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Functional analysis of schistosomes EF-hand domain-containing tegument proteins

chinese Science Bulletin 2007年第15期52卷 2100-2107页

作者： YU FuDong1,2,3,KANG Bin1,3,LI YuanYuan3,4.& LI YiXue1,3 1 Bioinformatics center,Key Laboratory of Systems Biology,shanghai institutes for biological {4.,chinese academy of Sci-ences,shanghai 2.0031,china 2 Graduate University of chinese academy of sciences,shanghai 2.0031,china 3 shanghai center for bioinformation Technology,shanghai 200235,china 4.Key Laboratory of Systems Biology,shanghai institutes for biological {4.,chinese academy of {4.,shanghai 2.0031,china Bioinformatics center Key Laboratory of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China Graduate University of chinese academy of sciences Shanghai China shanghai center for bioinformation Technology Shanghai China Key Laboratory of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China

Schistosomes cause schistosomiasis disease which severely threatens human health. Little is known about the functions of EF-hand domain containing schistosomes tegument proteins other than as an-tigens. More possible functions of these tegument proteins were investigated with in silico analyses including protein-protein functional interaction,site-specific variation and glycosylation modification. The analysis results suggested that schistosomes could actively modulate host immune responses for its own favor through functional interactions with host proteins with immunomodulatory function,and passively regulate host immune responses through sequence variation under positive selection and glycosylating the recognition sites of host immune attack. In addition,the analysis of the C-terminal domain of these tegument proteins indicated that they could assist schistosomes in escaping host immune attacks through inhibiting chemotaxis and non-complement fixing antibody (IgG4. responses. In summary,our results suggested that these tegument antigen proteins could assist schistosomes in escaping and modulating host immune responses for self-protection during the process of host-para-site interaction.

关键词：寄生虫血吸虫皮蛋白质健康

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Display of aggregation-prone ligand binding domain of human PPAR gamma on surface of bacteriophage lambda

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Acta Pharmacologica Sinica 2006年第1期27卷 91-99页

作者： Bo KONG~(2,4. Wei-jun MA~(2,3,5)2 Institute of Health sciences.shanghai institutes for biological sciences,chinese academy of sciences and Medical School of shanghai Jiao Tong University.shanghai 200025.china 3 Shaughai Research center of Biotechnology,shanghai institutes for biological sciences,Chiese academy og sciences,shanghai 200233.china 4.Graduate School of the chinese academy of sciences Institute of Health sciences Shanghai Institutes for Biological Sciences Chinese Academy of Sciences and Medical School of Shanghai Jiao Tong University Shanghai China Graduate School of the chinese academy of sciences China shanghai Research center of Biotechnology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China

Aim:To display the aggregation-prone ligand binding domain (LBD) of the hu-man peroxisome proliferator-activated receptor gamma (PPARγ) on the surface ofbacteriophages to establish an easy screening assay for the identification of PPARγ***:Plasmids were constructed for the expression of the PPARγLBD as a fusion to the N-terminus of the g3p protein of filamentous phage or theC-terminus of the capsid protein D (pD) of phage *** fusion proteinswere expressed in E coli and solubility characteristics were *** against the LBD as well as the pD protein were prepared for Westernblot analysis and phage capture ***:The pD-LBD fusion protein waspartially soluble,whereas the LBD-g3p fusion protein was detected only in theinsoluble *** pD-LBD fusion protein was efficiently incorporated inphage ***,the LBD was shown to be displayed on the surfaceof bacteriophage *** average,the pD-LBD fusion protein accounted for28% of the total pD protein in the lambda head ***:The hydro-phobic PPARγ LBD was expressed as a soluble form of fusion protein in E coli anddisplayed on the surface of bacteriophage lambda when it was fused to the lambdapD *** lambda pD fusion system could be used for improving the solu-bility of proteins that tend to form inclusion bodies when expressed in E *** phage particles displaying the LBD of PPARy may be of great value for theidentification of novel PPARγ ligands.

