小鼠糖皮质激素诱导的肿瘤坏死因子受体相关蛋白生物信息学分析

目的获取小鼠糖皮质激素诱导的肿瘤坏死因子受体相关蛋白(GITR)氨基酸序列,并预测其结构和功能。方法利用网络平台及相关生物学软件对小鼠GITR氨基酸序列进行生物信息学分析。结果小鼠GITR氨基酸序列与人等其他物种具有56%的同源性,具有信号肽、胞外区、跨膜区及胞内区等结构;小鼠GITR蛋白胞外区位于第22~153号氨基酸序列区间;可能含有4个N-糖基化位点、4个丝氨酸磷酸化位点、1个苏氨酸磷酸化位点以及1个酪氨酸磷酸化位点。结论小鼠GITR氨基酸序列的生物信息学分析为进一步表达该蛋白及其相关功能研究奠定了基础。     

小鼠CD226(PTA1)的基因克隆及其异型

目的 :克隆小鼠CD2 2 6 (PTA1)分子。方法 :从GenBank中检索出与人CD2 2 6分子在氨基酸水平上有 5 1%同源性的EST序列 ,设计并合成特异性引物 ,采用快速扩增cDNA末端的RACE方法 ,从 4周龄BALB c小鼠的胸腺中扩增小鼠CD2 2 6cDNA序列。结果 :克隆出完整的小鼠CD2 2 6cDNA ,长 2 2 2 3bp ,其中开放读框为 10 0 2bp ,编码含信号肽在内的 333个氨基酸 ,属免疫球蛋白超家族分子 ,较人CD2 2 6分子少了 3个氨基酸 ,在氨基酸水平上有 5 3%的同源性。此外 ,还克隆了小鼠CD2 2 6分子的 3种异型。结论 :成功克隆出小鼠CD2 2 6 (PTA1)cDNA ,并发现 3种异型 ,全面探讨该分子生物学特性 ,进行体内功能实验 ,基因敲除小鼠和转基因小鼠的研究提供了坚实的基础。     

癌基因PPO及其同源性基因的结构分析

目的采用PPO(proliferation and phosphorylation oncogene)基因与其同源性基因的结构分析,推测PPO并验证其功能。方法利用PPO的蛋白序列寻找同源基因,比较其结构并利用蛋白免疫杂交方法证实其功能。结果克隆了PPO基因,找到了PPO基因与小鼠、果蝇、蚊子、线虫以及酵母等的同源基因,比较发现PPO在进化上非常保守。人和小鼠的氨基酸序列有许多与磷酸化有关的功能域,并发现其中某些氨基酸在进化上非常保守。进一步研究表明PPO能使ERK2和MEK磷酸化。结论PPO基因在进化上非常保守,与磷酸化功能有关。     

中国猪种DQA新等位基因的克隆和分析

目的：克隆和序列分析中国猪种DQA基因cDNA，为猪异种器官移植的免疫识别机理的研究提供基础。方法：采用RT-PCR方法扩增广西巴马猪(GXP)、贵州香猪(GZP)及云南小耳猪(YNP)DQA基因cDNA，克隆入测序载体，然后进行测序及其序列分析。结果：获得具有阅读框架的3个结构和已有序列不同的DQA新等位基因(GXPDQA、GZPDQA和YNPDQA)，基因序列号分别为AY102473，AY102474和AY102475，其长度分别为765、768和768个核苷酸，除末端终止密码外，分别编码254、255和255个氨基酸残基。结论：发现了3个猪DQA新等位基因，同时发现中国猪种DQA基因及其推导的氨基酸与人相应基因的同源性职显高于小鼠。     

