研究: 核糖体失活蛋白及其在黄瓜中的表达分析

核糖体失活蛋白是一类具有高度特异性rRNA N-糖苷酶活性的蛋白,它们能够使原核或真核细胞的核糖体失活因而具有细胞毒性．由于其独特的生物学性质,核糖体失活蛋白被认为在农业和医学中都有着巨大的应用潜力．我们之前的研究表明,黄瓜的基因组中共包含2个2类核糖体失活蛋白基因,分别命名为CumsaAB1和CumsaAB2．以蓖麻毒蛋白Ricin为代表,2类核糖体失活蛋白通常由2条二硫键连接的肽链组成：具有N-糖苷酶活性的A链与具有凝集素活性的B链．本文研究了黄瓜中核糖体失活蛋白的表达情况．亚细胞定位研究表明CumsaAB1经过蛋白分泌通路表达于细胞外,这与蛋白质序列分析显示的CumsaAB1包含一个信号肽而不含转膜区域相一致．对黄瓜的不同生长阶段的不同组织中的转录水平分析表明,CumsaAB1在大部分组织中以极低的水平表达,而CumsaAB2表达水平则明显更高,尤其在第一片真叶阶段和刚开花的植物中．最后,我们使用分子模拟对黄瓜中核糖体失活蛋白的结构及糖结合位点进行了分析．本研究对黄瓜中核糖体失活蛋白的亚细胞定位、表达水平和可能的蛋白质结构进行了研究,为其进一步的生物学功能研究提供了重要信息．     

Translational machinery of channel catfish: II. Complementary DNA and expression of the complete set of 47 60S ribosomal proteins

Ribosomal protein genes have become widely used as markers for phylogenetic studies and comparative genomics, but they have not been available in fish. We have cloned and sequenced a complete set of all 47 60S ribosomal protein cDNAs from channel catfish (Ictalurus punctatus), of which 43 included the complete protein encoding regions. Most ribosomal protein mRNAs in channel catfish are highly similar to their mammalian counterparts. However, L4, L14, and L29 are significantly shorter in channel catfish than in mammals due to deletions in the 3' end of the gene. Two distantly related L5 cDNAs, L5a and L5b, were found in channel catfish. L5a is more similar to L5 in other vertebrates, while L5b showed significant levels of divergence, suggesting independent evolution of the two L5-encoding genes. The 47 ribosomal protein genes are generally highly expressed and together account for 11-14% of overall gene expression, depending on the tissues. Expression levels were highly variable both within a single tissue among different ribosomal protein genes, and among tissues with regard to a single ribosomal protein gene. Strong tissue preference expression was also observed for some ribosomal proteins. This set of ribosomal protein gene sequences represents one of the most complete sets from any single organism and will aid in fish phylogenetic and comparative genomic studies.     

Five geranylgeranyl diphosphate synthases expressed in different organs are localized into three subcellular compartments in Arabidopsis

Geranylgeranyl diphosphate (GGPP) is the precursor for the biosynthesis of gibberellins, carotenoids, chlorophylls, isoprenoid quinones, and geranylgeranylated proteins in plants. There is a small gene family for GGPP synthases encoding five isozymes and one related protein in Arabidopsis, and all homologs have a putative localization signal to translocate into specific subcellular compartments. Using a synthetic green fluorescent protein (sGFP), we studied the subcellular localization of these GGPP synthases. When these fusion proteins were expressed by the cauliflower mosaic virus 35S promoter in Arabidopsis, GGPS1-sGFP and GGPS3-sGFP proteins were translocated into the chloroplast, GGPS2-sGFP and GGPS4-sGFP proteins were localized in the endoplasmic reticulum, and the GGPS6-sGFP protein was localized in the mitochondria. Both GGPS1 and GGPS3 proteins synthesized in vitro were taken up into isolated intact pea chloroplasts and processed to the mature form. RNA-blot and promoter-beta-glucuronidase (GUS) analysis showed that these GGPP synthases genes are organ-specifically expressed in Arabidopsis. GGR and GGPS1 were ubiquitously expressed, while GGPS2, GGPS3, and GGPS4 were expressed specifically in the flower, root, and flower, respectively. These results suggest that each GGPP synthase gene is expressed in different tissues during plant development and GGPP is synthesized by the organelles themselves rather than being transported into the organelles. Therefore, we predict there will be specific pathways of GGPP production in each organelle.     

