白地霉的戊糖代谢 Ⅱ.L-阿拉伯糖代谢途径

用在L-阿拉伯糖上培养的白地霉(Geotrichum candidum Link)2.361无细胞提取液进行了L-阿拉伯糖代谢酶体系的研究。查明L-阿拉伯糖代谢的变化途径如下: L-阿拉伯糖+NADPH_2 戊醛糖还原酶L-阿拉伯糖醇+NADP L-阿拉伯糖醇+NAD L-阿拉伯糖醇脱氢酶L-木酮糖+NADH_2 L-木酮糖+NADPH_2 NADP-木糖醇脱氢酶木糖醇+NADP 木糖醇+NAD NAD-木糖醇脱氢酶D-木酮糖+NADH_2 D-木酮糖+ATP D-木酮糖激酶→D-木酮糖-5-磷酸+ADP L-阿拉伯糖醇脱氢酶仅存在于L-阿拉伯糖培养的菌体中,而不存在于木糖培养的菌体中。可见它与木糖醇脱氢酶不是同一个酶。这一点与文献报导的不同,在黄青霉中这两种酶活力被认为是同一种酶的作用。     

一类中草药有效成分与BCL2相互作用的分子模拟研究

以一类中草药有效成分为研究对象,使用分子对接和分子动力学方法,研究了其与BCL2酶的相互作用。结果表明,筛选出的人参皂苷Re、人参皂苷Rb1具有最好的对接结果。通过分子动力学方法分别获取了人参皂苷Re、人参皂苷Rb1与BCL2结合的稳定结构。其中,人参皂苷Re与Asn143、Arg146、Phe104等9个氨基酸残基有疏水作用,形成了2个稳定性不同的氢键,其中O原子与残基Glu136形成的氢键较为稳定。人参皂苷Rb1分别与残基Phe112、Glu136、Arg146等9个氨基酸残基有疏水作用,形成7个氢键,其中与残基Asp140和Asp103中的O原子形成的2个氢键最为稳定。     

一种基因工程改造的NADH高亲和力木糖还原酶突变基因可促进酿酒酵母发酵木糖生成乙醇

在导入表达毕赤酵母(Pichia stipitis)木糖还原酶(xylose reductase,XR)和木糖醇脱氢酶(xylitol dehydrogenase,XDH)基因的重组酿酒酵母中,木糖还原酶活性主要依赖辅酶NADPH,木糖醇脱氢酶活性依赖辅酶 NAD+,两者的辅助因子不同导致细胞内电子氧化还原的不平衡,是造成木糖醇积累,影响木糖代谢和乙醇产量的主要原因之一.将经过基因工程改造获得的NADH高亲和力的木糖还原酶突变基因m1,与毕赤酵母木糖醇脱氢酶(PsXDH)基因xyl2共转染酿酒酵母AH109,以转染毕赤酵母木糖还原酶(PsXR)基因xyl1和xyl2重组质粒的酵母细胞为对照菌株,在SC/-Leu/-Trp营养缺陷型培养基中进行筛选,获得的阳性转化子分别命名为AH-M-XDH和AH-XR-XDH.重组酵母在限制氧通气条件下对木糖和葡萄糖进行共发酵摇瓶培养,HPLC检测发酵底物的消耗和代谢产物的产出情况.结果显示,与对照菌株AH-XR-XDH相比,AH-M-XDH的木糖利用率明显提高,乙醇得率增加了16%,木糖醇产生下降了41.4%.结果证实,通过基因工程改造的木糖代谢关键酶,可用于酿酒酵母发酵木糖生产乙醇,其能通过改善酿酒酵母细胞内氧化还原失衡的问题,提高木糖利用率和乙醇产率.     

来自假单胞菌ZJU26的R-2-氯丙酸脱卤酶的手性识别过程研究

立体选择性是2-卤代酸脱卤酶最重要的性质之一,但目前其手性识别过程尚不明确,对其进行研究和解析具有重要意义。以来自假单胞菌ZJU26的R-2-氯丙酸脱卤酶dehDIV-R为模型,研究了R-2-卤代酸脱卤酶的手性识别过程。首先通过测定反应产物的构型,确定dehDIV-R催化底物为S_N2反应。通过Discovery Studio 3.0对dehDIV-R进行同源模建及底物分子对接,由对接结果和序列比对确定dehDIV-R立体选择性的关键位点Asn236,预测dehDIV-R的立体选择性与反应时底物到达反应位置的空间位阻密切相关。对dehDIV-R进行虚拟突变,将Asn236位点突变成具有不同空间位阻的残基Ala和Ser,并分别与底物分子进行分子对接,预测突变酶的立体选择性。根据预测结果,对Asn236氨基酸残基进行定点突变,发现在Asn236突变为Ala后的A1酶显示出对RS底物的活力;在Asn236突变为Ser后的S1酶显示出与原始酶相反的立体选择性,实现了立体选择性的反转。与模型的预测结果相符,证明了模型的合理性。     

