论文关于flask的参考文献

Synthesis of optically pure ethyl (S)-4-chloro-3-hydroxybutanoateby Escherichia coli transformant cells coexpressingthe carbonyl reductase and glucose dehydrogenase genes由共表达碳酰还原酶和葡萄糖脱氢酶的大肠杆菌转化细胞合成纯光学（S）-4-氯-3-羟基丁酸乙酯Abstract The asymmetric reduction of ethyl 4-chloro-3-oxobutanoate (COBE) to ethyl (S)-4-chloro-3-hydroxybutanoate((S)-CHBE) was investigated. Escherichia coli cells expressing both the carbonyl reductase (S1) gene from Candida magnoliae and the glucose dehydrogenase (GDH) gene from Bacillus megaterium were used as thecatalyst. In an organic-solvent-water two-phase system,(S)-CHBE formed in the organic phase amounted to M (430 g/l), the molar yield being 85%. E. coli transformant cells coproducing S1 and GDH accumulated M (208 g/l) (S)-CHBE in an aqueous monophase system by continuously feeding on COBE, which is unstable in an aqueous solution. In this case, the calculated turnover of NADP+ (the oxidized form of nicotinamide adenine dinucleotide phosphate) to CHBE was 21,600 mol/mol. The optical purity of the (S)-CHBE formed was 100% enantiomeric excess in both systems. The aqueous system used for the reduction reaction involving E. coli HB101 cells carrying a plasmid containing the S1 and GDH genes as a catalyst is simple. Furthermore, the system does not require the addition of commercially available GDH or an organic solvent. Therefore this system is highly advantageous for the practical synthesis of optically pure (S)-CHBE.本本篇文献研究了利用COBE不对称合成（S）-4-氯-3-羟基丁酸乙酯（CHBE）。大肠杆菌细胞作为催化剂同时表达了来自念珠菌属magnoliae的碳酰还原酶和来自巨大芽孢杆菌的葡萄糖脱氢酶基因。在水/有机溶剂两相体系中，(S)-CHBE在有机相中的浓度可以达到（430g/l），摩尔产率达到85%。大肠杆菌的副产物S1和GDH也达到了（208g/l），COBE在水相中不稳定，所以(S)-CHBE可以在水单相中不停的生成。在这种情况下，适当的从NADP+到CHBE的转变达到了21,600 mol/mol。所形成的CHBE的旋光度在这种体系中100%对映体过量。在水相中用携带含有S1和GDH基因质粒的E. coli HB101作为催化剂不对称还原是比较简单的。并且，这种体系并不额外需要商业GDH或者有机溶剂。因此，这种体系对于实际合成纯光学活性的(S)-CHBE是非常方便的。Optically active 4-chloro-3-hydroxybutanoic acid esters are useful chiral building blocks for the synthesis of pharmaceuticals. The (R)-enantiomer is a precursor of L-carnitine (Zhou et al. 1983), and (S)-enantiomer is an important starting material for hydroxymethylglutaryl- CoA (HMG-CoA) reductase inhibitors (Karanewsky et al. 1990). Many studies have described the microbial or enzymatic asymmetric reduction of 4-chloro-3-oxobutanoic acid esters (Aragozzini and Valenti 1992; Bare et ; Hallinan et al. 1995; Patel et al. 1992; Shimizu et al. 1990; Wong et al. 1985) based on the reduction by baker’s yeast (Zhou et al. 1983).We have previously showed that Candida magnoliae AKU4643 cells reduced ethyl 4-chloro-3-oxobutanoate (COBE) to (S)-CHBE with an optical purity of 96% enantiomeric excess (.) (Yasohara et al. 1999). As this yeast has at least three different stereoselective reductases (Wada et al. 1998, 1999a, b), the (S)-CHBE produced by this yeast was not optically pure. From among these three enzymes, an NADPH-dependent carbonyl reductase, designated as S1, was purified and characterized in some detail (Wada et al. 1998). We cloned and sequenced the gene encoding S1 and overexpressed it in Escherichia coli cells. This E. coli transformant reduced COBE to optically pure (S)-CHBE in the presence of glucose, NADP+, and commercially available glucose