The complete DNA sequence of yeast chromosome III.

The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined. This is the first complete sequence analysis of an entire chromosome from any organism. The 315-kilobase sequence reveals 182 open reading frames for proteins longer than 100 amino acids, of which 37 correspond to known genes and 29 more show some similarity to sequences in databases. Of 55 new open reading frames analysed by gene disruption, three are essential genes; of 42 non-essential genes that were tested, 14 show some discernible effect on phenotype and the remaining 28 have no overt function.     

Armillariella tabescens阿拉伯糖苷酶基因全长cDNA的克隆与表达

通过对假密环菌(Arm illariella tabescens)的表达cDNA克隆文库进行随机测序,获得一段与多形拟杆菌的阿拉伯糖苷酶序列同源性很高的EST序列(AJ620046).根据获得的EST序列用SMART-RACE技术成功从假密环菌中克隆出了阿拉伯糖苷酶基因的全长cDNA,用生物信息学的方法对所获的序列进行信息学分析.分析结果显示其全长cDNA为1 016 bp,其最长的开放阅读框架为924 bp,编码307个氨基酸,该全长cDNA序列与多形拟杆菌的阿拉伯糖苷酶序列具有较高同源性,80~279位氨基酸序列属于阿拉伯糖苷酶超家族,58~184位氨基酸是一个典型的结构功能域,蛋白分子质量预测为32 881 u,等电点为4.59.构建重组质粒pPIC9-AF,并在毕赤酵母菌GS115中对所获得的基因进行了表达,相对酶活达到了81.25%.     

Functional profiling of the Saccharomyces cerevisiae genome

Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.     

A combined algorithm for genome-wide prediction of protein function

The availability of over 20 fully sequenced genomes has driven the development of new methods to find protein function and interactions. Here we group proteins by correlated evolution, correlated messenger RNA expression patterns and patterns of domain fusion to determine functional relationships among the 6,217 proteins of the yeast Saccharomyces cerevisiae. Using these methods, we discover over 93,000 pairwise links between functionally related yeast proteins. Links between characterized and uncharacterized proteins allow a general function to be assigned to more than half of the 2,557 previously uncharacterized yeast proteins. Examples of functional links are given for a protein family of previously unknown function, a protein whose human homologues are implicated in colon cancer and the yeast prion Sup35.     

Large-scale analysis of the yeast genome by transposon tagging and gene disruption

Economical methods by which gene function may be analysed on a genomic scale are relatively scarce. To fill this need, we have developed a transposon-tagging strategy for the genome-wide analysis of disruption phenotypes, gene expression and protein localization, and have applied this method to the large-scale analysis of gene function in the budding yeast Saccharomyces cerevisiae. Here we present the largest collection of defined yeast mutants ever generated within a single genetic background--a collection of over 11,000 strains, each carrying a transposon inserted within a region of the genome expressed during vegetative growth and/or sporulation. These insertions affect nearly 2,000 annotated genes, representing about one-third of the 6,200 predicted genes in the yeast genome. We have used this collection to determine disruption phenotypes for nearly 8,000 strains using 20 different growth conditions; the resulting data sets were clustered to identify groups of functionally related genes. We have also identified over 300 previously non-annotated open reading frames and analysed by indirect immunofluorescence over 1,300 transposon-tagged proteins. In total, our study encompasses over 260,000 data points, constituting the largest functional analysis of the yeast genome ever undertaken.     

锯缘青蟹精氨酸激酶基因的克隆与表达

通过分子生物学方法,克隆得到锯缘青蟹（Scylla serrata）精氨酸激酶（Arginine Kinase,AK）开放阅读框基因序列.测序结果显示：该开放阅读框基因的序列长度为1 071 bp,编码356个氨基酸残基;该序列登录Genbank（GQ：851626）,序列比对结果显示,锯缘青蟹精氨酸激酶与凡纳滨对虾（...     

A retrovirus-like strategy for expression of a fusion protein encoded by yeast transposon Ty1

Eukaryotic transposons such as the Ty element of yeast or the copia-like sequences of Drosophila show structural and functional similarities to both prokaryotic transposons and retroviral proviruses, but the prokaryotic transposons and retroviral proviruses use markedly different expression strategies which yield products having entirely different functions. To determine the phylogenetic relationship between eukaryotic transposons, prokaryotic transposons and retroviruses, we have sought to identify and characterize the proteins encoded by the yeast Ty element and to describe the strategies used to express these proteins. We show here that the yeast transposon produces a fusion protein by a specific frameshifting event that fuses two out-of-phase open reading frames (ORFs). The process is remarkably similar to that used by retroviruses such as Rous sarcoma virus (RSV) to produce Pr180gag-pol.     