家蚕磷酸吡哆醇氧化酶的体外定点突变及其活性鉴定

[目的]研究家蚕Bombyx mori磷酸吡哆醇氧化酶(pyridoxine 5’-phosphate oxidase,PNPO)个别保守氨基酸残基对PNPO酶活性的影响.[方法]用重叠延伸法把氨基酸残基Lys111 (AAA)突变为Glu (GAA),Ser160(AGC)定点突变为Ala(GCC);构建重组表达载体...     

计算机模拟短小芽孢杆菌木聚糖酶与底物木聚糖的对接

克隆测序短小芽孢杆菌(Bacillus pumilus)木聚糖酶基因,在同源建模所得三维结构的基础上寻找底物结合可能的活性口袋,用计算机模拟其与底物木聚糖的对接,预测酶与催化反应过程的关键氨基酸残基。所得的信息对木聚糖酶的定向改造有重要意义。     

Gluconobacter oxydans NH-10中NAD+型阿拉伯糖醇脱氢酶基因敲除菌株的构建

氧化葡萄糖酸杆菌Gluconobacter oxydans NH-10能够转化D-阿拉伯糖醇,经木酮糖生成木糖醇,但该菌中存在的NAD+型D-阿拉伯糖醇脱氢酶可将中间产物D-木酮糖还原成D-阿拉伯糖醇,从而影响木糖醇的积累.利用同源重组基因敲除的方法构建G.oxydans NH-10 NAD+型D-阿拉伯糖醇脱氢酶( sArDH)基因敲除突变株.PCR结果显示:sArDH基因在1株重组菌中完全被卡那抗性基因替代,表明sArDH基因敲除突变体构建成功.生物学特性鉴定显示:突变菌在菌落形态,生长状态方面与原始菌无明显差异.静息细胞转化D-阿拉伯糖醇结果显示,突变株不存在还原D-木酮糖产D-阿拉伯糖醇的逆反应,终产物木糖醇的产量有所提高.     

计算机模拟短小芽孢杆菌木聚糖酶与底物木聚糖的对接

克隆测序短小芽孢杆菌（Bacillus pumilus）木聚糖酶基因,在同源建模所得三维结构的基础上寻找底物结合可能的活性口袋,用计算机模拟其与底物木聚糖的对接,预测酶与催化反应过程的关键氨基酸残基。所得的信息对木聚糖酶的定向改造有重要意义。     

嗜酸氧化亚铁硫杆菌的谷胱甘肽还原酶的结构模建和底物分子对接

极端环境微生物嗜酸氧化亚铁硫杆菌的谷胱甘肽还原酶(GR)可能在它的抵抗极端酸性,有毒和氧化性的生物浸出环境中发挥至关重要的作用.通过同源模建技术和分子动力学模拟,它的一个三维结构被构建,优化和检验了.获得的结构被进一步用于搜索绑定位点,跟辅因子黄素腺嘌呤二核苷酸(FAD)和底物谷胱甘肽(GSSG)进行分子柔性对接,并以此识别关健残基.对接结果显示,位于活性残基Cys42和Cys47之间的二硫键夹在FAD的活性位点和底物GSSG的二硫键之间.它们之间的距离非常靠近,这跟底物反应机理的初始步骤的情况十分一致.相互作用能表明8个酶中残基Cys42,Cys47,GIu443B,Glu444B,His438B,Ser14,Thr447B和Lys51是固定或激活GSSG的关键残基,这跟以前的实验事实相吻合.此外,根据相互作用能我们还新发现7个重要残基(Arg449B,Pro439B,Thr440B,Thr310,Va143,Gly46 and Va148).所有这些残基在其它物种中的相应物中也都是保守的.这些结果有助于进一步的实验研究和理解其催化机理,进而揭示这种细菌的抗毒机理,服务于工业应用.     

