检测DNA-蛋白质交联的新方法

将彗星实验进行改进以用于DNA-蛋白质交联作用的检测。利用甲醛对受试动物肝细胞的影响来判定此法是否适用于检测DNA-蛋白质交联。由于在实验中添加一定量的蛋白酶K, 可使单细胞在电泳时产生更大的迁移, 因此可以利用添加蛋白酶K前后的彗星尾距比来判断外来化合物对生物机体产生DNA损伤效应的时候是否有出现DNA-蛋白质交联作用。结果表明, 该方法快速、经济、灵敏度较高, 可以在单细胞水平对甲醛等强交联剂引发的不同组织的DNA-蛋白质交联效应进行检测, 希望该方法能成为指示DNA交联能力的有用工具。     

丙型肝炎病毒核心蛋白在大肠杆菌和毕赤酵母中表达的比较

为获得丙型肝炎病毒的核心蛋白（Core）,将克隆有Core基因的表达载体pBVIL1-Core转化大肠杆菌HB101,温度诱导表达Core蛋白。同时利用PCR方法以含有丙型肝炎病毒全基因的质粒PBR^TM／HCV为模板扩增Core基因,克隆进表达载体pPICZαA,构建表达载体pPICZαA-Core,转化毕赤酵母（Pichia pastoris）GS115,在甲醇诱导下表达Core蛋白。Western-blot显示Core蛋白在大肠杆菌中高效表达,表达蛋白量占菌体总蛋白的20％;在酵母培养上清中存在Core蛋白,证明Core蛋白在酵母系统中成功表达。     

抗病毒蛋白RC28在大肠杆菌和毕赤酵母中的表达及活性比较

RC28蛋白是从野生蕈类皱盖罗鳞伞中分离得到的新型抗病毒蛋白。前期通过3'-RACE方法,从皱盖罗鳞伞总RNA中克隆获得包含RC28编码区的c DNA,并通过TA克隆获得质粒p MD18-T-RC28。以该质粒为模板,设计特异性引物,PCR扩增RC28片段,分别插入大肠杆菌表达载体p ET28a(+)和毕赤酵母表达载体p PIC9K中,形成在N端表达组氨酸标签的重组RC28表达粒体。将这两种RC28表达质粒转化各自的宿主菌后,筛选阳性克隆,构建稳定表达体系。诱导表达后,用SDS-PAGE电泳和Western blot分析RC28的表达情况。放大表达体系后用Ni-NTA柱纯化获得RC28蛋白,并用MTT法测试重组表达蛋白质的抗病毒活性。在实验条件下,大肠杆菌和毕赤酵母中均能表达可溶性重组RC28,纯化后蛋白质得率分别是3.5mg/L发酵液及0.2mg/L发酵液。但抗病毒活性实验表明,大肠杆菌体系表达的RC28蛋白活性较差,而毕赤酵母系统表达的RC28蛋白的抗病毒活性与天然蛋白接近。     

丙型肝炎病毒核心蛋白在大肠杆菌和毕赤酵母中表达的比较*

为获得丙型肝炎病毒的核心蛋白(Core),将克隆有Core基因的表达载体pBVIL1-Core转化大肠杆菌HB101,温度诱导表达Core蛋白。同时利用PCR方法以含有丙型肝炎病毒全基因的质粒PBRTM/HCV为模板扩增Core基因,克隆进表达载体pPICZαA,构建表达载体pPICZαA-Core,转化毕赤酵母(Pichiapastoris)GS115,在甲醇诱导下表达Core蛋白。Western-blot显示Core蛋白在大肠杆菌中高效表达,表达蛋白量占菌体总蛋白的20%;在酵母培养上清     

体内甲醛交联及染色质免疫沉淀--研究DNA和蛋白质作用的新方法

甲醛交联及染色质免疫沉淀作用研究体内DNA和蛋白质相互作用的一种新方法,在染色质结构研究中获得了广泛的应用。该方法利用甲醛固定活细胞中的DNA与蛋白质,通过免疫沉淀分离复合物,从而分析蛋白质及其体内的DNA结合序列。     

