一色齿毛菌锰过氧化物酶2基因克隆及生物信息学分析

摘要 锰过氧化物酶（manganese peroxidase,MnP）是由一系列同功酶组成的木质素降解酶。我们前期工作克隆了一色齿毛菌（Cerrena unicolor) MnP1基因序列。在此基础上,本研究采用简并PCR、染色体步移和RACE等技术对C. unicolor mnp2基因(Cu-mnp2)序列进行克隆。同时,采用生物信息学软件对Cu-mnp2的基因结构、Cu-MnP2的蛋白质结构及多物种MnPs蛋白质序列的系统进化关系进行分析。克隆得到3 053 bp的Cu-mnp2 DNA序列(GenBank:JX270806.1)和1 429 bp的Cu-mnp2 cDNA序列(GenBank: JQ782580.1)。序列分析结果显示,Cu-mnp2 DNA序列包含14个外显子和13个内含子,启动子区域包含TATA-BOX、SP1和AP1等作用元件;Cu-mnp2 cDNA序列包含71 bp的5′UTR、230 bp的3′ UTR以及1 128 bp的开放阅读框(ORF)。Cu-mnp2 ORF序列的BLAST比对结果表明,Cu-mnp2与Trametes versicolor FP-101664 SS1 mnp序列覆盖度为53%,序列相似性为65%;与Heterobasidion irregulare mnp、C. unicolor mnp1等cDNA序列都有较高的序列相似性。Cu-mnp2的ORF编码(GenBank:AFK91530.1)由340个氨基酸残基组成的多肽链(Cu-MnP2)。Cu-MnP2蛋白质序列的BLAST比对和蛋白质三维结构均显示,Cu-MnP2包含Mn ²⁺ 、Ga ²⁺ 、血红素及芳香底物结合位点。对包含Cu-MnP1、Cu-MnP2蛋白质序列在内的多物种MnPs蛋白质序列的系统发育分析表明,多物种的MnPs分为两大类群,分别为包含4个二硫键的短MnPs和包含5个二硫键的长MnPs。其中,Cu-MnP1与Cu-MnP2均属于短MnPs,Cu-MnP2与Trametes versicolor MrP 的蛋白质序列亲缘关系最近。通过Cu-mnp2基因的克隆和序列分析,对继续研究C. uniclor的MnP同工酶基因结构和功能奠定基础。     

节杆菌A．pascens DMDC12中SOD基因的克隆和序列分析

根据基因库中细菌SOD的基因保守序列和Arthrobacter pascens DMDC12的N-末端氨基酸序列设计引物,采用PCR技术,以A.pascens DMDC12基因组为模板,克隆了A.pascens DMDC12中Mn-SOD的567 bp的基因片段;再结合该基因片段和A.pascens DMDC12中SOD的N-末端氨基酸序列的有关信息,设计包含该sod完整ORF区域的引物,成功扩增了A.pascens DMDC12中Mn-SOD的基因序列,新sod序列(sodAP)已提交Gen-Bank(收录号DQ779150)。利用生物学软件对该序列进行分析表明,该sodAP序列的ORF区域全长651 bp,编码216个氨基酸;该序列和Arthrobacter sp.FB24的SOD基因序列同源性为86%。     

