Characterization of equine cDNA sequences for alphaS1-, beta- and kappa-casein

Here we report the entire cDNA sequences for equine alphaS1-, beta- and kappa-casein. Based on interspecies comparison, nine exons were found in equine beta-casein and five in kappa-casein. In equine alphaS1-casein cDNA the exon 5 was missing, which resulted in the total of 18 exons instead of 19 theoretically possible exons in alphaS1-casein cDNA. Comparison of DNA sequences representing exon 5 in other species with corresponding equine genomic region confirmed the presence of cryptic exon in horse genomic DNA. Equine alphaS1-casein mRNA was present in three forms in the lactating mammary gland and we showed that the two shorter forms were produced by skipping either the exon 8 or exon 15. In horse, as in some other mammals, beta- and kappa-casein are considerably more conserved (sequence identity 53% to 59% and 57% to 67%, respectively) than alphaS1-casein which appears as the most variable casein among species (sequence identity 40% to 54%). Interestingly, horse caseins resemble human much more than bovine caseins which may also explain the high dietetic value of mares' milk.     

核盘菌诱导下甘蓝型油菜宁RS-1的SSH文库构建

以甘蓝型油菜宁RS-1为材料,用核盘菌（Sclerotinia sclerotiorum（Lib.）de Bary）对幼苗进行接种,提取经核盘菌诱导前和诱导后的宁RS-1叶片mRNA,经反转录成cDNA,以及经过酶解后加接头和两次杂交,构建差异表达的抑制消减（SSH）cDNA文库。正向消减文库是以诱导后的宁RS-1 cDNA为tester,以正常的宁RS-1 cD-NA为driver。所构建的正向文库重组率达到96.2%,反向文库重组率达到94.5%,文库容量均达到了2 190和2 780,表明所构建的文库质量良好。对从文库中随机挑取的克隆进行测序分析,获得了与抗病和代谢有关的基因,如γ-谷氨酰半胱氨酸酶基因、抗真菌蛋白基因、铁蛋白基因、ACC氧化酶基因等,为开展油菜抗菌核病重要功能基因的克隆和鉴定奠定了基础。     

Adequate design of customized cDNA macroarray for convenient multiple gene expression analysis

To establish a convenient, cost-effective, and reasonably reliable method for monitoring multiple gene expression using customized membrane-based macroarray, we constructed a cDNA macroarray with multiple probes for 13 human vascular endothelial genes and assessed the accuracy of the macroarray measurements. For each gene, two cDNA probes (450-550 bp) were designed from different regions (coding region and 3'-untranslated region [3'-UTR], respectively) on the basis of simple criteria concerning length and sequence specificity and spotted on the macroarray. In addition, unmodified oligonucleotide probes (80 mer) targeted to a unique sequence from the coding region of each gene were spotted on the same macroarray. Using this macroarray, shear stress-induced mRNA expression changes were analyzed in human coronary artery endothelial cells. Comparison of the expression ratios obtained with those measured using quantitative real-time polymerase chain reaction (PCR) as a reference method revealed that cDNA probes designed from a sequence within the coding region provided a highly accurate expression profile, whereas results obtained from oligonucleotide probes showed no correlation with real-time PCR data, which might be caused by inadequate immobilization of oligonucletotide probes on the nylon membrane. In addition, we observed that cDNA probes targeting different regions of a gene yielded different signal intensities. Most cDNA probes designed from a sequence within the coding region showed detectable signals, whereas few cDNA probes designed from 3'-UTR did.     

Isolation of the retinoblastoma cDNA from the marine flatfish dab (Limanda limanda) and evidence of mutational alterations in liver tumors

We have isolated a dab (Limanda limanda) homologue of the human retinoblastoma (Rb) tumor suppressor gene. The L. limanda partial Rb cDNA encodes a partial predicted protein of 753 amino acids. DNA sequence analysis with other vertebrate Rb sequences demonstrates that the L. limanda Rb cDNA is highly conserved in regions of functional importance. The sequence reported herein, combined with the high degree of conservation observed in critical domains, has also facilitated an investigation of the molecular etiology of environmentally induced liver tumor samples in a feral fish species. Mutational alterations were detected in liver adenoma samples, also in apparently "normal" regions of liver samples dissected from fish displaying adenoma, but not in normal liver samples from otherwise healthy feral fish. These results are the first reporting the appearance of Rb mutations in wild-caught fish and suggest that the molecular etiology of fish cancer appears to involve Rb-implicated tumorigenesis. The ecotoxicological relevance of the Rb mutations in feral fish liver tumors, in terms of future genome instability and possible development of a genotoxicity biomarker, is discussed.     

