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Identification and Characterization of glnA Promoter and its Corresponding Trans-regulatory Protein GlnR in the Rifamycin SV Producing Actinomycete,Amycolatopsis mediterranei U32

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Acta Biochimica et Biophysica Sinica 2006年第12期38卷 831-843页

作者： hao yu~(1&) wen-tao peng~1 yang liu~1 ting wu~2.yu-feng yao~1 ming-xue cui~1 wei-hong jiang~1 guo-ping zhao~(1,3,4*) 1 laboratory of molecular microbiology,institute of plant physiology and ecology,shanghai institutes for biological sciences,chinese academy of sciences,shanghai 2.0032.china 2 Department of Medicinal Chemistry,School of Pharmacy,Fudan University,shanghai 2.0032.china 3 State Key laboratory of Genetic Engineering & Department of microbiology,School of Life Science,Fudan University,shanghai 200433,china 4 laboratory of Disease and Health Genomics,chinese National Human Genome Center at shanghai,shanghai 201203,china laboratory of molecular microbiology Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China Department of Medicinal Chemistry School of Pharmacy Fudan University Shanghai 200032 China State Key laboratory of Genetic Engineering & Department of microbiology School of Life Science Fudan University Shanghai 200433 China laboratory of Disease and Health Genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China

The genetic requirements for the transcription of glnA,encoding the major glutaminesynthetase in a rifamycin SV-producing Amycolatopsis mediterranei strain,U32,were *** experiments showed that the promoter of U32 glnA （pglnA） was likely to have two transcriptioninitiation sites:P1and P2,located 157 and 45 nucleotides （nt） upstream of the translational start codon,*** mobility shift and DNase I footprinting analyses revealed a 30 bp cis-element locatedat 45 to 75 nt downstream of P1,or 38 to 68 nt upstream of *** sequence of the cis-element displayedhigh similarity to the corresponding regions of pglnA from Streptomyces coelicolor and *** as a reporter gene,the expression levels of U32 pglnA and its deletion derivatives under differentnitrogen-source conditions were analyzed by detecting the catechol dioxygenase activities in ***54,*** J508 and *** FS10 （glnR mutant）.These in vivo studies showed that theactivation of U32 pglnA in *** required GlnR,and its binding to the U32 pglnA was furtherconfirmed by the gel mobility shift *** and heterologous expression of the U32 glnR allowed usto detect the in vitro interaction between the U32 GlnR and the corresponding pglnA *** shown by in vivo glnR inactivation and complementation indicated that GlnR is essential for theactive transcription of glnA in U32.

关键词： glnA promoter cis-element glnR Amycolatopsis mediterranei

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Bacterial Type Ⅰ Glutamine Synthetase of the Rifamycin SV Producing Actinomycete,Amycolatopsis mediterranei U32,is the Only Enzyme Responsible for Glutamine Synthesis under Physiological Conditions

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Acta Biochimica et Biophysica Sinica 2006年第12期 821-830页

作者： wen-tao peng~(1&) Jin WANG~1 ting wu~2 Jian-Qiang HUANG~1 Jui-Shen CHIAO~1 guo-ping zhao~(1,3,4) 1 laboratory of molecular microbiology,institute of plant physiology and ecology,shanghai institutes for biological sciences,chinese academy of sciences,shanghai 2.0032.china 2 Department of Medicinal Chemistry,School of Pharmacy,Fudan University,shanghai 2.0032.china 3 State Key laboratory of Genetic Engineering/Department of microbiology,School of Life Science,Fudan University,shanghai 200433,china 4 laboratory of Health and Disease Genomics,chinese National Haman Genome Center at shanghai,shanghai 201203,china

The structural gene for glutamine synthetase,glnA,from Amycolatopsis mediterranei U32 wascloned via screening a genomic library using the analog gene from Streptomyces *** clone wasfunctionally verified by complementing for glutamine requirement of an Escherichia coli glnA null mutantunder the control of a lac *** analysis showed an open reading frame encoding a protein of466 amino acid *** deduced amino acid sequence bears significant homologies to other bacterialtype Ⅰ glutamine synthetases,specifically,71% and 72% identical to the enzymes of *** and Myco-bacterium tuberculosis,*** of this glnA gene in *** U32 led to glutamineauxotrophy with no detectable glutamine synthetase activity in *** contrast,the cloned glnA+gene cancomplement for both phenotypes in *** thus suggested that in *** U32,the glnA geneencoding glutamine synthetase is uniquely responsible for in vivo glutamine synthesis under our laboratorydefined physiological conditions.