酸性木聚糖酶XynⅡ活性中心关键氨基酸残基的鉴定

目的:鉴定来源于宇佐美曲霉(Aspergillus usamii)E001的酸性木聚糖酶XynⅡ活性中心关键氨基酸残基。方法:对XynⅡ进行SWISS-MODEL同源建模和BLAST序列比较,分析XynⅡ中所有可能作为催化残基的保守氨基酸,采用定点突变手段对其进行鉴定研究。结果:只有Glu-79和Glu-170位于酶与底物作用的活性中心,它们分别位于β折叠股B6和B4上,推测Glu-79和Glu-170为XynⅡ活性中心关键氨基酸残基。将Glu-79和Glu-170突变为酸性的Gln,突变酶E79Q,E170Q在大肠杆菌和毕赤酵母中表达后,活性均丧失。结论:79位、170位Glu是木聚糖酶XynⅡ活性中心的关键氨基酸残基,为该酶进一步的结构与功能研究提供了理论基础。     

Point mutation of the xylose reductase (XR) gene reduces xylitol accumulation and increases citric acid production in Aspergillus carbonarius

Aspergillus carbonarius accumulates xylitol when it grows on d-xylose. In fungi, d-xylose is reduced to xylitol by the NAD(P)H-dependent xylose reductase (XR). Xylitol is then further oxidized by the NAD⁺-dependent xylitol dehydrogenase (XDH). The cofactor impairment between the XR and XDH can lead to the accumulation of xylitol under oxygen-limiting conditions. Most of the XRs are NADPH dependent and contain a conserved Ile-Pro-Lys-Ser motif. The only known naturally occurring NADH-dependent XR (from Candida parapsilosis) carries an arginine residue instead of the lysine in this motif. In order to overcome xylitol accumulation in A. carbonarius a Lys-274 to Arg point mutation was introduced into the XR with the aim of changing the specificity toward NADH. The effect of the genetic engineering was examined in fermentation for citric acid production and xylitol accumulation by using d-xylose as the sole carbon source. Fermentation with the mutant strain showed a 2.8-fold reduction in xylitol accumulation and 4.5-fold increase in citric acid production compared to the wild-type strain. The fact that the mutant strain shows decreased xylitol levels is assumed to be associated with the capability of the mutated XR to use the NADH generated by the XDH, thus preventing the inhibition of XDH by the high levels of NADH and ensuring the flux of xylose through the pathway. This work shows that enhanced production of citric acid can be achieved using xylose as the sole carbon source by reducing accumulation of other by-products, such as xylitol.     

Gluconobacter oxydans木糖醇脱氢酶基因的克隆表达及木糖醇的转化分析

从氧化葡萄糖酸杆菌(Gluconobacter oxydans)的基因组DNA上扩增出木糖醇脱氢酶基因xdh,构建了诱导型表达载体pSE-xdh,导入E.coli JM109后获得了高效表达木糖醇脱氢酶基因的重组菌JM109/pSE-xdh。通过HisTrap HP亲和层析和SephacrylS 300分子筛两步纯化从细胞中得到纯酶,并对酶学性质进行研究。XDH最适还原反应的pH值为5.0,最适还原反应的温度为35℃;最适氧化反应的pH值为11.0,最适氧化反应的温度为30℃。重组菌中的XDH依赖NADH,对NADH的米氏常数Km=57.8 mmol/L,最大反应速率Vmax=1209.1 mmol/(ml·min)。重组菌的XDH酶活力为13.9 U/mg。利用重组菌和原始菌混合静止细胞转化D 木酮糖,16 h 28.0 g/L D木酮糖生成16.7 g/L木糖醇,而原始菌单独转化只生成8.3 g/L木糖醇。     

Heterologous expression of Aspergillus oryzae xylose reductase and xylitol dehydrogenase genes facilitated xylose utilization in the yeast Saccharomyces cerevisiae

The cDNA encoding a putative xylose reductase (xyrA) from Aspergillus oryzae was cloned and coexpressed in the yeast Saccharomyces cerevisiae with A. oryzae xylitol dehydrogenase cDNA (xdhA). XyrA exhibited NADPH-dependent xylose reductase activity. The S. cerevisiae strain, overexpressing the xyrA, xdhA, endogenous XKS1, and TAL1 genes, grew on xylose as sole carbon source, and produced ethanol.     

