7号淀粉酶链霉菌M1033木糖异构酶基因的启动子活性检测、转录起始点的确定

分别从重组质粒ｐＵＢ１及其Ｍ（１３）亚克隆Ｓ１中将７号淀粉酶链霉菌（ＳｔｒｅｐｔｏｍｙｃｅｓｄｉａｓｔａｔｉｃｕｓＮｏ．７）Ｍ１０３３（以下简称Ｓ．ｄｉ．Ｍ１０３３）木糖异构酶基因的－１９２－＋５８１ｂｐ片段克隆入链霉菌启动子探测质粒ｐＩＪ４０８３中,转化变铅青链霉菌（Ｓ．ｌｉｖｉｄａｎｓ）ＴＫ２４。通过对其邻苯二酚加双氧酶活性的检测表明,该片段具有启动子活性。应用Ｍ１３亚克隆Ｓ１和合成引物Ｐ６延伸制备放射性标记的单链ＤＮＡ探针;通过Ｓ．ｄｉ．Ｍ１０３３的总ＲＮＡ的Ｓ１核酸酶保护实验,确定了其转录的起始位点,并由此探讨了与木糖异构酶基因表达有关的一些因素。     

鸡马立克氏病病毒B抗原片段在大肠杆菌中表达

鸡马立克氏病病毒ＢａｍＨＩ基因文库Ｉ３质粒中含有编码Ｂ抗原膜外Ｄｏｍａｉｎ的ＤＮＡ序列。经ＳｃａＩ和ＳｐｈＩ双酶酶解Ｉ３质粒,分离获得７６４ｂｐＤＮＡ片段,并克隆进Ｍ１３ｍｐ１９中。ＤＮＡ序列测定分析表明克隆片段为ＭＤＶ－Ｂ抗原基因的４９４－１２５８ｂｐ部分序列。进一步分离ＮｃｏＩ－ＨｉｎｄＩＩＩ部分基因片（５３０ｂｐ）,克隆于ＰＬＰｒｏｍｏｔｅｒ控制下的含有修饰型ｃＩｔｓ８５７基因的表达载体中,     

7号淀粉酶链霉菌M1033木糖异构酶基因的启动子活性检测,转录起始点…

分别从重组质粒ＰＵＢ１及其Ｍ１３亚克隆Ｓ１中将７号淀粉酶链霉菌（Ｓｔｒｃｐｔｏｍｙｃｅｓ ｄｉａｓｔａｔｉｃｕｓ Ｎｏ．７）Ｍ１０３３（以下简称Ｓ。ｄｉ．Ｍ１０３３）木糖异构酶基因的－１９２－＋５８１ｂｐ片段克隆入链霉菌启动子探测质粒ＰＩＪ４０８３中,转化变铅青链霉菌（Ｓ。ｌｉｖｉｄａｎｓ）ＴＫ２４。通过对其邻苯二酚加双氧酶活性的检测表明,该片段具有启动子活性。应用Ｍ１３亚克隆Ｓ１和合成引物Ｐ６延     

麦迪霉素4″—O—丙酰基转移酶（mpt）基因结构的研究

对含有麦迪霉素４″－Ｏ－丙酰基转移酶（ｍｐｔ）基因的ＢａｍＨＩ－ＢａｍＨＩ８．０ｋｂ的ＤＮＡ片段进行限制性酶切分析,绘制出了含有２１个酶切位点的限制性酶切图谱。以含有碳霉素异戊酰基转移酶基因（ＣａｒＥ）的２．４ｋｂ ＤＮＡ片段为探针,经Ｓｏｕｔｈｅｒｎ ｂｌｏｔ分子杂交,将ｍｐｔ定位于一个ＥｃｏＲＩ－ＥｃｏＲＩ－ＰｓｔＩ３．０ｋｂ的ＤＮＡ片段上,将该片段克隆至大肠杆菌／链霉菌穿梭质粒载体ｐＷＨＭ３     

