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Genomic Analysis of MicroRNA Promoters and Their cis-acting elements in Soybean

Agricultural Sciences in China 2010年第11期9卷 1561-1570页

作者： LIU Yong-xin HAN Ying-peng CHANG Wei ZOU Quan GUO Mao-zu LI Wen-bin Key Laboratory of Soybean Biology Ministry of Education~Soybean Research Institute Northeast Agricultural University Harbin 150030 P.R.China School of lnformation Science and Technology Xiamen University Xiamen 361005 P.R.China Department of Computer Science and Technology Harbin Institute of Technology Harbin 150001 P.R.China

MicroRNAs （miRNAs） are derived from distinct loci in the genome and play crucial roles in RNA-mediated gene silencing mechanisms that regulate cellular processes during development and stress responses of plants. The miRNAs are approximately 21 nucleotides long and code for the complementary strand to a larger genic mRNA. They are often found within the complementary primary transcript （pri-miRNAs）. In the past few years, a growing number of soybean miRNAs have been discovered, however, little is known about the transcriptional regulation of these miRNAs. In this study, promoters and cis-acting elements of soybean miRNAs were analyzed using the genomic data for the first time. A total of 82 miRNAs were located among 122 loci in genome, some were present as double or multiple copies. Five clusters that included ten miRNAs were found in genome, and only one cluster share the same promoter. A total of 191 promoters from 122 loci of the soybean miRNA sequences were found and further analyzed. The results indicated that the conserved soybean miRNA genes had a greater proportion of promoters than that of non-conserved ones, and the distribution of the transcript start sites （TSSs） and TATA-boxes found had different motif styles between conserved and non-conserved miRNA genes. Furthermore, the cis-acting elements 5＇ of the TSSs were analyzed to obtain potential function and spatiotemporal expression pattern of miRNAs. The data obtained here may lead to the identification of specific sequences upstream of pre-miRNAs and the functional annotation of miRNAs in soybean.

关键词： miRNAs soybean promoter cis-acting elements miRNA clusters

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Harpin_(xoo) and Its Functional Domains Activate Pathogen-inducible Plant Promoters in Arabidopsis

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Acta Botanica Sinica 2004年第9期46卷 1083-1090页

作者： PENG Jian-Ling BAO Zhi-Long LI Ping CHEN Guang-Yong WANG Jin-Sheng DONG Han-Song Department of Plant Pathology Nanjing Agricultural UniversityNanjing 210095China

Harpins are bacterial proteins that can enhance plant growth and defense against pathogens and insects. To elaborate whether harpins perform the diverse functions in coordination with the activation of specific promoters that contain particular elements, we cloned pathogen-inducible plant promoters PPP1, PPP2, and PPP3 from tobacco and investigated their responses to harpinxoo or its truncated fragments DEG, DIR, and DPR (domains for enhancing plant growth, insect resistance and pathogen resistance). PPP1 contains an internal repeat composed of two tandem 111bp fragments; 111bp in the repeat was deleted in PPP2. PPP3 contains a bacteria-inducible element; PPP1 and PPP2 additionally contain TAC-1 and Eli boxes inducible correspondingly by salicylic acid (SA) and elicitors. Function of cloned PPPs was confirmed based on their activation in transgenic Arabidopsis plants by Ralstonia solanacearum (Ralston) or SA. Harpinxoo, DEG, DIR, or DPR activated PPP1 and PPP2 but not PPP3, consistent with the presence of Eli boxes in promoters. PPP1 was ca. 3-fold more active than PPP2, suggesting that the internal repeat affects levels of the promoter activation.

