Cloning and sequence analysis of Histoplasma capsulatum glucosamine-6-phosphate synthase gene fragment

The 3' part of the glucosamine-6-phosphate synthase gene from Histoplasma capsulatum was PCR amplified using degenerate primers designed from the known glucosamine-6-phosphate synthase gene sequences, cloned and sequenced. The computer analysis of the 676 bp sequence revealed the presence of two introns. The identities of the deduced amino acid sequence to the corresponding Saccharomyces cerevisiae and Candida albicans fragment are 65 and 63.8%, respectively. This revised version was published online in June 2006 with corrections to the Cover Date.     

Uracil DNA glycosylase-mediated cloning of polymerase chain reaction-amplified DNA: application to genomic and cDNA cloning.

A simple and rapid method for cloning of amplification products directly from the polymerase chain reaction (PCR) has been developed. The method is based on the addition of a 12-base dUMP-containing sequence (CUACUACUACUA) to the 5' end of PCR primers. Incorporation of these primers during PCR results in the selective placement of dUMP residues into the 5' end of amplification products. Selective degradation of the dUMP residues in the PCR products with uracil DNA glycosylase (UDG) disrupts base pairing at the termini and generates 3' overhangs. Annealing of 3' protruding termini to vector DNA containing complementary 3' ends results in chimeric molecules which can be transformed, with high efficiency, without in vitro ligation. Directional cloning of PCR products has also been accomplished by incorporating different dU-containing sequences at the end of each PCR primer. Substitution of all dT residues in PCR primers with dU eliminates cloning of aberrant "primer dimer" products and enriches cloning of genuine PCR products. The method has been applied to cloning of inter-Alu DNA sequences from human placental DNA. Using a single primer, DNA sequences between appropriately oriented Alu sequences were amplified and cloned. Cloning of cDNA for the glyceraldehyde-3'-phosphate dehydrogenase gene from rat brain RNA was also demonstrated. The 3' end region of this gene was amplified by the 3' RACE method and the amplified DNA was cloned after UDG digestion. Characterization of cloned DNAs by sequence analysis showed accurate repair of the cloning junctions. The ligase-free cloning method with UDG should prove to be a widely applicable procedure for rapid cloning of PCR-amplified DNA.     

斜纹夜蛾羧酸酯酶基因的克隆、序列分析及表达水平

为了明确斜纹夜蛾Spodoptera litura对溴氰菊酯产生抗性的分子机理, 本研究利用RT-PCR技术和RACE方法获得了1个斜纹夜蛾羧酸酯酶基因的全长cDNA序列, 命名为Slest2。序列分析表明, 该cDNA全长1 796 bp（GenBank 登录号: DQ445461）, 5′和3′UTR区分别长63和119 bp,开放阅读框编码一个由537个氨基酸残基组成的羧酸酯酶蛋白。通过对氨基酸同源性分析表明, 该羧酸酯酶与其他物种的酯酶均具有很高的氨基酸相似性,并具有多个在不同酯酶蛋白家族中均保守的区域。采用实时定量PCR技术比较了Slest2在斜纹夜蛾抗、感品系中的表达水平。当以cDNA为模板检测mRNA转录水平时发现, Slest2在抗性品系中的转录水平是敏感品系的46.85倍; 以基因组DNA为模板检测Slest2基因的拷贝数时发现, Slest2在抗、感性品系中的拷贝数无显著差异（前者为后者的1.16倍）。这些结果表明, 抗性与敏感品系具有相似的Slest2基因拷贝数, 但它们在抗性品系中的转录水平显著升高。由此推测Slest2基因的转录水平升高与斜纹夜蛾对溴氰菊酯的抗药性密切相关。     