粉尘螨变应原第6组分全长cDNA克隆及生物信息学分析

目的:获得粉尘螨变应原第6组分编码基因并了解其分子特征.方法:根据GeneBank已公布的Der f 6核酸序列设计引物,用RT-PCR扩增获得其编码基因,插入pMD19-T载体进行序列测定和生物信息学分析.结果:获得的Der f 6 cDNA全长为840 bp,与参考序列同源性达96.8%,含1个完整的开放读码框.推测编码蛋白由279个氨基酸组成,信号肽序列位于1～19 aa,亲水性指数为-0.139,跨膜区域位于1～19 aa,二级结构由α-螺旋(7.17%)、延伸主链(36.56%)和无规卷曲(56.27%)组成;亚细胞定位于细胞外,N-端第6位和第11位的亮氨酸有明显的序列核输出信号;可能为糜蛋白酶,具有cAMP和cGMP依赖的蛋白激酶磷酸化位点、蛋白激酶C磷酸化位点、酪蛋白激酶Ⅱ磷酸化位点、N端酰基化位点等.结论:获得了Der f 6基因全长,其编码的细胞外疏水性蛋白可能具有糜蛋白酶活性.     

中国猪种DQB新等位基因的克隆和分析

克隆和序列分析中国猪种DQB基因cDNA ,为猪异种器官移植的免疫识别机制的研究提供基础。采用RT PCR方法扩增猪DQB基因cDNA ,克隆入测序载体 ,然后进行测序及其序列分析。结果获得具有阅读框架的三个结构和已有序列不同的DQB新等位基因 ,基因序列号分别为AY10 2 4 76、AY10 2 4 77和AY10 2 4 78,其长度为 786个核苷酸 ,除末端终止密码外 ,编码 2 6 1个氨基酸残基。发现了三个猪DQB新等位基因 ,同时发现中国猪种DQB基因及其推导的氨基酸与人相应基因的同源性明显高于小鼠     

人类白细胞抗原新等位基因B*55:35的鉴定及家系调查

目的 鉴定人类白细胞抗原(human leukocyte antigen,HLA)基因B位点的1个新等位基因并调查其遗传情况.方法 应用聚合酶链反应-序列特异性寡核苷酸探针(polymerase chain reactionsequence specific oligonucleotide probe,PCR-SSOP) HLA分型技术发现1个疑似的新HLA等位基因,通过DNA测序鉴定其序列,并与同源性最高的HLA基因进行核苷酸序列比对,对携带者家系进行调查.结果应用PCR-SSOP进行HLA基因分型时,该样本HLA-B位点反应格局异常.DNA序列分析证实其为1个新HLA-B等位基因.与同源性最高的等位基因B*55:02比较,在第2外显子区域中有7个碱基发生改变,导致6个密码子发生了变化,造成2个氨基酸改变,即第69位的氨基酸由谷氨酸(Glu)变为甲硫氨酸(Met)、第70位的氨基酸由谷氨酸(Glu)变为丙氨酸(Ala).结论 发现并鉴定了HLA-B位点的1个新等位基因,GenBank注册号为FJ898284,被世界卫生组织HLA因子命名委员会正式命名为HLA-B* 55:35.     

6q25区域内一个新基因MTLC的克隆及特性分析

目的：克隆6q25区域内喉癌相关新基因。方法：以表达序列标签为电子探针，在人类基因组数据库中进行电子杂交，钓出相就基因组DNA克隆后进行基因预测。根据获得的基因序列设计引物，逆转录－聚合酶链反应扩增新基因cDNA。结果：克隆了1个6q25区域内的新基因。该基因全长约21kb，含两个外显子，其cDNA序列长1006bp，编码蛋白包括235个氨基酸。其5’侧翼序列存在癌蛋白c-Myc的结合位点，将其命名为MTLC（c-Myc target from laryngeal cancer cells）基因。同源性分析表明该基因编码蛋白与小鼠MT－MC1蛋白同源性达78％。MTLC蛋白一级结构含有一个核定位信号结构域，亚细胞定位实验证实该基因主要在细胞核表达，Northern印迹分析表明MTLC基因在心肌、肝、肾、脑等多个组织有表达。结论：成功克隆了1个新基因MTLC，该基因可能作为c-Myc的靶基因以转录因子形式参与维持细胞正常生理功能。     