dehydrogenase (GDH) as a cofactor generator (Yasoharaet al. 2000). Here, we describe the construction of three E. coli transformants coexpressing the S1 from C. magnoliae and GDH from Bacillus megaterium genes and analyze the reduction of COBE catalyzed by these strains. Previous reports on the enzymatic reduction of COBE to (R)-CHBE with an optical purity of 92% . (Kataoka et al. 1999; Shimizu et al. 1990) recommended an organic- solvent two-phase system reaction for an enzymatic or microbial reduction, because the substrate (COBE) is unstable in an aqueous solvent and inactivates enzymes. We examined the reduction of COBE to optically pure (S)-CHBE by E. coli transformants in a water monophase system reaction and discuss the possible use of this type of reaction system in industrial applications。具有旋光性的（S）-4-氯-3-羟基丁酸乙酯在药物制剂的合成中是重要的手性化合物。其右旋体是L-卡尼汀的前体，其左旋体是羟甲基戊二酰辅酶A还原酶抑制剂的起始材料。许多研究描述了以面包酵母为基础微生物或者酶的COBE的不对称还原。我们先前已经知道利用来自念珠菌属magnoliae AKU4643 细胞催化COBE生成光学纯度96%的CHBE。这种酵母至少有三种立体选择性的还原酶，这种酵母产生的CHBE并非纯光学的，在这三种酶之中，NADPH-依赖碳酰还原酶，我们克隆并测序编码S1的基因，并在大肠杆菌中过表达。大肠杆菌转化细胞在葡萄糖，NADP+和商业化的葡萄糖脱氢酶作为辅酶因子的启动子催化COBE生成纯光学的CHBE。我们构建这三种大肠杆菌转化细胞共表达来自的S1和来自巨大芽孢杆菌的GDH，并分析COBE被这几种菌株催化还原的反应机理。先前的报道表明，利用酶催化还原COBE生成CHBE光学纯度可达92%，也提到了因为底物（COBE）在水相中不稳定，并且酶容易钝化，所以利用酶或者微生物在有机溶剂/水两相体系中催化反应。我们研究了在水单相体系中由COBE还原生成纯光学的CHBE，还讨论了这种反应体系在工业应用中可能的用途。Materials and methodsBacterial strain and plasmids The E. coli strains used in this study were JM109 and pGDA2, in which the GDH gene from B. megaterium is inserted into pKK223-3, was kindly provided by Professor I. Urabe, Osaka University (Makino et al. 1989). Plasmids pSL301 and pTrc99A were purchased from Invitrogen (USA), and Amersham Pharmacia Biotech (UK), respectively. Plasmids pUC19 and pSTV28 (Homma et al. 1995; Takahashi et al. 1995) were purchased from Takara Shuzo (Japan).材料和方法菌株和质粒本次实验中使用的大肠杆菌是JM109 and HB101。来自B. megaterium的GDH基因插入到Pkk233-3质粒中，而带有GDH基因片段的pGDA2质粒由到由大阪大学的urabe教授提供。质粒pSL301和 pTrc99A是由美国的Invitrogen公司和英国的公司分别购买的。质粒pUC19和pST28是由日本takara公司购买的。The recombinant plasmid used in this study was constructed as follows (Fig. 1): Plasmid pGDA2 was double-digested with EcoRI and PstI to isolate a DNA fragment of about kilobase pairs (kb) including the GDH gene. This fragment was inserted into the EcoRI-PstI site of plasmid pSL301 to construct plasmid pSLG. Plasmid pSLG was double-digested with EcoRI and XhoI to isolate a DNA fragment of about kb including the GDH gene.这次实验使用的重组质粒构建如下：质粒pGDA2 被EcoRI 和 PstI双酶切从而分离出一个大小约为的包含有GDH基因的DNA片段。这个片段被插入到质粒Psl301的EcoRI-PstI酶切位点从而构建出质粒pSLG。质粒pSLG被EcoRI和XhoI To construct plasmid pNTS1G, this fragment was inserted into the EcoRI-SalI site of pNTS1, which was constructed to overproduce S1 as described previously (Yasohara et al. 2000). To construct plasmid pNTGS1, plasmid pNTG was first generated. Two synthetic primers (primer 1, TAGTCCATATGTATAAAGATTTAG,and primer 2 TCTGAGAATTCTTATCCGCGTCCT) were prepared for polymerase chain reaction (PCR) using pGDA2 as the template. The PCR-generated fragment was double- digested with NdeI and EcoRI and then inserted into the NdeI EcoRI site of plasmid pUCNT, which was constructed from pUC19 and pTrc99A, as reported (Nanba et al. 1999), to obtain pNTG. To construct plasmid pNTGS1, two synthetic primers (primer 3, GCCGAATTCTAAGGAGGTTAATAATGGCTAAGAACTTCTCCAACG, and primer 4, GCGGTCGACTTAGGGAAGCGTGTAGCCACCGTC) were prepared using pUCHE, which contains the S1 gene as the template. The PCR-generated fragment was double-digested with EcoRI and SalI and then inserted into the EcoRI-SalI site of pNTG to obtain pNTGS1. Plasmid pNTS1G, pNTGS1 or pNTG was transformed into E. coli HB101.