限制性酶

核酸限制性内切酶是识别双链DNA中专一序列的酶,主要从原核生物中提取。限制性内切酶可分为三类:第Ⅰ和第Ⅲ类酶在同一旦白中具有修饰作用(甲基化作用)和需要ATP的限制性裂解的活性。这两种酶都识别底物DNA中非甲基化的序列,不过第Ⅰ类酶的作用是随机的,第Ⅲ类酶则切DNA的专一位点。     

丁酰苷菌素产生菌Bacillus circulans3342质粒pBCl的分离及其性质

在氨基寡糖类抗生素丁酰苷菌素的产生菌Bacillus circulans 3342中发现了一种质粒DNApBC1,其分子量为9.0×10~6道尔顿。 用限制性内切酶BglⅠ、SmaⅠ和Hind Ⅲ酶切这种质粒DNA,构成了pBC1的限制性内切酶图谱。selⅠ、SmaⅠ和Hind Ⅲ分别将这种质粒DNA切为2、2和5条片段,EcoRI则切为4条片段,而SalⅠ、Bam HI和Pv(?) Ⅱ不能切这种质粒DNA。     

中国昆明(KM)小鼠线粒体DNA限制性内切酶图谱的研究

线粒体DNA的限制性内切酶图谱在不同的种系及亚种间存在多态性。我们分别用五种限制性内切酶BamHⅠ、EcoRⅡ、HidⅢ、PstⅠ、MspⅠ对60只中国KM小鼠(雌雄各半)的线粒体DNA进行了酶切电泳分析,结果未发现多态性,且这五种限制性内切酶图谱均与BALB/c小鼠相同。这表明中国KM小鼠与绝大多数实验小鼠一样,均起源于欧州的野鼠M.m.domesticu。未见到KM小鼠经其它亚种野鼠母系遗传污染的迹象。     

金秋梨和新高梨的分子遗传学对比分析

金秋梨和新高梨的形态性状、生物学性状以及酯酶同工酶、过氧化物酶同工酶、细胞色素氧化酶同工酶酶谱均产生了变化。利用异源DNA探针—小麦rDNA克隆pTA71,与四种核酸内切酶PstⅠ、BamHⅠ、EcoRⅠ及BglⅡ酶切消化的金秋梨和新高梨叶片总DNA杂交,结果表明,pTA71-PstⅠ和pTA71-BamHⅠ二种探针—酶组合可在金秋梨和新高梨中检测到RFLP差异。     

热带假丝酵母79线粒体DNA的研究

本文报道了热带假丝酵母线粒体DNA的分离纯化、性质和酶切图。此线粒体DNA用电镜观察有线状、开环状和闭环状三种形状;在氯化铯中浮力密度为1.691g/cm~3;解链温度为80.0℃。限制性内切酶EcoRⅠ、BamHⅠ和PstⅠ在此线粒体DNA上分别有6、5和3个切点。根据酶切片段计算分子量为22.97×10~6道尔顿。同时,用双酶切方法得到此线粒体DNA的内切酶图谱。     

Ⅱ型限制性核酸内切酶NcrⅠ的研究

 在肉色诺卡氏菌C-212株Nocardia carnea C-212中筛选到一种Ⅱ型限制性核酸内切酶NcrⅠ,经与BglⅡ的λDNA降解物的酶谱比较,以及酶识别特异性和切割位点的检测,证明了NcrⅠ是已知的限制酶BglⅡ的同切限制酶,而且其切割位点也与BglⅡ相同,其为:     

pBR322DNA与8-甲氧补骨脂素光化学反应部位的碱基顺序特异性

用限制性核酸内切酶酶切试验研究了质粒pBR322 DNA经8-MOP及近紫外线作用后损伤部位的碱基顺序特异性。实验研究发现PUVA损伤的DNA在HindⅢ及RsaⅠ识别位置上酶切反应受到严重抑制,而在SphⅠ,EcoRⅠ,PvuⅡ,BamHI,PstⅠ识到位置上抑制轻微。通过对不同识别位置上碱基顺序及其光化学反应敏感性的分析,推断出DNA的TpA顺序可能是最易接受8-MOP光化学反应的部位。     