Towards a proteome-scale map of the human protein-protein interaction network

Systematic mapping of protein-protein interactions, or 'interactome' mapping, was initiated in model organisms, starting with defined biological processes and then expanding to the scale of the proteome. Although far from complete, such maps have revealed global topological and dynamic features of interactome networks that relate to known biological properties, suggesting that a human interactome map will provide insight into development and disease mechanisms at a systems level. Here we describe an initial version of a proteome-scale map of human binary protein-protein interactions. Using a stringent, high-throughput yeast two-hybrid system, we tested pairwise interactions among the products of approximately 8,100 currently available Gateway-cloned open reading frames and detected approximately 2,800 interactions. This data set, called CCSB-HI1, has a verification rate of approximately 78% as revealed by an independent co-affinity purification assay, and correlates significantly with other biological attributes. The CCSB-HI1 data set increases by approximately 70% the set of available binary interactions within the tested space and reveals more than 300 new connections to over 100 disease-associated proteins. This work represents an important step towards a systematic and comprehensive human interactome project.     

筛选hALR的相互作用蛋白基因

为筛选与人肝再生增强因子(hALR)相互作用蛋白的基因，探讨肝再生增强因子在肝再生过程中的分子生物学机制，将人肝再生增强因子基因的开放读码框片断，重组入载体pGBKT7构建成“诱饵”质粒pGBKT7—hALR，然后用酵母双杂交系统从预转化酵母菌Y187的成人肝细胞cDNA文库中筛选与人肝再生增强因子相互作用蛋白的基因。筛出的阳性克隆基因序列被测出后，经GenBank查询，结果发现它们分别是血清白蛋白、金属硫蛋白、硒蛋白类似物、Na^ ／K^ ATPase和一个未知功能的蛋白的部分序列。这初步克隆了与hALR相互作用的蛋白基因，为进一步探讨ALR在肝再生过程中的作用机制奠定了基础。     

筛选hALR的相互作用蛋白基因(英)

为筛选与人肝再生增强因子(hALR)相互作用蛋白的基因,探讨肝再生增强因子在肝再生过程中的分子生物学机制,将人肝再生增强因子基因的开放读码框片断,重组入载体pGBKT7构建成“诱饵”质粒pGBKT7-hALR,然后用酵母双杂交系统从预转化酵母菌Y187的成人肝细胞cDNA文库中筛选与人肝再生增强因子相互作用蛋白的基因.筛出的阳性克隆基因序列被测出后,经GenBank查询,结果发现它们分别是血清白蛋白、金属硫蛋白、硒蛋白类似物、Na+/K+ ATPase和一个未知功能的蛋白的部分序列.这初步克隆了与hALR相互作用的蛋白基因,为进一步探讨ALR在肝再生过程中的作用机制奠定了基础.     

基于酵母基因组高通量数据的基因-基因相互作用预测

后基因组时代的显著特点是大规模基因组和蛋白质组实验平台所产生的大量高通量数据,整合并利用基因组和蛋白组信息成为这一时代的主要挑战之一. 因此,基因-基因相互作用将有助于理解细胞内基因之间的相互作用以及信号传导通路研究提供有价值的参考. 为预测酵母基因组中基因-基因相互作用,我们利用高通量数据中的蛋白-蛋白相互作用、遗传表型数据、基因微阵列表达数据以及功能基因注释数据等来分析酵母中的基因-基因相互作用. 本文建立的预测方法为在系统水平上理解酵母基因组中的基因功能提供了依据,也为揭示酵母基因组中的基因-基因相互作用网络奠定理论基础.     

Proteome survey reveals modularity of the yeast cell machinery

Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry. Through systematic tagging of open reading frames (ORFs), the majority of complexes were purified several times, suggesting screen saturation. The richness of the data set enabled a de novo characterization of the composition and organization of the cellular machinery. The ensemble of cellular proteins partitions into 491 complexes, of which 257 are novel, that differentially combine with additional attachment proteins or protein modules to enable a diversification of potential functions. Support for this modular organization of the proteome comes from integration with available data on expression, localization, function, evolutionary conservation, protein structure and binary interactions. This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling.     