Protein domains enriched in mammalian tissue-specific or widely expressed genes

In multicellular organisms some genes are expressed in essentially all tissues, whereas others are expressed predominantly in only one or a few tissues. In this study, we investigate the relationship between the tissue-specificity of gene expression and the type of protein encoded. We find that many protein domains are found to be enriched in either tissue-specific or widely expressed genes. Domains enriched in tissue-specific genes tend to be metazoan-specific; these same domains are also enriched in genes that are not essential for cell viability. These findings identify families of proteins that are probably used in the development or terminal differentiation of many different tissue types.     

Molecular cloning and identification of 3'-phosphoadenosine 5'-phosphosulfate transporter

Nucleotide sulfate, namely 3'-phosphoadenosine 5'-phosphosulfate (PAPS), is a universal sulfuryl donor for sulfation. Although a specific PAPS transporter is present in Golgi membrane, no study has reported the corresponding gene. We have identified a novel human gene encoding a PAPS transporter, which we have named PAPST1, and the Drosophila melanogaster ortholog, slalom (sll). The amino acid sequence of PAPST1 (432 amino acids) exhibited 48.1% identity with SLL (465 amino acids), and hydropathy analysis predicted the two to be type III transmembrane proteins. The transient expression of PAPST1 in SW480 cells showed a subcellular localization in Golgi membrane. The expression of PAPST1 and SLL in yeast Saccharomyces cerevisiae significantly increased the transport of PAPS into the Golgi membrane fraction. In human tissues, PAPST1 is highly expressed in the placenta and pancreas and present at lower levels in the colon and heart. An RNA interference fly of sll produced with a GAL4-UAS system revealed that the PAPS transporter is essential for viability. It is well known that mutations of some genes related to PAPS synthesis are responsible for human inherited disorders. Our findings provide insights into the significance of PAPS transport and post-translational sulfation.     

Genome-scale identification of membrane-associated human mRNAs

The subcellular localization of proteins is critical to their biological roles. Moreover, whether a protein is membrane-bound, secreted, or intracellular affects the usefulness of, and the strategies for, using a protein as a diagnostic marker or a target for therapy. We employed a rapid and efficient experimental approach to classify thousands of human gene products as either "membrane-associated/secreted" (MS) or "cytosolic/nuclear" (CN). Using subcellular fractionation methods, we separated mRNAs associated with membranes from those associated with the soluble cytosolic fraction and analyzed these two pools by comparative hybridization to DNA microarrays. Analysis of 11 different human cell lines, representing lymphoid, myeloid, breast, ovarian, hepatic, colon, and prostate tissues, identified more than 5,000 previously uncharacterized MS and more than 6,400 putative CN genes at high confidence levels. The experimentally determined localizations correlated well with in silico predictions of signal peptides and transmembrane domains, but also significantly increased the number of human genes that could be cataloged as encoding either MS or CN proteins. Using gene expression data from a variety of primary human malignancies and normal tissues, we rationally identified hundreds of MS gene products that are significantly overexpressed in tumors compared to normal tissues and thus represent candidates for serum diagnostic tests or monoclonal antibody-based therapies. Finally, we used the catalog of CN gene products to generate sets of candidate markers of organ-specific tissue injury. The large-scale annotation of subcellular localization reported here will serve as a reference database and will aid in the rational design of diagnostic tests and molecular therapies for diverse diseases.     