绒毛状烟草和林烟草全长cDNA文库构建及EST序列分析

表达序列标签（EST）广泛应用于基因功能研究和分子标记开发。以普通烟草两个二倍体祖先种绒毛状烟草（Nicotiana tomentosiformis,TT）和林烟草（Nicotiana sylvestris,SS）多个组织为试验材料,使用CloneMiner cDNA文库构建方法构建了均一化全长cDNA文库,测序并进行序列拼接、功能注释、进化分析和标记开发。绒毛状烟草和林烟草均一化全长cDNA文库容量分别为0.72×10⁶和1.12×10⁶ pfu/mL,重组率分别约为94%和93%,插入片段平均长度为1.4 kb。测序获得20 953条EST序列,拼接为10 504个unigenes。与普通烟草EST序列混合拼接,产生34 450条contigs,123 511条singletons,烟草异源四倍体中T和S基因与绒毛状烟草、林烟草之间的相似性远高于两个二倍体祖先种之间。预测获得104 915个编码序列,其中73 670个序列包含功能结构域,81% unigenes在番茄中具有同源基因。鉴定了11 869个微卫星位点（SSR）和25 209个单核苷酸多态性位点（SNP）。这些数据信息对于烟草基因功能研究和分子育种具有重要价值。     

In vivo construction of cDNA libraries for use in the yeast two‐hybrid system

We describe a simple and efficient one‐step method to make cDNA libraries using homologous recombination in yeast. cDNA from any source, together with a linear vector, is used to transform yeast. Through homologous recombination and gap repair, the cDNA is unidirectionally incorporated into the yeast expression vector in vivo. The cDNA‐encoded proteins can then be screened for potential protein–protein interactions with a bait already present in the yeast. This method allows rapid construction and screening of cDNA libraries, even from extremely small amounts of mRNA, and can replace the use of conventional cDNA libraries. Copyright © 1999 John Wiley & Sons, Ltd.     

Cloning of oleosin, a putative new hazelnut allergen, using a hazelnut cDNA library

The clinical presentation of non-pollen related allergy to hazelnut can be severe and systemic. So far, only a limited number of non-pollen related hazelnut allergens have been identified and characterized. The aim of this study was to identify and clone new hazelnut allergens. A lambda ZAP cDNA library of hazelnut was constructed. The library was screened with serum of six hazelnut allergic patients displaying different IgE-binding patterns on hazelnut immunoblot. Rapid amplification of cDNA ends (RACE) protocols were applied to obtain full-length clones. Expression experiments were carried out in Eschericchia coli. Expression was monitored by SDS-PAGE, protein staining and immunoblotting. A hazelnut cDNA library was constructed. IgE screening resulted in the cloning of two isoforms of a novel putative hazelnut allergen. The clones were identified as oleosins, with theoretical molecular masses of 16.7 and 14.7 kDa and pI of 10.5 and 10.0, respectively. The isoforms demonstrated only 37% amino acid sequence identity but contained the typical hydrophobic stretch in the middle of the protein (53% identity) with the characteristic oleosin proline knot region (11/12 amino acids identical). Expression in E. coli of the longer isoform resulted in a clear band on SDS-PAGE. The expressed protein was recognized on an immunodot blot by IgE from serum that was used for screening the cDNA library. Hazelnut contains multiple isoforms of oleosin. IgE binding of a hazelnut-allergic patient to a recombinant version suggest that hazelnut oleosin is an allergen, as has been described for peanut and sesame.     

