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Sequence analysis of mRNA polyadenylation signals of rice genes

chinese Science Bulletin 2006年第9期51卷 1069-1077页

作者： LU Ying1, 2, GAO Chenxi1,2,3.& HAN Bin1,3.41. National Center for Gene Research, shanghai institutes for biological Sciences, {3. academy of Sciences, shanghai 20023., china 2. Graduate School of the {3. academy of Sciences, Beijing 10003., china 3. institute of plant physiology and ecology, shanghai institutes for biological Sciences, {3. academy of Sciences, shanghai 20003., china National Center for Gene Research Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200233 China Graduate School of the chinese academy of Sciences Beijing 100039 China institute of plant physiology and {3. Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China

The formation of eukaryotic mRNAs involves the cleavage and polyadenylation of pre- mRNAs. To investigate the sequence requirement of putative polyadenylation signals (PASs), poly(A) sites and downstream elements (DUEs) in 3.-end-pro- cessing in rice, we compared expressed sequences tags (ESTs) with poly(A) extremity to full-length cDNA sequences and constructed a database of 12969 pre- mRNA sequences in ?40―+40 nt surrounding the poly(A) sites, which were from 9953.genes. The al- ternative poly(A) sites were revealed in approxi- mately 25% of mRNAs. Nearly 80% of pre-mRNAs showed stringent requirement of the YA (CA or UA) at poly (A) sites for polyadenylation. About 7.9% had the AAUAAA signals on ?40―?1 nt upstream of the poly(A) sites. Over 60% of mRNAs probably used the one- or two-base variants of AAUAAA hexamers as their PASs in 3. fragments. The single-base variants of AAUGAA revealed the high frequency in 11.5% of 3. fragments. The DUEs were detected in 90% of pre- mRNAs, especially more than half of the pre-mRNAs with multi-base variants of AAUAAA had the DUEs surrounding the poly(A) site. The location of DUE is also important for defining the cleavage site. Al- though most of the rice pre-mRNAs did not contain AAUAAA signal, the existence of downstream ele- ments ensured the efficiency of cleavage-polyade-

关键词：多聚腺苷酸序列分析 mRNA 水稻基因工程

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Expressional Analysis of an EREBP Transcription Factor Gene OsEBP-89 in Rice

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Acta Biochimica et Biophysica Sinica 2004年第1期36卷 21-26页

作者： Hui SHEN and Zong-Yang WANG( The State Key Laboratory of plant Molecular Genetics, institute of plant {3. & ecology, shanghai institutes for biological Sciences,the chinese academy of Sciences, shanghai 20003., china ) The State Key Laboratory of plant Molecular Genetics Institute of Plant Physiology & Ecology Shanghai Institutes for Biological Sciences the Chinese Academy of Sciences Shanghai 200032 China

OsEBP-89 gene encodes an ethylene responsive element binding protein (EREBP) transcription factor from rice (Oryza sativa). Northern blot analysis revealed that OsEBP-89 was expressed in root, stem, seeds, flowers and leaves. Histochemical assay showed that β-glucuronidase (GUS) was expressed mainly in phloem of vascular tissues of the root and stem transition region (RST), basal part of sheath roots, stem node and basal part of adventitious roots, also in endosperm of seeds in transgenic rice harboring OsEBP-89/GUS construct (pNSG). A sequence region from -279 to -97 was found to play an important role for OsEBP-89 gene expression through promoter deletion assay. The possible function of OsEBP-89 gene was discussed.

关键词： OsEBP-89 gene rice EREBP subfamily transcription factor tissue expression

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Positive Charges on Lysine Residues of the Extrinsic 18 kDa Protein Are Important to Its Electrostatic Interaction with Spinach Photosystem Ⅱ Membranes

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Acta Biochimica et Biophysica Sinica 2005年第11期37卷 737-742页

作者： Jin-Peng GAO Zhen-Hua YONG Feng ZHANG Kang-Cheng RUAN Chun-He XU Gen-Yun CHEN institute of plant physiology & {3..shanghai institutes for biological Sciences,chinese academy of Sciences,shanghai 20003.,china Laboratory of Proteomics,institute of Biochemistry and Cell Biology,shanghai institutes for biological Sciences,chinese academy of Sciences,shanghai 20003.,china College of Sciences,Zhejiang University.Hangzhou 3.0029,china Graduate School of the chinese academy of Sciences,shanghai 20003.,china institute of plant physiology & {3. Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200032 China Graduate School of the chinese academy of Sciencesshanghai {3. China College of Sciences Zhejiang UniversityHangzhou 310029 China Laboratory of Proteomics Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200031 China