卵巢癌肝转移灶高表达基因SFT2D1的生物信息学分析

目的:研究肿瘤原发灶和转移灶的基因表达差异,并采用生物信息学方法对一条卵巢癌肝转移灶高表达基因SFT2D1进行初步分析。方法:分别将卵巢癌原发灶和肝转移灶组织标本mRNA用Cy3-dUTP和Cy5-dUTP标记后与表达谱芯片杂交,通过信号扫描、处理后获得两者的表达差异基因。并用生物信息学方法对一条无功能研究的新基因SFT2D1进行初步分析,阐明了它的基因结构、染色体定位、编码蛋白质的理化性质、亚细胞定位、蛋白质功能域等信息。并对多物种中的相似性蛋白进行了系统进化分析。结果:表达谱芯片发现了共272条差异表达基因。对新基因SFT2D1的上述性质进行了有效的预测,基本明确了该基因编码蛋白为一内质网跨膜蛋白,可能参与肿瘤转移相关蛋白的合成与加工。结论:表达谱芯片技术是一种研究肿瘤转移基因表达差异的有效的高通量研究方法。通过生物信息学分析,表明新基因SFT2D1是一个有肿瘤转移研究价值的新靶点。     

Analysis of Arabidopsis genes encoding putative class III lipases

Triacylglycerol lipases are class of enzymes which catalyze the hydrolysis of long-chain triglycerides. They are widely found in the plant kingdom, numerous genes putatively encoding triacylglycerol lipases are sequenced but only a few of them have been characterized. Here we systematically analyzed Arabidopsis gene sequences deposited in public databases, and identified 38 putative class III lipase proteins, all of which contain a highly conserved lipase_3 domain (Pfam ID: PF01764). These 38 genes are randomly distributed on all chromosomes, and their genomic sequences consist of variable numbers of introns from zero to 13. They can be divided into four groups based on homology of protein sequences, and their potential subcellular localization is predicted to cytosol, chloroplast, mitochondria or endoplasmic reticulum. Furthermore, ten typical genes are selected to investigate their expression patterns. Most of them show weak tissue- or organ-specificity expression pattern. Several of them significantly accumulates in some tissues or organs in addition to germinated seedlings. Some of them are specifically transcribed during seed germination while others are not detected during stages of normal growth which are probably induced by stresses. In conclusion, putative Arabidopsis class III lipases display polymorphism in their sequences, gene structures and expression patterns.     

A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins II: public release of inaugural version of InGaP database containing gene/protein expression profiles for 127 mouse KIAA genes/proteins.

The inaugural version of the InGaP database (Integrative Gene and Protein expression database; http://www.kazusa.or.jp/ingap/index.html) is a comprehensive database of gene/protein expression profiles of 127 mKIAA genes/proteins related to hypothetical ones obtained in our ongoing cDNA project. Information about each gene/protein consists of cDNA microarray analysis, subcellular localization of the ectopically expressed gene, and experimental data using anti-mKIAA antibody such as Western blotting and immunohistochemical analyses. KIAA cDNAs and their mouse counterparts, mKIAA cDNAs, were mainly isolated from cDNA libraries derived from brain tissues, thus we expect our database to contribute to the field of neuroscience. In fact, cDNA microarray analysis revealed that nearly half of our gene collection is predominantly expressed in brain tissues. Immunohistochemical analysis of the mouse brain provides functional insight into the specific area and/or cell type of the brain. This database will be a resource for the neuroscience community by seamlessly integrating the genomic and proteomic information about the mouse KIAA genes/proteins.     

