SPR技术与功能基因组和蛋白质组研究

表面等离子体共振(surface plasmon resonance,SPR)依据光学—介质相互作用原理建立,属于实时和非标记的测试方法。SPR方法在研究分子间相互作用方面具有其独特的优势,其非标记和实时检测以及可以进行动力学分析的特点,给研究生物大分子的相互作用提供了诱人的解决方案。近来,随着SPR成像技术和SPR芯片制备技术的进展,将为功能基因组学和蛋白质组学研究提供重要的新的技术平台。     

嗜热四膜虫——具有发展潜力的功能基因组学研究模型

在真核生物的分子生物学和遗传学研究方面,纤毛类原生动物嗜热四膜虫(Tetrahymenathermophila)已经被证明是一种有价值的生物学模型。通过对它的研究,人们发现并且掌握了核酶的分子机制、RNA的自我拼接、端粒的结构和功能、DNA序列重组等机理。这种原生动物的基因组功能分别由两个细胞核执行,即二倍体的小核与生殖过程有关,而多倍体的大核决定细胞的基因转录,并为转化基因的表达提供了强有力的手段。     

Signal Sequence and Keyword Trap in silico for Selection of Full-Length Human cDNAs Encoding Secretion or Membrane Proteins from Oligo-Capped cDNA Libraries

We have developed an in silico method of selection of humanfull-length cDNAs encoding secretion or membrane proteins fromoligo-capped cDNA libraries. Fullness rates were increased toabout 80% by combination of the oligo-capping method and ATGpr,software for prediction of translation start point and the codingpotential. Then, using 5'-end single-pass sequences, cDNAs havingthe signal sequence were selected by PSORT (‘signal sequencetrap’). We also applied ‘secretion or membrane protein-relatedkeyword trap’ based on the result of BLAST search againstthe SWISS-PROT database for the cDNAs which could not be selectedby PSORT. Using the above procedures, 789 cDNAs were primarilyselected and subjected to full-length sequencing, and 334 ofthese cDNAs were finally selected as novel. Most of the cDNAs(295 cDNAs: 88.3%) were predicted to encode secretion or membraneproteins. In particular, 165(80.5%) of the 205 cDNAs selectedby PSORT were predicted to have signal sequences, while 70 (54.2%)of the 129 cDNAs selected by ‘keyword trap’ preservedthe secretion or membrane protein-related keywords. Many importantcDNAs were obtained, including transporters, receptors, andligands, involved in significant cellular functions. Thus, anefficient method of selecting secretion or membrane protein-encodingcDNAs was developed by combining the above four procedures.     

New adenovirus vectors for protein production and gene transfer

Based on two new adenovirus expression cassettes, we have constructed a series of Ad transfer vectors for the overexpression of one or two genes either in a dicistronic configuration or with separate expression cassettes. Inclusion of the green or blue fluorescent protein in the vectors accelerates the generation of adenovirus recombinants and facilitates the functional characterization of genes both in vitro and in vivo by allowing easy quantification of gene transfer and expression. With our optimized tetracycline-regulated promoter (TR5) we have generated recombinant adenoviruses expressing proteins, that are either cytotoxic or which interfere with adenovirus replication, at levels of 10–15% of total cell protein. Proteins that are not cytotoxic can be produced at levels greater than 20% of total cell protein. As well, these levels of protein production can be achieved with or without adenovirus replication. This yield is similar to what can be obtained with our optimized human cytomegalovirus-immediate early promoter-enhancer (CMV5) for constitutive protein expression in non-complementing cell lines. Using the green fluorescent protein as a reporter, we have shown that a pAdCMV5-derived adenovirus vector expresses about 6-fold more protein in complementing 293 cells and about 12-fold more in non- complementing HeLa cells than an adenovirus vector containing the standard cytomegalovirus promoter. Moreover, a red-shifted variant of green fluorescent protein incorporated in one series of vectors was 12-fold more fluorescent than the S65T mutant, making the detection of the reporter protein possible at much lower levels of expression. This revised version was published online in August 2006 with corrections to the Cover Date.     

A cDNA library functional screening strategy based on fluorescent protein complementation assays to identify novel components of signaling pathways

Progress towards a deeper understanding of cellular biochemical networks demands the development of methods to both identify and validate component proteins of these networks. Here, we describe a cDNA library screening strategy that achieves these aims, based on a protein-fragment complementation assay (PCA) using green fluorescent protein (GFP) as a reporter. The strategy combines a simple cell-based cDNA-screening approach (interactions of a "bait" protein of interest with "prey" cDNA products) with specific functional assays that use the same system and provide initial validation of the cDNA products as being biologically relevant. We applied this strategy to identify novel interacting partners of the protein kinase PKB/Akt. This method provides very general means of identifying and validating genes involved in any cellular process and is particularly designed for identifying enzyme substrates or regulatory proteins for which the enzyme specificity can only be defined by their interactions with other proteins in cells in which the proteins are normally expressed.     

