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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 2.003., china National Center for Gene Research Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China Graduate School of the chinese academy of Sciences Beijing China institute of plant {2. and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 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 12.69 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 2.% 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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Ultrafast excitation relaxation in light-harvesting complex LH2.from *** 601

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Science china Chemistry 2004年第3期47卷 192-199页

作者： GUO Lijun1,2. LIU Yuan3. LIU Weimin2. GUO Junhua1, XU Chunhe3.& QIAN Shixiong2.1. School of Physics and Information Optoelectronics, Henan University, Kaifeng 475001,{2. 2. Physics Department, Fudan University, shanghai 2.043.,{2. 3. shanghai institute of plant physiology, chinese {12. of Sciences, shanghai 2.003.,{2. School of Physics and Information Optoelectronics Henan University Kaifeng China Physics Department Fudan University Shanghai China shanghai institute of {2. {3. Chinese Academy of Sciences Shanghai China

The energy relaxation and kinetic evolution of transient spectra of bacteriochloro- phylls (BChls) in light-harvesting complex LH2.from Rb. sphaeroides 601 were investigated using femtosecond pump-probe technique. Upon 783.nm excitation, the energy at B800 BChls ex-periences an intramolecular redistribution with 0.3. ps time constant before transferring to B850 BChls. With tuning the excitation wavelength, the dynamical evolution of excited BChls was clearly observed, which indicates an obvious competition between the ground state bleaching and excited state absorption (ESA) of BChls involved and an isosbestic point near 818 nm, and also demonstrates that from the lower electronic excited state of B800 BChls to the higher exci-tonic state of B850 BChls is an efficient routine for energy transfer. The excitation energy in higher excitonic states of B850 BChls relaxes rapidly to the next lowest excitonic state by inter-conversion, delocalization to adjacent molecular, populating the lowest excitonic state and the change of molecular conformation.

关键词： photosynthesis, light-harvesting complex, energy transfer, ultrafast, dynamics, purple bacteria.

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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 2.003., 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 2.003., china 3.shanghai Center for Bioinformation Technology, shanghai 2.02.0}, 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 2.02.2. 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 2.02.and 2.03. 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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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 {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 2.003.. china National Center for Gene Research Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200233 China Graduate School of the chinese academy of SciencesBeijing 1000{2. China institute of plant {2. 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 C2.ompounds 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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cvhA Gene of Streptomyces hygroscopicus 10-2. Encodes a Negative Regulator for Mycelia Development

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Acta Biochimica et Biophysica Sinica 2006年第4期38卷 271-280页

作者： Heng-An WANG~(1,2.) Lei QIN~(2.) Ping LU~(1*) Zhi-Xuan PANG~2.Zi-Xin DENG~(3.) Guo-Ping ZHAO~(2.) 1 Biotechnology institute,School of Agriculture and Biology,{2. Jiaotong University,{2. 2.1101,{3. 2.Laboratory of Molecular Microbiology,institute of plant physiology and Ecology,{2. institute for Biological Sciences,chinese academy of Sciences,{2. 2.003.,{3. 3.Bio-X Life Science Research Center,{2. Jiaotong University,{2. 2.003.,{3.. Biotechnology institute School of Agriculture and Biology Shanghai Jiaotong UniversityShanghai 201101 China Laboratory of Molecular Microbiology Institute of Plant Physiology and Ecology Shanghai Institute for Biological Sciences Chinese Academy of SciencesShanghai 200032 China Bio-X Life Science Research Center Shanghai Jiaotong UniversityShanghai 200030 China.

A five-gene cluster cvhABCDE was identified from Streptomyces hygroscopicus *** thefirst gene of this cluster,cvhA encoded a putative sensor histidine kinase with a predicted sensor domainconsisting of two trans-membrane segments at the N-terminus and a conserved HATPasecdomain at the *** C-terminus polypeptide of CvhA expressed in Escherichia coli was purified and shown to beautophosphorylated with [γ-3.P]ATP in *** phosphoryl group was acid-labile and basic-stable,whichsupported histidine as the phosphorylation *** obvious difference of mycelia development was ob-served between the null mutant of cvhA generated by targeted gene replacement and the wild-type parentalstrain 10-2. grown on solid soya flour medium with 2.-8% glucose or sucrose,but the cvhA mutant couldform much more abundant aerial mycelia and spores than the wild-type strain on solid soya flour mediumsupplemented with 6%-8% mannitol,6%-8% sorbitol,4%-6% mannose,or 4%-6% *** pheno-type was complemented by the cloned wild-type cvhA gene,and no difference was observed for growthcurves of the cvhA mutant and the wild strain in liquid minimal medium with the tested sugars at a concen-tration of 4%,6% and 8%.We thus propose that CvhA is likely a sensor histidine kinase and negativelyregulates the morphological differentiation in a sugar-dependent manner in *** 10-2..