关键词： glnA glutamine synthetase Amycolatopsis mediterranei rifamycin SV

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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 200031, 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 2.0032, china 3 shanghai Center for Bioinformation Technology, shanghai 200235, china BioinformationCenter KeyLabofSystemsBiologyShanghaiInstitutesforBiologicalSciencesChineseAcademyofSciencesGraduateSchooloftheChineseAcademyofSciencesShanghai200031China

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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Tumor-derived neomorphic mutations in ASXL1 impairs the BAP1-ASXL1-FOXK1/K2 transcription network

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Protein & Cell 2021年第7期12卷 557-577页

作者： yu-Kun Xia Yi-Rong Zeng Meng-Li Zhang peng liu Fang liu hao Zhang Chen-Xi He Yi-ping Sun Jin-Ye Zhang Cheng Zhang Lei Song Chen Ding yu-Jie Tang Zhen yang Chen yang Pu Wang Kun-Liang Guan yue Xiong Dan Ye Huashan Hospital Fudan Universityand Molecular and Cell Biology LabInstitutes of Biomedical Sciencesand the Shanghai Key Laboratory of Medical Epigeneticsand the Key Laboratory of Metabolism and MolecularMinistry of EducationShanghai 200032China The International Co-laboratory of Medical Epigenetics and Metabolism Ministry of Science and TechnologyShanghai 200032China Department of Neurosurgery Huashan HospitalFudan UniversityShanghai 200032China Key laboratory of Cell Differentiation and Apoptosis of National Ministry of Education Department of PathophysiologyShanghai Jiao Tong University School of MedicineShanghai 200025China Key laboratory of Synthetic Biology Institute of Plant Physiology and EcologyShanghai 200032China institutes for biological sciences Chinese Academy of SciencesShanghai 200032China State Key laboratory of Proteomics Beijing Proteome Research CenterBeijing Institute of Radiation MedicineBeijing 102206China National Center for Protein sciences(The PHOENIX Center Beijing)Beijing 102206China State Key laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development School of Life SciencesInstitutes of Biomedical SciencesFudan UniversityShanghai 200032China Department of Pharmacology and Moores Cancer Center University of California San DiegoLa JollaCAUSA Lineberger Comprehensive Cancer Center Department of Biochemistry and BiophysicsUniversity of North CarolinaChapel HillNCUSA Department of General Surgery Huashan HospitalFudan UniversityShanghai 200032China

Additional sex combs-like 1(ASXL1)interacts with BRCA1-associated protein 1(BAP1)deubiquitinase to oppose the polycomb repressive complex 1(PRC1)-mediated histone H2A *** BAP1 mutations are found in a spectrum of human malignancies,while ASXL1 mutations recurrently occur in myeloid neoplasm and are associated with poor *** all ASXL1 mutations are heterozygous frameshift or nonsense mutations in the middle or to a less extent the C-terminal region,resulting in the production of C-terminally truncated mutant ASXL1 *** ASXL1 regulates specific target genes and how the C-terminal truncation of ASXL1 promotes leukemogen-esis are ***,we report that ASXL1 interacts with forkhead transcription factors FOXK1 and FOXK2 to regulate a subset of FOXK1/K2 target *** show that the C-terminally truncated mutant ASXL1 proteins are expressed at much higher levels than the wild-type protein in ASXL1 heterozygous leukemia cells,and lose the ability to interact with FOXK1/*** deletion of the mutant allele eliminates the expression of C-termi-nally truncated ASXL1 and increases the association of wild-type ASXL1 with BAP1,thereby restoring the expression of BAP1-ASXL1-FOXK1/K2 target genes,particularly those involved in glucose metabolism,oxygen sensing,and JAK-STAT3 signaling *** addition to FOXK1/K2,we also identify other DNA-bind-ing transcription regulators including transcription factors(TFs)which interact with wild-type ASXL1,but not C-terminally truncated *** results suggest that ASXL1 mutations result in neomorphic alleles that contribute to leukemogenesis at least in part through dominantly inhibiting the wild-type ASXL1 from interacting with BAP1 and thereby impairing the function of ASXL1-BAP1-TF in regulating target genes and leukemia cell growth.