To determine the contribution of charged amino acids to binding with the photosystem Ⅱcomplex(PSⅡ),the amino or carboxyl groups of the extrinsic 18 kDa protein were modified with N-succinimidyl propionate(NSP)or glycine methyl ester(GME)in the presence of a water-soluble carbodiimide,*** on isoelectric point shift,4-10 and 10-14 amino groups were modified in the presence of2 and 4 mM NSP,***,3.4 carboxyl groups were modified by reaction with *** of negatively charged carboxyl groups with GME did not alter the binding activity of theextrinsic 18 kDa ***,the NSP-modified 18 kDa protein,in which the positively charged aminogroups had been modified to uncharged methyl esters,failed to bind with the PSⅡ membrane in the presenceof the extrinsic 23.kDa *** defect can not be attributed to structural or conformational alterationsimposed by chemical modification,as the fluorescence and circular dichroism spectra among native,GME-and NSP-modified extrinsic 18 kDa proteins were ***,we have concluded that the positive chargesof lysyl residues in the extrinsic 18 kDa protein are important for its interaction with PSⅡ membranes in thepresence of the extrinsic 23.kDa ***,it was found that the negative charges of carboxylgroups of this protein did not participate in binding with the extrinsic 23.kDa protein associated with PSⅡmembranes.

关键词： extrinsic 18 kDa protein circular dichroism electrostatic interaction chemical modification

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Are small RNAs a big help to plants?

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Science china(Life Sciences) 2009年第3期52卷 212-223页

作者： MAO YingBo,XUE XueYi & CHEN XiaoYa National Key Laboratory of plant Molecular Genetics,institute of plant {3. and ecology,shanghai institutes for biological Sciences,chinese academy of Sciences,shanghai 20003.,china 1. National Key Laboratory of plant Molecular Genetics Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China

The discovery of RNA interference(RNAi) has augmented our knowledge of gene regulation and presents a fascinating technology that has a great potential for application in genetic analysis,disease therapy,plant protection,and many other *** this review,we will focus on the biological functions of RNAi and its application in agriculture with a brief introduction to the history of its discovery and molecular mechanism.

关键词： RNA interference gene regulation plant protection

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Agrobacterium tumefaciens-mediated transformation of rice with the spider insecticidal gene conferring resistance to leaffolder and striped stem borer

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Cell Research 2001年第2期11卷 149-155页

作者： HUANG JIAN QIU, ZHI MING WEI, HAI LONG AN, YU XIAN ZHU National Laboratory of plant Molecular Genetics, institute of plant {3. and ecology, shanghai institutes for biological Sciences, chinese academy of Sciences, shanghai 20003., china National La National Laboratory of plant Molecular Genetics Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai. jqhuang@***

Immature embryos of rice varieties 'Xiushui11' and 'Chunjiang 11' precultured for 4d were infected and transformed by Agrobacterium tumefaciens strain EHA101/pExT7 (containing the spider insecticidal gene). The resistant cant were transferred onto the differentiation medium and plants were regenerated. The transformation frequency reached 56%-72% measured as numbers of Geneticin (G418)-resistant calli produced and 3.%-60% measured as numbers of transgenic plants regenerated, respectively. PCR and Southern blot analysis of transgenic plants confirmed that the T-DNA had been integrated into the rice genome. Insect bioassays using T1 transgenic plants indicated that the mortality of the leaffolder (Cnaphalocrasis medinalis) after 7d of leaf feeding reached 3.%-61% and the corrected mortality of the striped stem borer (Chilo suppressalis) after 7d of leaf feeding reached 16%-75%. The insect bioassay results demonstrated that the transgenic plants expressing the spider insecticidal protein conferred enhanced resistance to these pests.

关键词： Rice Agrobacterium tumefaciens spider insecticidal gene transgenic plant Leaffolder striped stem borer insect bioassay.

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Regeneration of plants from callus tissues of hairy roots induced by Agrobacterium rhizogenes on Alhagi pseudoalhagi

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Cell Research 2001年第4期11卷 279-284页

作者： WANG YU MEI, JIANG BO WANG, DA LUO , JING FEN JIA National Laboratory of plant Molecular Genetics, institute of plant {3. and ecology, shanghai institutes for biological Sciences, chinese academy of Sciences, shanghai 20003., china Department of Bi institute of plant physiology and {3. Shanghai Institutes for Biological Sciences Chinese Academy of Sciences.

The legume forage Alhagi pseudoalhagi was transformed by the Agrobacterium rhizogenes strain A4 using cotyledon and hypocotyl segments as infection materials. Regenerated plants were achieved from sterile calli derived from hairy roots, which occurred at or near the infection sites. The regenerated plants from hairy root were characterized by normal leaf morphology and stem growth but a shallow and more extensive root system than normal plants. Opine synthesis, PCR and Southern blot confirmed that T- DNA had been integrated into the A. pseudoalhagi genome. Acetosyringone (AS) was found to be vital for successful transformation of A. pseudoalhagi.

关键词： Alhagi pseudoalhagi Agrobacterium rhizogenes hairy root regeneration.