构建pNTS1是为了过表达前文所提到的S1，这个大小的片段被插入到pNTS1的EcoRI-SalI酶切位点从而构建pNTS1G。为了构建质粒pNTGS1，首先需要构建pNTG。两个合成引物（引物1，TAGTCCATATGTATAAAGATTTAG和引物2，TCTGAGAATTCTTATCCGCGTCCT）和作为模板的pGDA2是PCR反应需要的。PCR得到的片段是由NdeI 和EcoRI双酶切和并插入到质粒pUCNT的NdeI EcoRI酶切位点来得到pNTG。根据报道，pUCNT是由pUC19和 pTrc99A构建而来。为了构建质粒pNTGS1，两个合成引物(引物 3, GCCGAATTCTAAGGAGGTTAATAATGGCTAAGAACTTCTCCAACG, and 引物 4, GCGGTCGACTTAGGGAAGCGTGTAGCCACCGTC)，包括了S1基因作为模板。Pcr产物片段被EcoRI和SalI双酶切然后被插入到pntg的EcoRI-SalI酶切位点得到pntg1.质粒pNTS1G, pNTGS1或者 pNTG都是导入大肠杆菌 pGDA2 was double-digested with EcoRI and PstI to isolate a DNA fragment of about kb including the GDH gene. To construct plasmid pSTVG, this fragment was inserted into the EcoRI-PstI site of plasmid pSTV28. Plasmid pSTVG was transformed into E. coli HB101. 质粒pGDA2被EcoRI 和 PstI双酶切得到包含GDH基因的大小的DNA片段。为了构建pSTVG质粒，这个片段被插入到pSTV28质粒的EcoRI-PstI的酶切位点。pSTVG质粒被导入到E. coli HB101。Medium and cultivationThe 2×YT medium comprised Bacto-tryptone, yeastextract, and NaCl, pH . E. coli HB 101 carrying pNTS1,pNTG, pNTS1G, or pNTGS1 was inoculated into a test tube containing2 ml 2×YT medium supplemented with mg/ml ampicillin,followed by incubation at 37 °C for 15 h with reciprocal preculture ( ml) was transferred to a 500-ml shakingflask containing 100 ml 2×YT medium. The cells were cultivatedat 37 °C for 13 h with reciprocal shaking. E. coli HB101 carryingpNTS1 and pSTVG was similarly cultivated in 2×YT mediumsupplemented with mg/ml ampicillin and mg/ml chloramphenicol.培养基和培菌2*YT培养基 包含有细菌用胰蛋白胨，酵母提取物， NaCl，.携带有pNTS1,pNTG, pNTS1G, 或 pNTGS1的大肠杆菌HB101被接种到有氨苄青霉素的2ml的2*YT培养基，37°C摇床15小时。将菌液接种到100ml2*YT培养基的500ml烧瓶中。在37°C摇床培养13小时。携带有pNTS1 和 pSTVG质粒的大肠杆菌HB101在2*YT培养基中培养方法相似，只是培养基中要加入 mg/ml的氨苄青霉素和 mg/ml的氯霉素。Preparation of cell-free extracts and the enzyme assay Cells were harvested from 100 ml of culture broth by centrifugation, suspended in 50 ml of 100 mM potassium phosphate buffer (pH ), and then disrupted by ultrasonication. The cell debris was removed by centrifugation; the supernatant was recovered as the cell-free extract. Carbonyl reductase S1 activity (COBE-reducing activity) was determined spectrophotometically as follows: The assay mixture consisted of 100 mM potassium phosphate buffer (pH ), mM NADPH, and 1 mM COBE. The reactions were incubated at 30 °C and monitored for the decrease in absorbance at 340 nm. The assay mixture for GDH activity consisted of 1 M Tris-HCl buffer (pH ), 100 mM glucose, and 2 mM NADP+. The reactions were incubated at 25 °C and monitored for the increase in absorbance at 340 nm. One unit of S1 or GDH was defined as the amount catalyzing the reduction of 1 μmol NADP+ or oxidation of 1 μmol NADPH per minute, respectively. Protein concentrations were measured with a proteinassay kit containing Coomassie brilliant blue (Nacalai Tesque, Japan),using bovine serum albumin as the standard (Bradford 1976).无细胞抽提液和酶鉴定将100ml培养液离心收获菌体，用为的磷酸缓冲液悬浮，然后超声粉碎。