六株成团肠杆菌 (Enterobacteragglomerans)接合子的分子生物学分析

对 6株成团肠杆菌 (Enterobacteragglomerans)接合子的分子生物学进行了分析 .6株菌与nifHDK基因有杂交 .菌株总DNA经BamHⅠ酶切后与pEA9 DNA进行Southern杂交 ,只有 2株菌具有完整的质粒DNA ,其余菌株质粒DNA发生了 15 3～ 137 7kb不同程度的缺失 .用切割位点较少的限制性内切酶XbaⅠ酶切 6株菌的总DNA ,经脉冲场凝胶电泳 (PFGE)后用pEA9 DNA为探针进行Southern杂交 ,每株菌的pEA9 DNA明显大于用BamHⅠ酶切后的杂交结果 ,表明质粒与染色体发生了整合 .转座子Tn5或插入序列IS 12 2 2和IS 12 71可能参与质粒与染色体的整合过程 .     

肝素结合的EGF样生长因子成熟肽的基因克隆

采用PCR方法扩增出肝素结合的EGF样生长因子(HB-EGF)成熟肽的cDNA。该cDNA用EcoR Ⅰ和BamH Ⅰ双酶切后,回收含HB-EGF成熟肽基因长约270bP的DNA片段,插入经EcoR Ⅰ和BamH Ⅰ双酶切的pUC18载体中,进行序列分析。结果表明所扩增出的片段与原设计完全一致。     

分子生物学技术讲座（二）——分子克隆中所用的酶

限制性内切酶及其它DNA与RNA修饰酶是分子克隆技术的基本工具。1限制性内切醉和DNA甲基化酶限制性内切酶能特异地结合于一段被称为限制性内切酶识别序列的特定的DNA序列或附近的序列,并在此切割DNA双链。它可以分成3类：Ⅰ类和Ⅲ类在同一蛋白分子中兼有修饰（甲基化）作用及依赖于ATP的限制（切割）活性。Ⅰ类酶结合于识别序列,但随机切割DNA;Ⅲ类酶能在识别序列位点切割DNA。在分子克隆中1类和皿类酶都不常用。D类限制一修饰系统限制性内切醇和修饰（甲基化）酶不在同一蛋白分子中,限制性内切酶能专一地切割识别序列,并不依…     

漠黄梅共生菌藻宏基因组文库的构建

为了从耐旱地衣漠黄梅的共生菌藻基因组中筛选功能基因,并为蛋白质类药物的基因筛选提供平台,采用改进的CTAB方法提取其总DNA,用Sau3AⅠ限制性内切酶部分酶切基因组DNA,以质粒pUC19为载体,转入大肠杆菌DH5α中,构建了漠黄梅共生菌藻的宏基因组文库。该文库包含了4.8×105个重组子,插入片段的平均大小为4kb,覆盖漠黄梅菌藻的整个基因组4次。     

碱性土壤微生物基因的克隆和多样性分析

从碱性土壤样品中直接抽提和分离宏基因组DNA, 首先构建了包含5 562个阳性克隆的碱性土壤16S rDNA文库, 随机抽取9个克隆测序后构建的系统进化树表明了碱性土壤环境微生物种群基因的多样性。纯化土壤宏基因组DNA后采用EcoRⅠ酶部分酶切处理, 我们又构建了以pGEM-3Zf(+)为载体的DNA部分文库AL01。AL01文库包含23650个克隆, 随机插入载体的外源DNA片段平均大小为3.2 kb左右, DNA文库的总容量为75.68 Mb。建库效率为从每克环境样品中获得6 000个左右的含随机外源DNA片段插入载体的克隆。采用酶活筛选策略, 我们从AL01文库中筛选到一个编号为pGXAA2011的阳性克隆携带有一个完整的碱性蛋白酶基因。蛋白酶活性检测其酶活作用最佳温度为40℃, 最适作用pH 值为9.5。另外, 我们还克隆和表达了一个新型b-葡萄糖苷酶基因unglu01, 该基因和现有数据库中的b-葡萄糖苷酶基因没有任何DNA或者氨基酸水平的同源性。将unglu01基因的ORF与表达载体pETBlue-2连接后导入宿主菌株Tuner(DE3)pLacI中, 该重组表达克隆在含柠檬酸高铁铵和七叶苷的LA平板上表现清晰的b-葡萄糖苷酶活性, SDS-PAGE电泳可以检测到29 kDa大小的目的蛋白。     