人脂联素在大肠杆菌中的可溶性表达

为了提高重组人脂联素在大肠杆菌中的可溶性,构建和表达了增溶标签与人脂联素的融合表达栽体.这些标签包括大肠杆茵硫氧还蛋白和NusA蛋白、酿酒酵母SUMO蛋白和噬热海洋茵Thermotoga maritime 的红素氧还蛋白.结果显示,所有的人脂联素融合蛋白在大肠杆茵中都获得了高水平的表达,但可溶性存在很大差异,说明不同融合标签对人脂联素可溶性表达的促进作用不同.其中,红素氧还蛋白与SUMO蛋白组合一起对人脂联素可溶性的增强作用最为显著,其相应的融合蛋白几乎全部可溶.另外,通过酵母SUMO/Ulp1反应,经His标签亲和层析纯化得到的人脂联素融合蛋白能被有效酶切,加工为人脂联素成熟肽产物.     

Interaction network containing conserved and essential protein complexes in Escherichia coli

Proteins often function as components of multi-subunit complexes. Despite its long history as a model organism, no large-scale analysis of protein complexes in Escherichia coli has yet been reported. To this end, we have targeted DNA cassettes into the E. coli chromosome to create carboxy-terminal, affinity-tagged alleles of 1,000 open reading frames (approximately 23% of the genome). A total of 857 proteins, including 198 of the most highly conserved, soluble non-ribosomal proteins essential in at least one bacterial species, were tagged successfully, whereas 648 could be purified to homogeneity and their interacting protein partners identified by mass spectrometry. An interaction network of protein complexes involved in diverse biological processes was uncovered and validated by sequential rounds of tagging and purification. This network includes many new interactions as well as interactions predicted based solely on genomic inference or limited phenotypic data. This study provides insight into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota.     

一种自剪切内含肽重组酿酒酵母表达优化研究

自剪切内含肽纯化系统在大肠杆菌中已经得到很好的应用。为了在真核生物中应用该系统,以酿酒酵母为宿主,p HR质粒为表达载体,构建微型内含肽ΔI-CM intein酿酒酵母表达系统。以猪免疫球蛋白Ig G的Fc domain为亲和标签,绿色荧光蛋白gfp为报告蛋白,在酿酒酵母GPD强启动子作用下,表达出融合的Fc-intein-gfp蛋白。检测发现融合序列在起始密码子ATG前加入一段Kozak序列有利于gfp表达。在此基础上,将微型内含肽ΔI-CM intein序列替换成密码子优化的ΔI-CMintein-O序列,显著促进gfp蛋白的表达量,初步实现了ΔI-CM intein融合蛋白的高效表达。为新型自剪切内含肽酿酒酵母表达系统的建立和重组蛋白高效纯化的实现奠定了基础。     

The Caenorhabditis elegans lin-12 gene encodes a transmembrane protein with overall similarity to Drosophila Notch

The lin-12 gene seems to control certain binary decisions during Caenorhabditis elegans development, from genetic and anatomical studies of lin-12 mutants that have either elevated or reduced levels of lin-12 activity. We report here the complete DNA sequence of lin-12: 13.5 kilobases (kb) derived from genomic clones and 4.5 kb from complementary DNA clones. It is of interest that the predicted product is a putative transmembrane protein, given that many of the decisions controlled by lin-12 activity require cell-cell interactions for the correct choice of cell fate. In addition, the predicted lin-12 product may be classified into several regions, based on amino acid sequence similarities to other proteins. These include extensive overall sequence similarity to the Drosophila Notch protein, which also is involved in cell-cell interactions that specify cell fate; a repeated motif found in proteins encoded by the yeast cell-cycle control genes cdc10 (Schizosaccharomyces pombe) and SWI6 (Saccharomyces cerevisiae); and a repeated motif exemplified by epidermal growth factor, found in many mammalian proteins.     

酵母双杂交系统筛选与HCMV pUL23蛋白相互作用的蛋白质

将UL23基因的ORF序列克隆到酵母表达载体pGBKT7构建诱饵质粒pGBKT7-UL23,用酵母双杂交技术筛选人胚肾cDNA文库中与人巨细胞病毒pUL23相互作用的宿主蛋白分子,再通过回复酵母双杂交再次确认两者之间的相互作用.结果表明:酵母双杂交,回复酵母双杂交试验证明宿主蛋白分子elF3e(eukaryotic trans-lation initiation factor 3,subunit E interacting protein)能够与人巨细胞病毒UL23蛋白相互作用.宿主蛋白分子elF3e能够与人巨细胞病毒UL23蛋白相互作用,这为进一步研究pUL23蛋白在HCMV生活周期中的作用机制提供依据.