恶臭假单胞菌丙氨酸消旋酶基因的克隆、序列分析及表达

从恶臭假单胞菌(Pseudomonas putida)200的基因组出发,用PCR方法克隆到两个独立作用的丙氨酸消旋酶基因,称之为dadX和alr。DadX编码357个氨基酸长的多肽,计算分子量为38.82kDa,alr编码409个氨基酸长的多肽,计算分子量为44.182kDa。序列分析显示,DadX的氨基酸序列与Pseudomonas putidaKT2440,铜绿假单胞菌(Pseudomonas aeruginosa),鼠伤寒沙门氏菌(Salmonella typhimurium)和大肠杆菌(Escherichia coli)的DadX比较,相似性分别为96.64%、71.99%、44.88%和47.37%。Alr的氨基酸序列与Pseudomonas putidaKT2440比较,同源性为94.38%,而与铜绿假单胞菌(P.aeruginosa)、鼠伤寒沙门氏菌(S.typhimurium)和大肠杆菌(E.coli)的Alr比较,同源性均较低,分别为22.89%、25.72%和26.44%。在P.putida200的DadX和Alr氨基酸序列中部发现有对于酶活性至关重要的保守区域,如磷酸吡哆醛(PLP)结合位点。DadX和alr在大肠杆菌中得到表达,DadX丙氨酸消旋酶只对丙氨酸有消旋作用,而Alr丙氨酸消旋酶可以作用于丙氨酸和丝氨酸两种底物,且对丝氨酸特异性更高。Alr的表达不依赖于外源启动子,说明在其结构基因上游存在启动子结构。     

恶臭假单胞菌CGMCC 1388对映选择性生物降解制备(S)-扁桃酸及其衍生物的研究

从土壤中分离得到一株（R）-扁桃酸选择性降解菌,经鉴定为恶臭假单胞菌,保存于中国普通微生物保藏中心,编号为CGMCC1388。考察了扁桃酸及其降解产物对扁桃酸脱氢酶活力的影响。研究表明,在培养基中添加少量扁桃酸、苯甲酰甲酸或苯甲酸均可显著提高其产量,以扁桃酸的诱导效果最佳。3种诱导物的最适添加质量浓度分别为4、4和2 g/L。当以消旋扁桃酸为反应底物时,该菌可高选择性降解（R）-扁桃酸,回收得到的（S）-扁桃酸对映体过量值（e.e.）高于99%,反应的对映选择率（E）达130。用静息细胞催化扁桃酸降解的最适温度和pH分别为30 ℃和6.0,最适底物浓度为60 mmol/L,以双倒数法求得Km为47 mmol/L。考察了该菌对扁桃酸苯环取代衍生物的生物转化,并以高产率制备获得高对映纯度的（S）-对羟基扁桃酸和（S）-对氯扁桃酸。     

恶臭假单胞菌JP-1腈水合酶的诱导形成

恶臭假单胞菌JP-1能利用乙腈、丙腈、异丁腈、乙酰胺和丙酰胺作为生长的碳源和氮源。培养液中丙腈的代谢产物经证明是丙酰胺、丙酸和氨。腈水合酶是诱导酶,经丙腈诱导的适应细胞的腈水合酶活力比未适应的细胞高得多。生长细胞用0.3%丙腈诱导14小时后,即具有很高的转化丙烯腈成丙烯酰胺的活力,丙烯腈转化率为90%。除丙腈外,丙酰胺、异丁腈、正丁腈都是腈水合酶的有效诱导物。     

新型扁桃酸消旋酶的基因挖掘和性能表征

消旋酶是实现手性化合物去消旋化制备光学纯化学品的重要工具,来源于恶臭假单胞菌的扁桃酸消旋酶(MR),是目前唯一可以催化两种构型扁桃酸互相转换的消旋酶。通过基因组数据挖掘获得了9个新的扁桃酸消旋酶基因及活性蛋白,其中来源于放射性土壤杆菌Agrobacterium radiobacter的Ar MR酶对扁桃酸和邻氯扁桃酸具有较高的催化活力,而且该酶的异源表达水平也较理想。ArMR催化扁桃酸消旋反应的最适温度为50℃,最适pH为7.8。该酶在30℃、40℃和50℃下的半衰期分别为70.7、7.2、0.17 h。ArMR对(R)-和(S)-扁桃酸的K_M值分别为1.44 mmol/L和0.81 mmol/L,k_(cat)值分别为410 s~(–1)和218 s~(–1);对(R)-和(S)-邻氯扁桃酸的KM值分别为6.48 mmol/L和6.37 mmol/L,而k_(cat)值为0.22 s~(–1)和0.23 s~(–1)。Mg~(2+)和Mn~(2+)对该酶的活力有促进作用,而Zn~(2+)使其完全失活。新型扁桃酸消旋酶的发现和表征为今后此类酶的深入研究和开发提供了更多资源和数据参考。     