沙葱萤叶甲表皮蛋白基因的鉴定及表达谱分析

【目的】表皮蛋白是昆虫体壁的主要组成部分,在昆虫生长发育中起着重要的作用。本研究旨在鉴定沙葱萤叶甲Galeruca daurica表皮蛋白基因,分析其表达模式,以期为进一步研究其在沙葱萤叶甲生长发育中的作用提供必要的基础。【方法】根据本实验室组装的沙葱萤叶甲转录组测序数据,应用生物信息学方法鉴定表皮蛋白基因全长开放阅读框(ORF);采用RT-qPCR技术测定鉴定的8个表皮蛋白基因在沙葱萤叶甲不同发育阶段和3龄幼虫不同组织(头部、体壁、消化道和脂肪体)中的表达谱。【结果】基于转录组数据鉴定到8条沙葱萤叶甲表皮蛋白基因的开放阅读框(ORF)全长序列,命名为GdauCP1-8(GenBank登录号: MN629000-MN629007),ORF长417~810 bp,编码138~269个氨基酸,预测分子量为15~28 kD,等电点pI为4.45~8.62;具有16~20个氨基酸的信号肽;GdauCP1具有典型的跨膜结构,其余7个GdauCP蛋白无跨膜结构。同源序列比对和系统发育分析表明,GdauCP3与马铃薯甲虫Leptinotarsa decemlineata CP的氨基酸序列一致性最高,为60.00%;其余的GdauCPs与玉米根萤叶甲Diabrotica virgifera virgifera CP的氨基酸序列一致性最高,为58.52%~80.00%。GdauCP1-4属于RR-2亚家族,GdauCP5-7属于RR-1亚家族,GdauCP8的亚家族归属未确定。RT-qPCR分析表明,8个GdauCP基因在沙葱萤叶甲不同发育阶段及3龄幼虫不同组织内均有表达,且表达量存在显著差异。GdauCP2, GdauCP4, GdauCP5和GdauCP6在1龄幼虫期高表达,GdauCP3, GdauCP7和GdauCP8在蛹期高表达,GdauCP1在3龄第3天幼虫期高表达;除GdauCP2在成虫中表达水平较高外,其他GdauCP基因在成虫中的表达水平均很低。GdauCP1在头部和体壁中高表达,GdauCP2和GdauCP8在脂肪体中高表达,GdauCP3, GdauCP4, GdauCP6和GdauCP7在消化道中高表达,而GdauCP5在体壁中高表达。【结论】8个GdauCP基因在沙葱萤叶甲不同发育阶段和组织间差异表达,且表达模式不同,意味着不同GdauCP可能具有不同的功能。     

Protein evolution is faster outside the cell

Some proteins are highly conserved across all species, whereas others diverge significantly even between closely related species. Attempts have been made to correlate the rate of protein evolution to amino acid composition, protein dispensability, and the number of protein-protein interactions, but in all cases, conflicting studies have shown that the theories are hard to confirm experimentally. The only correlation that is undisputed so far is that highly/broadly expressed proteins seem to evolve at a lower rate. Consequently, it has been suggested that correlations between evolution rate and factors like protein dispensability or the number of protein-protein interactions could be just secondary effects due to differences in expression. The purpose of this study was to analyze mammalian proteins/genes with known subcellular location for variations in evolution rates. We show that proteins that are exported (extracellular proteins) evolve faster than proteins that reside inside the cell (intracellular proteins). We find weak, but significant, correlations between evolution rates and expression levels, percentage of tissues in which the proteins are expressed (expression broadness), and the number of protein interaction partners. More important, we show that the observed difference in evolution rate between extra- and intracellular proteins is largely independent of expression levels, expression broadness, and the number of protein-protein interactions. We also find that the difference is not caused by an overrepresentation of immunological proteins or disulfide bridge-containing proteins among the extracellular data set. We conclude that the subcellular location of a mammalian protein has a larger effect on its evolution rate than any of the other factors studied in this paper, including expression levels/patterns. We observe a difference in evolution rates between extracellular and intracellular proteins for a yeast data set as well and again show that it is completely independent of expression levels.     

Evolutionary rate and gene expression across different brain regions

Background

The evolutionary rate of a protein is a basic measure of evolution at the molecular level. Previous studies have shown that genes expressed in the brain have significantly lower evolutionary rates than those expressed in somatic tissues.