细胞碎片通过离心可以去除，收集上层清液就是无细胞抽提物。碳酰还原酶S1的活性由分光光度计测量如下：测定的混合物包括：的磷酸二氢钾缓冲液，和1mMCOBE。反应在30°C条件下反应，并且随时监测其在340nm处的吸光值。测GDH混合物包括：1M pH 的Tris-HCl的缓冲液，100mM的葡萄糖，2mM的NADP+。反应在25°C下进行，监测其在340nm处的吸光值。一个单位S1或GDH被定义为每分钟催化还原1μmol NADP+或氧化1 μmol NADPH的量。蛋白质的测定通过含有考马斯亮蓝的蛋白质测定试剂利用牛血清白蛋白作为标准进行测定。Study of enzyme stabilityOne milliliter of 100 mM potassium phosphate buffer (pH ) containing the cell-free extracts of E. coli HB101 carrying pNTS1 (S1: 20 U/ml) was mixed with an equal volume of each test organic solvent in a closed vessel. After the mixture was shaken at 30 °C for 48 h, the remaining enzyme activities in an aqueous phase were assayed as described above. The mixture, containing 100 mM potassium phosphate buffer (pH ), S1 (20 U/ml), and various concentrations of CHBE, was incubated at 30 °C for 24 h in order to study the enzyme’s stability in the presence of remaining enzyme activities were assayed as described above.酶稳定性的研究一毫升含有含有pNTS1质粒的E. coli HB101的无细胞抽提液的100mM磷酸氢二钾缓冲液（）与等体积的有机溶剂混合。混合物在30 °C震摇48小时后，水相中残留的酶活力即是上述的酶活力。COBE reduction with E. coli cells expressing the S1 gene and E. coli cells expressing GDH genes in a two-phase system reaction The reaction mixture comprised 15 ml culture broth of E. coli HB101 carrying pNTG, 17 ml culture broth of E. coli HB101 carrying pNTS1, mg NADP+, 4 g glucose, g COBE, 25 ml n-butyl acetate, and about 25 mg Triton X-100. The pH of the reaction mixture was controlled at with 5 M sodium hydroxide. At 2 h, g COBE and g glucose were added to the reaction mixture. To compare the reaction by E. coli transformant coexpressing the GDH and S1 genes, 30 ml culture broth of E. coliHB101 carrying pNTS1G was used instead of culture broth of E. coli HB101 carrying pNTG and E. coli HB101 carrying pNTS1. Other components and the procedure were the same as described above.表达S1基因和GDH基因的大肠杆菌细胞在两相反应体系中的还原反应混合物包含有带有pNTG质粒的大肠杆菌HB101的菌液15ml，pNTS1质粒的大肠杆菌HB101的菌液17ml， mg NADP+，4 g葡萄糖，的COBE，25ml的n-butyl acetate丁酰醋酸盐和大约25mg的聚乙二醇辛基苯基醚Triton X-100。用5M的NaOH溶液将pH控制在。在反应两小时后，加入和葡萄糖到该混合物中。比较大肠杆菌转化细胞共表达GDH和S1基因，携带有pNTS1G质粒的大肠杆菌HB10130ml菌液取代了携带有pNTG和pNTS1质粒的大肠杆菌HB101菌液。其他的成分和步骤和上述的方法相似。 COBE reduction to (S)-CHBE in a two-phase system reaction The reaction mixture contained 50 ml of culture broth of an E. coli HB101 transformant, mg NADP+, 11 g glucose, 10 g COBE, 50 ml n-butyl acetate, and about 50 mg Triton X-100. The reaction mixture was stirred at 30 °C, and the pH was controlled at with 5 M sodium hydroxide. Five grams of COBE/ g glucose and 10 g COBE/11 g glucose were added to the reaction mixture at 3 h and 7 h, respectively; mg NADP+ was added at 26 在两相系统中还原生成（S）-CHBE反应混合物包含50ml E. coli HB101转化细胞的培养液，葡萄糖，10gCOBE，50ml丁酰醋酸，和大概50mg聚乙二醇辛基苯基醚Triton X-100.在30°C温度下将其混合均匀，并用5M的NaOH溶液将pH控制在。在第3小时加入5gCOBE和葡萄糖或者在第7小时加入10gCOBE和11g葡萄糖，分别在第26小时加入。 COBE reduction to (S)-CHBE in an aqueous system reaction The reaction mixture was made up of 50 ml of culture broth of an E. coli HB101 transformant, mg NADP+, 11 g glucose, and about 50 mg Triton X-100. The reaction mixture was stirred at 30 °C. Fifteen grams of COBE was fed continuously by means of a micro-feeding machine at a rate of about g/min for about 12 h. The pH of the reaction mixture was controlled at with 5 M sodium hydroxide. The reaction mixture was extracted with 100 ml ethyl acetate. The organic layer was dried over anhydrous sodium sulfate and then evaporated in vacuo. COBE在水相中还原成(S)-CHBE的反应反应的体系是由50ml大肠杆菌HB101转化细胞的菌液，，11g葡萄糖和大约50mg聚乙二醇辛基苯基醚Triton X-100。