关键词： harpin_(xoo) pathogen-inducible plant promoter(PPP) cis-acting elements transgenic Arabidopsis

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Grain proteomic analysis reveals central stress responsive proteins caused by wheat-Haynaldia villosa 6VS/6AL translocation

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Journal of Integrative Agriculture 2020年第11期19卷 2628-2642页

作者： ZOU Rong WU Ji-su WANG Ruo-mei YAN Yue-ming College of Life Science Capital Normal UniversityBeijing 100048P.R.China Hubei Collaborative Innovation Center for Grain Industry(HCICGI) Yangtze UniversityJingzhou 434023P.R.China

Haynaldia villosa(2n=14,VV),a wild grass of the subtribe Triticeae,serves as potential gene resources for wheat genetic *** this study,the proteome characterization during grain development of Yangmai 5 and Yangmai *** 6VS/6AL translocation line was investigated by a comparative proteomic ***-dimensional electrophoresis identified 81 differentially accumulated proteins(DAPs)during five grain developmental stages in *** translocation *** proteins were mainly involved in stress defense,storage protein,energy metabolism,protein metabolism and folding,carbon metabolism,nitrogen metabolism,and starch *** particular,6VS/6AL translocation led to significant upregulation of 36 DAPs and specific expression of 11 DAPs such as chitinase,thaumatin-like proteins,glutathione transferase,α-amylase inhibitor,heat shock proteins,and betaine aldehyde *** proteins mainly involved in biotic and abiotic stress *** analysis found that the upstream 1500 promoter regions of these stress-responsive DAP genes contained multiple high-frequency cis-acting elements related to stress defense such as abscisic acid response element ABRE,methyl jasmonate(MeJA)-response element TGACG-motif and CGTCA-motif involved in oxidative stress and antioxidant response element(ARE).RNA-seq and RT-qPCR analyses revealed the high expression of these stress-defensive DAP genes in the developing grains,particularly at the early-middle grain filling *** results demonstrated that 6VS chromosome of *** contains abundant stress-defensive proteins that have potential values for wheat genetic improvement.

关键词： 6VS/6AL translocation grain development proteome DAPs cis-acting elements adverse defense

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A novel cold-inducible promoter,PThCAP from Tamarix hispida,confers cold tolerance in transgenic Arabidopsis thaliana

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Journal of Forestry Research 2018年第2期29卷 330-336页

作者： Xiaohong Guo Yandong Lv Hongyu Li Nan Fu Guiping Zheng Lihua Liu Yuhua Li State Key Laboratory of Tree Genetics and Breeding Northeast Forestry University Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province Agronomy College Heilongjiang Bayi Agricultural University College of Life Science and Technology Heilongjiang Bayi Agricultural University College of Life Sciences Daqing Bio-tech Research InstituteNortheast Forestry University

Our previous studies have revealed that the Th CAP gene plays a vital role in transgenic Populus(*** 9 ***) in response to cold ***,the regulatory mechanism of Th CAP gene expression has been *** this study,the 50 flanking region of the Th CAP promoter(PTh CAP) was cloned using a genomewalking *** analyzing cis-acting regulatory elements of PTh CAP,a DRE motif and MYC and MYB elements were found to be located in the *** identify the regulatory elements that control the expression of the Th CAP gene promoter,a series of deletion derivatives ofPTh CAP,P1–P5,from the translation start code(-1538,-1190,-900,-718 and-375 bp),were fused to the GUS reporter gene,and then each deletion was stably introduced into Arabidopsis thaliana *** analysis of the promoter suggested that only the P2 fragment had strong GUS expression in leaves and roots of *** exposed to low temperature *** results suggest that this290-bp region(-1190 to-900 bp),as an important part in PTh CAP,was associated with cold tolerance of *** results provide evidence for the regulatory mechanism of Th CAP gene involved in the response to cold stress,and that the gene is promising candidate gene for genetic improvement of crops.

