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Variation at the transcriptional level among Chinese natural populations of Arabidopsis thaliana in response to cold stress

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Chinese Science Bulletin 2008年第19期53卷 2989-2999页

作者： HE Fei KANG JiuQing ZHOU Xin SU Zhen QU LiJia gu hongya National Laboratory of Protein Engineering and Plant Genetic Engineering Peking-Yale Joint Center for Plant Molecular Genetics and AgroBiotechnology College of Life Sciences Peking University Beijing 100871 China College of Biological Sciences China Agriculture University Beijing 100094 China National Plant Gene Research Center (Beijing) Beijing 100101 China

The Arabidopsis 25K GeneChip (ATH1, Affymetrix) was used to make a survey of the variation of the transcriptional profiles among 5 Chinese natural populations of Arabidopsis thaliana under cold treatment. In normal growth condition, the expression level of 2.26% (513 genes in the population from Jiujiang, Jiangxi, JXjjx) to 6.52% (1482 genes in the population from Tongliang, Chongqing, CQtlx) genes was 2-fold higher than that of Col ecotype. Under cold treatment, the expression of 12.84% (2920 genes in the population from Chenggu, Shaanxi, SXcgx) to 19.46% (4426 genes in the population from Qinghe, Xinjiang, XJqhx) genes was up- or down-regulated by at least two-fold that of their controls. In general, most of up-regulated genes might be the genes essential for plant surviving at low temperature, such as genes in CBF pathway and the genes responsible for synthesizing molecules accumulated for cold tolerance. However, each natural population had some specific genes induced under cold treatment. The data indicated that some of the cold-responding genes were differentiated among the populations distributed in the natural habitats with different climate conditions. CBF3, one of the key tran-scription factor genes in cold responding pathway, showed significant differences in expression among populations. The sequence analysis indicated that the changes in its regulation region caused the dramatic difference in the expression pattern. Further studies on the correlation of the function of the differentially expressed genes and the cold tolerance in different populations may provide some new insight into the molecular mechanism of adaptation to local environment in Arabidopsis thaliana in China.

关键词：中国人口调查基因转录实验研究

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The Features and Regulation of Co-transcriptional Splicing in Arabidopsis

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Molecular Plant 2020年第2期13卷 278-294页

作者： Danling Zhu Fei Mao Yuanchun Tian Xiaoya Lin Lianfeng gu hongya gu Li-jia Qu Yufeng Wu Zhe Wu SUSTech-PKU Institute of Plant and Food Science Department of BiologySouthern University of Science and TechnologyShenzhen 518055China State Key Laboratory for Crop Genetics and Germplasm Enhancement Bioinformatics CenterNanjing Agriculture UniversityNanjingJiangsu 210095China State Key Laboratory of Protein and Plant Gene Research Peking-Tsinghua Center for Life SciencesCollege of Life SciencesPeking UniversityBeijing 100871China Basic Forestry and Proteomics Research Center College of ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China Present address:School of Life Sciences Guangzhou UniversityGuangzhou 510006China

Precursor mRNA(pre-mRNA)splicing is essential for gene expression in most eukaryotic *** studies from mammals,Drosophila,and yeast show that the majority of splicing events occurs *** plants,however,the features of co-transcriptional splicing(CTS)and its regulation still remain largely ***,we used chromatin-bound RNA sequencing to study CTS in Arabidopsis *** found that CTS is widespread in Arabidopsis seedlings,with a large proportion of alternative splicing events determined *** efficiency correlated with gene expression level,the chromatin landscape and,most surprisingly,the number of introns and exons of individual genes,but is independent of gene *** combination with enhanced crosslinking and immunoprecipitation sequencing analysis,we further showed that the hnRNP-like proteins RZ-1B and RZ-1C promote efficient CTS globally through direct binding,frequently to exonic ***,this general effect of RZ-1B/1C on splicing promotion is mainly observed at the chromatin level,not at the mRNA ***-1C promotes CTS of multiple-exon genes in association with its binding to regions both proximal and distal to the regulated *** propose that RZ-1C promotes efficient CTS of genes with multiple exons through cooperative interactions with many exons,introns,and splicing *** work thus reveals important features of CTS in plants and provides methodologies for the investigation of CTS and RNA-binding proteins in plants.