6种重要经济鱼类生长激素完整cDNA的克隆和序列分析

通过RT-PCR、3′RACE、5′-RACE方法,从6种重要经济鱼类——大眼鳜(Siniperca kneri)、石斑鱼(Epinephelus coioides)、黄鳝(Monopterus albus)、鲶鱼(Silurus asotus)、泥鳅(Misgurnus anguillicaudatus)和方正银鲫(Carassius auratus gibelio Bloch,Fang Zheng crucian carp)中克隆了生长激素(Growth Hormone,GH)的完整cDNA序列(除石斑鱼序列外,其他生长激素序列均系第一次克隆),并详细分析了其序列特征。测序结果显示,克隆的6种GH cDNA长度依次为953bp、1023bp、825bp、1082bp、1154bp和1180bp,它们均包含一个长度为600个左右核苷酸的完整阅读框,分别编码一个200个左右氨基酸的蛋白：大眼鳜、石斑鱼和黄鳝GH为204个氨基酸,鲶鱼GH为200个氨基酸,泥鳅和方正银鲫GH为210个氨基酸。这6种蛋白序列与其他已知的鱼类GH序列都有较高的同源性,特别是与相同目的鱼类序列相比。通过序列比对,在这些蛋白序列内鉴定了许多保守的氨基酸残基,其中的大多数聚集而成5个保守域。基于这6种鱼类序列的编码区和其他鱼类的GH编码序列进行分子系统学分析,结果(MP和NJ树)与根据形态特征构建的系统发育树基本一致,特别是在硬骨鱼类较大分类阶元(目间、目以上)的系统发育研究方面比较一致,尽管仍存在一定差异,说明生长激素基因的编码区应该在硬骨鱼类系统发育研究领域得到更多的重视。     

絮凝基因(FLOIG)的序列测定及分析

虽然酵母细胞絮凝的确切机制至今尚无定论,但已克隆了多个与絮凝相关的基因,如FLOI、FLO5、FLO11等[1-3].这些基因的表达可以赋予非絮凝酵母细胞以絮凝能力.酵母细胞的絮凝特性在酿造工业、固定化酶、精细化工和物生制药等领域具有广泛的应用价值[4,5].从一株强絮凝酿酒酵母菌株中克隆到一个约4.3kb的NDA片段,酵母转化实验证明该DNA片段能够赋予非絮凝酵母菌株以絮凝能力[6].本文简要报道对该DNA片段进行序列测定和分析的结果.     

A yeast nuclear gene, MRS1, involved in mitochondrial RNA splicing: nucleotide sequence and mutational analysis of two overlapping open reading frames on opposite strands.

We have cloned a 1.6-kb fragment of yeast nuclear DNA, which complements pet- mutant MK3 (mrs1). This mutant was shown to be defective in mitochondrial RNA splicing: the excision of intron 3 from the mitochondrial COB pre-RNA is blocked. The DNA sequence of the nuclear DNA fragment revealed two open reading frames (ORF1 with 1092 bp; ORF2 with 735 bp) on opposite strands, which overlap by 656 bp. As shown by in vitro mutagenesis, ORF1, but not ORF2, is responsible for complementation of the splice defect. Hence, ORF1 represents the nuclear MRS1 gene. Disruption of the gene (both ORFs) in the chromosomal DNA of the respiratory competent yeast strain DBY747 (long form COB gene) leads to a stable pet- phenotype and to the accumulation of the same mitochondrial RNA precursors as in strain MK3. The amino acid sequence of the putative ORF1 product does not exhibit any homology with other known proteins, except for a small region of homology with the gene product of another nuclear yeast gene involved in mitochondrial RNA splicing, CBP2. The function of the MRS1 (ORF1) gene in mitochondrial RNA splicing and the significance of the overlapping ORFs in this gene are discussed.     

黄河裸裂尻鱼细胞色素C氧化酶Ⅰ、Ⅱ和Ⅲ亚基基因的克隆及序列特征分析

采用RT-PCR技术克隆获得了黄河裸裂尻鱼(Schizopygopsis pylzovi)CO Ⅰ、Ⅱ、Ⅲ基因的编码序列,并对此进行了初步分析.结果表明,黄河裸裂尻鱼CO I基因全长为1 551 bp,开放阅读框(ORF)由基因全长组成,编码516个氨基酸;COⅡ基因全长为691 bp,开放阅读框为690 bp,编码2...     

