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Horticulture Research 2023年第4期10卷 238-248页

作者： Hongtao Song Qi Wang Zhonghua Zhang Kui Lin Erli Pang MOE key laboratory for Biodiversity Science and Ecological Engineering and beijing key laboratory of gene resource and molecular development College of Life SciencesBeijing Normal UniversityBeijing 100875China college of Horticulture Qingdao Agricultural UniversityQingdao 266109China

Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of *** conserved non-coding sequences(CNSs)function as cis-regulatory *** control the development of various ***-ever,predicting clade-wide cis-regulatory elements across several closely related species remains *** on the relationship between CNSs and cis-regulatory elements,we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae *** 12-way whole-genome alignment,we first obtained 632112 CNSs in ***,we identified 16552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae ***,we predicted 3271 potential regulatory pairs in the cucumber genome,of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development *** CNSs,Cucurbitaceae-wide cis-regulatory elements,and their target genes are accessible at http://***/cisRCNEs_cucurbit/.These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.

关键词： elements conserved sequences

Over-Expression of ScMnSOD,a SOD gene Derived from Jojoba, Improve Drought Tolerance in Arabidopsis

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Journal of Integrative Agriculture 2013年第10期12卷 1722-1730页

作者： LIU Xiao-fei SUN Wei-min LI Ze-qin BAI Rui-xue LI Jing-xiao SHI Zi-han GENG Hong-wei ZHENG Ying ZHANG Jun ZHANG Gen-fa beijing key laboratory of gene resource and molecular development Beijing Normal University college of life sciences Beijing Normal University COE For Neuroscience Departments of AnesthesiologyBiomedical SciencesTexas Tech University Health Sciences CenterTexas79905USA

Jojoba（Simmondsia chinensis） is mainly distributed in desert,and the molecular mechanisms of jojoba in response to abiotic stress still remain *** this paper,we cloned and characterized a SOD gene from jojoba named as ScMnSOD,and introduced into Arabidopsis to investigate its functions of responding to drought *** transgenic Arabidopsis showed an improvement in drought ***,under a water deficit condition,the accumulation of reactive oxygen species（ROS） was remarkably decreased in the transgenic lines compared to the ***,the ScMnSOD promoter was cloned to the 5′-upstream of GUS coding region in a binary vector,and introduced into *** results showed that ScMnSOD expression can be induced by drought,salt,ABA,and low *** conclusion,ScMnSOD plays an important role in drought tolerance which is,at least partially,attributed to its role in ROS detoxification.

关键词： drought jojoba promoter ROS ScMnSOD stress tolerance

Deafening-induced rapid changes to spine synaptic connectivity in the adult avian vocal basal ganglia

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Integrative Zoology 2022年第6期17卷 1136-1146页

作者： Xiaojuan ZHOU Yalan CHEN Jikan PENG Mingxue ZUO Yingyu SUN beijing key laboratory of gene resource and molecular development College of Life SciencesBejiing Normal UniversityBeijingChina Chinese Institute for Brain Research(CIBR) BeijingChina Technology Center for Protein sciences Tsinghua UniversityBeijingChina School of life sciences Westlake UniversityHangzhouChina

The basal ganglia have been implicated in auditory-dependent vocal learning and plasticity in human and songbirds,but the underlying neural phenotype remains to be clariﬁ***,using confocal imaging and three-dimensional electron microscopy,we investigated striatal structural plasticity in response to hearing loss in Area X,the avian vocal basal ganglia,in adult male zebraﬁnch(Taeniopygia guttata).We observed a rapid elongation of dendritic spines,by approximately 13%,by day 3 after deafening,and a considerable increase in spine synapse density,by approximately 61%,by day 14 after deafening,compared with the controls with an intact ***ﬁnd-ings reveal structural sensitivity of Area X to auditory deprivation and suggest that this striatal plasticity might contribute to deafening-induced changes to learned vocal behavior.