甲1型流感病毒新分离株HA基因的序列分析

目的 研究新分离的H1N1亚型流感病毒株的HA1基因序列。方法 甲型流感病毒通过鸡胚增殖后提取RNA、逆转录合成cDNA,经PCR扩增和产物纯化构建重组质粒,用双脱氧链终止法进行核苷酸序列测定;并进行基因特性分析。结果 新分离到的3株流感病毒株（H1N1）HA1区基因长度为981bp,编码327个氨基酸;与A/桂防/10/94和A/Bayern/07/95（H1N1）标准株比较其同源性分别为92.8%和91.3%,丢失了第130位氨基酸和304位糖基化位点;新分离的3株甲型流感病毒（H1地）标准株比较其同源性分别为92.8%和91.3%,丢失了第130位氨基酸和304位糖基化位点,新分离的3株甲型流感病毒株（H1N1）HA1区氨基酸同源性高达98%;A/桂防/10/94和A/Bayern/07/95(H1N1)毒株HN1氨基酸的同源性高达96%。结论 新分离到的3株H1N1毒株HA编码氨基酸不同于A/Baydrn/07/95(H1N1)和A/桂防/10/94（H1N1）标准株,它们可能为新的甲型流感病毒变异性。     

中国基因3型乙型脑炎病毒E基因分子特征

目的 以减毒活疫苗(SA14-14-2株)为对照,分析我国分离的基因3型乙脑病毒E基因区段核苷酸及氨基酸序列分子特征.方法 从GenBank中获取相应乙脑病毒株E基因区段核苷酸序列,通过Clustal X(1.81)、DNAStar、GENEDOC(3.2)等生物学软件进行核苷酸和氨基酸位点差异分析.以蜱传脑炎病毒可溶性蛋白晶体结构为模板进行乙脑病毒E蛋白氨基酸位点分析.结果 我国不同地域、不同宿主分离的基因3型乙脑病毒与SA14-14-2株核苷酸同源性分别在96%和95%以上,氨基酸同源性在95%和94%以上.在同一地域、同一宿主类型分离的毒株之间核苷酸和氨基酸同源性非常高.在E基因区段存在10处共同的氨基酸位点差异,在结构域Ⅰ(E160)、结构域Ⅱ(E123和E227)和两个未在结构域中的氨基酸位点(E441和E487)等5个位点在部分基因3型乙脑病毒中存在差异.结论 我国分离的基因3型乙脑病毒与减毒活疫苗株(SA14-14-2株)E基因区段同源性高,存在5处基因3型乙脑病毒特异的氨基酸位点差异,但现行减毒活疫苗株理论上可以保护我国分离的基因3型乙脑病毒野毒株.     

The gene encoding the stem cell antigen, CD34, is conserved in mouse and expressed in haemopoietic progenitor cell lines, brain, and embryonic fibroblasts.

The human haemopoietic cell surface antigen, CD34, is a 105 - 120 kd cell surface glycoprotein whose stage-specific expression by stem cells and lineage-specific progenitor cells suggests a role in regulating early events in blood cell differentiation. A murine gene and cDNA encoding a closely homologous protein have been isolated. The gene is organized in eight exons in 22 kb of DNA. The first exon lies in a GC- and CpG-rich island. The sequence of the gene and the cDNA predict a 382 amino acid-long protein containing an N-terminal signal peptide and one transmembrane region 73 amino acids from the C-terminus. The extracellular part of the protein contains: a 140 amino acid-long-N-terminal region, 40% of whose residues are serine or threonine potential attachment sites for O-linked carbohydrate, as well as five potential attachment sites for N-linked carbohydrate. Proximal to the extracellular membrane there is a 79 amino acid-long cysteine-rich region. The homology with the human sequence is highest in the intracellular domain (90% amino acid identity) and lowest in the N-terminal region (43% amino acid identity). The protein is not homologous with any other proteins currently in the databases. The expression of the murine gene by a number of haemopoietic progenitor cell lines suggests that the CD34 function in haemopoiesis may be conserved between man and mouse. The high level of expression in a number of embryonic fibroblast cell lines and in brain imply a function outside of haemopoiesis.     

