小麦丛矮病毒M蛋白基因的序列测定,表达和鉴定

从小麦丛矮病毒（ＷＲＳＶ）基因文库含磷蛋白ＮＳ基因的质粒中,经亚克隆、测序,得到ＮＳ蛋白基因的下游序列,其中含有一读框４５３ｎｔ、编码一分子量约１７ｋＤ蛋白。用ＰＣＲ方法获得该读框全长片段并克隆到表达载体ｐＧＥＸ－３Ｘ,在大肠杆菌ＢＬ２１（ＤＥ３）菌株中以ＩＰＴＧ诱导表达,产物由谷胱甘肽Ｓ－转移酶（ＧＳＴ）亲和层析柱纯化后,用蛋白质印迹分析鉴定,结果表明,该读框为编码病毒基质蛋白Ｍ的基因。     

人肝癌组织中的一个Lis1基因的阅读框移码突变

将ＧＳＴ融合蛋白表达与蛋白质截短检测法（ＰＴＴ）法相结合,检测Ｌｉｓ１基因在肝癌组织中的阅读框移码突变。即从肝癌组织中通过ＲＴ－ＰＣＲ扩增的Ｌｉａ１基因克隆人ＧＳＴ融合蛋白表达载体ｐＧＥＸ０１,并于大肠杆菌ＤＨ５α中进行表达。通过ＳＤＳ－ＰＡＧＥ电泳发现肝癌组织中有截短的ＧＳＴ－Ｌｉｓ１融合蛋白,大小为３３ＫＤ,而全长融合蛋白大小应为７１ＫＤ。经测序验证,发现产生截短蛋白的Ｌｉａ１基因在第１６３位     

日本血吸虫26kD抗原基因在BCG中的表达

研究了外源基因日本血吸虫２６ｋＤ抗原（Ｓｊ２６ＧＳＴ）在卡介苗（ｂａｃｉｌｕｓＣａｌｍｅｔｅ－Ｇｕｅｒｉｎ,ＢＣＧ）、耻垢分枝杆菌（Ｍ．ｓｍｅｇｍａｔｉｓ）和大肠杆菌（Ｅ．ｃｏｌｉ）中的表达．运用重组ＤＮＡ和聚合酶链反应（ＰＣＲ）等分子生物学技术,以表达Ｓｊ２６ＧＳＴ的Ｅ．ｃｏｌｉｐＧＥＸ衍生质粒为模板,经ＰＣＲ得到编码Ｓｊ２６ＧＳＴ的全长ｃＤＮＡ片段．将其按正确的阅读框顺序,克隆到人结核杆菌热休克蛋白（ｈｅａｔｓｈｏｃｋｐｒｏｔｅｉｎ,ＨＳＰ）７０的启动子下游,再将ＨＳＰ７０启动子和Ｓｊ２６ＧＳＴ基因一起亚克隆到Ｅ．ｃｏｌｉ－分枝杆菌穿梭质粒ｐＢＣＧ－２０００中,得到Ｅ．ｃｏｌｉ－分枝杆菌穿梭表达质粒ｐＢＣＧ－Ｓｊ２６．ｐＢＣＧ－Ｓｊ２６电转化入ＢＣＧ和Ｍ．ｓｍｅｇｍａｔｉｓｍｃ２１５５中表达Ｓｊ２６ＧＳＴ抗原,所表达的天然重组Ｓｊ２６ＧＳＴ（ｒＳｊ２６ＧＳＴ）为可溶性蛋白,在ＳＤＳ－ＰＡＧＥ上分子量为２６ｋＤ处可见明显的表达蛋白带．其表达量分别占ＢＣＧ和Ｍ．ｓｍｅｇｍａｔｉｓ菌体总蛋白的１５％和１０％．可见,Ｓｊ２６ＧＳＴ基因能在ＢＣＧ中高效表达．     

细胞色素P450超家族蛋白质基于结构知识的序列联配

应用计算机程序对细胞色素Ｐ４５０蛋白２０个家族的代表序列进行初步多序列联配后,利用结构知识对匹配结果加以调整,调整的依据是Ｐ４５０蛋白二级结构特征和某些超二级结构特征的保守性,三维结构空间配置的保守性,在结构与功能重要残基的保守性,亲水和疏水片段的保守性。大量定点突变实验、选择性化学修饰实验、抗多肽抗体结合实验等能很好地确证该联配结果的正确性。联配结果对真核Ｐ４５０蛋白膜结合方式、活性位点残基分布、与氧化还原偶联蛋白有相互作用的残基的分布等作出了合理的推断。细胞色素Ｐ４５０超家族蛋白基于结构知识的序列联配的尝试对Ｐ４５０蛋白结构与功能关系研究提供了参考     