Results

We study the evolutionary rates of genes expressed in 21 different human brain regions. We find that genes highly expressed in the more recent cortical regions of the brain have lower evolutionary rates than genes highly expressed in subcortical regions. This may partially result from the observation that genes that are highly expressed in cortical regions tend to be highly expressed in subcortical regions, and thus their evolution faces a richer set of functional constraints. The frequency of mammal-specific and primate-specific genes is higher in the highly expressed gene sets of subcortical brain regions than in those of cortical brain regions. The basic inverse correlation between evolutionary rate and gene expression is significantly stronger in brain versus nonbrain tissues, and in cortical versus subcortical regions. Extending upon this cortical/subcortical trend, this inverse correlation is generally more marked for tissues that are located higher along the cranial vertical axis during development, giving rise to the possibility that these tissues are also more evolutionarily recent.

Conclusions

We find that cortically expressed genes are more conserved than subcortical ones, and that gene expression levels exert stronger constraints on sequence evolution in cortical versus subcortical regions. Taken together, these findings suggest that cortically expressed genes are under stronger selective pressure than subcortically expressed genes.     

An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development

Xylans constitute the major non-cellulosic component of plant biomass. Xylan biosynthesis is particularly pronounced in cells with secondary walls, implying that the synthesis network consists of a set of highly expressed genes in such cells. To improve the understanding of xylan biosynthesis, we performed a comparative analysis of co-expression networks between Arabidopsis and rice as reference species with different wall types. Many co-expressed genes were represented by orthologs in both species, which implies common biological features, while some gene families were only found in one of the species, and therefore likely to be related to differences in their cell walls. To predict the subcellular location of the identified proteins, we developed a new method, PFANTOM (plant protein family information-based predictor for endomembrane), which was shown to perform better for proteins in the endomembrane system than other available prediction methods. Based on the combined approach of co-expression and predicted cellular localization, we propose a model for Arabidopsis and rice xylan synthesis in the Golgi apparatus and signaling from plasma membrane to nucleus for secondary cell wall differentiation. As an experimental validation of the model, we show that an Arabidopsis mutant in the PGSIP1 gene encoding one of the Golgi localized candidate proteins has a highly decreased content of glucuronic acid in secondary cell walls and substantially reduced xylan glucuronosyltransferase activity.     

Characterization of the Bex gene family in humans, mice, and rats

To better understand the development of ventral mesencephalic dopamine neurons, we performed subtractive hybridization screens to find ventral mesencephalic genes expressed at rat embryonic day 10 when these neurons begin to differentiate. The most commonly identified genes in these screens were members of the Bex (Brain expressed X-linked) gene family, rat Bex1 (Rex3), and a novel gene, rat Bex4. After identifying these genes, we then sought to characterize the Bex gene family. Two additional novel Bex genes (human Bex5 and mouse Bex6) were discovered through genomic databases. Bex5 is present in humans and monkeys, but not rodents, while Bex6 exists in mice, but not humans. Bex4 and Bex5 are localized to the X chromosome, are expressed in brain, and are similar in sequence. Bex4 and Bex5 are 54% and 56% identical to human Bex3 (pHGR74, NADE). Mouse Bex6 is on chromosome 16 and is 67% identical to mouse Bex4. Human Bex gene expression was studied with tissue expression arrays probed with specific oligonucleotides. Human Bex1 and Bex2 have similar expression patterns in the central nervous system with high levels in pituitary, cerebellum, and temporal lobe, and Bex1 is widely expressed outside of the central nervous system with high expression in the liver. Human Bex4 is highly expressed in heart, skeletal muscle, and liver, while Bex3 and Bex5 are more widely expressed. The subcellular localization of the Bex proteins varies from nuclear (rat Bex1) to cytoplasmic (rat Bex3, human Bex5, and mouse Bex6) and to both nuclear and cytoplasmic (rat Bex2 and rat Bex4). Rat Bex3, rat Bex4, human Bex5, and mouse Bex6 are degraded by the proteasome, while rat Bex1 or Bex2 are not. Rat Bex3 protein can likely bind transition metals through a histidine-rich domain. Because this gene family was originally named Bex and because these genes are unified by sequence similarity and gene structure, we believe the Bex nomenclature should prevail over nomenclature based on function (NADE) that has not been extended to the other Bex genes. We conclude that the Bex gene family members are highly homologous but differ in their expression patterns, subcellular localization, and degradation by the proteasome.     