Molecular characterization of the TCP11 gene which is the human homologue of the mouse gene encoding the receptor of fertilization promoting peptide.

A human testis-specific gene was isolated by subtractive hybridization between the cDNA pools of adult and fetal testes, followed by rapid amplification of cDNA ends (RACE). This gene sequence is highly homologous to a large portion of the mouse Tcp11 gene which is important in sperm function because it encodes the receptor for fertilization-promoting peptide (FPP). The gene was mapped to human chromosome band 6p21 by fluorescence in-situ hybridization. The 9 exon gene spans a 22.8 kp genomic DNA sequence. The mature processed message encodes a 441 amino acid protein that is highly homologous to the mouse 566 amino acid protein after the first 142 amino acids. Results of Northern blot and RT-PCR analyses of RNA extracted from human tissues revealed that the gene is only expressed in fertile adult testes, but not in azoospermic testes, fetal testes nor in other human tissues. Taken together, our results along with the mouse Tcp11 function suggest that TCP11 gene is important in sperm function and fertility.     

Molecular cloning and characterization of a novel human gene homologous to the murine ecotropic retroviral receptor.

A novel human cDNA homologous to the murine ecotropic retroviral receptor was cloned from a cDNA library derived from a human T-cell line. The human cDNA is highly homologous to the murine counterpart (87.6% amino acid identity), and its sequence predicts a protein with 629 amino acids (approximately 68 kDa), which is 7 amino acids more than the murine counterpart (622 amino acids). The predicted protein is highly hydrophobic and contains 14 potential transmembrane-spanning domains. No other gene and protein with significant homology to the cloned human gene and the predicted protein were identified by a computer-based search of sequence data banks other than the murine T-cell early activation gene (52.5% amino acid identity) and the murine ecotropic retroviral receptor gene. The human gene is ubiquitously expressed in human tissues and conserved among mammalian species. The genomic gene was also isolated from a cosmid library derived from human lymphocytes, and its organization was elucidated. The gene mapped to human chromosome 13.     

Slc19a2: cloning and characterization of the murine thiamin transporter cDNA and genomic sequence, the orthologue of the human TRMA gene

Recently, our group and others cloned the TRMA disease gene, SLC19A2, which encodes a thiamin transporter. Here, we report the cloning and characterization of the full-length cDNA and genomic sequences of mouse Slc19a2. The Slc19a2 cDNA contained a 1494-bp open-reading frame, and had 5'- and 3'-untranslated regions of 189 and 1857 bp, respectively. A putative GC-rich, TATA-less promoter was identified in genomic sequence directly upstream of the identified 5' end. The Slc19a2 gene spanned 16.3 kb and was organized into six exons, a gene structure conserved with the human orthologue. The predicted Slc19a2 protein, like SLC19A2, was predicted to have 12 transmembrane domains and shared a number of other conserved sequence motifs with the human orthologue, including one potential N-glycosylation site (N(63)) and several potential phosphorylation sites. Comparison of the Slc19a2 amino acid sequence with those of the other known SLC19A solute carriers highlighted interesting patterns of conservation and divergence in various domains, allowing insight into potential structure-function relationships. The identification of the mouse Slc19a2 cDNA and genomic sequences will facilitate the generation of an animal model of TRMA, permitting future studies of disease pathogenesis.     

Characterization of the human jumonji gene

While constructing a cDNA library of human embryos, we have isolated a clone homologous to jumonji, a mouse gene required for neural tube formation. We have determined the complete coding sequence of the human homologue (JMJ) and deduced the amino acid sequence of the putative protein. We show here that human and mouse jumonji putative proteins are homologous and present 90% identity. During human embryogenesis, JMJ mRNAs are predominantly expressed in neurons and particularly in dorsal root ganglion cells. They are also expressed in neurons of human adult cerebral cortex. In view of these observations, we propose JMJ as a candidate gene for developmental defects of the central nervous system in the human. The human JMJ gene maps at position 6p24-6p23.      