反应混合物在30°C15mg的COBE通过微量添加机器以 g/min的速率连续12小时恒定的加入到体系中。用5M的NaOH溶液将pH控制在。反应混合物用100ml乙酸乙酯萃取。有机层用无水硫酸钠吸干，并在真空中脱水。Analysis The organic layer was obtained on centrifugation of the reaction mixture and was assayed for CHBE and COBE by gas chromatography. Optical purity of CHBE was analyzed by high-performance liquid chromatography (HPLC), as described previously (Yasohara et al. 1999).Enzymes and chemicals Restriction enzymes and DNA polymerase were purchased fromTakara Shuzo (Japan). COBE (molecular weight: ) was purchasedfrom Tokyo Kasei Kogyo (Japan). Racemic CHBE (molecularweight: ) was synthesized by reduction of COBE withNaBH4. All other chemicals used were of analytical grade andcommercially available.分析离心反应混合物得到的有机层通过气相色谱法测定其CHBE和COBE。COBE的光学纯度如前所述通过高效液相色谱法进行分析。酶和化学试剂限制性内切酶和DNA聚合酶由takara公司购得，COBE（分子量：）由东京Tokyo Kasei Kogyo公司购得，消旋体CHBE（分子量）通过COBE及NaBH4合成。所有其他化学试剂都是分析等级和商业化的试剂。Construction of E. coli transformants overproducing S1 and GDHTo express the carbonyl reductase S1 and GDH genes in the same E. coli cells, four expression vectors were constructed (Fig. 1). Plasmids pNTS1G and pNTGS1 contain the S1 gene from C. magnoliae, the GDH gene from B. megaterium, the lac promoter derived from pUC19, and the terminator derived from pTrc99A. Plasmid pNTS1 contains the S1 gene, the lac promoter derived from pUC19, and the terminator derived from pTrc99A. The enzyme activities in cell-free extracts of the E. coli transformants are shown in Table 1. E. coli HB101 cells carrying the vector plasmid pUCNT had no detectable S1 or GDH activity. E. coli HB101 carrying either pNTS1G or pNTGS1 showed S1 and GDH activity without isopropyl-β-D-thiogalactopyranoside (IPTG) induction. The S1 activities of these two transformants were lower than the GDH activities. To obtain a transformant whose S1 activity was equal to or greater than the level of GDH activity, we used a lower copy vector, pSTV28 (Homma et al. 1995; Takahashi et al. 1995), to express the GDH gene. It may be possible to raise the S1 activity by lowering the GDH activity. Plasmid pSTVG contains the GDH gene, the lac promoter, the chloramphenicol resistance gene, and the replicative origin derived from pACYC184 for compatibility with the plasmid pNTS1. In E. coli HB101 carrying pNTS1 and pSTVG, the S1 activity was higher than the GDH activity, but this GDHlevel may be too low to regenerate in a COBE reduction reaction as described below.过产生S1和GDH的大肠杆菌转化细胞的构建为了在同一大肠杆菌细胞中表达碳酰还原酶S1和GDH基因，要构建四个表达型载体。质粒pNTS1G 和 pNTGS1包含有来自C. magnoliae的S1基因，来自B. megaterium的GDH基因，来自pUC19的LAC启动子，从pTrc99A的来的终止子，质粒pNTS1包含有S1基因，来自pUC19的LAC启动子，从pTrc99A的来的终止子。在大肠杆菌转化细胞的无细胞抽提物的酶活力如表一所示。携带有运输质粒pUCNT的大肠杆菌细胞无法检测到其S1和GDH活性。携带有pNTS1G 或 pNTGS1质粒在没有IPTG的诱导下有S1和GDH的活性。在这两个转化菌种中，S1的活力小于GDH的活力。为了得到S1活性等于或者大于GDH的大肠杆菌转化菌株，我们使用低拷贝的载体pSTV28，来表达GDH基因。它可能可以通过降低GDH的活性从而提高S1的活性。质粒pSTVG包含有GDH基因，lac启动子，和氯霉素抗性基因，以及与pNTS1具有相容性的从pACYC184得来的复制起始位点。在携带有pNTS1和pSTVG的大肠杆菌转化细胞中，S1的活性要高于GDH的活性，但是GDH的活性可能会太低而在COBE还原反应中不能再生。 太长了，字数有限制，所以不能发完。分数我无所谓啦，我很少登录的。这应该算是基因工程的吧，是我以前自己翻的，不是很好。如果你要的话可以联系我的邮箱。

