Cloning, nucleotide sequencing, and expression of tetanus toxin fragment C in Escherichia coli.

The amino acid sequence of the first 30 residues of fragment C of tetanus toxin was determined, and a mixture of 32 complementary oligonucleotides, each 17 bases long, was synthesized. A 2-kilobase (kb) EcoI fragment of Clostridium tetani DNA was identified by Southern blotting and was cloned into the Escherichia coli plasmid vector pAT153 with the 32P-labeled oligonucleotide mixture as a probe. A second 3.2-kb Bg/II fragment was identified and cloned with the 2-kb EcoRI fragment as a probe. The nucleotide sequence of 1.8 kb of this DNA was determined and was shown to encode the entire fragment C and a portion of fragment B of tetanus toxin. The tetanus DNA was expressed in E. coli with pWRL507, a plasmid vector containing the trp promoter and a portion of the trpE gene. The trpE-tetanus fusion proteins were visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and were shown to react with anti-fragment C antibody.     

α-葡萄糖苷酶基因序列分析及真核表达载体构建

目的：Aspergillus niger（CU-1）菌株α-葡萄糖苷酶基因（agdA）克隆并对其序列进行分析,构建该基因的真核表达载体。方法：设计合成的一对特异性引物,采用PCR以总DNA为模板,扩增得到DNA片段（D1）;采用RT-PCR方法扩增得到DNA片段（D2）。将DNA片段D1和D2转入大肠杆菌中并进行了序列测定,序列进行BLAST比对分析。将α-葡萄糖苷酶基因的cDNA片段与表达载体pGAPZαA连接,构建重组表达载体。结果：基因agdA大小为3 127bp,含有3个外显子和4个内含子。该基因的cDNA序列大小为2 958bp,包含完整的编码框,编码985个氨基酸。agdA基因序列与已发表的α-葡萄糖苷基因序列同源性达99%,其中有6个位置的碱基发生了变化。已成功构建重组表达载体pGAPZαA-agdA。结论：Aspergillus niger（CU-1）菌株α-葡萄糖苷酶基因序列分析及重组表达载体pGAPZαA-agdA的构建为在毕赤酵母中表达Aspergillus niger（CU-1）菌株的α-葡萄糖苷酶奠定基础。     

基于λ-Red重组酶系统的Ⅳa2基因缺失及重组腺病毒的包装

本研究用λ-Red重组酶介导的PCR打靶方法缺失腺病毒基因组上Ⅳa2基因的大部分编码序列(1104 bp),并获得一种Ⅳa2基因缺失的重组腺病毒。首先构建PCR打靶的含有卡那霉素抗性表达盒的模板质粒pAK,再以pAK为模板扩增出两端含39 bp同源臂的线性DNA片段;将pFG140质粒及线性DNA片段依次转化到宿主菌BW25113/pIJ790中,通过λ-Red重组酶介导的同源重组获得了缺失Ⅳa2基因的腺病毒基因组质粒pFG140-ΔⅣa2(1104)。酶切及DNA测序结果显示,用λ-Red重组酶介导的PCR打靶方法在pFG140上精确地缺失了预计的Ⅳa2基因3’端的1104bp片段。用PCR方法扩增获得Ⅳa2基因全长ORF,插入表达载体pAAV2neo中,构建成Ⅳa2基因表达质粒pAAV2neo-Ⅳa2。将pFG140-ΔⅣa2(1104)与pAAV2neo-Ⅳa2共转染HEK293细胞,成功地获得了重组腺病毒Ad5ΔⅣa2(1104)。Western Blot的结果表明,Ad5ΔⅣa2(1104)病毒感染的HEK293细胞检测不到Ⅳa2蛋白的表达。本研究建立了一种对腺病毒基因组直接进行缺失操作的λ-Red重组酶介导的PCR打靶方法,并获得了一种IVa2基因大部分缺失的重组腺病毒。     

兽疫链球菌透明质酸分解酶基因的敲除

以透明质酸分解酶基因（Hyl）为改造目标, 利用同源重组技术获得 Hyl基因敲除的重组菌。首先以兽疫链球菌的基因组DNA为模板扩增出部分透明质酸分解酶基因（Hyl-1）,然后将其克隆到载体pMD19-T上,再以质粒pUC19为模板, PCR扩增得到氨苄青霉素抗性基因,通过反向PCR将其插入Hyl-1基因的中部,得到基因敲除载体pMD19T-SA。该载体与质粒pBR322分别用EcoRⅠ、PstⅠ双酶切后进行连接,得到基因敲除的重组载体pBR322 SA,PCR 及限制性酶切分析,构建的敲除载体与设计结果相符。最后,利用这两种敲除载体通过同源重组技术得到一株重组菌,经PCR 及酶活鉴定,这株菌的Hyl 基因已缺失。     