关键词： sensor histidine kinase aerial mycelia sugar metabolism

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Transiently Expressed Short Hairpin RNA Targeting 12. kDa Protein of Tobacco Mosaic Virus Interferes with Virus Infection

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Acta Biochimica et Biophysica Sinica 2006年第1期38卷 22-28页

作者： Ming-Min ZHAO~(1,2.,De-Rong AN~(1*),Jian ZHAO~2.Guang-Hua HUANG~3.Zu-Hua HE~4,and Jiang-Ye CHEN~3. ~1 College of {2. Protection,Northwest Science and Technology University of Agriculture and Forestry,Yangling 712.00,china ~2.College of Agriculture,Yangtze University,Jingzhou 43.02.,china ~3.State Key Laboratory of Molecular Biology,{3. of Biochemistry and Cell Biology,shanghai {3.s for Biological Sciences, chinese academy of Sciences,shanghai 2.003.,china ~4 State Key Laboratory of {2. Molecular Genetics,{3. of {2. physiology and Ecology,shanghai {3.s for Biological Sciences, chinese academy of Sciences,shanghai 2.003.,china College of plant Protection Northwest Science and Technology University of Agriculture and Forestry Yang ling 712100 China College of Agriculture Yangtze University Jingzhou 434025 China State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China State Key Laboratory of plant Molecular Genetics Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China

RNA-interference (RNAi) silences gene expression by'guiding mRNA degradation in asequence-specific *** interfering RNA (siRNA),an intermediate of the RNAi pathway,has beenshown to be very effective in inhibiting virus infection in mammalian cells and cultured plant ***,wereport that Agrobacterium tumefaciens-mediated transient expression of short hairpin RNA (shRNA) couldinhibit tobacco mosaic virus (TMV) RNA accumulation by targeting the gene encoding the replication-asso-ciated 12. kDa protein in intact plant *** results indicate that transiently expressed shRNA efficientlyinterfered with TMV *** interference observed is sequence-specific,and time-and *** expressed shRNA corresponding to the TMV 12. kDa protein gene did not inhibit cucumbermosaic virus (CMV),an unrelated *** order to interfere with TMV accumulation in tobaccoleaves,it is essential for the shRNA constructs to be infiltrated into the same leaves as TMV *** support the view that RNAi opens the door for novel therapeutic procedures against virus *** propose that a combination of the RNAi technique and Agrobacterium-mediated transient expressioncould be employed as a potent antiviral treatment in plants.

关键词： tobacco mosaic virus 12. kDa protein RNA interference short hairpin RNA

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Morphology and mapping analysis of rice(Oryza sativa L.)clustered spikelets(Cl)mutant

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chinese Science Bulletin 2003年第6期48卷 559-562页

作者： ZHENG Leiying1, ZHU Xudong2. QIAN Qian2. ZHAO Zhong1, ZHANG Jianjun3. HU Xiaohe1, LIN Hongxuan1,4 & LUO Da1 1. National Key Laboratory of plant Molecular Genetics, {2. In-stitute of plant {3. and Ecology, chinese academy of Sci-ences, shanghai 2.003., china 2. china National Rice Research institute, Hangzhou 3.0006, china 3. Crop institute of Breeding and Cultivation, {2. Agricultural academy, {2. 2.1106, china 4. {2. Anxin Research Foundation Laboratory, shanghai 2.003., china National Key Laboratory of plant Molecular Genetics Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China china National Rice Research institute Hangzhou China Crop institute of Breeding and Cultivation Shanghai Agricultural Academy Shanghai China shanghai Anxin Research Foundation Laboratory Shanghai China

The rice clustered spikelets (Cl) mutant exhib-its a phenotype that most of branch apical have 2.3.spikelets clustered together. SEM (scanning electron microscope) ob-servation suggested that the Cl gene controlled branch apical development, and influenced the terminal spikelets elonga-tion. The spikelet number was reduced in mutant, indicating that Cl may also have an effect on spikelet number. To map Cl locus, two F2.mapping populations derived from the crosses between the Cl and ZhongHua11, and Cl and ZheFu802.were constructed, respectively. The Cl locus was roughly mapped between two CAPS markers, CK02.4 and SS03.4. A further fine mapping analysis showed that the Cl locus was mapped between makers R0674E and Cl2.60, with genetic distances of 0.2.and 2.1 cM, respectively. Then we found a PAC contig spanning Cl locus, the region was delim-ited to 196 kb. This result was useful for cloning of the Cl gene. Allelism test demonstrated that Cl was allelic to Cl2. another rice clustered spikelets mutant.