热激对恶臭假单胞菌S1胞内海藻糖合成酶的影响

研究了热激对恶臭假单胞菌S1胞内海藻糖合成酶的影响。通过正交试验确定了热激的最佳条件:热激在产酶初期(培养20 h)进行,热激时培养温度由20℃升高至30℃,处理时间30 min。在此条件下,海藻糖合成酶的酶活提高了76%。同时在热激后菌体的耐盐性也有较大增强。     

冷风干燥制备高活菌的恶臭假单胞菌菌粉

【目的】获得高活菌恶臭假单胞菌菌粉,提高菌体干燥及保藏存活率。【方法】选用冷风干燥法制备活菌粉,并优化吸附载体与保护剂。【结果】冷风干燥制备恶臭假单胞菌菌粉干燥存活率普遍达到65%以上,显著优于喷雾干燥(24%);对载体与保护剂进行正交试验优化,确定了载体为混合的硅藻土和碱处理玉米芯粉,混合比为1:2,保护剂(质量比)为甘露醇7%、谷氨酸钠5%、甘油1%,制得菌粉活菌数为1.03×1011 CFU/g,室温保藏30 d和4 °C保藏60 d存活率分别达到40.54%和71.67%。【结论】冷风干燥温度相对较低(10?40 °C),对菌体损伤小,碱处理玉米芯粉、甘露醇和谷氨酸钠是提高菌粉保藏存活率的重要因子,此法克服了革兰氏阴性菌菌粉不易制备和不耐保藏的瓶颈。     

恶臭假单胞菌S1产胞内海藻糖合成酶发酵培养基的优化

采用摇瓶发酵法研究了不同碳源、氮源对恶臭假单胞菌S1干重和胞内海藻糖合成酶酶活力的影响。通过正交试验得出其最佳培养基配方为(g.L-1):葡萄糖25,玉米浆15,麦芽糖20,豆粕水解液10 mL.L-1,Na3C6H5O7.2 H2O 0.5,Na2HPO4.12 H2O 0.5。优化后菌体密度、单位细胞产酶活力分别提高了1.44倍和72.16%。     

假单胞菌海因酶基因在大肠杆菌中的高效表达(英文)

为实现利用生物酶转化法进行D 对羟基苯甘氨酸的工业化生产 ,构建了 3株海因酶基因工程菌 .利用PCR技术从恶臭假单胞菌 (Pseudomonasputida)CPU 980 1染色体DNA中扩增得到长约1.8kb的含编码区和自身启动子的海因酶全基因 .通过将海因酶全基因插入pMD18 T质粒、海因酶基因的编码区与pET 17 b质粒重组、海因酶基因编码区和T7强启动子一起插入pMD18 T质粒分别得到重组质粒pMD dht、pET dht和pMD T7 dht.将上述重组质粒分别转化大肠杆菌 (Escherichiacoli) ,通过地高辛标记菌落原位杂交和海因酶活力测定两种方法 ,筛选出具有海因酶活力的阳性转化子 .结果表明 ,大肠杆菌的RNA聚合酶能够识别和结合来自恶臭假单胞菌海因酶基因的自身启动子 ,该启动子在大肠杆菌中能够工作 .基因工程菌E .coliBL2 1 pMD dht、E .coliBL2 1 pET dht和E .coliBL2 1 pMD T7 dht的海因酶活力分别为 170 0U L、190 0U L和 2 5 0 0U L ,比野生菌P .putidaCPU 980 1的海因酶活力分别提高了 8倍、9倍和 12倍 .薄层扫描结果显示 ,这些工程菌的海因酶表达量分别约占菌体总可溶性蛋白质的 2 0 %、31%和 5 7%.SDS PAGE显示 ,海因酶的单体分子量约为 5 0kD .经工程菌E .coliBL2 1 pMD T7 dht催化 ,底物对羟基苯海因的转化率在 13h内可达到 9     

Virtual screening of mandelate racemase mutants with enhanced activity based on binding energy in the transition state