利用互联网预测cDNA蛋白质产物的结构和功能

人类基因组计划预计近两三年内即可完成,我们将会得到许多序列已知但未知功能的cDNA。本简单介绍利用互联网上信息资源分析cDNA序列和预测它所编码的蛋白质的结构和功能的方法和常用工具。     

The oligosaccharyltransferase complex from pig liver: cDNA cloning, expression and functional characterisation

Oligosaccharyltransferase (OST) is an oligomeric protein complex which catalyses the transfer en bloc of Glc₃-Man₉-GlcNAc₂ from Dol-PP to specific asparagine residues in the nascent polypeptide chain. In order to study the function of the pig enzyme subunits, we have cloned OST48, ribophorin I and ribophorin II and characterized these proteins after in vitro translation as well as after expression in COS-1 cells. The individual full-length cDNAs contained open reading frames (ORFs) encoding polypeptides with calculated molecular masses of 48.9[emsp4 ]kDa (OST48), 68.7[emsp4 ]kDa (ribophorin I) and 69.3[emsp4 ]kDa (ribophorin II), respectively. A Kyte and Doolittle hydrophobicity analysis revealed that OST48, ribophorin I and ribophorin II possess a type I membrane topology with the bulk of their polypeptide chains directed towards the ER-lumen. In contrast to OST48, ribophorin I and II contain, respectively, three or two potential N-glycosylation sites of the Asn-Xaa-Thr/Ser type; only one is found to function as the acceptor site in each protein.Transfection of COS-1 cells with vector constructs encoding either OST48, ribophorin I, or a ribophorin I variant tagged with a myc-peptide sequence, resulted in the over-expression of polypeptides whose molecular masses were similar to those calculated from the respective cDNA ORFs. None of these three polypeptides, or ribophorin II, were found to display OST activity when over-expressed alone. By contrast, a modest but reproducible 25% increase of activity was observed when OST48 together with ribophorin I, or OST48 and myc-tagged ribophorin I, were co-expressed, indicating that these two subunits are probably responsible for the catalytic activity in the hetero-oligomeric OST complex. The only modest over-expression of transferase activity suggests that either the dimeric enzyme complex is catalytically unstable, or that the OST48 and ribophorin I polypeptides are unable to fold properly when other subunit components of the hetero-oligomeric OST complex are lacking. OST48 as well as ribophorin I are expressed in COS-1 cells as ER-resident proteins. Whereas OST48 carries a double-lysine motif in the –3/–5 position of its cytosolic C-terminal domain, ribophorin I does not contain recognizable ER-retention information. Replacing the lysine residue in the –3 position by leucine resulted in plasma membrane expression of the OST48-Leu polypeptide, indicating that this sequence motif may be able to influence OST48 localisation. No cell surface staining was observed when OST48-Leu was co-expressed with ribophorin I. This suggests that localisation of OST48 in the ER is mediated by interaction with ribophorin I rather than by the double-lysine motif.     

Prediction of the Coding Sequences of Unidentified Human Genes. III. The Coding Sequences of 40 New Genes (KIAA0081-KIAA0120) Deduced by Analysis of cDNA Clones from Human Cell Line KG-1

We isolated full-length cDNA clones from size-fractionated cDNAlibraries of human immature myeloid cell line KG-1, and thecoding sequences of 40 genes were newly predicted. A computersearch of the GenBank/EMBL databases indicated that the sequencesof 14 genes were unrelated to any reported genes, while theremaining 26 genes carried some sequences with similaritiesto known genes. Significant transmembrane domains were identifiedin 17 genes, and protein motifs that matched those in the PROSITEmotif database were identified in 11 genes. Northern hybridizationanalysis with 18 different cells and tissues demonstrated that10 genes were apparently expressed in a cell-specific or tissue-specificmanner. Among the genes predicted, half were isolated from themedium-sized cDNA library and the other half from the small-sizedcDNA library, and their average sizes were 4 kb and 1.4 kb,respectively. As judged by Northern hybridization profiles,small-sized cDNAs appeared to be expressed more ubiquitouslyand abundantly in various tissues, compared with that of medium-sizedcDNAs.     