烟草优质品种叶片全长cDNA文库的构建和质量分析

为研究优质烟叶的分子基础,以翠碧一号不同生长时期的叶片为材料,CTAB法提取总RNA,利用SMART技术合成全长cDNA,之后按经修改的Clontech技术成功构建了烟草叶片全长cDNA文库.经鉴定,初级文库库容为3.85×106个克隆,重组率为100％,重组子插入片段集中在750-2000 bp之间.随机挑取25个克隆测序后,经生物信息学分析表明,烟草上已经报道的基因占10条,11条为全长基因序列;20条序列有功能注释.综合分析表明,所构建的文库质量较高,达到了基因的分离、筛选和克隆的建库目的.     

黑曲霉糖化酶基因在毕赤酵母中的克隆和表达

从高产糖化酶的黑曲霉的cDNA文库中筛选出糖化酶基因,并研究在毕赤酵母中的表达情况。运用RT-PCR从黑曲霉cDNA文库中克隆糖化酶基因的cDNA片段与载体pPIC9K相连,构建重组载体,电转化毕赤酵母GS115,筛选阳性克隆并进行研究。阳性克隆在MM培养基中发酵72 h和1%的甲醇的诱导的情况下,重组毕赤酵母产生的糖化酶酶活最大为15.6 U/mL。测定结果显示,其糖化酶大小为1 908 bp,编码636个氨基酸残基组成的蛋白质。经柱分离纯化其发酵上清液后,用SDS-PAGE电泳方法,测得分子质量大约为80 ku。黑曲霉糖化酶基因在毕赤酵母GS115中成功得到了表达。     

Identification of novel IgE-binding soybean allergens using serological analysis of a recombinant cDNA expression library (SEREX)

New immunoglobulin E (IgE)-binding proteins from soybean (Glycine max L.) were identified using serological analysis of a recombinant cDNA expression library (SEREX) derived from soybean seeds and an enzyme-linked immunosorbent assay (ELISA). A soybean cDNA expression library was synthesized using the lambda ZAP express phage vector system and screened using sera of soybean-sensitive patients with atopic dermatitis (AD). A total of 3 new IgE-binding soybean proteins were identified as enolase, triosephosphate isomerase (TPI), and malate dehydrogenase (MDH). Full-length cDNAs were cloned into the expression vector pET15b, and expressed in Escherichia coli BL21 (DE3). The recombinant proteins were purified using affinity chromatography, followed by ELISA, with the sera of AD patients, resulting in positive reactions. The cDNA sequences were submitted to the GenBank Nucleotide Sequence Database with the accession numbers AY496909 (enolase), AY631048 (TPI), and AY496910 (MDH).     

一种酿酒酵母表达cDNA文库分离纤维质降解酶系基因的方法

目的:建立一种筛选自然界产纤维质降解酶系基因的新方法。方法:对酿酒酵母表达载体pYES2多克隆位点加入真核生物稀有限制性酶切位点SfiI进行改造,利用SMART技术,以大肠杆菌文库为转导,构建了拟青霉(Paecilomyces sp.H28)的酿酒酵母全长cDNA表达文库。结果:利用纤维质-刚果红染色法从文库筛选到多种纤维素和半纤维素降解酶系基因。结论:成功构建了拟青霉的酿酒酵母表达cDNA文库,加快了纤维质降解酶系基因的快速分离,也为其它相关基因的快速分离提供了有益的借鉴。     

盐藻八氢番茄红素脱氢酶cDNA的分离及序列分析

采用5’和3’RACE技术和梯度PCR方法从盐藻中克隆了八氢番茄红素脱氢酶(Pds)全长cDNA,序列分析表明,该cDNA长2198bp,包含1个1752bp的开放阅读框(ORF),编码一段583氨基酸残基的多肽链。氨基酸序列的同源性分析表明,它与高等植物和蓝藻的八氢番茄红素脱氢酶序列一致性高达67%,而与细菌和酵母的序列同源性较差;在N端具有一段转运序列和辅助因子结合结构域,C端则有一胡萝卜素结合域。这些序列特征预示,盐藻Pds与其他绿藻、高等植物和蓝藻中的同源基因一样催化八氢番茄红素发生前2步脱氢反应,并且需要与另一个脱氢酶联合作用合成番茄红素。     