这章是跟着上一章讲的，如有不适应请点击 上一章 服务器里的路由是一个非常重要的角色，它控制了路径与视图函数的关联。 url的是统一资源定位符，对可以从 互联网 上得到的资源的位置和访问方法的一种简洁的表示，是互联网上标准资源的地址。互联网上的每个文件都有一个唯一的URL，它包含的信息指出文件的位置以及浏览器应该怎么处理它。 常见的url是： 可以分成：

通俗的讲

Werkzeug 库的routing模块的主要功能在于URL解析。对于WSGI应用来讲，不同的URL对应不同的视图函数，routing模块则会对请求信息的URL进行解析并匹配，触发URL对应的视图函数，以此生成一个响应信息。routing模块的解析和匹配功能主要体现在三个类上：Rule、Map和MapAdapter。

Rule类继承自RuleFactory类。一个Rule的实例代表一个URL模式，一个WSGI应用可以处理很多不同的URL模式，这也就是说可以产生很多不同的Rule实例。这些Rule实例最终会作为参数传递给Map类，形成一个包含所有URL模式的对象，通过这个对象可以解析并匹配请求对应的视图函数。

关于Rule类有一些常用的方法：

rule实例化时至少接受一个参数，其他的都是默认参数。这个类实现了match,build等方法。主要的方法有get_url方法，这个方法重写了父类RuleFactory的方法，返回的是自身的生成器。这个方法与submain等其他的类的实现方法不同，在submain类中，这个类本身包含了rule类，故调用get_urls方法首先获得rule实例，再一次调用get_url得到一个生成器。 另外一个方法是bind方法，这个方法将rule实例绑定到map实例上,绑定后的rule能够使用map属性的方法。

通过Map类构造的实例可以存储所有的URL规则，这些规则是Rule类的实例。Map实例可以 通过后续的调用和给定的URL进行匹配。

关于Map类有一些常用的方法：

map类相当于一个存放Rule类的容器，实现的方法能对rule进行操作，也是url进入特定视图函数的中介。

MapAdapter主要是获取请求的url参数，将参数传递至相关视图函数中，进行处理。