关键词： ASXL1 BAP1 FOXK1/K2 leukemia epigenetics

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Toward understanding genetic mechanisms of complex traits in rice

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Journal of Genetics and Genomics 2010年第10期37卷 653-666页

作者： wei hao hong-Xuan Li National Key laboratory of plant molecular Genetics Shanghai Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China

Rice is the primary carbohydrate staple cereal feeding the world population. Many genes, known as quantitative trait loci （QTLs）, con- trol most of the agronomically important traits in rice. The identification of QTLs controlling agricultural traits is vital to increase yield and meet the needs of the increasing human population, but the progress met with challenges due to complex QTL inheritance. To date, many QTLs have been detected in rice, including those responsible for yield and grain quality; salt, drought and submergence tolerance; disease and insect resistance; and nutrient utilization efficiency. Map-based cloning techniques have enabled scientists to successfully fine map and clone approximately seventeen QTLs for several traits. Additional in-depth functional analyses and characterizations of these genes will provide valuable assistance in rice molecular breeding.

关键词： rice quantitative trait loci (QTLs) mapping populations marker-assisted selection (MAS) map-based cloning

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Identification of Quantitative Trait Loci for Rice Quality in a Population of Chromosome Segment Substitution Lines

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Journal of Integrative plant Biology 2009年第5期51卷 500-512页

作者： wei hao Mei-Zhen Zhu Ji-ping Gao Shi-Yong Sun hong-Xuan Lin National Key laboratory of plant molecular Genetics Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences the Chinese Academy of Sciences Shanghai 200032 China

The demand for high quality rice represents a major issue in rice production. The primary components of rice grain quality include appearance, eating, cooking, physico-chemical, milling and nutritional qualities. Most of these traits are complex and controlled by quantitative trait loci （QTLs）, so the genetic characterization of these traits is more difficult than that of traits controlled by a single gene. The detection and genetic identification of QTLs can provide insights into the genetic mechanisms underlying quality traits. Chromosome segment substitution lines （CSSLs） are effectivetools used in mapping QTLs. In this study, we constructed 154 CSSLs from backcross progeny （BC3F2） derived from a cross between ＇Koshihikari＇（an Oryza sativa L. ssp. japonica variety） as the recurrent parent and ＇Nona Bokra＇（an O. sativa L. ssp. indica variety） as the donor parent. In this process, we carried out marker-assisted selection by using 102 cleaved amplified polymorphic sequence and simple sequence repeat markers covering most of the rice genome. Finally, this set of CSSLs was used to identify QTLs for rice quality traits. Ten QTLs for rice appearance quality traits were detected and eight QTLs concerned physico-chemical traits. These results supply the foundation for further genetic studies and breeding for the improvement of grain quality.

关键词： appearance quality traits chromosome segment substitution lines Oryza sativa physico-chemical quality traits quantitative trait loci

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Production of very-high-amylose cassava by post-transcriptional silencing of branching enzyme genes

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Journal of Integrative plant Biology 2020年第6期62卷 832-846页

作者： wenzhi Zhou Shanshan zhao Shutao He Qiuxiang Ma Xinlu Lu Xiaomeng hao hongxia Wang Jun yang peng Zhang National Key laboratory of plant molecular Genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological Sciencesthe Chinese Academy of SciencesShanghai 200032China shanghai Key laboratory of plant Functional Genomics and Resources Shanghai Chenshan Plant Science Research CenterShanghai Chenshan Botanical Gardenthe Chinese Academy of SciencesShanghai 201602China University of chinese academy of sciences Beijing 100049China

High amylose starch can be produced by plants deficient in the function of branching enzymes(BEs).Here we report the production of transgenic cassava(Manihot esculenta Crantz)with starches containing up to 50%amylose due to the constitutive expression of hair-pin ds RNAs targeting the BE1 or BE2 *** BE1-RNAi plant lines(BE1i)and BE2-RNAi plant lines(BE2i)were grown up in the field,but with reduced total biomass *** high amylose content in the storage roots of BE2i plant lines was *** starch granules of BE1i and BE2i plants had similar morphology as wild type(WT),however,the size of BE1i starch granules were bigger than that of *** of amylograms and thermograms of all three sources of storage starches revealed dramatic changes to the pasting properties and a higher melting temperature for BE2i *** chain length distribution analysis showed a slight increase in chains of DP>36 in BE1i lines and a dramatic increase in glucan chains between DP 10-20 and DP>40 in BE2i ***,BE2i starches displayed a B-type X-ray diffraction pattern instead of the A-type pattern found in BE1i and WT ***,cassava BE1 and BE2 function differently in storage root starch biosynthesis.