关键词： protein expression lambda phage surface display nuclear receptor peroxisome proliferator-activated receptors ligand binding domain

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Comparative Analysis of Two-component Signal Transduction System in Two Streptomycete Genomes

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Acta Biochimica et Biophysica Sinica 2007年第5期39卷 317-325页

作者： WU WEI~(1,3#), Weihua WANG~(2#), Zhiwei CAO~(3#), Hong YU~3, Xiaojing WANG~1, Jing ZHAO~3, Hao TAN~3, Hao XU~3, Weihong JIANG~(2*), and Yixue LI~(1,3*) 1 bioinformation center, Key Lab of Systems Biology, shanghai institutes for biological sciences, chinese academy of sciences, Graduate School of the chinese academy of sciences, shanghai 2.0031, china 2 Laboratory of Molecular Microbiology, Institute of Plant Physiology and Ecology, shanghai institutes for biological sciences, chinese academy of sciences, Graduate School of the chinese academy of sciences, shanghai 200032, china 3 shanghai center for bioinformation Technology, shanghai 200235, china bioinformation center Key Lab of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200031 China shanghai center for bioinformation Technologyshanghai 200235 China Laboratory of Molecular Microbiology Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200032 China

Species of the genus Streptomyces are major bacteria responsible for producing most natural antibiotics. Streptomyces coelicolor A3(2) and Streptomyces avermitilis were sequenced in 2002 and 2003, respectively. Two-component signal transduction systems (TCSs), consisting of a histidine sensor kinase (SK) and a cognate response regulator (RR), form the most common mechanism of transmembrane signal transduction in prokaryotes. TCSs in S. coelicolor A3(2) have been analyzed in detail. Here, we identify and classify the SK and RR of S. avermitilis and compare the TCSs with those of S. coelicolor A3(2) by computational approaches. Phylogenetic analysis of the cognate SK-RR pairs of the two species indicated that the cognate SK-RR pairs fall into four classes according to the distribution of their orthologs in other organisms. In addition to the cognate SK-RR pairs, some potential partners of non-cognate SK-RR were found, including those of unpaired SK and orphan RR and the cross-talk between different components in either strain. Our study provides new clues for further exploration of the molecular regulation mechanism of streptomycetes with industrial importance.

关键词： Streptomyces two-component system cross-talk phylogenetic analysis

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EMMA:An Efficient Massive Mapping Algorithm Using Improved Approximate Mapping Filtering

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Acta Biochimica et Biophysica Sinica 2006年第12期38卷 857-864页

作者： Xin ZHANG~1 Zhi-Wei CAO~2 Zhi-Xin LIN~3 Qing-Kang WANG~1* Yi-Xue LI~4. 1 Institute of Micro/Nano Science and Technology,shanghai Jiaotong University,shanghai 200030,china 2 shanghai {4. for bioinformation Technology,shanghai 200235,china 3 College of Life Science and Technology,shanghai Jiaotong University,shanghai 200030,china 4.bioinformation {4. of shanghai institutes for biological sciences,{14. academy of sciences,shanghai 2.0031,china Institute of Micro/Nano Science and Technology Shanghai Jiaotong UniversityShanghai 200030 China shanghai center for bioinformation Technology Shanghai 200235 China College of Life Science and Technology Shanghai Jiaotong UniversityShanghai 200030 China bioinformation center of shanghai institutes for biological sciences Chinese Academy of SciencesShanghai 200031 China

Efficient massive mapping algorithm (EMMA),an algorithm on efficiently mapping massivecDNAs onto genomic sequences,has recently been *** process of mapping massive cDNAsonto genomic sequences has been improved using more approximate mapping filtering based on an enhancedsuffix array coupled with a pruned fast hash table,algorithms of block alignment extensions,and *** compared with the classical BLAT software in this field,the computing of EMMA ranges fromtwo to forty-one times faster under similar prediction precisions.