絮凝基因(FLO1G)的序列测定及分析

虽然酵母细胞絮凝的确切机制至今尚无定论 ,但已克隆了多个与絮凝相关的基因 ,如ＦＬＯ1、ＦＬＯ5、ＦＬＯ1 1等[1～3 ] 。这些基因的表达可以赋予非絮凝酵母细胞以絮凝能力。酵母细胞的絮凝特性在酿造工业、固定化酶、精细化工和物生制药等领域具有广泛的应用价值[4 ,5] 。从一株强絮凝酿酒酵母菌株中克隆到一个约 4 3ｋｂ的ＮＤＡ片段 ,酵母转化实验证明该ＤＮＡ片段能够赋予非絮凝酵母菌株以絮凝能力[6] 。本文简要报道对该ＤＮＡ片段进行序列测定和分析的结果。1　材料和方法1 .1　菌株和质粒实验所用菌株和质粒见表 1。表 1　菌株和质…     

哈氏弧菌dam基因的克隆与分析

利用兼并PCR的方法克隆得到哈氏弧菌T4的DNA腺嘌呤甲基化酶(dam)基因,序列分析表明该基因编码279个氨基酸,与其它已知弧菌的Dam具有较高的同源性,其中与副溶血弧菌Dam的相同性达95%。功能检验表明所克隆的dam基因在大肠杆菌中具有DNA腺嘌呤甲基化酶活性,能够甲基化大肠杆菌染色体DNA GATC序列中的腺嘌呤。运用染色体步移法获得dam基因上游的3251 bp DNA,发现该区域含有3个基因,其与dam在染色体上的相对排列顺序为:莽草酸激酶-脱氢奎尼酸合成酶-damX-dam。对dam上游DNA序列研究发现位于翻译起点ATG上游的78bp、112bp和477bpDNA片段皆具有启动子活性,但前者的活性明显高于后二者。     

Localization of the T4 phage ribonucleotide reductase B1 subunit gene and the nucleotide sequence of its upstream and 5' coding regions

The nucleotide (nt) sequence in a 757-bp [corrected] segment downstream from the intron-containing T4 phage thymidylate synthase gene (td) has been determined. This region was found to contain two open reading frames (ORFs). The first ORF(ORF2) [corrected] 261 bp [corrected] in length, is 24 [corrected] nt downstream from the td gene. The second ORF(ORF3) [corrected]) is 200 bp long at 558 [corrected] nt from the td gene and extends to the end of the Eco RI fragment. The amino acid (aa) sequence (66 aa residues) deduced from the second truncated ORF shows 59% homology to the sequence of the N-terminal portion of the ribonucleotide reductase large subunit of either Escherichia coli (B1 subunit) or mouse (M1 subunit). This tentatively identifies the truncated gene to be the 5' end of the T4 phage ribonucleotide reductase subunit B1 (nrdA) gene and pinpoints its exact location on the T4 phage genomic map. Southern hybridization analysis suggests good sequence homology among the nrdA genes of various T-even phages.     

紫杆柽柳与其它物种脂质转运蛋白基因编码蛋白的同源性比较

根据从柽柳cDNA文库克隆获得的脂质转运蛋白(LTP)的部分序列,用RACE技术克隆出其全长cDNA序列.基因的5'非翻译区96bp,3'非翻译区222bp,开放阅读框285bp,编码94个氨基酸,预计蛋白的分子量为9.9 kD,等电点为8.02.此基因有8个位置保守的Cys残基及26个氨基酸的信号肽,为典型的植物脂质转运蛋白基因.其基因序列数据库(GenBank)登录号为AY574218(基因)和AAS79106(蛋白).     

Cloning and molecular characterization of a new fungal xylanase gene from Sclerotinia sclerotiorum S2

Sclerotinia sclerotiorum fungus has three endoxylanases induced by wheat bran. In the first part, a partial xylanase sequence gene (90 bp) was isolated by PCR corresponding to catalytic domains (β 5 and β 6 strands of this protein). The high homology of this sequence with xylanase of Botryotinia fuckeliana has permitted in the second part to amplify the XYN1 gene. Sequence analysis of DNA and cDNA revealed an ORF of 746 bp interrupted by a 65 bp intron, thus encoding a predicted protein of 226 amino acids. The mature enzyme (20.06 kDa), is coded by 188 amino acid (pI 9.26). XYN1 belongs to G/11 glycosyl hydrolases family with a conserved catalytic domain containing E(86) and E(178) residues. Bioinformatics analysis revealed that there was no Asn-X-Ser/Thr motif required for N-linked glycosylation in the deduced sequence however, five O-glycosylation sites could intervene in the different folding of xylanses isoforms and in their secretary pathway.     