Mandelate racemase (MR) is a promising candidate for the dynamic kinetic resolution of racemates. However, the poor activity of MR towards most of its non-natural substrates limits its widespread application. In this work, a virtual screening method based on the binding energy in the transition state was established to assist in the screening of MR mutants with enhanced catalytic efficiency. Using R-3-chloromandelic acid as a model substrate, a total of 53 mutants were constructed based on rational design in the two rounds of screening. The number of mutants for experimental validation was brought down to 17 by the virtual screening method, among which 14 variants turned out to possess improved catalytic efficiency. The variant V26I/Y54V showed 5.2-fold higher catalytic efficiency (k_cat/K_m) towards R-3-chloromandelic acid than that observed for the wild-type enzyme. Using this strategy, mutants were successfully obtained for two other substrates, R-mandelamide and R-2-naphthylglycolate (V26I and V29L, respectively), both with a 2-fold improvement in catalytic efficiency. These results demonstrated that this method could effectively predict the trend of mutational effects on catalysis. Analysis from the energetic and structural assays indicated that the enhanced interactions between the active sites and the substrate in the transition state led to improved catalytic efficiency. It was concluded that this virtual screening method based on the binding energy in the transition state was beneficial in enzyme rational redesign and helped to better understand the catalytic properties of the enzyme.     

Stabilization and activity-enhancement of mandelate racemase from Pseudomonas putida ATCC 12336 by immobilization

Mandelate racemase [EC 5.1.2.2] from Pseudomonas putida ATCC 12336 was efficiently immobilized through ionic binding onto DEAE- and TEAE 23-cellulose. The activity of the immobilized enzyme was significantly enhanced as compared to the native protein, i.e., 2.7- and 2.5-fold, respectively. DEAE-cellulose-immobilized mandelate racemase could be efficiently used in repeated batch reactions for the racemization of (R)-mandelic acid under mild conditions.     

Racemization of undesired enantiomers: Immobilization of mandelate racemase and application in a fixed bed reactor

Production of optically pure products can be based on simple unselective synthesis of racemic mixtures combined with a subsequent separation of the enantiomers; however, this approach suffers from a 50% yield limitation which can be overcome by racemization of the undesired enantiomer and recycling. Application of biocatalyst for the racemization steps offers an attractive option for high‐yield manufacturing of commercially valuable compounds. Our work focuses on exploiting the potential of racemization with immobilized mandelate racemase. Immobilization of crude mandelate racemase via covalent attachment was optimized for two supports: Eupergit^® CM and CNBr‐activated Sepharose 4 Fast Flow. To allow coupling of enzymatic reaction with enantioselective chromatography, a mobile phase composition compatible with both processes was used in enzymatic reactor. Kinetic parameters obtained analyzing experiments carried out in a batch reactor could be successfully used to predict fixed‐bed reactor performance. The applicability of the immobilized enzyme and the determined kinetic parameters were validated in transient experiments recording responses to pulse injections of R‐mandelic acid. The approach investigated can be used for futher design and optimization of high yield combined resolution processes. The characterized fixed‐bed enzymatic reactor can be integrated e.g. with chromatographic single‐ or multicolumn steps in various configurations.     

Substrate spectrum of mandelate racemase: Part 2. (Hetero)-aryl-substituted mandelate derivatives and modulation of activity

Efficient enzymatic racemization of 2-hydroxy-2-heteroaryl-acetic acid derivatives by mandelate racemase under mild conditions is reported for the first time. (i) Steric limitations for aryl-substituted mandelate derivatives were elucidated to be particularly striking for o-substituents, whereas m- and p-analogues were freely accepted, as well as heteroaryl- and naphthyl-analogs. (ii) The electronic character of substituents was found to play an important role: whereas electron-withdrawing substituents dramatically enhanced the racemization rates, electron-donating analogs caused a depletion. This effect could be ascribed to an α-carbanion-stabilization in accordance with the known enzyme mechanism. The latter was modeled by comparison of gas phase deprotonation energies as a useful parameter to describe resonance stabilization. The calculated data nicely correlate with the experimentally observed activities for a specific substrate as long as other parameters, such as steric restrictions, are absent or play a minor role.     