Cloning and expression of uridine/cytidine kinase cDNA from human fibrosarcoma cells

Uridine/cytidine kinase which converts uridine and cytidine to their corresponding monophosphates is a rate-limiting enzyme involved in the salvage pathway of pyrimidine synthesis. We isolated cDNA encoding the enzyme from human fibrosarcoma cells, then determined its nucleotide sequence by the 5'-RACE method followed by confirmation employing the human genome DNA library. The isolated uridine/cytidine kinase cDNA (UCK cDNA) consisted of 786 nucleotides encoding 261 amino acids and was found to have approximately 70% homology with mouse UCK cDNA. Northern blot analysis of human leukemia RNAs with labeled UCK gene showed a single band at 1.6 kb to be UCK mRNA, and southern blot analysis of the UCK cDNA after digestion with BamHI, SacI and XbaI enzymes showed four band signals, suggesting the UCK gene to have at least 4 exons. A truncated form of UCK cDNA was expressed as the His-tag conjugated protein in Escherichia coli. The expressed and purified protein specifically converted uridine and cytidine to their corresponding monophosphates and also phosphorylated antitumor nucleosides such as 5-fluorouridine, cyclopentenyl-cytosine and 3'-C-ethynylcytidine. The present results suggest that our cloned human UCK cDNA encodes the correct amino acid sequence for UCK protein, showing high intracellular phosphorylation activity forward natural and synthetic pyrimidine nucleosides.     

Cloning of cDNA for the bovine IL-2 receptor (bovine Tac antigen).

We have cloned the Tac analog of the bovine IL-2 receptor (IL-2R) cDNA. Using mouse and human cDNA probes, we isolated five bovine IL-2R clones from a lambda gt11 bovine long-term lymphocyte cDNA library. Three of the clones had inserts of 2600 base pairs (bp), the same size as the bovine IL-2R mRNA visualized on Northern blots. The full-length cDNA contain a 190-bp 5' untranslated region, followed by a 825-bp coding region, and a 3' untranslated region that contain 1600 bp. Comparison of the bovine and human IL-2R-coding sequences revealed 71% homology at the nucleotide level. The 3' and 5' non-coding regions were not as homologous, apart from a specific site in the 5'-untranslated region that contained a 5'-upstream start codon. In this region, 24 of 26 nucleotides were identical for the human and bovine cDNAs. Further analysis of the bovine IL-2R sequence also revealed the following: (i) the hydrophobic domains of the IL-2R protein were more conserved between species than the hydrophilic domains, (ii) the predominant site of intracellular IL-2R phosphorylation in mouse and human was a conserved Ser which was not conserved in the bovine sequence, and (iii) there exists a statistically significant amino acid homology with the AIDS gag protein.     

Cloning and characterization of a novel gene which encodes a protein interacting with the mitosis-associated kinase-like protein NTKL

NTKL is an evolutionarily conserved kinase-like protein. The cell-cycle-dependent centrosomal localization of NTKL suggested that it was involved in centrosome-related cellular function. The mouse NTKL protein is highly homologous with human NTKL. A novel mouse protein was identified as an NTKL-binding protein (NTKL-BP1) by yeast two-hybrid screening, and the full-length cDNA was amplified based on the result of a sequence data analysis cloning strategy. The full-length cDNA sequence of the NTKL-BP1 gene consists of 2,537 bp, which encode 368 amino acids. A database search revealed that homologues of NTKL-BP1 exist in different organisms, including Arabidopsis thaliana, Drosophila melanogaster, Plasmodium falciparum, Geobacter metallireducens, Anopheles gambiae and human. It suggests that NTKL-BP1 is an evolutionarily conserved protein. The expression of NTKL-BP1 was observed in multiple normal mouse tissues. The interaction of the two proteins was confirmed by co-immunoprecipitation. Moreover, immunofluorescent staining indicated that NTKL and NTKL-BP1 were all localized in the cytoplasm.