葡萄糖酸氧化杆菌木糖醇脱氢酶基因的克隆与表达

【目的】获得葡萄糖酸氧化杆菌(Gluconobacter oxydans CGMCC 1.637)的木糖醇脱氢酶基因,研究其酶学性质及碳源特别是D-阿拉伯醇和木糖醇对该酶活性的影响。【方法】通过已报道序列的木糖醇脱氢酶的保守区设计引物,用聚合酶链式反应(polymerase chain reaction,PCR)扩增获得目的基因片段。根据获得的片段序列设计引物克隆目的基因的5’和3’片段,将所获得的片段拼接,获得完整的木糖醇脱氢酶基因。通过构建工程菌获得重组蛋白,并利用氧化还原反应测定重组酶的活性。用含不同碳源的培养基培养G.oxydans CGMCC 1.637,并测定其破胞上清液木糖醇脱氢酶氧化木糖醇的活性;用不同碳源培养的G.oxydans CGMCC 1.637转化木酮糖,用高效液相色谱法测定木糖醇的产量。【结果】获得一个新的798bp的木糖醇脱氢酶基因,所编码的木糖醇脱氢酶含265个氨基酸,属于短链脱氢酶家族。酶学性质研究发现,该木糖醇脱氢酶催化木糖醇氧化的最适合条件为35℃、pH 10.0,最高活性为23.27 U/mg,催化木酮糖还原为木糖醇的最适条件为30℃、pH 6.0。最高活性为255.55 U/mg;该木糖醇脱氢酶的对木糖醇的Km和Vmax分别为78.97 mmol/L和40.17 U/mg。碳源诱导实验表明,d-山梨醇对G.oxydans CGMCC 1.637木糖醇脱氢酶的活性有明显的促进作用,而葡萄糖、果糖、木糖、木糖醇、D-阿拉伯醇对木糖醇脱氢酶活性有明显的抑制作用。而在转化实验中,用d-甘露糖培养的G.oxydans CGMCC 1.637的转化能力明显高于其他碳源培养的G.oxydans CGMCC 1.637的转化能力,其中,用阿拉伯醇培养的G.oxydans CGMCC 1.637的转化能力最低,仅为对照的35%。【结论】克隆自G.oxydans CGMCC 1.637的木糖醇脱氢酶基因是一个新的基因,用阿拉伯醇培养的G.oxydans CGMCC 1.637破胞液木糖醇脱氢酶活性低;且阿拉伯醇对G.oxydans CGMCC 1.637木酮糖的还原能力具有抑制作用。     

Antisense inhibition of xylitol dehydrogenase gene, xdh1 from Trichoderma reesei

AIMS: To inhibit xylitol dehydrogenase (XDH) in Trichoderma reesei by antisense inhibition strategy and construct novel strains capable of accumulating xylitol. METHODS AND RESULTS: The xdh1 antisense expression plasmid pGTA-xdh was constructed by inserting xdh1 DNA fragment inversely between the gpdA promoter and the trpC terminator from Aspergillus nidulans into a pUC19 plasmid backbone. Trichoderma reesei protoplasts were co-transformated with pGTA-xdh and hygromycin B resistance plasmid pAN7-1. Of 20 transformants screened from the selective medium, one transformant with the highest xylitol accumulation, designated ZY15, showed a distinct reduction (c. 52%) in XDH activity compared with the original strain Rut-C30. The results of Southern hybridization and PCR assay showed that the antisense expression cassette of xdh1 was integrated into the genome of T. reesei. The RT-PCR analysis proved that antisense RNA effectively inhibited XDH expression (c. 65%). Xylitol accumulation (2.37 mg ml(-1)) of ZY15 was five times higher than that (0.46 mg ml(-1)) of the original strain Rut-C30. CONCLUSIONS: Strain ZY15 successfully downregulated XDH production and exhibited xylitol accumulation in xylose liquid medium. SIGNIFICANCE AND IMPACT OF THE STUDY: This study contributed to the budding field of fungal genetics in two points. First, it confirmed that antisense RNA strategy could be used as a means of reducing gene expression in the filamentous fungus T. reesei. Secondly, it verified that the strategy appears most promising for creating novel filamentous fungi strains capable of accumulating intermediary metabolites.     