Construction and transduction of a shuttle vector bearing the cos site of Streptomyces phage phi C31 and determination of its cohesive ends

A plasmid has been constructed which is a bifunctional vector for Escherichia coli and for streptomycetes, containing the cos site of Streptomyces phage phi C31. It can be efficiently transduced into S. lividans 66 and into several other Streptomyces species. The nucleotide sequence of a 311-bp DNA fragment containing the cohesive ends has been determined. The cohesive ends consist of 10 bases protruding at the 3'-end of the phage genome.     

Preferential uptake of restriction fragments from a gonococcal cryptic plasmid by competent Neisseria gonorrhoeae

Factors involved in the specificity of DNA uptake by competent Neisseria gonorrhoeae were examined. Host-controlled modification did not affect uptake. Certain restriction fragments of the 4.2 kb gonococcal cryptic plasmid pFA1 and of the replicative form of the bacteriophage M13 were taken up in preference to others, independent of differences in fragment size. A 600 bp fragment from the 4.2 kb plasmid was cloned into pLES2, a gonococcal-Escherichia coli shuttle vector; the 600 bp fragment was taken up into a DNAase-I-resistant state in preference to the vector fragment. A second 370 bp fragment in pFA1 was also taken up preferentially. The 600 bp and 370 bp fragments share a 10 bp sequence, which is found in pFA1 only on fragments that were taken up readily. However, a fragment from M13 which was efficiently taken up did not contain this 10 bp sequence. In addition, this sequence was not sufficient to direct preferential DNA uptake by gonococci, since a recombinant plasmid containing this 10 bp sequence was not taken up appreciably better than the vector plasmid or another recombinant plasmid containing an unrelated 10 bp sequence. Sequence comparisons of the three restriction fragments which were preferentially taken up did not yield any consensus sequences greater than 7 bp. Although it is likely that efficient uptake of DNA by gonococci is determined by DNA structure, a single short sequence could not be found that accounted for specific uptake.     

Nonrandom DNA sequencing of exonuclease III-deleted complementary DNA

The nonrandom DNA sequence analysis procedure of Poncz et al. [Proc. Natl. Acad. Sci. USA 79, 4298-4302 (1982)] was extensively modified to permit the determination of complementary DNA (cDNA) sequences containing G-C homopolymer regions. The recombinant cDNA plasmid was cleaved at a unique restriction enzyme site close to the cDNA and treated with Exonuclease III under controlled conditions to generate a set of overlapping fragments having deletions 50-1500 bases in length at the free 3' termini. After removal of single-stranded DNA regions by Bal31 and DNA polymerase I large fragment, the unique restriction enzyme site was recreated by blunt end ligation of synthetic oligonucleotides to the deleted DNA fragments and restriction enzyme digestion. The cDNA fragment was excised from the cloning vector using a second different restriction enzyme having a unique site that flanks the cDNA fragment and subsequently force-cloned into either M13 mp10 or mp11. This method should also be particularly useful for the sequencing of other types of DNA molecules with lengths 1500 bp or smaller.     

Cloning of rfaG, B, I, and J genes for glycosyltransferase enzymes for synthesis of the lipopolysaccharide core of Salmonella typhimurium.

R-prime plasmids carrying the pyrE-rfa-cysE region of the chromosome of Salmonella typhimurium were isolated by using the vector pULB113 (RP4::mini-Mu). One of the R-prime plasmids was used as a source of DNA to clone the rfa genes for lipopolysaccharide synthesis to pBR322. The following three hybrid plasmids were constructed: pKZ15, with a 4.0-kilobase EcoRI fragment of S. typhimurium DNA, containing the rfaG gene; pKZ27, a 9-kilobase BglII fragment with the rfaG, rfaB, and rfaI genes; and pKZ26, a 7.7-kilobase HindIII fragment with the rfaG, rfaB, rfaI, and rfaJ genes. We propose that these cloned genes code for four glycosyltransferases used for synthesis of the lipopolysaccharide core region (rfaG for glucosyltransferase I; rfaI for galactosyltransferase I; rfaB for galactosyltransferase II; and rfaJ for glucosyltransferase II). For all four genes, mutants which lacked the appropriate enzyme activity were complemented by the plasmids to give completed core lipopolysaccharide with O (somatic) side chains; for rfaG, rfaB, and rfaI, mutants gave restored or even amplified levels of the appropriate glycosyltransferase in in vitro assays. We show that the order of genes in the region is pyrE-rfaG-(rfaB-rfaI)-rfaJ-rfaL-rfaF -cysE.     