关键词： co-transcriptional splicing CB-RNA-seq eClip-seq RNA binding protein chromatin transcription

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The precise regulation of different COR genes by individual CBF transcription factors in Arabidopsis thaliana

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Journal of Integrative Plant Biology 2017年第2期59卷 118-133页

作者： Yihao Shi Jiaying Huang Tianshu Sun Xuefei Wang Chenqi Zhu Yuxi Ai hongya gu State Key Laboratory for Protein and Plant Gene Research College of Life Sciences Peking University Beijing 100871 China

The transcription factors CBF1/2/3 are reported to play a dominant role in the cold responsive network of Arabidopsis by directly regulating the expression levels of cold responsive （COR） genes. In this study, we obtained CRISPR/Casg-mediated loss-of-function mutants of cbf1-3. Over 3,ooo COR genes identified by RNA-seq analysis showed a slight but significant change in their expression levels in the mutants compared to the wild- type plants after being treated at 4 ℃ for 12 h. The C-repeat （CRT） motif （5＇-CCGAC-3＇） was enriched in promoters of genes that were up-regulated by CBF2 and CBF3 but not in promoters of genes up-regulated by CBFI. These data suggest that CBF2 and CBF3 play a more important role in directing the cold response by regulating different sets of downstream COR genes. More than 2/3 of COR genes were co-regulated by two or three CBFs and were involved mainly in cellular signal transduction and metabolic processes; less than 1[3 of the genes were regulated by one CBF, and those genes up-regulated were enriched in cold-related abiotic stress responses. Our results indicate that CBFs play an important role in the trade-off between cold tolerance and plant growth through the precise regulation of COR genes in the complicated transcriptional network.

关键词： CRISPR Cas9 CBF cold tolerance COR single CBF-regulated genes

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Cloning and expression of a cDNA encoding ribosomal protein S4 from Rice (Oryza sativa)

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Chinese Science Bulletin 2000年第2期45卷 168-173页

作者： QU Lijia LI Donghui ZHANG Yi LIU Meihua gu hongya CHEN Zhangliang National Laboratory of Protein Engineering and Plant Genetic Engineering Peking UniversityBeijing 100871China De Montfort University The GatewayLeicester LE1 9BHUK

A cDNA clone, pS4, has been isolated from a cDNA library prepared from rice anthers of about 1.0 mm in length. DNA sequence analysis and database search show that the cDNA encodes a protein which is highly homologous to eukaryotic 80S ribosomal protein subunit 4 (S4). Northern hybridization indicates that this gene expresses in all tissues analyzed although the expression level varies and it cannot be induced by mechanical wounding in leaves. Southern blot analysis demonstrates that this rice S4 gene is from a multigene

关键词： ribosomal protein S4 cDNA clone monocotyledonous plant tissue specificity(rice) 1) The nucleotide sequence data reported is in the EMBL Nucleotide Sequence Database under the accession number Y15009.

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Structural and expressional analysis of a cDNA that expresses predominantly in rice stamens

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Chinese Science Bulletin 1998年第9期43卷 765-769页

作者： Yi Zhang Lijia Qu Meihua Liu Xiaoli Qin hongya gu Zhangliang Chen Peking Univ Key Lab Prot Engn & Plant Genet Engn Beijing 100871 Peoples R China

The development of stamen is an important stage during the sexual reproduction in higher plants. Studying the genes that predominantly or even specifically expressed in stamens will aid in understanding the molecular mechanism of stamen development. The structure of a rice CHS-like gene (D5) which predominantly expressed in anthers has been analysized, showing high structural similarity with two other anther-specific genes (A1 and BA42) from Brassica napus. Northern analysis also reveals that the three genes share a similar expression pattern and that the expression of D5 may relate to the early development of pollens. It is concluded that D5, A1 and BA42 represent a group of diverged CHS-like genes which are related to stamen development.