关键词： basal ganglia dendritic spine songbird synapse vocal plasticity

Let there be light： a bright future for Ca2＋ signaling

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Science Bulletin 2018年第16期63卷 1029-1031页

作者： Guolin Ma Jindou Liu Nhung T. Nguyen Yubin Zhou Youjun Wang Center for Translational Cancer Research Institute of Biosciences and Technology College of Medicine Texas A&M University Houston TX 77030 USA beijing key laboratory of gene resource and molecular development College of Life Sciences Beijing Normal University Beijing 100875 China

Calcium ion(Ca^(2+))is a ubiquitous second messenger in eukaryotic *** response to electrical,hormonal,or mechanical stimulation,cytosolic Ca^(2+)levels increase due to Ca^(2+) influxes through ion channels embedded i... 详细信息

关键词： Ca2+ 信号控制真核细胞肌肉收缩新陈代谢钙离子细胞内神经质

Identification of salinity-related genes in ENO2 mutant (eno2~–) of Arabidopsis thaliana

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Journal of Integrative Agriculture 2018年第1期17卷 94-110页

作者： ZHANG Yong-hua CHEN Chao SHI Zi-han CHENG Hui-mei BING Jie MA Xiao-feng ZHENGChao-xing LI Hong-jie ZHANG Gen-fa beijing key laboratory of gene resource and molecular development/college of life sciences Beijing Normal University Beijing 100875 P.R.China beijing Normal University Zhuhai 519087 P.R.China National key Facility for Crop gene resources and genetic Improvement/Institute of Crop sciences Chinese Academy of Agricultural Sciences Beijing 100081 P.R. China

Abiotic stress poses a great threat to plant growth and can lead to huge losses in yield. gene enolase2 （EN02） is important in resistance to abiotic stress in various organisms. ENO2 T-DNA insertion mutant （enoZ） plants of Arabidopsis thaliana showed complete susceptibility to sodium chloride treatment when were analyzed either as whole plants or by measuring root growth during NaCl treatment. Quantitative real-time RT-PCR （RT-qPCR） was performed to investigate the expression profile of EN02 in response to NaCl stress in Arabidopsis. The transcript level of EN02 was rapidly elevated in 300 mmol L-1 NaCl treatment. ENO2 also responded to 300 mmol L 1 NaCl treatment at the protein level. To illuminate the mechanism underlying EN02 resistance to salt at the transcriptional level, we studied the wild-type and enoZ Arabidopsis lines that were treated with 300 mmol L 1 NaCl for 18 h using 454 GS FLX, which resulted in an expressed sequence tag （EST） dataset. A total of 961 up-regulated and 746 down-regulated differentially expressed genes （DEGs） were identified in the pairwise comparison w-r-18 h：eno2^-18 h. The DEGs were identified and functionally annotated using the databases of gene Ontology （GO） and the Kyoto encyclopedia of genes and genomes （KEGG）. The identified unigenes were subjected to GO analysis to determine biological, molecular, and cellular functions. The biological process was enriched in a total of 20 GO terms, the cellular component was enriched in 13 GO terms, and the molecular function was enriched in 11 GO terms. Using KEGG mapping, DEGs with pathway annotations contributed to 115 pathways. The top 3 pathways based on a statistical analysis were biosynthesis of the secondary metabolites （KO01110）, plant-pathogen interactions （KO04626）, and plant hormone signal transduction （KO04075）. Based on these results, EN02 contributes to increased resistance to abiotic stress. In particular, EN02 is involved in some of the metabolic stress response pathways in

关键词： EN02 NaCI tolerance abiotic stress 454 GS FLX sequencing GO KEGG

Using Genome-Referenced Expressed Sequence Tag Assembly to Analyze the Origin and Expression Patterns of Gossypium hirsutum Transcripts

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Journal of Integrative Plant Biology 2013年第7期55卷 576-585页

作者： Xiang Jin Qin Li Guanghui Xiao Yu-Xian Zhu State key laboratory of Protein and Plant gene Research College of Life SciencesPeking University National Center for Plant gene Research(beijing)