毕赤酵母表达蛋白质的糖基化

毕赤酵母表达系统可对表达产物进行翻译后加工如糖基化等。通过研究其糖基化的特点、影响因素以及对重组蛋白质质产量、功能的影响,介绍如何避免过度糖基化以使表达产物更加符合人类需求。     

抗菌肽magainin Ⅱ的密码子优化及在大肠杆菌和毕赤酵母中的表达

Magainin Ⅱ是非洲爪蟾皮肤分泌的一种抗菌肽,在低浓度下即能够对细菌、真菌、原虫、肿瘤等都具有杀伤作用,并且与同是来源于非洲爪蟾皮肤的另一种抗菌肽PGLa在杀菌、抗肿瘤等方面具有很好的协同效应。文中分别按照大肠杆菌和毕赤酵母的密码子利用频率,对抗菌肽magainin Ⅱ以及杂合抗菌肽magainin Ⅱ-PGLa,进行了密码子优化。构建了高效表达抗菌肽magainin Ⅱ的原核表达载体,经过蛋白酶切割获得纯化的抗菌肽magainin Ⅱ。同时进一步构建了杂合抗菌肽magainin Ⅱ-PGLa的分泌型毕赤酵母表达载体,实现了杂合抗菌肽在毕赤酵母中的分泌表达。本研究为magainin Ⅱ和magainin Ⅱ-PGLa的生产与应用奠定了基础。     

毕赤酵母菌高效表达乙肝表面抗原的研究

目的:筛选高效表达HBsAg的毕赤酵母茵,制备目的蛋白.方法:从已确诊的乙肝病人血清中提取DNA,PCR扩增HBVS基因,将其分别克隆入毕赤酵母胞内表达栽体pPICZA中.构建重组质粒pPICZA-S和pPICZA-SH,经Sac I线性化后,LiCI化学法转化入酵母茵株GS115、X-33、KM71H和SMD1168.结果:诱导表达后的GS115工程茼单位体积的培养基所得的抗原含量最高,诱导培养基中加入0.1%酪蛋氨基酸后,可抑制目的蛋白的水解,有利于目的蛋白的表达,粗略估算表达量为15.3mg/L,最佳收获时间为72 h.结论:经SDS-PAGE和Westcrn-blot分析表明,所得产物为乙肝表面抗原S蛋白.     

HPV18晚期蛋白L1在毕赤酵母菌中的表达及鉴定

目的:用毕赤酵母胞内表达载体构建含人乳头瘤病毒18型(HPV18)L1基因质粒,诱导表达并进行鉴定。方法:按照毕赤酵母密码子偏爱性原则,合成全长L1基因,然后克隆到pAO819表达载体上,在体外分别构建含一个拷贝和二个拷贝的L1基因载体。线形化后转化到GS115酵母细胞,经G418抗性筛选,获高拷贝重组子并经甲醇诱导表达,表达产物采用化学发光Western blot鉴定,一抗为抗HPV18L1蛋白鼠抗血清。结果:在55kDa处有诱导蛋白免疫印迹出现,并在电镜下观察到HPV18的病毒样颗粒(VLPs),证明该表达系统能表达出HPV18 L1蛋白。结论:本实验构建的毕赤酵母表达菌株,可经甲醇诱导表达HPV18L1晚期蛋白,为进一步研制人乳头瘤病毒18型基因工程疫苗打下基础。     

极端耐热木聚糖酶基因在大肠杆菌和毕赤酵母中的高效表达

以海栖热袍菌 (Thermotoga maritima) MSB8菌株基因组DNA为模板,通过PCR扩增出木聚糖酶（XylanaseB）基因, 将此基因克隆至大肠杆菌表达载体pET_28a（+）和毕赤酵母表达载体pPIC9K,并分别转化大肠杆菌 BL21和毕赤酵母GS115。该木聚糖酶在大肠杆菌细胞中表达量高, 但不能分泌; 而在毕赤酵母细胞的表达产物可分泌至胞外。酶学性质分析表明,此酶分子量约为40kD,其最适反应温度为90℃, 最适反应pH值为6.65,且在碱性条件下稳定,具有重要的工业应用前景。     

Comparison of protein quantification and extraction methods suitable for E. coli cultures