关键词： cDNA mapping maximal exact match enhanced suffix array pruned fast hash table extension algorithm

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Anaerobic Induction of Isocitrate Lyase and Malate Synthase in Submerged Rice Seedlings Indicates the Important Metabolic Role of the Glyoxylate Cycle

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Acta Biochimica et Biophysica Sinica 2005年第6期37卷 406-414页

作者： Ying LU~(1.2) Yong-Rui WU~(1.2) Bin HAN~(1.3) 1 National center for Gene Research. shanghai institutes for biological sciences. chinese academy of sciences. shanghai 200233.{4.. 2 Graduate School of the chinese academy of sciences. Beijing 100039.china 3 Institute of Plant Physiology and Ecology. shanghai institutes for biological sciences. chinese academy of sciences. shanghai 200032.{4. National center for Gene Research Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200233 China Graduate School of the chinese academy of sciencesBeijing 100039 China Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200032 China

The glyoxylate cycle is a modified form of the tricarboxylic acid cycle that converts C2compounds into C4.dicarboxylic acids at plant developmental *** studying submerged rice seedlings,we revealed the activation of the glyoxylate cycle by identifying the increased transcripts of mRNAs of thegenes of isocitrate lyase(ICL)and malate synthase(MS),two characteristic enzymes of the *** blot analysis showed that ICL and MS were activated in the prolonged anaerobic *** activity assay of pyruvate decarboxylase and ICL in the submerged seedlings indicated an 8.8-fold and3.5-fold increase over that in the unsubmerged seedlings,*** activity assay of acetyl-coen-zyme A synthetase in the submerged seedlings indicated a 3-fold increase over that in the unsubmergedseedlings,which is important for initiating acetate ***,we concluded that the glyoxylatecycle was involved in acetate metabolism under anaerobic conditions.

关键词： Oryza sativa glyoxylate cycle isocitrate lyase malate synthase acetyl-coenzyme A synthetase anoxia

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Semantic Search among Heterogeneous biological Databases Based on Gene Ontology

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Acta Biochimica et Biophysica Sinica 2004年第5期36卷 365-370页

作者： Shun-Liang CAO, Lei QIN1, Wei-Zhong HE1, Yang ZHONG2, Yang-Yong ZHU, and Yi-Xue LI1,3* Department of Computing and Information Technology, Fudan University, shanghai 2004.3, china shanghai center for {4. 1 Technology, shanghai 200235, china School of Life sciences, Fudan University, shanghai 2004.3, china {4. center of shanghai institutes for biological sciences, the chinese academy of sciences,{14., china Department of Computing and Information Technology Fudan University Shanghai 200433 China shanghai center for bioinformation Technology shanghai 200235 China School of Life sciences Fudan University Shanghai 200433 China bioinformation center of shanghai institutes for biological sciences the Chinese Academy of Sciences Shanghai 200031 China

Semantic search is a key issue in integration of heterogeneous biological databases. In this paper, we present a methodology for implementing semantic search in BioDW, an integrated biological data warehouse. Two tables are presented: the DB2GO table to correlate Gene Ontology (GO) annotated entries from BioDW data sources with GO, and the semantic similarity table to record similarity scores derived from any pair of GO terms. Based on the two tables, multifarious ways for semantic search are provided and the corresponding entries in heterogeneous biological databases in semantic terms can be expediently searched.

关键词： Gene Ontology semantic search BioDW

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Association between Alcohol, Smoking and HLA-DQA1*0201 Genotype in Psoriasis

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Acta Biochimica et Biophysica Sinica 2004年第9期36卷 597-602页

作者： Guang-Yong ZHENG1,2#, Sheng-Cai WEI3#, Tie-Liu SHI1, and Yi-Xue LI1* 1Bioinformatics center, shanghai institutes for biological sciences, chinese academy of sciences, Graduate School of the chinese academy of sciences, {4., china Research center for Proteome Analysis, Institute of Biochemistry and Cell Biology, shanghai institutes for biological sciences, chinese academy of sciences, Graduate School of the chinese academy of sciences,{4., china 3Guangzhou Institute of Dermatology, Guangzhou 510095, china Bioinformatics center Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200031 China Research center for Proteome Analysis Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200031 China Guangzhou Institute of DermatologyGuangzhou 510095 China

Psoriasis is a chronic skin disease triggered by genetic, environment or other risk factors such as infection, drugs, stress, moisture, alcohol, and smoking. A major psoriasis susceptibility locus at 6p21.3 has been identified. Further studies found that HLA-DQA1*0201 allele was associated with psoriasis. However, there were few data exploring an association between the environmental factors and susceptibility genes. In this study, the samples of 189 patients with psoriasis and 333 healthy controls were collected with their consent and were carried on analysis through polymerase chain reaction sequence-specific primer (PCR- SSP) method. The proportion of male psoriasis patients engaging in the smoking and alcohol was much higher than that of the control group (P4.25, P6.91, P4..