中国棉铃虫核型多角体病毒DNA聚合酶基因的克隆和序列分析

应用谷实夜蛾核型多角体病毒（ＨｚＳＮＰＶ）ＤＮＡ聚合酶基因ＨｉｎｄⅢ／ＰｓｔⅠ３５９６ｂｐ片段作探针,经Ｓｏｕｒｔｈｅｒｎｂｌｏｔ杂交,克隆了中国棉铃虫核型多角体病毒（ＨａＳＮＰＶ）完整的ＤＮＡ聚合酶基因,大小约为３．４ｋｂ。限制性内切酶分析表明,ＨａＳＮＰＶＤＮＡ聚合酶基因限制性内切酶图谱与ＨｚＳＮＰＶ相似。用双脱氧链终止法测定该基因部分核苷酸序列（８０５ｂｐ）,推导出编码区２０６ａ。序列同源性比较显示,ＨａＳＮＰＶＤＮＡ聚合酶与ＨｚＳＮＰＶ之间具有高度的同源性;与ＬｄＭＮＰＶ、ＡｃＭＮＰＶ、ＢｍＳＮＰＶ、ＣｆＭＮＰＶ和ＯｐＭＮＰＶ也具有一定的同源性     

CS3纤毛抗原表达调控机理的研究

ＣＳ３是某些肠毒素大肠杆菌菌体表面上的多聚物,它能使病原菌粘附于宿主的小肠上皮细胞上,是致病的重要因素．为了探索ＣＳ３菌毛抗原基因的表达调控机制,根据ＣＳ３亚基结构基因的核苷酸序列分析表明,在其翻译起始位点的上游存在着ｒｂｓ位点及原核启动子的－１０区和－３５区ＤＮＡ序列．采用基因重组技术将ＣＳ３结构基因上游１２０ｂｐ的ＤＮＡ片段亚克隆进缺乏启动子而只含报告基因ｌａｃＺ的质粒ｐＣＢ２６７中．凝胶滞留和启动报告基因表达的实验证明了ＣＳ３亚基结构基因具有自身的启动子（Ｐｓ）．将该启动子上游区域不同长度的核苷酸片段克隆进ｐＣＢ２６７中,报告基因表达结果表明ＣＳ３结构基因的表达受其上游区域的抑制．核苷酸序列分析发现,在Ｐｓ－３５区上游５５０ｂｐ和８４０ｂｐ处各存在一个富Ａ－Ｔ簇．结合原核启动子的一般作用规律推知,ＣＳ３的表达可能受ＤＮＡ结合蛋白型的正向调节因子的作用．用ＣＦＡ／１菌毛抗原基因的正向调节基因ｃｆａＤ对ＣＳ３基因进行的互补表达试验表明ｃｆａＤ基因不仅可消除上游区对Ｐｓ的抑制,而且可大幅度地提高Ｐｓ的启动能力．在分析表达调控的基础上获得ＣＳ３重组高效表达．同时提出了其表达调控模型．     

绿色木霉纤维素酶CBHⅡ基因的结构研究

实验经限制性酶切和双向Ｓｏｕｔｈｅｒｎ杂交将重组质粒ｐＣＢＨＩＩ－１４的１４ｋｂ外源片段上的绿色木霉纤维素酶ＣＢＨＩＩ基因定位于４．４ｋｂ的ＥｃｏＲＩ片段上,将该片段克隆于质粒ｐＵＣ１９,获得重组质粒ｐＣＢＨＩＩ。通过限制性分析构建了ｐＣＢＨＩＩ上４．４ｋｂＥｃｏＲＩ片段的物理图谱。在此基础上用质粒制作该片段的亚克隆,采用Ｓａｎｇｅｒ双脱氧链终止法测定了含绿色木霉纤维素酶ＣＢＨＩＩ基因的４０７４ｂｐ的ＤＮＡ序列,由ＧＴ－ＡＧ规则和ｃＤＮＡ序列推知该结构基因由４个外显子和３个内含子组成,总长１６１３ｂｐ,５′端存在与一般真核基因类似的两个特征性调控序列,但３′端不存在真核基因通常具有的特征序列而存在功能未明的短重复序列和嘧啶富集区。并对纤维素酶基因间的同源性和可能的功能作了初步的探讨。     