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Auxin distribution and transport during embryogenesis and seed germi-nation of Arabidopsis

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Cell Research 2001年第4期11卷 273-278页

作者： NI DI AN, LING JIAN WANG, CHUN HONG DING, ZHI HONG XU, institute of plant physiology and {3., shanghai institutes for biological Sciences, chinese academy of Sciences, shanghai 20003., china College of Bioscience, East china Normal University, Shangha 1institute of plant physiology and {3. Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China 1institute of plant physiology and {3. Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China 2College of Bioscience East China Normal University Shanghai 200062 China 3.ollege of Life Sciences Peking University Beijing 100871 China

Auxin distribution during embryogenesis and seed germination were studied with transgenic Arabidopsis plants expressing GUS gene driven by a synthetic DR5 promoter,an auxin responsive promoter. The results showed that GUS activity is higher in ends of hypophysis and cotyledon primordia of heart-, torpedo- and cotyledon-stage embryos, leaf tip area, lateral root primordia, root apex and cotyledon of young seedlings. And GUS accumulated in root apex of the seedlings grown on auxin transport inhibitor containing media. All these suggested that above-mentioned part of the organs and tissues have a higher level of auxin, and auxin polar transport inhibitor could cause the accumulation of auxin in root apex. And auxin transport inhibitor also resulted in aberration of Arabidopsis leaf pattern formation, root gravitropism and elongation.

关键词： Auxin auxin distribution auxin polar transport auxin-responsive promoter transgenic Ara- bidopsis.

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Tissue Distribution and Purification of Prophenoloxidase in Larvae of Asian Corn Borer, Ostrinia furnacalis Guenée (Lepidoptera: Pyralidae)

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Acta Biochimica et Biophysica Sinica 2004年第5期36卷 360-364页

作者： Cong-Jing FENG1,2 and Wen-Jun FU1* 1institute of plant physiology and {3., shanghai institute for biological Sciences, the chinese academy of Sciences, shanghai 200025, china 2The GraduateSchool of the chinese academy of Sciences, Beijing 10003., china institute of plant physiology and {3. Shanghai Institute for Biological Sciences the Chinese Academy of Sciences The Graduate School of the chinese academy of Sciences

Using ammonium sulphate precipitation, Blue-Sepharose CL-6B, Phenyl-Sepharose CL-4B, prophenoloxidase (PPO) was isolated and purified from hemolymph of Ostrinia furnacalis larvae. This zy- mogen was a heterodimer, and composed of two subunits with the relative molecular mass ranging from 66.2 kD to 97.4 kD determined by SDS-PAGE. Western blotting and indirect immunofluorescence test showed that PPO was present in integument, hemolymph plasma and cell membrane of granular hemocytes and oenocytoids of O. furnacalis larvae.

关键词： Ostrinia furnacalis prophenoloxidase tissue distribution purification

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Overview of Rim2/Hipa transposon superfamily:Structure, distribution, transposition and utilization

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Progress in Natural Science:Materials International 2008年第4期18卷 375-379页

作者： Pingfang Tian a, Zuhua He b a College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, china b shanghai institute of {3. physiology and ecology, shanghai institute for biological Sciences, chinese academy of Sciences, shanghai 20003., china College of Life Science and Technology Beijing University of Chemical Technology Beijing 100029 China shanghai institute of plant {3. and ecology Shanghai Institute for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China

The rice Rim2/Hipa is a unique transposon superfamily in Oryza genomes, which can be transcriptionally activated by the infection of the rice blast pathogen Magnaporthe grisea and its elicitors. Rim2/Hipa elements belong to En/Spm family, with perfect terminal inverted repeats in both ends, direct and inverted sub-terminal repeats, and 3.bp target site duplication upon insertion. Intriguingly, the typical ’CACTG’ end sequences in the terminal inverted repeats of most Rim2/Hipa elements distinguish them from previously reported CACTA elements, such as En/Spm, Tam1, and Tgm1, which harbor ’CACTA’ sequence in their terminal inverted repeats. In particular, the plentiful Rim2/Hipa elements unevenly distribute over all 12 chromosomes and make up at least 1% of the entire genome. Southern hybridization revealed the existence of Rim2/Hipa elements in all rice varieties examined and the Rim2/Hipa core sequence is unique to rice genomes. Evidence derived from sequence analysis indicated the occurrence of transposition events during the long evolution. The abundance and insertion polymorphisms suggested their applications as novel molecular marker in rice fingerprinting and fine chromo- some mapping. This paper aims at outlining the Rim2/Hipa elements with respect to their structure, distribution, transposition and utilization.

关键词： Rim2/Hipa elements Structure Distribution Transposition Utilization

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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. {3. academy of Sciences. shanghai 20023.. china. 2 Graduate School of the {3. academy of Sciences. Beijing 10003..china 3.institute of plant physiology and {13.. shanghai institutes for biological Sciences. {3. academy of Sciences. shanghai 20003.. china NationalCenterforGeneResearch ShanghaiInstitutesforBiologicalSciencesChineseAcademyofSciencesShanghai200233

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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