苏云金芽孢杆菌分子伴侣串联基因p19-p29的克隆和表达载体的构建

根据已知序列设计一对PCR引物(ORF5S,ORF3N),可从cry2Aa或cry2Ac操纵子中扩增出包含串联分子伴侣基因p19p29的DNA片段,预期大小分别为16kb和20kb。对150株苏云金芽孢杆菌菌株进行PCR检测,从26株中获得了大小为16kb的扩增片段,但未获得20kb的片段。这表明cry2Aa型操纵子p19p29基因存在较广泛,而cry2Ac型较罕见。将来自Y2菌株的16kb片段回收,通过一系列亚克隆,最终构建成一个含有p19p29串联基因的Bt表达载体,为进一步研究p19p29串联基因的功能奠定了基础。     

Efficient combination of large DNA in vitro: in gel site specific recombination (IGSSR) of PAC fragments containing alpha satellite DNA and the human HPRT gene locus.

In an attempt to combine a cloned genomic copy of a selectable gene with different cloned centromeric sequences to develop mammalian artificial chromosomes (MAC) we used site specific recombination mediated by purified Cre recombinase acting on the loxP sequence in PAC vector DNA. A new method was required to purify highly concentrated, virtually 100% intact PAC DNA which could be stored for a long period. Here we show the efficient linking of linearized PACs containing alpha satellite DNA from chromosomes X and 17 with sizes of 125 and 140 kb, respectively, to a 95 kb restriction fragment derived from a 175 kb PAC containing the intact human HPRT gene locus.     

ACA基因启动子的克隆及功能初探

根据已知的ACA基因的5’端序列设计三个基因特异的反向引物(GSP-1,GSP-2,GSP-3)分别与11个简并引物(AD1-AD11)配对,进行热不对称嵌套PCR(Thermal asymmetric interlaced PCR,TAIL-PCR)扩增,获得了ACA基因起始密码子上游约700bp的片段。为检测其表达特性,构建了该片段与Gus嵌合基因的表达载体pBpAG,在真空条件下通过农杆菌介导,转化了植物的叶、果实、种子三种不同组织,Gus瞬时表达染色结果显示,该DNA片段具有种子特异的启动子活性?对该启动子的一些顺式元件进行了讨论。     

An improved chemico-enzymatic method of synthesizing long DNA segments

A simple and economy method of the biochemical assembling of long double-stranded DNA segments is described. A single-stranded polydeoxynucleotide 122 bases long representing a fragment of synthetic gene of human beta-interferon was assembled from three synthetic fragments 36 (two) and 50 bases long on four complementary 12-mers as templates. This single-stranded polynucleotide was converted, in the presence of DNA polymerase 1 and a 12-meric primer, in to the full-length double-stranded DNA (the beta-interferon gene segment). It was cloned into an E. coli plasmid vector pBR322 and its sequence confirmed.     

An unusual accumulation of repetitive sequences in the rat genome

We have found in the rat genomic DNA a fragment 1300 bp long, containing an unusual concentration of members of different repetitive families. Three different repeats were noticed. An Alu-like repeat, homologous to the mouse B1 sequence, was followed by a fragment containing alternating purine-pyrimidine bases as in Z-DNA. Finally, a third repeat was identified, containing 38 TAGA tetranucleotides as described for reptile DNA.     

用同源重组法修饰含人α类珠蛋白基因簇的细菌人工染色体

采用RecA蛋白介导的同源重组的方法,对本实验室筛选出的包含完整人α-类珠蛋白基因簇的细菌人工染色体（BAC）DNA进行删除修饰。首先采用PCR的方法,分别在预删除的HS-40增强子区域的上游和下游克隆长度约为500bp的两段同源序列,并一起克隆到构建载体pBV的XbaI和HindIII位点上,SalI酶切后回收1kb左右的片段并克隆到温度敏感的穿梭质粒pSV-RecA中,转化带有人α-类珠蛋白基因簇的BACDNA的感受态大肠杆菌DH10B,经氯霉素正筛选和镰孢菌酸的负筛选,获得发生两次同源重组后只含BACDNA而穿梭载体已丢失的菌株,经Southern杂交鉴定,获得了HS-40被定位删除的BAC突变体克隆。表明同源重组的方法可以对含有较多重复序列的BACDNA进行准确的删除修饰。 Abstract：By RecA protein mediated homologous recombination method, we successfully delet ed the HS-40 fragment from a bacterial artificial chromosome containing complete human α-globin gene cluster screened by our lab. Two mutant boxes(A and B) fra gments located at the two terminals of HS-40 were cloned into the XbaⅠ and HindIII sites of pBV building vector, then the 1.1kb A+B fragment was recove red from the building vector and inserted into the SalⅠ site of the shuttle vector pSV-RecA, competent DH10B E. Coli containing BAC DNA was tranformed by t he shuttle vector,after chloramphenicol positive selection and fusatic acid neg ative selection,two times of homologous recombination happened and the HS-40 fra gment was successfully deleted from the BAC DNA which is characterized by Southe rn blot,suggested that this method could modified BAC DNA accurately containing high percentage of repeat sequence.     