BRCA1基因结构及其在乳腺癌中的表达

利用ＭＰＣＲ技术从乳腺组织分离到抑癌基因ＢＲＣＡ１的ｃＤＮＡ片段,将此９１４ｂｐ的片段克隆进质粒ｐＵＣ１１８,并经全序列测定证实。序列分析表明,ＢＲＣＡＩｃＤＮＡ编码的肽链ＮＮ２－末端有一锌指结构,抑癌基因ＢＲＣＡＩ的产物可能是ＤＮＡ结合蛋白,ｃＤＮＡ序列存在两个变异位点：一个是第４０９位的Ｃ→Ａ（Ａｓｐ→Ｇｌｕ）：另一个是第８７９位的Ａ→Ｔ（ＭＩａ同义突变）。以该片段为探针,检测６例乳腺癌组织中ＢＲＣＡＩｍＩＭＡ表达,一例表达明显下降,一例没检测到表达的ｍＩＭＡ产物,说明一些乳腺癌组织的ＢＲＣＡ１基因转录水平降低     

葡萄叶绿体rbcL基因的结构分析

以玫瑰香葡萄（Ｖｉｔｉｓｖｉｎｉｆｅｒａ Ｌ．）为材料,克隆了含有叶绿体ｒｂｃ Ｌ基因的３．１ ｋｂ Ｂａｍ ＨⅠ片段,构建了该基因的限制性酶切图谱,测定了该基因的核苷酸序列。所测的核苷酸序列总长度为２００４ ｂｐ,其中基因的编码区为１４２８ ｂｐ,编码一个含４７５ 个氨基酸的蛋白质,其分子量约为５３ ｋＤ;测定基因的５上游含启动子的部分共３５８ ｂｐ,包括－ １０ 区（ＴＡＡＡＡＴ）、－ ３５区（ＴＴＧＣＧＣ）和ＳＤ 序列（ＧＧＡＧＧ）;基因的３下游区共２１８ ｂｐ,含有３ 个转录茎环终止结构。玫瑰香葡萄ｒｂｃ Ｌ基因编码区的核苷酸序列与烟草、矮牵牛、菠菜、苜蓿、水稻和玉米之间的同源性分别为９１．５％ 、９１．４％ 、９０．２％ 、８９．８％ 、８６．３％ 和８４．５％ ;推导出的氨基酸序列的同源性分别为９２．２％ 、９１．６％ 、９２．２％ 、９３．７％ 、９３．５％ 和９０．１％ 。     

变铅青链霉菌66中对噬菌ΦHAU3显示抗性的基因（ψHAU3￣R）的核苷酸定序和分析

杂合质粒ｐＩＪ８３１０是链霉菌低拷贝质粒ｐＩＪ９２２１携带了１０．８ｋｂ来自变铅青链霉菌ＪＴ４６菌株,编码对噬菌体ΦＨＡＵ３抗性的ＤＮＡ片段。已知Ｔｎ４５６０插到该克隆中３ｋｂ的ＥｃｏＲＩ或３．３ｋｂ的ＢａｍＨＩ片段（这两个片段之间有２．５ｋｂ的重叠区）上,中断了ΦＨＡＵ３抗性基因的表达。已将３．０ｋｂ的ＢｃｏＡＩ片段分别以两种不同的取向克隆到ｐＢｌｕｅｓｃｒｉｐｔＳＫ（＋）上。核苷酸序列分析揭示出一个１．３ｋｂ的ＯＲＦ的存在,其所编码的４７８个氨基酸组成的蛋白与λ噬菌体的ｅａ５９基因所编码的氨基酸序列显示了高度的同源性,其氨基酸序列的同一性高达３７％,相似性达５８％,而λ噬菌体的ｅａ５９基因是编码赖ＡＴＰ和单键ＤＮＡ的核酸内切酶Ｉ的,该区域与λ的复制无关。此外,这段具有高度同源性的ＤＮＡ区域的Ｇ＋Ｃ％只有６０％,低于变铅青霉菌ＤＮＡＧ＋Ｃ％的平均值（７４％）。     