关键词：水稻簇生小穗突变体分子标记基因图遗传分析植物形态 SEM

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Change of proton motive force across thylakoid membrane in soybean leaf during state transitions

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chinese Science Bulletin 2003年第7期48卷 652-657页

作者： SU Jihu & SHEN Yungang shanghai institute of {2. {3., chinese academy of Sciences, shanghai 2.003., china shanghai institute of {2. {3. Chinese Academy of Sciences Shanghai 200032 China

Change of proton gradient across thylakoid membrane in soybean leaves was studied with millisecond delayed light emission (ms-DLE) during the course of state transitions which were indicated by the chlorophyll fluores-cence at room temperature and 77 K. When dark-adapted leaves were induced to stateⅠ with far-red light, Fm/Fo, F685/F73. and the intensity of fast phase of ms-DLE were af-fected slightly. However, during the induction to stateⅡ with red light, both Fm/Fo and F685/F73. decreased immedi-ately and the former were quicker than the latter. In this interval, the intensity of fast phase of ms-DLE increased to a maximum and then decreased to a lower value during the transition to stateⅡ. Nigericin, an uncoupler which elimi-nates the proton gradient across thylakoid membrane, inhib-ited the increase in the intensity of fast phase of ms-DLE during the transition to stateⅡ. Another uncoupler, valino-mycin, which eliminates the membrane potential, did not affect the changes of the intensity of fast phase. These results suggest that the prompt increase in the intensity of fast phase of ms-DLE at the beginning of transitions to stateⅡ is cor-related mainly with the proton gradient released from water oxidation in photosystemⅡ.

关键词：大豆叶状态转换类囊体膜质子运动力量毫秒滞后光发射光合体系

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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 {2. and Ecology, {3. institute for Biological Sciences, the chinese academy of Sciences, {3. 2.002., china 2.he GraduateSchool of the chinese academy of Sciences, Beijing 10003., china institute of plant {2. and Ecology Shanghai Institute for Biological Sciences the Chinese Academy of Sciences Shanghai 200025 China The Graduate School of the chinese academy of Sciences Beijing 1000{2. China

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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Evaluation of 10 plant barcodes in Bryophyta (Mosses)

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Journal of Systematics and Evolution 2010年第1期48卷 36-46页

作者： 1,2.Yan LIU 3.Hai-Fei YAN 4 Tong CAO 3.Xue-Jun GE 1({2. of Applied Ecology, chinese academy of Sciences, Shenyang 110016,{3.) 2.Graduate University of the chinese academy of Sciences, Beijing 100049,{3.) 3.Key Laboratory of plant Resources Conservation and Sustainable Utilization, South{3. Botanical Garden, chinese academy of Sciences, Guangzhou 510650,{3.) 4(College of Life & Environment Sciences, shanghai Normal University, shanghai 2.02.0},{3.) (institute of Applied Ecology Chinese Academy of Sciences Shenyang 110016 China) (Graduate University of the chinese academy of Sciences Beijing 100049 China) (Key Laboratory of plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou 510650 China) (College of Life & Environment Sciences Shanghai Normal University Shanghai 200234 China)

DNA barcoding is a molecular tool that uses a standardized DNA region to identify *** preliminary study reported here is the first attempt to specifically focus on universality and attributes of candidate barcodes across a wide systematic range of *** tested eight previously proposed plant barcoding regions(atpF-atpH, ITS2. matK, psbK-psbI, rbcL, rpoB, rpoC1, and trnH-psbA) and two popular phylogenetic markers(rps4 and trnL-trnF of cpDNA) in 49 moss species and 9 liverwort species, representing half of the orders in moss *** ITS2. rbcL, rpoC1, rps4, trnH-psbA and trnL-trnF regions showed good universality, and therefore the efficacy of these loci as DNA barcodes was further evaluated in 3. mosses and 2.liverworts, each of which included two to three individuals per *** five loci, ***, rpoC1, rps4, trnH-psbA and trnL-trnF, were easy to amplify and sequence and showed significant inter-specific genetic variability, making them potentially useful DNA barcodes for *** best performing single loci were the rbcL and rpoC1 coding *** loci showed equivalent performance and combinations of them did not greatly increase their discrimination *** addition, phylogenies generated from each of the separate regions and multi-locus combinations by using best-fit and Kimura 2.parameter models were compared, but no significant difference was found.

关键词： Bryophyta DNA barcoding rbcL rpoC1 rps4 trnH-psbA trnL-trnF.

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