We assembled a total of 297,239 Gossypium hirsutum （Gh, a tetraploid cotton, AADD） expressed sequence tag （EST） sequences that were available in the National Center for Biotechnology Information database, with reference to the recently published G. raimondii （Gr, a diploid cotton, DD） genome, and obtained 49,125 Unigenes. The average lengths of the U nigenes were increased from 804 and 791 bp in two previous EST assemblies to 1,019 bp in the current analysis. The number of putative cotton Unigenes with lengths of 3 kb or more increased from 25 or 34 to 1,223. As a result, thousands of originally independent G. hirsutum ESTs were aligned to produce large contigs encoding transcripts with very long open reading frames, indicating that the G. raimondii genome sequence provided remarkable advantages to assemble the tetraploid cotton transcriptome. Significant different distribution patterns within several GO terms, including transcription factor activity, were observed between D- and A-derived assemblies. Tran- scriptome analysis showed that, in a tetraploid cotton cell, 29,547 Unigenes were possibly derived from the D subgenome while another 19,578 may come from the A subgenome. Finally, some of the in silico data were confirmed by reverse transcription polymerase chain reaction experiments to show the changes in transcript levels for several gene families known to play key role in cotton fiber development. We believe that our work provides a useful platform for functional and evolutionary genomic studies in cotton.

关键词： Cotton fiber deep sequencing expressed sequence tag assembly functional genomics Gossypium.

gene Network Analysis and Functional Studies of Senescence-associated genes Reveal Novel Regulators of Arabidopsis Leaf Senescence

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Journal of Integrative Plant Biology 2012年第8期54卷 526-539页

作者： Zhonahai Li Jinying Peng Xing Wen Hongwei Guo State key laboratory of Protein and Plant gene Research College of Life SciencesPeking UniversityPeking-Tsinghua Center for Life SciencesBeijing 100871China

Plant leaf senescence has been recognized as the last phase of plant development, a highly ordered process regulated by genes known as senescence associated genes （SAGs）. However, the function of most of SAGs in regulating leaf senescence as well as regulators of those functionally known SAGs are still unclear. We have previously developed a curated database of genes potentially associated with leaf senescence, the Leaf Senescence Database （LSD）. In this study, we built gene networks to identify common regulators of leaf senescence in Arabidopsis thaliana using promoting or delaying senescence genes in LSD. Our results demonstrated that plant hormones cytokinin, auxin, nitric oxide as well as small molecules, such as Ca2＋, delay leaf senescence. By contrast, ethylene, ABA, SA and JA as well as small molecules, such as oxygen, promote leaf senescence, altogether supporting the idea that phytohormones play a critical role in regulating leaf senescence. Functional analysis of candidate SAGs in LSD revealed that a WRKY transcription factor WRKY75 and a Cys2/His2-type transcription factor AZF2 are positive regulators of leaf senescence and loss-of-function of WRKY75 or AZF2 delayed leaf senescence. We also found that silencing of a protein phosphatase, AtMKP2, promoted early senescence. Collectively, LSD can serve as a comprehensive resource for systematic study of the molecular mechanism of leaf senescence as well as offer candidate genes for functional analyses.

关键词： Arabidopsis leaf senescence SAG phytohormone systems biology.

Novel DYW-type pentatricopeptide repeat(PPR) protein BLX controls mitochondrial RNA editing and splicing essential for early seed development of Arabidopsis

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Journal of genetics and Genomics 2018年第3期45卷 155-168页

作者： Yan Sun Jiaying Huang Sheng Zhong Hongya Gu Shan He Li-Jia Qu State key laboratory for Protein and Plant gene Research Peking-Tsinghua Center for Life Sciences at College of Life Sciences Peking University Beijing 100871 China The National Plant gene Research Center (beijing) Beijing 100101 China