一株南极嗜冷杆菌产丙酮酸脱氢酶的 性质研究及基因克隆

从南极普利兹湾深海沉积物中筛选到一株嗜冷杆菌7195。其16SrDNA序列分析表明谊菌株属于嗜冷杆菌属（Psychrobacter）,从该菌的全基因组DNA中克隆到编码丙酮酸脱氢酶系E1（PDHcEI）的完整ORF,全长为2817bp,使用DNAMAN5．1对其全长ORF的PDHcEI基因进行分析,PDHcE1基因编码一个由939AA残基组成、分子量预计为100663Da的PDHcEI蛋白质,与Psychrobacter sp．273—4的PDHcE1有78．53％的相似性。     

棉花咖啡酰辅酶A-O-甲基转移酶基因的克隆及表达

根据棉花纤维特异表达cDNA文库分析得到的咖啡酰辅酶A-O-甲基转移酶(CCoAOMT)基因EST序列设计引物,采用RT-PCR技术首次从棉花中克隆了一个CCoAOMT基因,命名为GhCCoAOMT1(GenBank登录号为FJ848871).研究结果表明:GhCCoAOMT1基因cDNA全长960 bp,具有一个753 bp的开放阅读框,5'非编码区为9 bp,3'非编码区为198 bp,编码250个氨基酸,预测分子量约为28.306 kDa,等电点为5.39.利用PCR方法克隆了GhCCoAOMT1基因的基因组序列,长度为1 311 bp,包含5个外显子和4个内含子.氨基酸同源性分析发现,GhCCoAOMT1与来自毛白杨、烟草和苎麻的CCoAOMT同源性较高.半定量RT-PCR检测表明,GhCCoAOMT1基因在棉花各个组织中都有表达,其中茎部的表达量最高,其次表达量依次为根>花瓣>子叶>10 d纤维>雄蕊>胚珠>叶.     

大熊猫Sjogren综合症/硬皮病自身抗原1基因(SSSCA1)的克隆及比较

硬皮病或称系统性硬化症(systemic sclerosis,SSc),又名sjogren's综合症,是一种以局限性或弥漫性皮肤及内脏器官结缔组织纤维化或硬化,最后发展至萎缩为特点的疾病.根据受累范围、程度、病程分为局限性SSc和弥漫性SSc两类,累及的内脏器官为肺脏、食管,患者常死于肺部感染、肾衰竭、心力衰竭等.     

Cloning and characterization of a novel trypsin inhibitor (BTIomega1) gene from Fagopyrum esculentum.

Based on the amino acid information of trypsin inhibitor of buckwheat (Fagopyrum Esculentum Moench), degenerated primers were designed and a full-length cDNA sequence named BTIomega1 (Buckwheat Trypsin Inhibitor) was amplified from the leaves RNA by using RT-PCR and rapid amplification of cDNA ends (RACE) methods. Sequence analysis shows that the 392 bp cDNA contained an open reading frame (ORF) of 216 bp, encoding 72 amino acids residues. The deduced amino acid sequence exhibits 96 and 93% homology with BWI-1 and BTI-2, a natural trypsin inhibitor from buckwheat seeds. Southern blotting suggested that three copies of BTIomega1 gene existed in the buckwheat genome. Moreover, a predicted secondary structure and 3D-structural model was constructed by homology modeling. To our knowledge, this is the first all-round report of the gene BTIomega1. The novel BTIomega1 gene has been submitted to the GeneBank under Accession No. DQ289792.     

The primary structure and expression of the second open reading frame of the polymerase gene of the coronavirus MHV-A59; a highly conserved polymerase is expressed by an efficient ribosomal frameshifting mechanism.