Isolation of five laccase gene sequences from the white-rot fungus Trametes sanguinea by PCR, and cloning, characterization and expression of the laccase cDNA in yeasts

To obtain laccase-gene-specific sequences from the white-rot fungus Trametes sanguinea M85-2, a PCR screening method was used. Degenerate primers were designed based on highly conserved copper-binding regions I and IV of known laccases and used to amplify laccase sequences from T. sanguinea M85-2 genomic DNA. A single 1.6-kbp DNA band was amplified and cloned into a vector. Partial sequences of 21 clones were classified into five groups (lcc1-5) and the deduced amino acid sequences were all homologous to known laccase sequences. Based on the partial sequence of lcc1, the 5'-end of its cDNA was obtained by a PCR termed 5' rapid amplification of cDNA ends (5'-RACE), and RT-PCR was then carried out using the 5'-primer and the poly-dT primer to obtain the full-length lcc1 cDNA. The obtained cDNA encoded a protein consisting of 518 amino acid residues and its first 21 amino acid residues were predicted to be the signal peptide for secretion. The conserved characteristic structures of laccase, such as copper-binding ligands, N-glycosylation sites, and cysteine residues for disulfide bridges, were observed. The genomic DNA sequence of the lcc1 gene was also cloned by PCR method and the sequence revealed 10 introns. The lcc1 cDNA was inserted into yeast vectors for heterologous expression by Saccharomyces cerevisiae and Pichia pastoris. Phenol-oxidizing activity was detected from transformants of the yeasts, indicating that the obtained cDNA encodes a laccase. Previously, two laccase isozymes were biochemically characterized and purified from T. sanguinea M85-2. Using the sequential PCR method presented here, we have obtained partial sequences of at least five laccase genes and one cDNA clone encoding a protein with laccase activity but without any enzymatic information, suggesting that expressed enzymes under restricted conditions may not represent all the isozymes in target microorganisms. PCR cloning and heterologous expression of the cloned genes can be an alternative method of screening enzymes if these enzymes have conserved sequences.     

Cloning and sequencing of the chromosomal DNA and cDNA encoding the mitochondrial citrate synthase of Aspergillus niger WU-2223L

The complementary DNA (cDNA) and chromosomal DNA encoding the citrate synthase (EC 4.1.3.7) gene (cit1) of Aspergillus niger WU-2223L, a citric acid-producing strain, were cloned. Synthetic oligonucleotide primers were designed according to the amino acid sequences of already known eukaryotic citrate synthases and the codon bias of A. niger genes. The 920-bp DNA fragment was amplified by polymerase chain reaction with these primers using chromosomal DNA of WU-2223L as a template, and was employed to screen a cDNA library of A. niger. One full-length cDNA clone was isolated and sequenced, within which an ORF of 1425 by encoding a protein of 475 as with a molecular weight of 52,153 Da was found. Its N-terminal region contains a typical mitochondrial-targeting motif. The predicted as sequence was 82, 68, and 65% homologous with the mitochondrial citrate synthases of Neurospora crassa, Saccharomyces cerevisiae, and pig, respectively, but it showed lower homology to bacterial citrate synthases. The full-length cDNA clone was used to screen a chromosomal library of A. niger WU-2223L, and a 7.5 kb-SalI fragment containing the corresponding chromosomal gene was isolated. Comparison of the chromosomal and cDNA sequences revealed that the cit1 gene is interrupted by six introns. In the chromosomal DNA, upstream of the coding region, a CT-rich region, but not the TATAAA or CAAT motifs, was found. Escherichia coli MOB150, a citrate synthase-deficient mutant showing a glutamate-requiring phenotype, was transformed with the plasmid pKAC-35S, which is the expression vector pKK223-3 containing the cDNA fragment encoding a putative mature protein of A. niger citrate synthase. The transformant harboring pKAC-35S showed citrate synthase activity and a glutamate-nonrequiring phenotype.     