Cloning of the xylitol dehydrogenase gene from Gluconobacter oxydans and improved production of xylitol from D-arabitol

Xylitol dehydrogenase (XDH) was purified from the cytoplasmic fraction of Gluconobacter oxydans ATCC 621. The purified enzyme reduced D-xylulose to xylitol in the presence of NADH with an optimum pH of around 5.0. Based on the determined NH2-terminal amino acid sequence, the gene encoding xdh was cloned, and its identity was confirmed by expression in Escherichia coli. The xdh gene encodes a polypeptide composed of 262 amino acid residues, with an estimated molecular mass of 27.8 kDa. The deduced amino acid sequence suggested that the enzyme belongs to the short-chain dehydrogenase/reductase family. Expression plasmids for the xdh gene were constructed and used to produce recombinant strains of G. oxydans that had up to 11-fold greater XDH activity than the wild-type strain. When used in the production of xylitol from D-arabitol under controlled aeration and pH conditions, the strain harboring the xdh expression plasmids produced 57 g/l xylitol from 225 g/l D-arabitol, whereas the control strain produced 27 g/l xylitol. These results demonstrated that increasing XDH activity in G. oxydans improved xylitol productivity.     

Ethanol production from xylose by recombinant Saccharomyces cerevisiae expressing protein engineered NADP+-dependent xylitol dehydrogenase

Effects of reversal coenzyme specificity toward NADP+ and thermostabilization of xylitol dehydrogenase (XDH) from Pichia stipitis on fermentation of xylose to ethanol were estimated using a recombinant Saccharomyces cerevisiae expressing together with a native xylose reductase from P. stipitis. The mutated XDHs performed the similar enzyme properties in S. cerevisiae cells, compared with those in vitro. The significant enhancement(s) was found in Y-ARSdR strain, in which NADP+-dependent XDH was expressed; 86% decrease of unfavorable xylitol excretion with 41% increased ethanol production, when compared with the reference strain expressing the wild-type XDH.     

Metabolic control analysis of xylose catabolism in Aspergillus

A kinetic model for xylose catabolism in Aspergillus is proposed. From a thermodynamic analysis it was found that the intermediate xylitol will accumulate during xylose catabolism. Use of the kinetic model allowed metabolic control analysis (MCA) of the xylose catabolic pathway to be carried out, and flux control was shown to be dependent on the metabolite levels. Due to thermodynamic constraints, flux control may reside at the first step in the pathway, i.e., at the xylose reductase, even when the intracellular xylitol concentration is high. On the basis of the kinetic analysis, the general dogma specifying that flux control often resides at the step following an intermediate present at high concentrations was, therefore, shown not to hold. The intracellular xylitol concentration was measured in batch cultivations of two different strains of Aspergillus niger and two different strains of Aspergillus nidulans grown on media containing xylose, and a concentration up to 30 mM was found. Applying MCA showed that the first polyol dehydrogenase (XDH) in the catabolic pathway of xylose exerted the main flux control in the two strains of A. nidulans and A. niger NW324, but the flux control was exerted mainly at the first enzyme of the pathway (XR) of A. niger NW 296.     

Analysis and prediction of the physiological effects of altered coenzyme specificity in xylose reductase and xylitol dehydrogenase during xylose fermentation by Saccharomyces cerevisiae

An advanced strategy of Saccharomyces cerevisiae strain development for fermentation of xylose applies tailored enzymes in the process of metabolic engineering. The coenzyme specificities of the NADPH-preferring xylose reductase (XR) and the NAD?-dependent xylitol dehydrogenase (XDH) have been targeted in previous studies by protein design or evolution with the aim of improving the recycling of NADH or NADPH in their two-step pathway, converting xylose to xylulose. Yeast strains expressing variant pairs of XR and XDH that according to in vitro kinetic data were suggested to be much better matched in coenzyme usage than the corresponding pair of wild-type enzymes, exhibit widely varying capabilities for xylose fermentation. To achieve coherence between enzyme properties and the observed strain performance during fermentation, we explored the published kinetic parameters for wild-type and engineered forms of XR and XDH as possible predictors of xylitol by-product formation (Y(xylitol)) in yeast physiology. We found that the ratio of enzymatic reaction rates using NADP(H) and NAD(H) that was calculated by applying intracellular reactant concentrations to rate equations derived from bi-substrate kinetic analysis, succeeded in giving a statistically reliable forecast of the trend effect on Y(xylitol). Prediction based solely on catalytic efficiencies with or without binding affinities for NADP(H) and NAD(H) were not dependable, and we define a minimum demand on the enzyme kinetic characterization to be performed for this purpose. An immediate explanation is provided for the typically lower Y(xylitol) in the current strains harboring XR engineered for utilization of NADH as compared to strains harboring XDH engineered for utilization of NADP?. The known XDH enzymes all exhibit a relatively high K(m) for NADP? so that physiological boundary conditions are somewhat unfavorable for xylitol oxidation by NADP?. A criterion of physiological fitness is developed for engineered XR working together with wild-type XDH.