关键词： pollen development meiosis stage rice anther cDNA chalcone synthase.

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The Arabidopsis Anaphase-Promoting Complex/Cyclosome Subunit 1 is Critical for Both Female Gametogenesis and Embryogenesis

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Journal of Integrative Plant Biology 2013年第1期55卷 64-74页

作者： Yanbing Wang Yingnan Hou hongya gu Dingming Kang Zhang-Liang Chen Jingjing Liu Li-Jia Qu State Key Laboratory of Protein and Plant Gene Research College of Life Sciences Peking University College of Agronomy and Biotechnology China Agricultural University The National Plant Gene Research Center

Anaphase-promoting complex/cyclosome （APC/C）, a multisubunit E3 ligase, plays a critical role in cell cycle control, but the functional characterization of each subunit has not yet been completed. To investigate the function of APC1 in Arabidopsis, we analyzed four mutant alleles of APC1, and found that mutation in APC1 resulted in significantly reduced plant fertility, accumulation of cyclin B, and disrupted auxin distribution in embryos. The three mutant alleles apcl-1, apcl-2 and apcl-3 shared variable defects in female gametogenesis including degradation, abnormal nuclear number, and disrupted polarity of nuclei in the embryo sac as well as in embryogenesis, in which embryos were arrested at multiple stages. All of these defects are similar to those previously identified in apc4. The mutant apcl-4, in which the T-DNA was inserted after the transmembrane domain at the C-terminus, showed much more severe phenotypes; that is, most of the ovules were arrested at the one-nucleate female gametophyte stage （stage FG1）. In the apcl apc4 double mutants, the fertility was further reduced by one-third in apcl-ll＋ apc4-1/＋, and in some cases no ovules even survived in siliques of apcl-4/＋ apc4-1/＋. Our data thus suggest that APC1, an essential component of APC/C, plays a synergistic role with APC4 both in female gametogenesis and in embryogenesis.

关键词： Arabidopsis anaphase-promoting complex/cyclosome (APC/C) APC1 APC4 female gametogenesis embryogenesis synergistic role

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Construction of chimeric inducible promoters by elicitors of rice fungal blast pathogen and their expression in transgenic rice

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Chinese Science Bulletin 2000年第3期45卷 242-246页

作者： LU Huafei MING Xiaotian QU Lijia LIU Meihua LI Jing gu hongya CHEN Zhangliang State Key Laboratory of Protein Engineering and Plant Genetic Engineering Peking UniversityBeijing 100871China Demontfort University The GatewaysLeicester LEI 9BHUK

The promoter fragments of wheat GstA1 and potato Gst1 have been amplified by PCR, cloned and fused respectively to the minimal promoter sequence of rice actin gene (Act1)) and its 5’ untranslated leader sequence together with guS. The constructs with 2 chimeric promoters (WGA and PGA) have been transferred into rice in order to analyze their inducibility patterns in transgenic rice plants. The results show that: WGA and PGA are both inducible by elicitors of Pyricularia oryzae in transgenic rice cells; the intron I of rice Act1 gene is important for the heterogenic expression of monocot and dicot promoter elements in rice; and the Act1 minimal promoter and its 5’untranslated leader sequence produced low level background expression in rice.

关键词： pathogen-inducible chimeric promoter gene expression and regulation transgenic rice rice fungal blast disease.