草鱼AMBP基因cDNA的克隆与序列分析

α1-微球蛋白和Bikunin是由同一基因翻译表达出的两种功能不相关联的血浆蛋白。本文通过快速扩增cDNA末端的方法,首次从草鱼肝脏组织克隆了α1-微球蛋白和Bikunin前体蛋白(α1-microglobulin/Bulinin precursor, AMBP）基因全长cDNA。其cDNA全长1230bp,包含5′非翻译区23 bp,3′非翻译区160 bp和开放读码框1047 bp。开放读码框编码348个氨基酸,包含182个氨基酸的α1-微球蛋白和145个氨基酸的Bikunin。草鱼AMBP与其他物种的氨基酸序列分析结果表明,它们具有较高的同源性(44.7%－84.4%),其中草鱼与斑马鱼同源性最高(84.4%)。结果表明AMBP序列结构和α1-微球蛋白与Bikunin共翻译表达特点在动物机体中具有着重要的生理意义。     

HSP70基因上游调控序列对GST基因在耻垢分枝杆菌中表达效率的 影响

将外源基因———日本血吸虫２６ｋＤ抗原（Ｓｊ２６ＧＳＴ）基因克隆到大肠杆菌分枝杆菌穿梭质粒中,构建成四个不同的表达截体,研究它们在耻垢后分枝杆菌（Ｍｙｃｏｂａｃｔｅｒｉｕｍｓｍｅｇｍａｔｉｓ）中的表达效率。首先将含有结核杆菌热休克蛋白７０（ＨｅａｔＳｈｏｃｋＰｒｏｔｅｉｎ,ＨＳＰ７０）的启动子的质粒ｐＭＴ７０用ＮｃｏＩ切,进行两种不同的修饰后,得到不同的ＳＤ序列;将Ｓｊ２６ＧＳＴ基因克隆进去。再将含ＨＳＰ７０启动子和Ｓｊ２６ＧＳＴ基因的片段切下,克隆到分枝杆菌大肠杆菌穿梭质粒ｐＢＣＧ２０００中,筛选出不同ＳＤ序列、不同方向和不同拷贝数的分枝杆菌表达载体四个。所表达的重组天然Ｓｊ２６ＧＳＴ（ｒＳｊ２６ＧＳＴ）为可溶性蛋白,在ＳＤＳＰＡＧＥ上分子量为２６ｋＤ处可见明显的表达蛋白带。通过薄层扫描分析,发现表达质粒中双拷贝启动子外源基因组合,表达效率最高,是单拷贝组合的１６倍,占分枝杆菌菌体总蛋白的２８％。而不同的克隆方向和不同的ＳＤ序列（两者相差３个碱基）对表达效率的影响不明显。     

汉坦病毒陈株S基因编码区的克隆,序列分析及表达

从汉坦病毒陈株感染的ＶｅｒｏＥ６细胞裂解液中提取病毒ＲＮＡ,经逆转录ＰＣＲ获得病毒Ｓ基因编码区约１．３ｋｂｃＤＮＡ片段,克隆该片段后进行核苷酸序列测定,并与汉坦病毒７６１１８株进行同源性比较,结果二者核苷酸序列同源性为８６％,推导的氨基酸序列同源性为９７％。将该基因片段插入原核表达载体ｐＧＥＸ４Ｔ１,在大肠杆菌中获得高效表达。表达产物为ＧＳＴＮＰ融合蛋白。ＳＤＳＰＡＧＥ检测表达蛋白分子约７２ｋＤ左右。Ｗｅｓｔｅｒｎｂｌｏｔｉｎｇ和ＥＬＩＳＡ试验结果表明,表达产物可与多株抗汉坦病毒核蛋白的ＭｃＡｂ发生反应,其抗原表位及ＭｃＡｂ反应谱与７６１１８株相比存在某些差异。     

鲑鱼降钙素基因在大肠杆菌中的克隆与表达

以鲑鱼基因组ＤＮＡ为模板,采用ＰＣＲ获得ｓＣＴ基因,并为ＤＮＡ序列分析所证实。以ｐＧＥＸ－３Ｘ为表达载体,利用体外定点突变技术成功地构建了融合蛋白ＧＳＴ－ｓＣＴ的重组表达质粒ｐＧＥＸ－３Ｘ－ｓＣＴ,在大肠杆菌中得到高效表达,其表达量约为菌体总蛋白的３０％;利用亲合层析法对融合蛋白ＧＳＴ－ｓＣＴ进行纯化,再经Ｆａｃｔｏｒ Ｘａ酶切后获得了重组ｓＣＴ,并对其进行活性检测。初步实验证明,重组ｓＣＴ具有较     