Cloning of pig prostaglandin F2alphaFP receptor cDNA and expression of its mRNA in the corpora lutea

Changes in the expression and localization of luteal mRNA for PGF(2alpha) (FP) receptors may be critical in determining the luteolytic action of PGF(2alpha) in pig corpora lutea. In this study, a full-length FP receptor (FPr) cDNA was isolated and cloned from pig corpora lutea. This isolate (GenBank accession no. U91520) contains an open reading frame of 1086 bases coding for a protein of 362 amino acids with seven potential transmembrane domains. The predicted amino acid sequence of this isolate was 83% identical to the FPr amino acid sequence of other species including sheep, cattle and humans. Northern blot analysis showed the presence of an FPr message of about 5 kb in mRNA from pig corpora lutea. Relatively weak FPr mRNA expression was detected on day 4 and day 7 of the oestrous cycle. The expression was greater (P < 0.05) on days 10, 13 and 15 than on days 4 and 7. In situ hybridization analysis revealed that mRNA for FPr was expressed predominantly in the steroidogenic large luteal subtype of cell, although there was some expression in small luteal cells, with histological appearance of steroidogenic small cells. Localization of hybridization signals of FPr was observed in luteal tissue at all stages examined. These data demonstrate that FPr is expressed in pig corpora lutea throughout the oestrous cycle and that upregulation of the FPr mRNA occurs when the corpora lutea becomes sensitive to PGF(2alpha). Direct luteal targets of PGF(2alpha) appear to be primarily large steroidogenic cells in this species.     

Cloning and sequencing of cDNA and genomic DNA encoding serine carboxypeptidase of Fusarium moniliforme that was copurified with phosphatase

A previous study [Yoshida, H. et al., J. Biochem., 140, 813-823 (2006)] revealed that a protein of unknown nature was copurified with PDM phosphatase of Fusarium moniliforme. In this study, the identity of this protein was investigated. The results of homology search for the tryptic peptides derived from the purified preparation of PDM phosphatase strongly suggested that it might be serine carboxypeptidase. In fact, carboxypeptidase activity was demonstrated in the preparation and partial separation of carboxypeptidase from PDM phosphatase was achieved by gel filtration high-performance liquid chromatography. Cloning and sequencing of the full-length cDNA encoding the carboxypeptidase was successfully conducted. The cDNA possessed an open reading frame for a protein of 575 amino acid residues with a molecular mass of 64,650 Da, which was highly homologous to certain fungal serine carboxypeptidases. Comparison of the deduced amino acid sequence with the N-terminal sequence of the separated carboxypeptidase revealed that the mature enzyme starts at serine 56 of the precursor and has a molecular mass of 58,487 Da. Cloning and sequencing of the genomic DNA corresponding to the cDNA demonstrated that the gene of carboxypeptidase consists of four exons. A limited number of close homologs of F. moniliforme carboxypeptidase were detected among fungi by homology search and their evolutionary relationship was discussed.     

Global cDNA amplification combined with real-time RT-PCR: accurate quantification of multiple human potassium channel genes at the single cell level

We have developed a sensitive quantitative RT-PCR procedure suitable for the analysis of small samples, including single cells, and have used it to measure levels of potassium channel mRNAs in a panel of human tissues and small numbers of cells grown in culture. The method involves an initial global amplification of cDNA derived from all added polyadenylated mRNA followed by quantitative RT-PCR of individual genes using specific primers. In order to facilitate rapid and accurate processing of samples, we have adapted the approach to allow use of TaqMan real-time quantitative PCR. We demonstrate that the approach represents a major improvement over existing conventional and real-time quantitative PCR approaches, since it can be applied to samples equivalent to a single cell, is able to accurately measure expression levels equivalent to less than 1/100th copy/cell (one specific cDNA molecule present amongst 10(8) total cDNA molecules). Furthermore, since the initial step involves a global amplification of all expressed genes, a permanent cDNA archive is generated from each sample, which can be regenerated indefinitely for further expression analysis.     

Systematic transient assays of promoter activities for leaf-specific genes identified by gene-expression profiling with cDNA microarrays in Arabidopsis thaliana

We identified 85 genes highly expressed in leaves using an Arabidopsis cDNA microarray. A vector, pRAB5, was designed to allow cloning and assaying of the promoters. Fifty-one promoters from the selected genes were cloned and then assayed using a microprojectile bombardment and dual luciferase reporter assay system. This system allowed efficient systematic assays of promoter activity.