Isolation of High Molecular Weight DNA from Marine Sponge Bacteria for BAC Library Construction

Metagenomics is a powerful tool for mining the genetic repositories from environmental microorganisms. Bacteria associated with marine sponges (phylum Porifera) are rich sources of biologically active natural products. However, to date, few compounds are discovered from the sponge metagenomic libraries, and the main reason might be the difficulties in recovery of high molecular weight (HMW) DNA from sponge symbionts to construct large insert libraries. Here, we describe a method to recover HMW bacterial DNA from diverse sponges with high quality for bacterial artificial chromosome (BAC) library construction. Microorganisms concentrated from sponges by differential centrifugation were embedded in agarose plugs to lyse out the HMW DNA for recovery. DNA fragments over 436 kb size were recovered from three different types of sponges, Halichondria sp., Haliclona sp., and Xestospongia sp. To evaluate the recovered DNA quality, the diversity of bacterial DNA comprised in the HMW DNA derived from sponge Halichondria sp. was analyzed, and this HMW DNA sample was also cloned into a shuttle BAC vector between Escherichia coli and Streptomyces sp. The results showed that more than five types of bacterial DNA, i.e., Proteobacteria, Nitrospirae, Cyanobacteria, Planctomycetes, and unidentified bacteria, had been recovered by this method, and an average 100 kb size insert DNA in a constructed BAC library demonstrated that the recovered HMW DNA is suitable for metagenomic library construction.     

沼气池宏基因组文库中未培养微生物β-葡萄糖苷酶基因的克隆与鉴定

以间接提取法提取了沼气池样品的微生物宏基因组DNA,用柯斯质粒载体pWEB:TNC构建了一个含三万个克隆的沼气池宏基因组文库,对文库中的克隆随机分析表明,该文库的外源片段平均长度为40 kb,文库的总容量为1 .2×106kb。对其中的一个在七叶苷平板上显色的阳性克隆pGXN100进行进一步亚克隆、测序和序列分析。结果表明,pGXN100上有一个全长为1 863bp的ORF,编码621个氨基酸组成的蛋白质。将该基因命名为Unglu100。与产气克雷伯菌属的一个β-葡萄糖苷酶基因AN292在核苷酸和氨基酸水平上分别有76%和85%的同源性,利用SMART软件进行预测表明,Unglu100可能是PTS中β-葡萄糖苷酶特异性的转运蛋白组件。     

Isolation of a low-temperature adapted lipolytic enzyme from uncultivated micro-organism

Aims: The aim of the study was to isolate a novel lipolytic enzyme from the activated sludge of uncultured micro‐organisms. Methods and Results: The metagenomic DNA was directly extracted from the activated sludge, and a metagenomic library was constructed by using the pUC vector. The library was screened for lipolytic enzyme activity on 1% tributyrin agar plate. A clone among c. 100 000 recombinant libraries showed the lipolytic activity. The putative lipolytic gene encoding lipo1 from the metagenomic library was subcloned and expressed in Escherichia coli BL21 using the pET expression system. The expressed recombinant enzyme was purified by Ni‐nitrilotriacetic acid affinity chromatography and characterized using general substrates of lipolytic property. The gene consisted of 972 bp encoding a polypeptide of 324 amino acids with a molecular mass of 35·6 kDa. Typical residues essential for lipolytic activity such as penta‐peptide (GXSXG) and catalytic triad sequences (Ser166, Asp221 and His258) were detected. The deduced amino acid sequence of lipo1 showed low identity with amino acid sequences of esterase/lipase (32%, ZP_01528487 ) from Pseudomonas mendocina ymp and esterase (31%, AAY45707 ) from uncultured bacterium. This lipolytic enzyme exhibited the highest activity at pH 7·5 and 10°C. At thermal stability analysis, lipo1 was more unstable at 40°C than 10°C. Conclusions: An activity based strategy has been an effective method for fishing out a low‐temperature adapted lipolytic enzyme from the metagenomic library. This lipo1 enzyme can be considered to belong to the hormone‐sensitive lipase family due to the enzyme’s oxyanion hole by the sequence HGGG. Significance and Impact of the Study: Lipo1 is a novel psychrophilic esterase obtained directly from the metagenomic library. Owing its support of significant activity at low temperature, this enzyme is expected to be useful for potential application as a biocatalyst in organic chemistry.     