金龟子绿僵菌中性海藻糖酶基因的克隆及其表达特性分析

根据中性海藻糖酶NTL基因的同源序列设计引物,PCR扩增出杀蝗专一菌株———金龟子绿僵菌CQMa102NTL基因片段,利用5′_RACE和3′_RACE扩增出NTLcDNA的5′和3′端序列,经拼接得到CQMa102NTL基因cDNA全长。根据其全长cDNA序列,设计引物PCR扩增出CQMa102NTL的完整基因。为了解该基因的上游调控信息,采用PanhandlePolymeraseChainReactionAmplification方法扩增其上游序列。序列分析表明,CQMa102NTL全长DNA3484bp,cDNA全长2385bp,编码737个氨基酸的蛋白,推测蛋白分子量为83.1kD;含有3个内含子,包含一个依赖于cAMP的磷酸化作用位点(RRGS)和一个钙附着位点(DTDGNMQITIED);上游序列含有一个压力反应元件(CCCCT);与金龟子绿僵菌广谱性菌株ME1NTL的核苷酸序列和氨基酸序列分别具有93%和99%同源性,由此确定该序列为金龟子绿僵菌中性海藻糖酶基因序列。Southern杂交表明,NTL基因在CQMa102基因组中为单拷贝。Northern杂交表明,NTL基因转录出约2.5kb的mRNA单带,在液体培养条件下,对数生长前期表达水平最高,对数生长后期降到最低,进入稳定生长期后表达水平又有所提高。金龟子绿僵菌CQMa102中性海藻糖酶基因DNA全长和cDNA全长登录GenBank,登录号分别为:AY557613,AY557612。     

Isolation of a subtilisin-like serine protease gene (MyxSubtSP) from spores of Myxobolus cerebralis, the causative agent of whirling disease

Proteases play important roles in parasite life cycles and host-parasite interactions. They are pathogenesis factors of many pathogenic organisms and are hence potential targets for chemotherapeutic treatment of disease. We identified a subtilisin-like serine protease gene, MyxSubtSP, expressed by Myxobolus cerebralis. After PCR with subtilisin-like serine protease primers, the gene was cloned, sequenced and aligned against the NCBI database. Its corresponding amino acid sequence included the putative conserved domains of Peptidase_S8, subtilase family and AprE, subtilisin-like serine proteases. Rapid amplification of 5' and 3' cDNA ends (RACE) was used to generate the full length (1385 bp) gene, with a 429 bp open reading frame. The gene encompasses coding regions for a catalytic triad formed by Asp-74, His-100 and Ser-110.     

Inverse polymerase chain reaction mediated chromosome walking within the human glutamic acid decarboxylase gene

Using inverse polymerase chain reaction (PCR), we have cloned partial intronic sequences from human glutamic acid decarboxylase (GAD) gene. A small 153 bp core region was selected from the GAD cDNA sequence to design outward primers corresponding to its 3′ and 5′ ends. EcoRI digested human DNA which had been circularized by self-ligation and then linearized withSacII was used as a substrate to can.y out PCR. This gave a 900 bp long product which was cloned into pUC19. The sequence analysis of this fragment revealed the presence of introns in the region flanking the selected core DNA. In this work we used this technique to walk into the upsteam region of the GAD gene using sequence information from its cloned cDNA.     

内含子中正筛选标记neo基因在转录中的剪切研究

目的:研究插入内含子中的正筛选标记基因neo在转录中的剪切情况。方法:克隆了猪血清白蛋白基因5'端调控序列,以猪基因组DNA为模板,P10/P11为引物,PCR扩增猪血清白蛋白基因翻译终止密码子后2.9kb的3'端调控序列;以pEGFP-1为模板,P400/P401为引物PCR扩增绿色荧光蛋白(EGFP)基因,插入猪血清白蛋白基因5'端调控区之后,在3'端调控序列的内含子中靠近N端的序列中插入正筛选标记基因neo,构建了表达EGFP的真核表达载体pEXp11。转染人肝癌细胞系HepG2,通过G418药物筛选获得稳定转染的抗药性细胞克隆。提取抗性细胞克隆基因组RNA并进行反转录,获得cDNA序列。结果:用引物D400/D401及分别位于neo基因和3'端调控序列上的一对引物D394/D357进行PCR检测,其中D394/D357并未扩增出目的条带。结论:插入内含子中的neo基因在转录过程中可随内含子一起被剪切。     

Sequence of the cDNA encoding ovine tumor necrosis factor-alpha: problems with cloning by inverse PCR.