关键词： chains branching pattern

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Fine Mapping of Spr3, a Locus for Spreading Panicle from African Cultivated Rice （Oryza glaberrima Steud.）

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molecular plant 2008年第5期1卷 830-838页

作者： Ji-Jing Luo wei hao Jian Jin Ji-ping Gao hong-Xuan Lin National Key laboratory of plant molecular Genetics Shanghai Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences The Chinese Academy of Sciences Graduate School of the Chinese Academy of Sciences 300 Fenglin Road Shanghai 200032 China

A CSSL （chromosome segment substitution line）, SG-64, carrying a segment of chromosome 4 from African cultivated rice （CG-14） in the genetic background of var. wuyujing-7 （japonica）, showed a spreading panicle, which was different significantly from that of wuyujing-7 with an erect compact panicle. The gene controlling a spreading panicle is referred to as Spr3, and is mapped on chromosome 4. To uncover the genetic basis of Spr3, a large F2 population derived from cross between SG-64 and wuyujing-7 was constructed for fine mapping of the Spr3 locus. The high-resolution linkage analysis revealed that the Spr3 locus was narrowed down to a 4.6-kb region. The delimited genomic DNA regions of wuyujing-7 and CG-14 were sequenced and compared. Sequence mutations between wuyujing-7 and CG-14 were evident and the candidate genes for the locus were predicted. Publicly available databases were searched for homologous cDNA sequences. However, any coding regions or other meaningful sequences for the Spr3 locus were not found within this delimited region. This result suggested that Spr3 is an unknown genetic factor in controlling the outspreading of the primary branches in rice inflorescence. In addition, NIL（Spr3） exhibited seed shattering. The formation of spreading panicle was accompanied by a few undesirable traits and the spreading panicle links with seed shattering suggest that the spreading panicle was likely lost during the domestication and selection for high seed productivity of cultivated rice.

关键词： rice spreading panicle fine mapping molecular marker.

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Computation-Based Development of Therapeutic Strategy for Fragile X Syndrome

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神经药理学报 2019年第Z1期 59-60页

作者： DING Qi Ferzin Sethna wu xue-ting MIAO Zhuang CHEN ping ZHANG yue-qi XIAO Hua feng wei feng yue LI Xuan 王红兵 Department of physiology 2Genetics ProgramMichigan State University Key laboratory of Synthetic Biology Institute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of Sciences Department of Pharmacology and Chemical Biology Emory University School of Medicine 密西根州立大学生理系

Fragile X syndrome(FXS),caused by mutations in fragile X mental retardation 1 gene(FMR1),is a prevailing genetic disorder of intellectual disability and autism. Currently,there is no efficacious medication for FXS. Here,we use transcriptome landscape as a holistic molecular phenotype/endpoint to identify potential therapeutic intervention. Through in silico screening with public gene signature database,computational analysis of transcriptome profile in Fmr1 knockout(KO) neurons predicts therapeutic value of an FDA-approved drug trifluoperazine. Through experimental validation,we find that systemic administration of trifluoperazine attenuates multiple FXS-and autism-related behavioral symptoms. Moreover,computational analysis of transcriptome alteration caused by trifluoperazine suggests a new mechanism of action against PI3 K(Phosphatidylinositol-4,5-bisphosphate 3-kinase) activity. Consistently,trifluoperazine suppresses PI3 K activity and its down-stream targets Akt(protein kinase B) and S6 K1(S6 kinase 1) in neurons. In conclusion,our data demonstrate promising value of gene signature-based computation in identification of therapeutic strategy and repurposing drugs for neurological disorders,and suggest trifluoperazine as a potential practical treatment for FXS.

关键词： fragile X syndrome transcriptome signature connectivity MAP mouse model therapeutic development

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Cryo–EM structure of the CRY2 and CIB1 fragment complex provides insights into CIB1-mediated photosignaling

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plant Communications 2023年第2期4卷 4-7页

作者： Yahui hao xue Zhang Yaqi liu Miaolian Ma Xiaowei Huang hongtao liu peng Zhang National Key laboratory of plant molecular Genetics Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina University of chinese academy of sciences BeijingChina

Dear Editor,Cryptochromes(CRYs)are blue-light photoreceptors that mediate various light responses in plants(Wang and Lin,2020;Wang et al.,2021).Two CRYs have been identified in Arabidopsis thaliana(At),AtCRY1 and AtCRY2,which mediate hypocotyl elongation and floral initiation(Ahmad and Cashmore,1993;guo et al.,1998).CRYs are comprised of a conserved N-terminal photolyase-related(PHR)domain for chromophore FAD binding and a C-terminal domain(CCE)of variable length,and different plant CRYs have been found to exert overlapping biological functions(Lin et al.,1998;Rosenfeldt et al.,2008).

关键词： CRY1 CRY2 structure

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