Availability of short amino acid sequences in proteins

Much attention is being paid to protein databases as an important information source for proteome research. Although used extensively for similarity searches, protein databases themselves have not fully been characterized. In a systematic attempt to reveal protein-database characters that could contribute to revealing how protein chains are constructed, frequency distributions of all possible combinatorial sets of three, four, and five amino acids ("triplets," "quartets," and "pentats"; collectively called constituent sequences) have been examined in the nonredundant (nr) protein database, demonstrating the existence of nonrandom bias in their "availability" at the population level. Nonexistent short sequences of pentats were found that showed low availability in biological proteins against their expected probabilities of occurrence. Among them, six representative ones were successfully synthesized as peptides with reasonably high yields in a conventional Fmoc method, excluding the possibility that a putative physicochemical energy barrier in forming them could be a direct cause for the low availability. They were also expressed as soluble fusion proteins in a conventional Escherichia coli BL21Star(DE3) system with reasonably high yield, again excluding a possible difficulty in their biological synthesis. Together, these results suggest that information on three-dimensional structures and functions of proteins exists in the context of connections of short constituent sequences, and that proteins are composed of evolutionarily selected constituent sequences, which are reflected in their availability differences in the database. These results may have biological implications for protein structural studies.     

The Primary Structure of an Entamoeba histolyticaβ-Hexosaminidase A Subunit

ABSTRACT. An Entamoeba histolytica gene ( hex-A1 ) that encodes subunit A of the lysosomal enzyme β-hexosaminidase has been cloned and sequenced. The inferred 59 kDa hex-A1 protein has the same molecular weight and 32% amino acid residue identity with the human and mouse proteins and 28% residue identity with the Dictyostelium protein. Northern blot analysis identified a mRNA of approximately 1.6 kb, which is in agreement with the expected size of a mRNA encoding the 522 amino acid hex-A1 protein. Southern blot analysis indicated the presence of at least two β-hexosaminidase A subunit genes.     

Sequencing and analysis of a genomic fragment provide an insight into the Dunaliella viridis genomic sequence

Dunaliella is a genus of wall-less unicellular eukaryotic green alga.Its exceptional resistancesto salt and various other stresses have made it an ideal model for stress tolerance study.However,very littleis known about its genome and genomic sequences.In this study,we sequenced and analyzed a 29,268 bpgenomic fragment from DunalieIla viridis.The fragment showed low sequence homology to the GenBankdatabase.At the nucleotide level,only a segment with significant sequence homology to 18S rRNA wasfound.The fragment contained six putative genes,but only one gene showed significant homology at theprotein level to GenBank database.The average GC content of this sequence was 51.1%,which was muchlower than that of close related green algae Chlamydomonas (65.7%).Significant segmental duplicationswere found within this fragment.The duplicated sequences accounted for about 35.7% of the entireregion.Large amounts of simple sequence repeats (microsatellites) were found,with strong bias towards(AC)_n type (76%).Analysis of other Dunaliella genomic sequences in the GenBank database (total 25,749bp) was in agreement with these findings.These sequence features made it difficult to sequence Dunaliellagenomic sequences.Further investigation should be made to reveal the biological significance of these uniquesequence features.     