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SNAIL1 is essential for female gametogenesis in Arabidopsis thaliana

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Journal of Integrative Plant Biology 2017年第9期59卷 629-641页

作者： Lihong Hao Xiaolin Wei Jiulei Zhu Jiao Shi Jingjing Liu hongya gu Tomohiko Tsuge Li-Jia Qu State Key Laboratory for Protein and Plant Gene Research Peking-Tsinghua Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing 100871China National Plant Gene Research Center(Beijing) Bejing 100101China Institute for Chemical Research Kyoto UniversityGokasho UjiKyoto 611-0011Japan

Two yeast Brix family members Ssfl and Ssf2, involved in large ribosomal subunit synthesis, are essential for yeast cell viability and mating efficiency. Their putative homologs exist in the Arabidopsis genome; however, their role in plant development is unknown. Here, we show that Arabidopsis thaliana SNAIL1 （AtSNAIL1）, a protein sharing high sequence identity with yeast Ssfl and Ssf2, is critical to mitosis progression of female gametophyte development. The snail1 homozygous mutant was nonviable and its heterozygous mutant was semi-sterile with shorter siliques. The mutation in SNAIL1 led to absence of female transmission and reduced male transmission. Further phenotypic analysis showed that the synchronic development of female gametophyte in the snail1 heterozygous mutant was greatly impaired and the snaih pollen tube growth, in vivo, was also compromised. Furthermore, SNAIL1 was a nucleolar- localized protein with a putative role in protein synthesis. Our data suggest that SNAIL1 may function in ribosome biogenesis like Ssf1 and Ssf2 and plays an important role during megagametogenesis in Arabidopsis.

关键词： SNAIL1 is essential for female gametogenesis in Arabidopsis thaliana Figure

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Expression and inhibitory activity analysis of a 25-kD Bowman-Birk protease inhibitor in rice

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Chinese Science Bulletin 2006年第1期51卷 54-62页

作者： CHEN Jun MAO Shengji XlE Yang CAO Zhongren ZHANG Yan LIU jing CHEN Zhangliang QU Lijia gu hongya Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology National Laboratory of Protein Engineering and Plant Genetic Engineering College of Life Sciences Peking University Beijing 100871 China National Plant Gene Research Center (Beijing) Beijing 100101 China

Rice Bowman-Birk inhibitors (RBBI), with one (8 kD) or two homologous domains (16 kD), were found to be effective trypsin inhibitors in vitro. In this study, we demonstrate that the 25-kD protein corresponding to the three-domain RBBI indeed ex- ists in rice in planta, and that the RBBIs are regulated by development and wounding. We also found by inhibitory activity assay that the 3:13 disulfide bond, but not the 4:5 disulfide bond, suppresses the tryp- sin-inhibitory activity, and the D3 domain of RBBI3-1 has no inhibitory activity against trypsin, chymotryp- sin, paparin or subtilisin. Mutation analyses showed that conversion from Lys to Leu or Tyr in the N-terminal P1 site in D1 domain did not create chy- motrypsin-inhibitory activity, suggesting that the structure of the reactive loop in D1 domain hinder the new inhibitory specificity at P1 site, and the chy- motrypsin-inhibitory activity might need the participa- tion of other structures, e.g. 3:13 disulfide bond.

关键词：水稻 RBBI 双硫键胰凝乳蛋白酶胰岛素

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An anther-specific chalcone synthase-like gene D5 related to rice pollen development

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Chinese Science Bulletin 2000年第21期45卷 1921-1926页

作者： Honghong Zheng Lijia Qu Meihua Liu Yi Zhang Yunping Shen Junming Wei Naisui Pan hongya gu Zhangliang Chen Beijing Univ Natl Lab Prot Engn & Plant Genet Engn Beijing 100871 Peoples R China

It was shown in a previous analysis that D5 gene from rice (Oryza sativa L.) was an anther-specific gene encoding a chalcone synthase-related protein. In this study, D5 gene was found specifically expressed in tapetum cells as well as in the peripheral cells of the vascular bundle of rice anthers by RNA in situ hybridization. In order to study its function, D5 was transformed into rice in both sense and antisense directions driven by a rice Actin 1 promoter. It has been observed that the pollen grains from the antisense D5 transgenic rice plants are abnormal, indicating that D5 plays a critical role in rice pollen development.

关键词： antisense in situ hybridization pollen development Oryza sativa.

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