette was constructed to express DAO in S. pombe even in the absence of G418. The newly established integrant, ASP417-7, did not exhibit any catalase activity so that heat treatment was not required. The obtained integrant and its biocatalyst were significantly improved in GL-7ACA conversion ability and mechanical strength. This study demonstrates that the established integrant is a potential candidate as an alternative source of DAO enzyme.     

Structures of reduced and ligand‐bound nitric oxide reductase provide insights into functional differences in respiratory enzymes

Nitric oxide reductase (NOR) catalyzes the generation of nitrous oxide (N₂O) via the reductive coupling of two nitric oxide (NO) molecules at a heme/non‐heme Fe center. We report herein on the structures of the reduced and ligand‐bound forms of cytochrome c‐dependent NOR (cNOR) from Pseudomonas aeruginosa at a resolution of 2.3–2.7 Å, to elucidate structure‐function relationships in NOR, and compare them to those of cytochrome c oxidase (CCO) that is evolutionarily related to NOR. Comprehensive crystallographic refinement of the CO‐bound form of cNOR suggested that a total of four atoms can be accommodated at the binuclear center. Consistent with this, binding of bulky acetaldoxime (CH₃‐CH=N‐OH) to the binuclear center of cNOR was confirmed by the structural analysis. Active site reduction and ligand binding in cNOR induced only ～0.5 Å increase in the heme/non‐heme Fe distance, but no significant structural change in the protein. The highly localized structural change is consistent with the lack of proton‐pumping activity in cNOR, because redox‐coupled conformational changes are thought to be crucial for proton pumping in CCO. It also permits the rapid decomposition of cytotoxic NO in denitrification. In addition, the shorter heme/non‐heme Fe distance even in the bulky ligand‐bound form of cNOR (～4.5 Å) than the heme/Cu distance in CCO (～5 Å) suggests the ability of NOR to maintain two NO molecules within a short distance in the confined space of the active site, thereby facilitating N‐N coupling to produce a hyponitrite intermediate for the generation of N₂O. Proteins 2014; 82:1258–1271. © 2013 Wiley Periodicals, Inc.