窄叶鲜卑花(Sibiraea angustata)nrDNA ITS和cpDNA trnL-F序列分子进化特点的分析

应用PCR产物直接测序法分析了窄叶鲜卑花居群间nrDNA(核糖体DNA)ITS序列和cpDNA(叶绿体DNA)trnL-F的碱基差异,并与cpDNAtrnS-G序列和rpl20-rps12序列进行比较,从而初步研究两套植物基因组的变异速率。采用改良的CTAB法从硅胶干燥的窄叶鲜卑花叶片中提取总DNA,并对nrDNA ITS和cpDNAtrnL-F区域进行扩增、纯化、测序。nrDNA ITS序列共有601 bp,有变异位点3处,变异位点百分率为0.05%,(G+C)含量为41.4%。cpDNAtrnL-F序列共有927 bp,有变异位点1处,变异位点百分率0.01%,(G+C)含量为32.6%,两种序列的核苷酸多样性非常低。比较发现,窄叶鲜卑花nrDNA ITS区域较cpDNAtrnS-G序列和rpl20-rps12序列保守,变异速率较慢,比cpDNAtrnL-F序列变异速率稍快。通过对ITS序列单倍型(haplotype)进行分析发现,窄叶鲜卑花现有分布范围经历了居群近期范围扩张,与叶绿体基因组(trnS-G和rpl20-rps12序列)得出的结论一致。因此,窄叶鲜卑花nrDNA ITS序列适合该种的谱系地理学研究。     

A method to recognize distant repeats in protein sequences

An automated algorithm is presented that delineates protein sequence fragments which display similarity. The method incorporates a selection of a number of local nonoverlapping sequence alignments with the highest similarity scores and a graphtheoretical approach to elucidate the consistent start and end points of the fragments comprising one or more ensembles of related subsequences. The procedure allows the simultaneous identification of different types of repeats within one sequence. A multiple alignment of the resulting fragments is performed and a consensus sequence derived from the ensemble(s). Finally, a profile is constructed form the multiple alignment to detect possible and more distant members within the sequence. The method tolerates mutations in the repeats as well as insertions and deletions. The sequence spans between the various repeats or repeat clusters may be of different lengths. The technique has been applied to a number of proteins where the repeating fragments have been derived from information additional to the protein sequences. © 1993 Wiley-Liss, Inc.     

EMBOSS软件包序列分析程序应用实例

本文介绍欧洲分子生物学开放软件包EMBOSS序列分析程序应用实例。第1节简单介绍EMBOSS软件包的概况和基本用法。第2节介绍格式转换、序列提取、序列变换和序列显示等常用序列处理程序。第3节介绍序列比对程序,包括双序列比对、多序列比对和点阵图程序。第4节介绍常用核酸序列分析程序,可用于核苷酸组分统计、开放读码框分析、CpG岛识别、密码子使用统计和重复序列寻找等。第5节介绍常用蛋白质序列分析程序,包括氨基酸组分统计、序列特征位点识别、二级结构分析等。文中结合教学实例,选择部分常用程序,给出具体运行方式,并扼要说明分析结果的生物学意义。文末对程序运行过程中需要注意的地方加以讨论,并用表格列出部分常用程序的名称和用途,以便读者查阅。     

基于核糖体基因的鳞钙皮菌种内分子关系分析

为探讨不同地域的鳞钙皮菌Didymium squamulosum种内分子亲缘关系,通过PCR扩增鳞钙皮菌子实体及原质团DNA,得到SSU、ITS1-5.8S-ITS2 rRNA基因区域,并以SSU、5.8S rRNA基因片段构建NJ亲缘关系树。     

Protein sequence redundancy reduction: comparison of various method

Non-redundant protein datasets are of utmost importance in bioinformatics. Constructing such datasets means removing protein sequences that overreach certain similarity thresholds. Several programs such as 'Decrease redundancy', 'cd-hit', 'Pisces', 'BlastClust' and 'SkipRedundant' are available. The issue that we focus on here is to what extent the non-redundant datasets produced by different programs are similar to each other. A systematic comparison of the features and of the outputs of these programs, by using subsets of the UniProt database, was performed and is described here. The results show high level of overlap between non-redundant datasets obtained with the same program fed with the same initial dataset but different percentage of identity threshold, and moderate levels of similarity between results obtained with different programs fed with the same initial dataset and the same percentage of identity threshold. We must be aware that some differences may arise and the use of more than one computer application is advisable.