Sequence analysis of a substantial part of the polymerase gene of the murine coronavirus MHV-A59 revealed the 3' end of an open reading frame (ORF1a) overlapping with a large ORF (ORF1b; 2733 amino acids) which covers the 3' half of the polymerase gene. The expression of ORF1b occurs by a ribosomal frameshifting mechanism since the ORF1a/ORF1b overlapping nucleotide sequence is capable of inducing ribosomal frameshifting in vitro as well as in vivo. A stem-loop structure and a pseudoknot are predicted in the nucleotide sequence involved in ribosomal frameshifting. Comparison of the predicted amino acid sequence of MHV ORF1b with the amino acid sequence deduced from the corresponding gene of the avian coronavirus IBV demonstrated that in contrast to the other viral genes this ORF is extremely conserved. Detailed analysis of the predicted amino acid sequence revealed sequence elements which are conserved in many DNA and RNA polymerases.     

Sequence of a cDNA encoding turtle high mobility group 1 protein

In order to understand sequence information about turtle HMG1 gene, a cDNA encoding HMG1 protein of the Chinese soft-shell turtle (Pelodiscus sinensis) was amplified by RT-PCR from kidney total RNA, and was cloned, sequenced and analyzed. The results revealed that the open reading frame (ORF) of turtle HMG1 cDNA is 606 bp long. The ORF codifies 202 amino acid residues, from which two DNA-binding domains and one polyacidic region are derived. The DNA-binding domains share higher amino acid identity with homologues sequences of chicken (96.5%) and mammalian (74%) than homologues sequence of rainbow trout (67%). The polyacidic region shows 84.6% amino acid homology with the equivalent region of chicken HMG1 cDNA. Turtle HMG1 protein contains 3 Cys residues located at completely conserved positions. Conservation in sequence and structure suggests that the functions of turtle HMG1 cDNA may be highly conserved during evolution. To our knowledge, this is the first report of HMG1 cDNA sequence in any reptilian.     

Isolation, sequence, and expression in Escherichia coli of the Pseudomonas sp. strain ACP gene encoding 1-aminocyclopropane-1-carboxylate deaminase.

Pseudomonas sp. strain ACP is capable of growth on 1-aminocyclopropane-1-carboxylate (ACC) as a nitrogen source owing to induction of the enzyme ACC deaminase and the subsequent conversion of ACC to alpha-ketobutyrate and ammonia (M. Honma, Agric. Biol. Chem. 49:567-571, 1985). The complete amino acid sequence of purified ACC deaminase was determined, and the sequence information was used to clone the ACC deaminase gene from a 6-kb EcoRI fragment of Pseudomonas sp. strain ACP DNA. DNA sequence analysis of an EcoRI-PstI subclone demonstrated an open reading frame (ORF) encoding a polypeptide with a deduced amino acid sequence identical to the protein sequence determined chemically and a predicted molecular mass of 36,674 Da. The ORF also contained an additional 72 bp of upstream sequence not predicted by the amino acid sequence. Escherichia coli minicells containing the 6-kb clone expressed a major polypeptide of the size expected for ACC deaminase which was reactive with ACC deaminase antiserum. Furthermore, a lacZ fusion with the ACC deaminase ORF resulted in the expression of active enzyme in E. coli. ACC is a key intermediate in the biosynthesis of ethylene in plants, and the use of the ACC deaminase gene to manipulate this pathway is discussed.     

草鱼α1-抗胰蛋白酶基因cDNA全长克隆与表达分析

采用RACE技术获得α1-抗胰蛋白酶基因cDNA全长序列为1 469 bp,开放阅读框为1 329 bp,可编码442个氨基酸。5′非编码区长19 bp,3′非编码区长121 bp。核苷酸序列分析表明,在N端可能存在一个由1～21位氨基酸残基组成的信号肽;与斑马鱼的同源性最好,其次是虹鳟;在系统进化上,与在斑马鱼、虹鳟共聚为一个大支。用半定量RT-PCR分析正常及细菌诱导下草鱼α1-抗胰蛋白酶基因在不同组织中的表达分布。结果显示:正常情况下,草鱼α1-抗胰蛋白酶在肝脏表达最丰富,在脾脏、前肾、前肠、中肠、后肠和也有少量表达;细菌诱导下,肝脏中表达最强,前肾、脾脏、肠道中表达均明显提高,心脏和后肾中也出现较高表达。提示α1-抗胰蛋白酶可能参与了机体对嗜水气单胞菌感染的免疫应答。