Molecular dynamics perspective on the thermal stability of mandelate racemase

Mandelate racemase from Pseudomonas putida is a promising candidate for the dynamic kinetic resolution of α-hydroxy carboxylic acids. In the present study, the thermal stability of mandelate racemase was investigated through molecular dynamics simulations in the temperature range of 303–363 K, which can guide the design of mandelate racemase with higher stability. The basic features such as radius of gyration, surface accessibility, and secondary structure content suggested the instability of mandelate racemase at high temperatures. With increase in temperature, α-helix content reduced significantly, especially the α-helices exposed to the environment. At the simulation time scale considered, intra-protein hydrogen bonds, hydrogen bonds between protein and water decreased at 363 K, while the number of salt-bridges increased. The long-distance networks remarkably changed at 363 K. A considerable number of long-lived (percentage existence time higher than 90%) hydrogen bonds and Cα contacts were lost. Root mean square fluctuation analysis revealed regions with high fluctuation, which should be helpful in the reengineering of mandelate racemase for enhanced thermal stability.     

Improvement in thermostability and psychrophilicity of psychrophilic alanine racemase by site-directed mutagenesis

A psychrophilic alanine racemase from Bacillus psychrosaccharolyticus has a higher catalytic activity than a thermophilic alanine racemase from Bacillus stearothermophilus even at 60 °C in the presence of pyridoxal 5′-phosphate (PLP), although the thermostability of the former enzyme is lower than that of the latter one [FEMS Microbial. Lett. 192 (2000) 169]. In order to improve the thermostability of the psychrophilic enzyme, two hydrophilic amino acid residues (Glu150 and Arg151) at a surface loop surrounding the active site of the enzyme were substituted with the corresponding residues (Val and Ala) in the B. stearothermophilus alanine racemase. The mutant enzyme (ER150,151VA) showed a higher thermostability, and a markedly lower K_m value for PLP, than the wild type one. In addition, the catalytic activities at low temperatures and kinetic parameters of the two enzymes indicated that the mutant enzyme was more psychrophilic than the wild type one. Thus, the psychrophilic alanine racemase was improved in both psychrophilicity and thermostability by the site-directed mutagenesis. The mutant enzyme may be useful for the production of stereospecifically deuterated NADH and various -amino acids.     

The effect of a non-metabolizable analog on mandelate catabolism in Pseudomonas putida

Dl-2,3,4,5,6-pentafluoromandelic acid (PFM) specifically inhibits the growth of Pseudomonas putida (ATCC 12633) on medium containing mandelate as sole carbon and energy source by competitive inhibition of mandelate dehydrogenase. PFM is not metabolized and is neither an inducer of the mandelate catabolic enzymes nor an antagonist of induction. Mutants resistant to the inhibitory effects of PFM (PFM^r) were isolated; most prove to be superinducible, i.e. synthesize coordinately the mandelatespecific catabolic enzymes at elevated levels following induction. In at least one case the PFM^r mutation maps very near the structural genes that encode the enzymes functional in the first two steps of mandelate catabolism. It is reasoned that the PFM^r mutation is of the promotor type. Resistance to substrate analogs such as PFM offers a general method for isolation of regulatory mutants in catabolic metabolism.Dedicated to Prof. Roger Y. Stanier on the occasion of his 60th birthday     

Modeling of Transition State by Molecular Dynamics. Prediction of Catalytic Efficiency of the Mutants of Mandelate Racemase

Abstract

Modeling of transition state by molecular dynamic method often requires modification of the force field parameters to describe energy profile accurately. In this work, we avoided the modification by modeling a series of mutants at binding-related site. In predicting the catalytic efficiency (k _cat /K _m ) of the mutants of mandelate racemase (MR), the prediction performance of three energy subsets was investigated. It was indicated that the interaction-energy subset exhibited better prediction performance than whole-system subset and binding-site subset in both quantity and trend. When prediction error (PE) criterion was equal to 5%, 10 out of 12 samples were predicted correctly within interaction-energy subset, which demonstrated a great application potential of this method in prediction of enzyme catalytic efficiency and enzyme rational design.     

Substrate spectrum of mandelate racemase: Part 1: Variation of the α-hydroxy acid moiety

Enzymatic racemization of mandelic acid derivatives modified at the α-hydroxy acid moiety was achieved using mandelate racemase [EC 5.1.2.2]. Whereas α-amino acid derivatives, such as phenyl glycine and mandelic acid hydrazide were not accepted, the mandelic acid amide was racemized at an acceptable rate. The latter was significantly enhanced by an electron-withdrawing substituent in the phenyl moiety. Based on the catalytic mechanism of the enzyme, the relative activities of non-natural substrates could be explained by steric and electronic reasons.