人天然免疫基因TRIM5α的序列及进化分析

目的：克隆人TRIM5α基因,对其编码序列进行分析,并进行分子进化研究。方法：以HeLa细胞cDNA为模板,用RT-PCR方法克隆人TRIM5α基因,与人基因组序列对比分析其结构;用BioEdit、Genedoc和MEGA4.1软件进行蛋白序列联配和进化分析。结果：扩增了长1482bp的人TRIM5α基因片段,序列分析表明其覆盖了完整编码框,编码由493个氨基酸残基组成的人TRIM5α蛋白;人TRIM5α蛋白与黑猩猩、大猩猩、猩猩、猕猴TRIM5α蛋白的相似度分别为98.2%、96.8%、93.7%和87.6%。结论：克隆了人TRIM5α基因,为进一步研究该基因的功能奠定了基础。     

鲑鱼降钙素基因在大肠杆菌中的克隆与表达

以鲑鱼基因组ＤＮＡ为模板,采用ＰＣＲ获得ｓＣＴ基因,并为ＤＮＡ序列分析所证实．以ｐＧＥＸ－３Ｘ为表达载体,利用体外定点突变技术成功地构建了融合蛋白ＧＳＴ－ｓＣＴ的重组表达质粒ｐＧＥＸ－３Ｘ－ｓＣＴ,在大肠杆菌中得到高效表达,其表达量约为菌体总蛋白的３０％;利用亲合层析法对融合蛋白ＧＳＴ－ｓＣＴ进行纯化,再经Ｆａｃ－ｔｏｒΧａ酶切后获得了重组ｓＣＴ,并对其进行活性检测．初步实验证明,重组ｓＣＴ具有较强的生物活性     

MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.MACSE is distributed as an open-source java file executable with freely available source code and can be used via a web interface at: http://mbb.univ-montp2.fr/macse.     

ZmDB,an integrated database for maize genome research

Zea mays DataBase (ZmDB) seeks to provide a comprehensive view of maize (corn) genetics by linking genomic sequence data with gene expression analysis and phenotypes of mutant plants. ZmDB originated in 1999 as the Web portal for a large project of maize gene discovery, sequencing and phenotypic analysis using a transposon tagging strategy and expressed sequence tag (EST) sequencing. Recently, ZmDB has broadened its scope to include all public maize ESTs, genome survey sequences (GSSs), and protein sequences. More than 170 000 ESTs are currently clustered into approximately 20 000 contigs and about an equal number of apparent singlets. These clusters are continuously updated and annotated with respect to potential encoded protein products. More than 100 000 GSSs are similarly assembled and annotated by spliced alignment with EST and protein sequences. The ZmDB interface provides quick access to analytical tools for further sequence analysis. Every sequence record is linked to several display options and similarity search tools, including services for multiple sequence alignment, protein domain determination and spliced alignment. Furthermore, ZmDB provides web-based ordering of materials generated in the project, including ESTs, ordered collections of genomic sequences tagged with the RescueMu transposon and microarrays of amplified ESTs. ZmDB can be accessed at http://zmdb.iastate.edu/.     

Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP

AutoSNP is a program to detect single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (indels) in expressed sequence tag (EST) data. The program uses d2cluster and cap3 to cluster and align EST sequences, and uses redundancy to differentiate between candidate SNPs and sequence errors. Candidate polymorphisms are identified as occurring in multiple reads within an alignment. For each candidate SNP, two measures of confidence are calculated, the redundancy of the polymorphism at a SNP locus and the co segregation of the candidate SNP with other SNPs in the alignment. AVAILABILITY: The program was written in PERL and is freely available to non-commercial users by request from the authors.     

FramePlus: aligning DNA to protein sequences

MOTIVATION: Automated annotation of Expressed Sequence Tags (ESTs) is becoming increasingly important as EST databases continue to grow rapidly. A common approach to annotation is to align the gene fragments against well-documented databases of protein sequences. The sensitivity of the alignment algorithm is key to the success of such methods. RESULTS: This paper introduces a new algorithm, FramePlus, for DNA-protein sequence alignment. The SCOP database was used to develop a general framework for testing the sensitivity of such alignment algorithms when searching large databases. Using this framework, the performance of FramePlus was found to be somewhat better than other algorithms in the presence of moderate and high rates of frameshift errors, and comparable to Translated Search in the absence of sequencing errors. AVAILABILITY: The source code for FramePlus and the testing datasets are freely available at ftp.compugen.co.il/pub/research. CONTACT: raveh@compugen.co.il.     

QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species

Background  

Single nucleotide polymorphisms (SNPs) are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs)) and are considered to be faster and more cost-effective than experimental procedures. A major challenge in computational SNP discovery is distinguishing allelic variation from sequence variation between paralogous sequences, in addition to recognizing sequencing errors. For the majority of the public EST sequences, trace or quality files are lacking which makes detection of reliable SNPs even more difficult because it has to rely on sequence comparisons only.     

Highly improved homopolymer aware nucleotide-protein alignments with 454 data

ABSTRACT: BACKGROUND: Roche 454 sequencing is the leading sequencing technology for producing long read high throughput sequence data. Unlike most methods where sequencing errors translate to base uncertainties, 454 sequencing inaccuracies create nucleotide gaps. These gaps are particularly troublesome for translated search tools such as BLASTx where they introduce frame-shifts and result in regions of decreased identity and/or terminated alignments, which affect further analysis. RESULTS: To address this issue, the Homopolymer Aware Cross Alignment Tool (HAXAT) was developed. HAXAT uses a novel dynamic programming algorithm for solving the optimal local alignment between a 454 nucleotide and a protein sequence by allowing frame-shifts, guided by 454 flowpeak values. The algorithm is an efficient minimal extension of the Smith-Waterman-Gotoh algorithm that easily fits in into other tools.Experiments using HAXAT demonstrate, through the introduction of 454 specific frame-shift penalties, significantly increased accuracy of alignments spanning homopolymer sequence errors. The full effect of the new parameters introduced with this novel alignment model is explored. Experimental results evaluating homopolymer inaccuracy through alignments show a two to five-fold increase in Matthews Correlation Coefficient over previous algorithms, for 454-derived data. CONCLUSIONS: This increased accuracy provided by HAXAT does not only result in improved homologue estimations, but also provides un-interrupted reading-frames, which greatly facilitate further analysis of protein space, for example phylogenetic analysis.The alignment tool is available at http://bioinfo.ifm.liu.se/454tools/haxat.     

An interactive bovine <Emphasis Type="Italic">in silico</Emphasis> SNP database (IBISS)

An interactive bovine in silico SNP (IBISS) database has been created through the clustering and aligning of bovine EST and mRNA sequences. Approximately 324,000 EST and mRNA sequences were clustered to produce 29,965 clusters (producing 48,679 consensus sequences) and 48,565 singletons. A SNP screening regime was placed on variations detected in the multiple sequence alignment files to determine which SNPs are more likely to be real rather than sequencing errors. A small subset of predicted SNPs was validated on a diverse set of bovine DNA samples using PCR amplification and sequencing. Fifty percent of the predicted SNPs in the putative >1 category were polymorphic in the population sampled. The IBISS database represents more than just a SNP database; it is also a genomic database containing uniformly annotated predicted gene mRNA and protein sequences, gene structure, and genomic organization information.     

Gene discovery using the maize genome database ZmDB

Zea mays DataBase (ZmDB) is a repository and analysis tool for sequence, expression and phenotype data of the major crop plant maize. The data accessible in ZmDB are mostly generated in a large collaborative project of maize gene discovery, sequencing and phenotypic analysis using a transposon tagging strategy and expressed sequence tag (EST) sequencing. ESTs constitute most of the current content. Database search tools, convenient links to external databases, and novel sequence analysis programs for spliced alignment are provided and together serve as an efficient protocol for gene discovery by sequence inspection. ZmDB can be accessed at http://zmdb. iastate.edu. ZmDB also provides web-based ordering of materials generated in the project, including EST and genomic DNA clones, seeds of mutant plants and microarrays of amplified EST and genomic DNA sequences.     

Motifer, a search tool for finding amino acid sequence patterns from nucleotide sequence databases.

Motifer is a software tool able to find directly in nucleotide databases very distant homologues to an amino acid query sequence. It focuses searches on a specific amino acid pattern, scoring the matching and intervening residues as specified by the user. The program has been developed for searching databases of expressed sequence tags (ESTs), but it is also well suited to search genomic sequences. The query sequence can be a variable pattern with alternative amino acids or gaps and the sequences searched can contain introns or sequencing errors with accompanying frame shifts. Other features include options to generate a searchable output, set the maximal sequencing error frequency, limit searches to given species, or exclude already known matches. Motifer can find sequence homologues that other search algorithms would deem unrelated or would not find because of sequencing errors or a too large number of other homologues. The ability of Motifer to find relatives to a given sequence is exemplified by searches for members of the transforming growth factor-beta family and for proteins containing a WW-domain. The functions aimed at enhancing EST searches are illustrated by the 'in silico' cloning of a novel cytochrome P450 enzyme.