Many different extraction and analysis methods exist to determine the protein fraction of microbial cells. For metabolic engineering purposes it is important to have precise and accurate measurements. Therefore six different protein extraction protocols and seven protein quantification methods were tested and compared. Comparison was based on the reliability of the methods and boxplots of the normalized residuals. Some extraction techniques (SDS/chloroform and toluene) should never be used: the measurements are neither precise nor accurate. Bugbuster extraction combined with UV280 quantification gives the best results, followed by the combinations Sonication-UV280 and EasyLyse-UV280. However, if one does not want to use the quantification method UV280, one can opt to use Bugbuster, EasyLyse or sonication extraction combined with any quantification method with exception of the EasyLyse-BCA_P and Sonication-BCA_P combinations.     

基于卷积神经网络的大肠杆菌启动子预测

目的 基于位点特异性打分矩阵（position-specific scoring matrices,PSSM）的预测模型已经取得了良好的效果,基于PSSM的各种优化方法也在不断发展,但准确率相对较低,为了进一步提高预测准确率,本文基于卷积神经网络（convolutional neural networks,CNN）算法做了进一步研究。方法 采用PSSM将启动子序列处理成数值矩阵,通过CNN算法进行分类。大肠杆菌K-12（Escherichia coli K-12,E.coli K-12,下文简称大肠杆菌）的Sigma38、Sigma54和Sigma70 3种启动子序列被作为正集,编码（Coding）区和非编码（Non-coding）区的序列为负集。结果 在预测大肠杆菌启动子的二分类中,准确率达到99%,启动子预测的成功率接近100%;在对Sigma38、Sigma54、Sigma70 3种启动子的三分类中,预测准确率为98%,并且针对每一种序列的预测准确率均可以达到98%以上。最后,本文以Sigma38、Sigma54、Sigma70 3种启动子分别和Coding区或者Non-coding区序列做四分类,预测得到的准确性为0.98,对3种Sigma启动子均衡样本的十交叉检验预测精度均可以达到0.95以上,海明距离为0.016,Kappa系数为0.97。结论 相较于支持向量机（support vector machine,SVM）等其他分类算法,CNN分类算法更具优势,并且基于CNN的分类优势,编码方式亦可以得到简化。     

A novel plasmid-mediated DNA restriction-modification system in E. coli

R plasmids from 101 clinical isolates were transferred to E. coli J62 by conjugation and tested for the presence of R plasmid-mediated restriction-modification DNA systems. Thirty R plasmids were found to inhibit phage λ. vir development. Ten plasmids determined restriction modification system; nine of them proved identical with R.M. EcoRII. One transconjugant, E. coli J62 pLG74, was shown to have a restriction-modification system different from all the known R plasmid-mediated systems. Site-specific endonuclease has been isolated from E. coli J62 pLG74 which differed from all the known restriction endonucleases in the number of cleavage sites on phages λ, φX 174, virus SV40, plasmid pBR322 DNA molecules.     

Optimization of bio-indigo production by recombinant E. coli harboring fmo gene

A bacterial flavin-containing monooxygenase (FMO) gene was cloned from Methylophaga aminisulfidivorans MP^T, and a plasmid pBlue 2.0 was constructed to express the bacterial fmo gene in E. coli. To increase the production of bio-indigo, upstream sequence size of fmo gene was optimized and response surface methodology was used. The pBlue 1.7 plasmid (1686 bp) was prepared by the deletion of upstream sequence of pBlue 2.0. The recombinant E. coli harboring the pBlue 1.7 plasmid produced 662 mg l⁻¹ of bio-indigo in tryptophan medium after 24 h of cultivation in flask. The production of bio-indigo was optimized using a response surface methodology with a 2ⁿ central composite design. The optimal combination of media constituents for the maximum production of bio-indigo was determined as tryptophan 2.4 g l⁻¹, yeast extract 4.5 g l⁻¹ and sodium chloride 11.4 g l⁻¹. In addition, the optimum culture temperature and pH were 30 °C and pH 7.0, respectively. Under the optimized conditions mentioned above, the recombinant E. coli harboring pBlue 1.7 plasmid produced 920 mg of bio-indigo per liter in optimum tryptophan medium after 24 h of cultivation in fermentor. The combination of truncated insert sizes and culture optimization resulted in a 575% increase in the production of bio-indigo.     