暗黑鳃金龟气味结合蛋白HparOBP15a基因的克隆及功能分析

【目的】暗黑鳃金龟Holotrichia parallela通过气味结合蛋白(odorant binding protein,OBP)识别性信息素和植物挥发物准确而迅速地定位配偶、寄主植物。本研究通过克隆暗黑鳃金龟气味结合蛋白15a(Hpar OBP15a)基因,解析该基因的编码蛋白特征、组织表达模式及与寄主植物气味等化合物的结合特性方面的研究,为阐明暗黑鳃金龟基于嗅觉识别的寄主植物选择机理奠定理论基础。【方法】根据暗黑鳃金龟成虫触角转录组测序的结果,利用RT-PCR克隆了Hpar OBP15a基因;Real-time PCR方法分析了该基因在成虫不同部位的表达量差异;荧光竞争结合测定了Hpar OBP15a蛋白和58种候选化合物的结合特征。【结果】暗黑鳃金龟Hpar OBP15a基因全长534 bp,编码147个氨基酸,Gen Bank登录号为AK1834747。Hpar OBP15a在触角中特异表达,且在雌虫触角中表达量显著高于雄虫。在被测的58种化合物中,Hpar OBP15a与46种气味化合物具有较好的亲和性,其中与十二烷、十二醇结合能力最强,其解离常数分别为8.5和11.3μmol/L;同时,对性信息素(L-异亮氨酸甲酯和R-芳樟醇)也有一定的结合能力(解离常数分别为21.0和18.5μmol/L)。【结论】Hpar OBP15a具有广泛的气味结合谱,其中对榆树挥发物十二烷的结合能力最强,因此该蛋白可能在暗黑鳃金龟对榆树的定位过程中具有重要作用。     

On the structure of hisH: protein structure prediction in the context of structural and functional genomics

We predict a structure of the glutamine amidotransferase subunit (hisH) of imidazole glycerol phosphate synthase (IGPS) which catalyzes the fifth step of the histidine biosynthesis in Escherichia coli. The model is constructed using an energy-based threading program augmented by a multiple sequence to structure profile analysis. In developing our model we identified a conserved core region within hisH and a variable domain which is the likely site of interaction with the synthase subunit (hisF) of IGPS. Information available from structural and functional genomics studies was used to improve the structure prediction, to discuss parallels between histidine biosynthesis and other amino acid and nucleotide metabolic pathways, and to better understand the protein-protein interactions between the hisH and hisF domains of IGPS. This work allows us to develop a preliminary model for the structure of the entire IGPS holoenzyme.     

Isolation,characterization, and chromosomal mapping of a novel cDNA clone encoding human selenium binding protein

We have isolated the full-length human 56 kDa selenium binding protein (hSP56) cDNA clone, which is the human homolog of mouse 56 kDa selenium binding protein. The cDNA is 1,668 bp long and has an open reading frame encoding 472 amino acids. The calculated molecular weight is 52.25 kDa and the estimated isoelectric point is 6.13. Using Northern blot hybridization, we found that this 56 kDa selenium binding protein is expressed in mouse heart with an intermediate level between those found in liver/lung/kidney and intestine. We have also successfully expressed hSP56 in Escherichia coli using the expression vector-pAED4. The hSP56 gene is located at human chromosome 1q21–22. J. Cell. Biochem. 64:217–224. © 1997 Wiley-Liss, Inc.     

Prediction of the Coding Sequences of Unidentified Human Genes. IV. The Coding Sequences of 40 New Genes (KIAA0121-KIAA0160) Deduced by Analysis of cDNA Clones from Human Cell Line KG-1

In this series of projects regarding the accumulation of sequenceinformation of unidentified human genes, we newly deduced thesequences of 40 full-length cDNA clones of human cell line KG-1,and predicted the coding sequences of the corresponding genes,named KIAA0121 to 0160. The results of a computer search ofpublic databases indicated that the sequences of 13 genes wereunrelated to any reported genes, while the remaining 27 genescarried sequences which showed some similarities to known genes.Obvious unique sequences noted were as follows. A stretch oftriplet repeats was contained in each of three genes: Thesewere GAG(Glu) in KIAA0122 and KIAA0147, and TCC(Ser) in KIAA0150.A stretch of 10 amino acidresidues was repeated 21 times inKIAA0139, and a homologous sequence of 76–78 nucleotideswas found repeated 6 times in the untranslated region of KIAA0125.northern hybridization analysis demonstrated that 13 genes wereexpressed in a cell- or tissue-specific manner. Although a vastnumber of expressed sequence tags (ESTs) have been registeredfor comprehensive analysis of cDNA clones, our sequence dataindicated that their distribution is very unbalanced: e.g. whileno EST hit 7 genes, 85 ESTs fell in a single gene.