We have cloned and sequenced the ovine tumor necrosis factor-alpha (TNF-alpha)-encoding cDNA, using gene amplification by polymerase chain reaction (PCR) technology, to aid studies of assorted diseases in this species. We used primers selected from published TnfA sequences of other species on a cDNA template prepared from lipopolysaccharide-stimulated ovine alveolar macrophages, to generate a product representing the central region of the molecule. We then used a novel method based on 'inverse PCR' to generate a product containing the 5' and 3' ends of the molecule. Here, we present the complete sequence of the ovine TNF-alpha cDNA and compare it with other published TNF sequences. The cloned cDNA has a leader sequence of 156 bp followed by a protein-coding sequence of 702 bp and a 3'-untranslated region of 800 bp. The protein product of the gene is a protein of Mr = 25,586, 79% homologous to human TNF-alpha. An mRNA produced by alveolar macrophages, which hybridises to the cloned gene, is induced greatly, with a peak induction time of approx. 135 min, in response to stimulation by lipopolysaccharide and to plating on plastic. We also discuss the resolution of some artefacts of the inverse PCR technique.     

The cDNA and genomic DNA organization of a novel toxin SHT-I from spider Ornithoctonus huwena

Spider venoms are complex mixtures of neurotoxicpeptides, proteins and low molecular mass organicmolecules. Their neurotoxic activity is due to the interac-tion of the venom components with cellular receptors, inparticular ion channels. Spider venoms have…     

The plasma membrane H+-ATPase gene family in Arabidopsis: genomic sequence of AHA10 which is expressed primarily in developing seeds

The plasma membrane H+-ATPases in Arabidopsis thaliana represent the largest family of cation translocating P-type ATPases identified in plants or animals. We report here seven new isoforms, which were identified by polymerase chain reaction (PCR) amplification of genomic DNA. Amplifications were performed with degenerate primers corresponding to two short conserved sequence motifs (“CSDK” and “GDGV”) found in most P-type ATPases. A comparison was made of three CSDK-side primers, which were used either as totally degenerate mixtures or rendered less degenerate by substitution with deoxyinosine or fluorodeoxyuridine. Amplified genomic fragments were cloned, partially sequenced and shown to correspond to Arabidopsis genes by Southern blot analysis with gene-specific probes. One newly identified isoform, AHA10, was isolated as a cosmid clone and sequenced. The 5′ and 3′ ends of the gene were determined by comparison with the AHA10 cDNA sequence. AHA10 is the most divergent isoform characterized in the Arabidopsis family. AHA10 appears to be expressed primarily in developing seeds, as indicated by Northern blot analysis of AHA10 mRNA and by the analysis of transgenic plants expressing a β-glucuronidase (GUS) reporter gene fused to an AHA10 promoter. Our results indicate that one function of this unusually large H⁺-ATPase gene family is to allow for expression of different isoforms in different cell types.     

程序化设计简并引物与克隆小菜蛾酯酶基因

利用遗传密码简并性 ,针对特定的氨基酸序列设计简并引物 ,是克隆蛋白质家族cDNA的常规方法。文章介绍了利用blastp ,blockmaker,CodeHop ,SwissProt,SpTrEMBL等网络工具及数据库设计昆虫抗性酯酶的简并引物。用这对引物从抗有机磷杀虫剂的小菜蛾Plutellaxylostella中克隆了 1段cDNA。经blastx检索genebank,发现此cDNA产物与其它昆虫抗性酯酶基因有高度的相似性。研究表明 ,程序化设计的简并引物可信性强 ,阳性率高 ,能迅速得到满意结果     