关键词： psoriasis HLA-DQA1*0201 allele smoking alcohol association

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Inducible nitric oxide synthase contributes to intermittent hypoxia against ischemia/reperfusion injury

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Acta Pharmacologica Sinica 2005年第3期26卷 315-322页

作者： Hai-lei DING~2 Hai-feng ZHU~2 Jian-wen DONG~2 Wei-zhong ZHU~2 Wei-wei YANG~3 Huang-tian YANG~3 Zhao-nian ZHOU~(2,4.2 Physiological Laboratory of Hypoxia,shanghai institutes for biological sciences,{4. academy of sciences,shanghai 2.0031,china 3 Laboratory of Molecular Cardiology,Health Science center,shanghai institutes for biological sciences,{4. academy of sciences and shanghai Second Medical University,shanghai 200025,china Physiological Laboratory of Hypoxia Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China Laboratory of Molecular Cardiology Health Science Center Shanghai Institutes for Biological Sciences Chinese Academy of Sciences and Shanghai Second Medical University Shanghai China

Aim:To investigate the role of inducible nitric oxide synthase (iNOS)-derivednitric oxide (NO) in the cardioprotection of intermittent hypoxia (IH) against is-chemia/reperfusion (I/R) ***:Langendorff-perfused isolated rathearts were used to measure variables of left ventricular function during baselineperfusion,ischemia,and reperfusion *** plus nitrite (NOx) content inmyocardium was measured using a biochemical method,iNOS mRNA and pro-tein expression in rat left ventricles were detected using reverse transcription poly-merase chain reaction (RT-PCR) and Western blot,***:Myo-cardial function recovered better in IH rat hearts than in normoxic control *** iNOS-selective inhibitor aminoguanidine (AG) (100μmol/L) significantlyinhibited the protective effects of IH,but had no influence on normoxic rat *** baseline content of NOx in IH hearts was higher than that in normoxic *** 30 min ischemia,the NOx level in normoxic hearts increased compared tothe corresponding baseline level,whereas there was no significant change in ***,the NOx level in IH hearts was still higher than that of normoxichearts during ischemia and reperfusion *** 100μmol/L significantly di-minished the NOx content in IH and normoxic hearts during ischemia and *** baseline levels of iNOS mRNA and protein in IH hearts were higherthan those of normoxic *** to the corresponding baseline level,iNOS mRNA and protein levels in normoxic rat hearts increased and those in IH rathearts decreased after *** addition of AG 100μmol/L significantlydecreased iNOS mRNA and protein expression in IH rat hearts after I/***:IH upregulated the baseline level of iNOS mRNA and protein expres-sion leading to an increase in NO production,which may play an important role inthe cardiac protection of IH against I/R injury.

关键词： intermittent hypoxia ischemia/reperfusion inducible nitric oxide synthase aminoguanidine: rats

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Expression and Comparative Analysis of Genes Encoding Outer Membrane Proteins LipL21,LipL32 and OmpL1 in Epidemic Leptospires

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Acta Biochimica et Biophysica Sinica 2005年第10期37卷 7+650-656页

作者： Xiang-Yan ZHANG~(1#) Yang YU~(2,3#) Ping HE~1 Yi-Xuan ZHANG~(2,3) Bao-Yu HU~1 Yang YANG~1 Yi-Xin NIE~4.Xiu-Gao JIANG~4.Guo-Ping ZHAO~(2,3) Xiao-Kui GUO~(1*) 1 Department of Medical Microbiology and Parasitology,shanghai Jiaotong University,shanghai 200025,china 2 Research center of Biotechnology,shanghai institutes for biological sciences,chinese academy of sciences,shanghai 2.0031,china 3 chinese National Human Genome center at shanghai,Zhangjiang High Tech Park,shanghai 201203,china 4.Institute for Infectious Disease Control and Prevention,chinese center for Disease Control and Prevention,Beijing 102206,china Department of Medical Microbiology and Parasitology Shanghai Jiaotong UniversityShanghai 200025 China Research center of Biotechnology Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200031 China chinese National Human Genome center at shanghai Zhangjiang High Tech ParkShanghai 201203 China Institute for Infectious Disease Control and Prevention Chinese Center for Disease Control and PreventionBeijing 102206 China