Isolation of the ARO1 cluster gene of Saccharomyces cerevisiae.

The AROl cluster gene was isolated by complementation in Saccharomyces cerevisiae after transformation with a comprehensive yeast DNA library of BamHI restriction fragments inserted into the shuttle vector YEp13. Most of the transformants exhibited the expected episomal inheritance of the ARO+ phenotype; however, one stable transformant has been shown to be an integration of the AROl fragment and the vector YEp13 at the arol locus. The insert containing AROl is a 17.2-kilobase pair (kbp) BamHI fragment which complements both nonsense and missense alleles of arol. Subcloning by Sau3AI partial digestion further locates the AROl segment to a 6.2-kbp region. An autonomously replicating sequence (ars) was found on the 17.2-kbp fragment. Yeast arol mutants transformed with the AROl episome express 5 to 12 times the normal level of the five AROl enzyme activities and possess elevated amounts of the AROl protein. The yeast AROl fragment also complemented aroA, aroB, aroD, and aroE mutants of Escherichia coli. The expression of AROl in both S. cerevisiae and E. coli was independent of the orientation of the fragment with respect to the vector.     

Purification and properties of an Arthrobacter oxydans P52 carbamate hydrolase specific for the herbicide phenmedipham and nucleotide sequence of the corresponding gene.

Arthrobacter oxydans P52 isolated from soil samples was found to degrade the phenylcarbamate herbicides phenmedipham and desmedipham cometabolically by hydrolyzing their central carbamate linkages. The phenylcarbamate hydrolase (phenmedipham hydrolase) responsible for the degradative reaction was purified to homogeneity. The enzyme was shown to be a monomer with a molecular weight of 55,000. A 41-kb wild-type plasmid (pHP52) was identified in A. oxydans P52, but not in a derivative of this strain that had spontaneously lost the ability to hydrolyze phenylcarbamates, indicating that the gene for phenylcarbamate degradation (pcd) is plasmid encoded. Determination of two partial amino acid sequences allowed the localization of the coding sequence of the pcd gene on a 3.3-kb PstI restriction fragment within pHP52 DNA by hybridization with synthetic oligonucleotides. The phenylcarbamate hydrolase was functionally expressed in Escherichia coli under control of the lacZ promoter after the 3.3-kb PstI fragment was subcloned into the vector pUC19. A stretch of 1,864 bases within the cloned Pst fragment was sequenced. Sequence analysis revealed an open reading frame of 1,479 bases containing the amino acid partial sequences determined for the purified enzyme. Sequence comparisons revealed significant homology between the pcd gene product and the amino acid sequences of esterases of eukaryotic origin. Subsequently, it was demonstrated that the esterase substrate p-nitrophenylbutyrate is hydrolyzed by phenmedipham hydrolase.     

Construction of plasmid vectors that facilitate subcloning and recovery of yeast and Escherichia coli DNA fragments

We have constructed a plasmid vector (pNF2) which is a derivative of the multicopy yeast cloning vehicle YEp24. This derivative contains a single BamHI site flanked immediately on each side by SalI sites. The latter site was selected because it appears to be infrequent in yeast nuclear DNA. Thus, DNA fragments produced by partial digestion with enzymes (such as Sau3A) that cut at frequent intervals and leave single-stranded ends that have sequence homology with BamHI sites, can be conveniently subcloned into this site. Such fragments can then be excised intact by digestion with SalI enzyme. Plasmid pNF2 also contains the kanamycin-resistance (kanR) gene derived from Tn903 and confers resistance in yeast to the antibiotic G418. pNF2 was converted into an integrating vector (pNF3) by deleting a 2.2-kb EcoRI fragment containing a sequence that determines autonomous replication in yeast. Further deletion of a HindIII fragment containing the yeast URA3 gene converts the plasmid into one containing only pBR322 sequences plus the kanR gene (pNF4).