Retrieval of glycoside hydrolase family 9 cellulase genes from environmental DNA by metagenomic gene specific multi-primer PCR

A new method, termed metagenomic gene specific multi-primer PCR (MGSM-PCR), is presented that uses multiple gene specific primers derived from an isolated gene from a constructed metagenomic library rather than degenerate primers designed based on a known enzyme family. The utility of MGSM-PCR was shown by applying it to search for homologues of the glycoside hydrolase family 9 cellulase in metagenomic DNA. The success of the multiplex PCR was verified by visualizing products on an agarose gel following gel electrophoresis. A total of 127 homologous genes were amplified with combinatorial multi-primer reactions from 34 soil DNA samples. Multiple alignments revealed extensive sequence diversity among these captured sequences with sequence identity varying from 26 to 99.7%. These results indicated that significantly diverse homologous genes were indeed readily accessible when using multiple metagenomic gene specific primers.     

Cloning and identification of cellulase genes from uncultured microorganisms in pulp sediments from paper mill effluent]

The metagenomic DNA of pulp sediments from paper mill effluent was extracted and purified. The 16S rDNA was amplified using the purified metagenomic DNA as template and a 16S rDNA library was prepared. Sequence analysis of 16S rDNA clones showed that diverse of uncultured bacteria inhabit in this environment, which can be classified into 4 clusters as Spirochaetes, Proteobacteria, Bacteroidetes and Firmicutes. A metagenomic library containing 10000 clones was constructed into cosmid vector, and the capacity of inserted DNA of which was 3.53 x 10(8) bp. Functional screening of the library resulted in isolation of two independent clones expressing endoglucanase activity, three independent clones expressing exoglucanase activity and two independent clones expressing beta-glucosidase activity. One clone expressing strongest enzyme activity from each activity category was chosen to be further analyzed. Three novel cellulase genes designated as umcel5L, umcel5M and umbgl3D were identified by subcloning, sequencing and expression. The umcel5L encodes an endoglucanase belonging to glycosyl hydrolase family 5, which is most related to an endoglucanase from Bradyrhizobium japonicum at 43% identity and 59% similarity. The umcel5M encodes a cellodextrinase belonging to glycosyl hydrolase family 5, which is most similar to a cellodextrinase from Fibrobacter succinogenes at 48% identity and 69% similarity. The umbgl3D encodes a putative beta-glucosidase belonging to glycosyl hydrolase family 3, which shares highest homology with a beta-glucosidase from Thermotoga maritima at 46% identity and 61% similarity. It is the first time to reveal the bacterial diversity of pulp sediments from paper mill effluent and clone novel cellulase genes from the bacteria by culture-independent method.     

Mining the metagenome of activated biomass of an industrial wastewater treatment plant by a novel method

Metagenomic libraries herald the era of magnifying the microbial world, tapping into the vast metabolic potential of uncultivated microbes, and enhancing the rate of discovery of novel genes and pathways. In this paper, we describe a method that facilitates the extraction of metagenomic DNA from activated sludge of an industrial wastewater treatment plant and its use in mining the metagenome via library construction. The efficiency of this method was demonstrated by the large representation of the bacterial genome in the constructed metagenomic libraries and by the functional clones obtained. The BAC library represented 95.6 times the bacterial genome, while, the pUC library represented 41.7 times the bacterial genome. Twelve clones in the BAC library demonstrated lipolytic activity, while four clones demonstrated dioxygenase activity. Four clones in pUC library tested positive for cellulase activity. This method, using FTA cards, not only can be used for library construction, but can also store the metagenome at room temperature.     

荷斯坦奶牛瘤胃微生物元基因组BAC文库的构建与分析

采用未培养技术和脉冲场电泳技术直接从瘤胃微生物提取到大小在2Mb左右混合微生物DNA,经HindⅢ不完全酶切获得50～100kbDNA片段,将其连接在pCC1BAC载体上,转化E.coliEPI300,得到瘤胃微生物BAC文库,经对文库的鉴定分析,该文库的平均插入片段54.5kb,空载体率小于2%,库容837Mb,共保存15360个克隆。通过对该文库进行部分酶活性筛选,获得具有淀粉酶活性的克隆16个;纤维素酶活性的克隆26个,而且能降解纤维素的克隆中25个呈现多酶活性。这些结果表明该文库具有重要研究价值。