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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, chinese {3. of sciences, shanghai 20023., China 2. Graduate school of the chinese {3. of sciences, Beijing 10003., China 3. Institute of plant physiology and ecology, shanghai Institutes for biological sciences, chinese {3. 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 ecology 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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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 ecology, {3. Institute for biological sciences, the chinese academy of sciences, {3. 200025, China 2The Graduateschool of the chinese academy of sciences, Beijing 10003., China Institute of plant physiology and ecology 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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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 physiology & {3., 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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salt-responsive genes in rice revealed by cDNA microarray analysis

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Cell Research 2005年第10期 50-64页

作者： Dai Yin CHAO1,3. Yong Hai LUO1,3. Min sHI1, Da LUO1,2, Hong Xuan LIN1,2,* 1National Key Laboratory of plant Molecular Genetics, shanghai Institute of plant {3. and ecology, shanghai Institutes for biological sciences, chinese academy of sciences, 3.0 Fenglin Road, shanghai 20003., China, 2sHARF Laboratory, shanghai Institute of plant {3. and ecology, shanghai Institutes for biological sciences, chinese academy of sciences, 3.0 Fenglin Road, shanghai 20003., China, 3.raduate school of the chinese academy of sciences (D.C.), 19 Yuquan Road, Beijing 10003., China

We used cDNA microarrays containing ~9,000 unigenes to identify 486 salt responsive expressed sequence tags (EsTs) (representing ~450 unigenes) in shoots of the highly salt-tolerant rice variety, Nona Bokra (Oryza sativa L. ssp. Indica pv. Nona). some of the genes identified in this study had previously been associated with salt stress. However the majority were novel, indicating that there is a great number of genes that are induced by salt exposure. Analysis of the salt stress expression profile data of Nona provided clues regarding some putative cellular and molecular processes that are undertaken by this tolerant rice variety in response to salt stress. Namely, we found that multiple transcription factors were induced during the initial salt response of shoots. Many genes whose encoded proteins are implicated in detoxification, protectant and transport were rapidly induced. Genes supporting photosynthesis were repressed and those supporting carbohydrate metabolism were altered. Commonality among the genes induced by salt exposure with those induced during senescence and biotic stress responses suggests that there are shared signaling pathways among these processes. We further compared the transcriptome changes of the salt-sensitive cultivar, IR28, with that of Nona rice. Many genes that are salt responsive in Nona were found to be differentially regulated in IR28. This study identified a large number of candidate functional genes that appear to be involved in salt tolerance and further examination of these genes may enable the molecular basis of salt tolerance to be elucidated.

关键词： cDNA microarray rice salt stress signaling crosstalk transcriptome.

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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 {3. of sciences, Graduate school of the chinese {3. of sciences, shanghai 20003., China 2 Laboratory of Molecular Microbiology, Institute of plant physiology and ecology, shanghai Institutes for biological sciences, chinese {3. of sciences, Graduate school of the chinese {3. of sciences, shanghai 20003., China 3.shanghai Center for Bioinformation Technology, shanghai 20023., 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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The tricks plants use to reach appropriate light

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science China(Life sciences) 2010年第8期53卷 916-926页

作者： CHAO DaiYin1 & LIN HongXuan2 1Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, UsA 2National Key Laboratory of plant Molecular Genetics, shanghai Institute of plant {3. and ecology, shanghai Institutes for biological sciences, chinese academy of sciences, shanghai 20003., China 1. Department of Horticulture and Landscape Architecture Purdue University West Lafayette Indiana 47907 USA2. 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

The perception of ambient light signals that produce a relevant response to ensure exposure to appropriate levels of light energy is vital for plants. In response to this, intricate molecular mechanisms to mediate light signaling have evolved in plants. Among the responses induced by light, seedling extension is a determining event for plant survival in darkness, especially in the initial stage of plant growth. Here we review previous studies and recent progress towards an understanding of light signaling that regulates seedling elongation. We focus on the three regions of the sunlight spectrum that primarily control seedling elongation, namely red/far-red light, blue/UV-A light and UV-B light, and summarize the four signaling pathways that correspond to the three effective spectra.

关键词： photomorphogenesis light signaling photoreceptors cell elongation cell division

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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 U3.

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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,{3. Institutes for biological sciences,chinese academy of sciences,{3. 20003.,China 2 Department of Medicinal Chemistry,school of Pharmacy,Fudan University,{3. 20003.,China 3.state Key Laboratory of Genetic Engineering & Department of Microbiology,school of Life science,Fudan University,{3. 20043.,China 4 Laboratory of Disease and Health Genomics,chinese National Human Genome Center at {3.,{3. 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,U3.,were *** experiments showed that the promoter of U3. 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 3. bp cis-element locatedat 45 to 75 nt downstream of P1,or 3. 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 U3. 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 U3. pglnA in *** required GlnR,and its binding to the U3. pglnA was furtherconfirmed by the gel mobility shift *** and heterologous expression of the U3. glnR allowed usto detect the in vitro interaction between the U3. GlnR and the corresponding pglnA *** shown by in vivo glnR inactivation and complementation indicated that GlnR is essential for theactive transcription of glnA in U3..

关键词： glnA promoter cis-element glnR Amycolatopsis mediterranei

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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 physiology and {3.,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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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 physiology and {3., shanghai Institutes for biological sciences, chinese academy of sciences, shanghai 20003., China Department of Bi Institute of plant physiology and ecology 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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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 physiology and {3., 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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