A bifunctional plasmid carrying the recA gene of E. coli

Summary To investigate the effect of an active, plasmid-carried recA gene on the stability and/or the expression of plasmid genes in different genetic backgrounds, we have constructed a bifunctional plasmid (able to replicate in Escherichia coli and in Bacillus subtilis). Chimeric plasmids were obtained by inserting pC194 (Ehrlich 1977) into pDR1453 (Sancar and Rupp 1979). pDR1453 is a 12.9 Kbp plasmid constructed by inserting an E. coli chromosome fragment carrying the recA gene into pBR322. The expected bifunctional recombinant (pMR22/1) (15.7 Kbp) was easily obtained but surprisingly the Cm resistance was expressed only at a very low level in E. coli (as compared, for example, to pHV14, pHV15). We attribute this effect to the presence of multiple recA genes in the cell. On the contrary, Cm^r E. coli transformants bear a recombinant plasmid (pMR22/n) containing tandemly repeated copies of pC194 in equilibrium with excised free pC194. Such amplification has never been observed in a Rec^- background and is therefore mediated by the recA genes. Growth of these clones in the absence of Cm causes the loss of the extra copies, yielding a plasmid with a single copy of pC194, indistingishable from pMR22/1. Interestingly, we have observed that deletions occur at high frequency in pC194, which drastically increase Cm^r in E. coli containing plasmids with a single copy of pC194. Two types of such deletions were detected: (a) large 1050 bp deletions covering about onethird of pC194 and (b) small 120–150 bp deletions (near the MspI site) in the region containing the replicative functions of pC194 (Horinouchi and Weisblum 1982). Both types of deletion render the recombinant plasmid unable to replicate in B. subtilis. pM22/1 replicates, although with a low copy-number, and is stable in B. subtilis wild type; the recA gene of E. coli does not complement any of the rec ^- mutations of B. subtilis. A strong instability, mainly of the E. coli and pBR322 sequences, was observed in many dna and rec mutants of B. subtilis yielding smaller plasmid with a much higher copy-number.     

Replication of E. coli duplex DNA in vitro

Summary An E. coli lysate after being gently washed to remove soluble components, supports replicative DNA synthesis, if soluble proteins and the deoxyribonucleotide triphosphates are added. This DNA synthesis is dependent on ATP and on the presence of the gene products of the dnaB, dnaG, and polC (DNA polymerase III) genes. It continues at the replication forks preformed in vivo and Okazaki fragments are intermediate products of the reaction.Two different methods were used to prepare the washed DNA containing fraction. The one method involves washing of a cell lysate situated on a dialysis membrane. The other method involves DNAase treatment of a lysate and sedimentation of the degraded DNA through a glycerol gradient. Both washed preparations contain not only the DNA and the replication forks but also functional amounts of DNA polymerase III and of the dnaB gene product. Other factors, that are essential for replicative DNA synthesis, including the dnaG gene product, are washed out of the DNA containing preparations and the system is reconstituted by readdition of the soluble proteins.     

大肠杆菌基因组中存在Era亲和蛋白的基因

构建了一个大肠杆菌基因组DNA λ ZAP表达文库,以Dig标记的Era为探针,从4×10⁴噬斑中筛选到一个与探针呈特异结合的噬斑,说明大肠杆菌基因组中确有Era亲和蛋白基因存在.将该噬菌体中插段DNA前800 bp的测序结果与1996年底完成的大肠杆菌基因组全序列作同源性比较,发现该插段序列位于大肠杆菌基因组的第267 section.     

大肠杆菌的蛋白分泌机制

大肠杆菌的分泌蛋白定位于内膜、外膜、周质空间和胞外环境,它们在N端或C端带有一定的结构包含着分泌信号,这两类分泌蛋白在各自特定的一组蛋白因子的协助下跨越内膜,再通过目前尚不清楚的方式实现其最终定位.N端带有信号肽的分子在跨越内膜时得到Sec家族蛋白因子协助,信号肽在跨膜过程中可能被切除,该过程由ATP和电化学势提供能量.C端带分泌信号的分子主要受到Hly家族分子协助,一次穿过内膜和外膜而不经过周质空间.