Amplification and sequence analysis of the full length toxR gene in Vibrio harveyi

This study was focused on obtaining the complete gene sequence of the toxR gene in V. harveyi by using toxR-targeted PCR to amplify 5' and 3' regions flanking the 576-bp Vibrio harveyi (NBRC 15634) toxR gene fragment previously amplified using degenerate PCR. To obtain the 5' flanking sequences, a forward PCR primer (VhtoxRpv) was designed based on known sequences upstream of toxR in V. parahaemolyticus and V. vulnificus. The reverse primer (VctoxR2R) was based on the sequence of the 576-bp Vibrio harveyi toxR fragment. The resulting 750-bp amplicon was sequenced, providing the 5' sequences of the V. harveyi (NBRC 15634) toxR gene. The 3' flanking region was amplified using a primer pair toxRS1 and toxRS2 based on V. parahaemolyticus and V. vulnificus toxR and toxS, resulting in a 900-bp amplicon that contained the remaining 3' sequences of the V. harveyi NBRC 15634 toxR. This paper reports, for the first time, a complete 882-bp nucleotide sequence for toxR in Vibrio harveyi. Sequence analysis and alignment revealed that the complete toxR gene in V. harveyi shares 87% sequence similarity with toxR of V. parahaemolyticus, 84% similarity with V. fluvialis, 83% with V. vulnificus and partial sequence of V. campbellii. The phylogenetic trees revealed wider divergence in toxR compared to 16S rRNA genes, so that V. harveyi could easily be distinguished from V. campbellii and V. parahaemolyticus.     

Molecular characterization of the first heat shock protein 70 from a reef coral.

The branching coral Stylophora pistillata, one of the most abundant hermatypic corals along the coasts of the Red Sea, has been used for many years as a model species for coral biological studies. Here we characterize the first coral heat shock protein 70 gene (SP-HSP70), cloned from S. pistillata, to be used as a tool for studying coral stress response. The cloning was carried out by a combination of PCR methods using heterologous, degenerate HSP70-based primers, followed by plaque-lift screening of a genomic library. The sequenced clone (5212 bp), contains a complete 1953 bp, intronless open reading frame, and 5' and 3' flanking regions of 1,935 and 1,324 bp, respectively. TATA, CAAT, and ATF boxes as well as 11 putative heat shock elements were identified in the SP-HSP70 5' flanking region. A polyadenylation site was identified in the 3' flanking region. SP-HSP70 protein sequence resembles the cytosolic/nuclear HSP70 cluster. RT-PCR studies confirmed SP-HSP70 mRNA expression in corals grown within their normal physiological conditions. Furthermore, SP-HSP70 has been shown to belong to the coral genome and not to its symbiotic algae one, as revealed by SP-HSP70 PCR amplification, using purified algal and coral DNA templates.     

四甲基氯化铵在PCR扩增小麦基因中的关键作用

利用高简并性引物,用PCR法从小麦DNA或cDNA中合成小麦几丁质酶基因、葡 聚糖酶基因和苯丙氨酸解氨酶基因片段。在PCR反应中添加四甲基氯化铵(TMACl)是合成这些特异基因片段的关键。合成的PCR片段都经末端补齐和磷酸化后用于克隆。核酸序列分析证实,这些PCR产物分别与用于设计PCR引物的基因具有高度的同源性。 Abstract:In the presence of tetramethy1 ammonium chloride(TMAC1),a chitinase gene sequence,a phenylalanine ammonia-lyase gene sequence and a glucanase cDNA sequence of wheat were amplified with highly degenerate primers by PCR.The inclusion of TMAC1 in the PCR reactions was essential for successful amplification of the desired sequences from genomic DNA or cDNA in wheat.The ends of the PCR fragments were made flush and phosphorylated prior to cloning.Sequence analyses of the above PCR fragments confirmed their identities,showing high sequence similarities to the genes used for the design of PCR primers.