Leptospiral outer membrane proteins (OMPs) are highly conserved in different species,andplay an essential role in the development of new immunoprotection and serodiagnosis *** genesencoding LipL21,LipL32 and OmpL1 were cloned from the complete genome sequence of Leptospirainterrogans serovar lai strain Lai and expressed in *** comparison analysis revealed that the threegenes were highly conserved among distinct epidemic leptospires,including three major epidemic speciesLeptospira interrogans,Leptospira borgpetersenii and Leptospira weilii,in *** analysis wasfurther performed to scrutinize 15 epidemic Leptospira reference strains using the antisera of the *** immunoblot assay and reverse transcription-polymerase chain reaction demonstrated that thesethree OMPs were conservatively expressed in pathogenic *** strains and other pathogenic ***,the use of these recombinant OMPs as antigens in enzyme-linked immunosorbent assay (ELISA)for serodiagnosis of leptospirosis was *** recombinant LipL32 and OmpL1 proteins showed ahigh degree of ELISA reactivity with sera from patients infected with *** strain Lai and otherpathogenic *** results may contribute to the identification of candidates for broad-rangevaccines and immunodiagnostic antigens in further research.

关键词： outer membrane protein expression comparative analysis epidemic leptospire

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Reconstruction of the most recent common ancestor sequences of SARS-Cov S gene and detection of adaptive evolution in the spike protein

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chinese Science Bulletin 2004年第12期49卷 1311-1313页

作者： ZHANG Yuan1, ZHENG Nan2,3, HAO Pei4.5 & ZHONG Yang6 1. Laboratory of Systematic and Evolutionary Botany, Institute of Bot- any, chinese academy of sciences, Beijing 100093, china 2. College of Life sciences, Beijing Normal University, Beijing 100875, china 3. Institute of Viral Disease Control and Prevention, {4. CDC, Beijing 100052, china 4. bioinformation center, shanghai institutes for biological sciences, chinese academy of sciences, shanghai 2.0031, china 5. shanghai center for bioinformation Technology, shanghai 200235, china 6. School of Life sciences, Fudan University, shanghai 2004.3, china 1Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences 100093 Beijing China. 2College of Life sciences Beijing Normal University 100875 Beijing China. 3Institute of Viral Disease Control and Prevention Chinese CDC 100052 Beijing China. 4.0} center Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 200031 Shanghai China. 5shanghai center for bioinformation Technology 200235 Shanghai China. 6School of Life sciences Fudan University 200433 Shanghai China.

The genome organization and expression strategy of severe acute respiratory syndrome coronavirus (SARSCoV) have been described extensivelyl1- 10]. As a structural glycoprotein on the virion surface, the spike protein is responsible for binding to host cellular receptors and for the fusion between the viral envelope and the cellular membrane. It also induces neutralizing antibodies in the host and mediates cellular immunity[11]. Previous studies suggested that amino acid replacements in the spike protein could dramatically alter the pathogenesis and virulence of some coronaviruses[11]. It is therefore reasonable to test the hypothesis that radical amino acid replacements in the spike protein, favored by environmental selective pressure during the process of SARS-CoV interspecific transmission[10], might make this pathogen adapt to a new host. In this study, we investigated a total of 108complete sequences of the SARS-CoV S gene from GenBank (until March 23, 2004.. After omission of those records containing frame-shift mutations or low quality sequences, e.g. ZJ01, and selection of one sequence for identical records, an alignment of 4. sequences was obtained using the program Clustal-X[13]. Then, we reconstructed the most recent common ancestor (MRCA) sequences of the SARS-CoV S gene and detected the adaptive evolution in the spike protein.

关键词： SARS冠状病毒自适应进化基因表达糖蛋白分子免疫学波峰病毒

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