家蚕ABP与ABPX基因定位与表达分析

气味结合蛋白（odorant binding proteins, OBPs）在昆虫与外界环境化学信息交流过程中起着重要作用, 对昆虫的觅食、 求偶、 繁殖具有重要意义。触角结合蛋白（antennal binding protein, ABP）是OBP家族中的重要成员之一。为进一步探明家蚕Bombyx mori ABP与ABPX基因的结构、 表达及功能, 本研究利用染色体定位、 基因分析及半定量表达分析方法对其进行了研究。染色体定位分析表明, BmABP和BmABPX分别位于家蚕第5和第26染色体上, 基因结构差异较大, 可能功能上有较大差异。对家蚕胚胎、 幼虫和成虫不同发育阶段的雌、 雄虫多种组织进行基因表达谱分析发现, BmABP在家蚕发育的各个虫态、 多种组织器官中都有较高表达, 无时间特异性和组织特异性; BmABPX在不同发育时期和不同组织间差异显著（P<0.05）, 相对表达量以触角中最高, 其他非嗅觉组织中也多有表达, 性别间差异不大。结果提示, BmABP和BmABPX除了具有嗅觉相关功能外, 很可能还具有其他未知的生理功能。     

Molecular cloning and gene expression of endoplasmic reticulum stress proteins in Japanese monkey, Macaca fuscata

BACKGROUND: Immunoglobulin heavy-chain binding protein (BiP), calreticulin (Crt), and protein disulfide isomerase (PDI), are major resident endoplasmic reticulum (ER) stress proteins which are involved in diverse roles relating to successful folding, assembly, intracellular localization, and degradation of other proteins. METHODS: In this study, we molecular cloned cDNAs for BiP, Crt, and PDI from Japanese monkey (Macaca fuscata), and analyzed tissue-specific expression of respective genes. RESULTS AND CONCLUSIONS: The lengths of protein-coding regions of these cDNAs for BiP, Crt and PDI are 1965, 1254, and 1533 bp, respectively. Each protein has a signal peptide and a KDEL motif in N- and C-terminal parts respectively, showing its intracellular localization to be the lumen of the ER. These stress proteins are highly conserved, showing that their similarities among mammals are more than 90% in the level of amino acid. The expression of the genes for stress proteins differed among the monkey tissues examined. BiP and PDI gene expression was predominant in secretory tissues such as liver and kidney, and brain tissues. But Crt gene expressed rather ubiquitously in a variety of tissues.     

Highly expressed and alien genes of the Synechocystis genome

Comparisons of codon frequencies of genes to several gene classes are used to characterize highly expressed and alien genes on the SYNECHOCYSTIS: PCC6803 genome. The primary gene classes include the ensemble of all genes (average gene), ribosomal protein (RP) genes, translation processing factors (TF) and genes encoding chaperone/degradation proteins (CH). A gene is predicted highly expressed (PHX) if its codon usage is close to that of the RP/TF/CH standards but strongly deviant from the average gene. Putative alien (PA) genes are those for which codon usage is significantly different from all four classes of gene standards. In SYNECHOCYSTIS:, 380 genes were identified as PHX. The genes with the highest predicted expression levels include many that encode proteins vital for photosynthesis. Nearly all of the genes of the RP/TF/CH gene classes are PHX. The principal glycolysis enzymes, which may also function in CO(2) fixation, are PHX, while none of the genes encoding TCA cycle enzymes are PHX. The PA genes are mostly of unknown function or encode transposases. Several PA genes encode polypeptides that function in lipopolysaccharide biosynthesis. Both PHX and PA genes often form significant clusters (operons). The proteins encoded by PHX and PA genes are described with respect to functional classifications, their organization in the genome and their stoichiometry in multi-subunit complexes.