In plants, RNA editing is a post-transcriptional process that changes specific cytidine to uridine in both mitochondria and plastids. Most pentatricopeptide repeat（PPR） proteins are involved in organelle RNA editing by recognizing specific RNA sequences. We here report the functional characterization of a PPR protein from the DYW subclass, Baili Xi（BLX）, which contains five PPR motifs and a DYW domain. BLX is essential for early seed development, as plants lacking the BLX gene was embryo lethal and the endosperm failed to initiate cellularization. BLX was highly expressed in the embryo and endosperm, and the BLX protein was specifically localized in mitochondria, which is essential for BLX function. We found that BLX was required for the efficient editing of 36 editing sites in mitochondria. Moreover, BLX was involved in the splicing regulation of the fourth intron of nad1 and the first intron of nad2. The loss of BLX function impaired the mitochondrial function and increased the reactive oxygen species（ROS） level. genetic complementation with truncated variants of BLX revealed that, in addition to the DYW domain, only the fifth PPR motif was essential for BLX function. The upstream sequences of the BLX-targeted editing sites are not conserved, suggesting that BLX serves as a novel and major mitochondrial editing factor（MEF） via a new non-RNA-interacting manner. This finding provides new insights into how a DYW-type PPR protein with fewer PPR motifs regulates RNA editing in plants.

关键词： Arabidopsis PPR RNA editing RNA splicing Embryo and endosperm development

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Journal of Integrative Plant Biology 2012年第10期54卷 814-827页

作者： Guo Luo Hongya Gu Jingjing Liu Li-Jia Qu State key laboratory for Protein and Plant gene Research College of Life SciencesPeking-Tsinghua Center of Life SciencesPeking UniversityBeijing 100871China The National Plant gene Research Center Beijing 100101China

Ubiquitination of proteins is one of the critical regulatory mechanisms in eukaryotes. In higher plants, protein ubiquitination plays an essential role in many biological processes, including hormone signaling, photomorphogenesis, and pathogen defense. However, the roles of protein ubiquitination in the repro- ductive process are not clear. In this study, we identified four plant-specific RING-finger genes designated Aberrant_Pollen development 1_ （APD1） to APD4, as regulators of pollen mitosis II （PMII） in Arabidopsis thaliana （L.）. The apdl apd2 double mutant showed a significantly increased percentage of bicellular-like pollen at the mature pollen stage. Further downregulation of the APD3 and APD4 transcripts in apdl apd2 by RNA interference （RNAi） resulted in more severe abnormal bicellular-like pollen phenotypes than in apdl apd2, suggesting that cell division was defective in male gametogenesis. All of the four genes were expressed in multiple stages at different levels during male gametophyte development. Confocal analysis using green florescence fusion proteins （GFP） GFP-APD1 and GFP-APD2 showed that APDs are associated with intracellular membranes. Furthermore, APD2 had E2-dependent E3 ligase activity in vitro, and five APD2-interacting proteins were identified. Our results suggest that these four genes may be involved, redundantly, in regulating the PMII process during male gametogenesis.

关键词： Male gametogenesis pollen mitosis II RING-finger E3 ligase Arabidopsis.

Plant Mediator complex and its critical functions in transcription regulation

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Journal of Integrative Plant Biology 2016年第2期58卷 106-118页

作者： Yan Yang Ling Li Li-Jia Qu State key laboratory of Protein and Plant gene Research Peking-Tsinghua Center for Life Sciences College of Life Sciences Peking University Beijing 100871 China The National Plant gene Research Center (beijing) Beijing 100101 China.

The Mediator complex is an important component of the eukaryotic transcriptional machinery. As an essential link between transcription factors and RNA polymerase II, the Mediator complex transduces diverse signals to genes involved in different pathways. The plant Mediator complex was recently purified and comprises conserved and specific subunits. It functions in concert with transcription factors to modulate various responses. In this review, we summarize the recent advances in understanding the plant Mediator complex and its diverse roles in plant growth, development, defense, non-coding RNA production, response to abiotic stresses, flowering, genomic stability and metabolic homeostasis. In addition, the transcription factors interacting with the Mediator complex are also highlighted.

关键词： Mediator complex transcription factors transcription regulation