关键词： Arabidopsis thaliana cis-acting elements GUS expression PThCAP ThCAP gene

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A Proximal Promoter Region of Arabidopsis DREB2C Confers Tissue-specific Expression under Heat Stress

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Journal of Integrative Plant Biology 2012年第9期54卷 640-651页

作者： Jihyun Je Chieun Song Jung Eun Hwang Chae Oh Lim Systems and Synthetic Agrobiotech Center and PMBBRC Division of Applied Life Science Gyeongsang National University

The dehydration-responsive element-binding factor 2C （DREB2C） is a member of the CBF/DREB subfamily of proteins, which contains a single APETALA2/Ethylene responsive element-binding factor （AP2/ERF） domain. To identify the expression pattern of the DREB2C gene, which contains multiple transcription cis-regulatory elements in its promoter, an approximately 1.4 kb upstream DREB2C sequence was fused to the β-glucuronidase reporter gene （GUS） and the recombinant p1244 construct was transformed into Arabidopsis thaliana （L.） Heynh. The promoter of the gene directed prominent GUS activity in the vasculature in diverse young dividing tissues. Upon applying heat stress （HS）, GUS staining was also enhanced in the vasculature of the growing tissues. Analysis of a series of 5＇-deletions of the DREB2C promoter revealed that a proximal upstream sequence sufficient for the tissue-specific spatial and temporal induction of GUS expression by HS is localized in the promoter region between -204 and -34 bps relative to the transcriptional start site. Furthermore, electrophoretic mobility shift assay （EMSA） demonstrated that nuclear protein binding activities specific to a -120 to -32 bp promoter fragment increased after HS. These results indicate that the TATA-proximal region and some latent trans-acting factors may cooperate in HS-induced activation of the Arabidopsis DREB2C promoter.

关键词： cis-acting elements β-glucuronidase gene expression histochemical assay promoter deletion transgenic plant.

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Genome-wide identification and in silico gene expression analysis of the related to ABI3/VP1(RAV)transcription factor family in barley(Hordeum vulgare L.)

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BIOCELL 2021年第6期45卷 1673-1685页

作者： CÜNEYT UÇARLI Department of Molecular Biology and Genetics Istanbul UniversityIstanbul34134Turkey

RAV(Related to ABI3/VP1)transcription factors are unique members of the AP2-ERF superfamily with AP2 and B3 domains and play important roles in the regulation of seed germination,plant growth,and stress *** the study,7 RAV genes,named HvRAVs,were identified in barley based on the available genome *** five of the seven HvRAVs were located on chromosome 3,HvRAV5 and HvRAV7 were located on chromosome 1 and 4,*** of the predicted HvRAVs were intron-less,except HvRAV2,which had one *** proteins have shown basic,instable,and hydrophilic *** AP2 domain specific RAYD and WLG motifs were detected in all HvRAV ***,B3 repression domain,R/KLFGV,is also found in the C-terminal of *** were found to have stress-related cis-acting elements,including MYB,MYC,and ***2 was predicted to have no GARE motifs,TATCCCA or TAACAA(G/A),and *** drought conditions,the expression level of HvRAVs did not significantly change in a drought-sensitive barley genotype,whereas HvRAV5 and HvRAV7 were dramatically down-regulated in a drought-tolerant *** of HvRAV5 was also inhibited by ***7 was strongly induced by plant pathogen *** HvRAV6 was induced by exogenous gibberellin application and during the germination ***,HvRAV6 transcript was detected higher than other HvRAVs in all stress and control conditions as well as during *** silico analyses have shown that HvRAVs play a role in response to different abiotic and biotic stresses as well as in plant ***,the extensive biological roles of HvRAV genes in plant development and in response to abiotic and biotic stresses need further investigation.

关键词： Barley RAV AP2 domain B3 domain AP2/ERF family cis-acting elements

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Cloning and Analysis of the Promoters of Two OsRhoGDIs Genes from Rice

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Agricultural Sciences in China 2008年第7期7卷 789-795页

作者： ZHANG Li-juan LIANG Wei-hong LIU Yue-xia LIU Xiao-fei HOU Cheng-qian BI Jia-jia College of Life Science Henan Normal University Xinxiang 453007 P.R. China

OsRacD, belonging to rice （Oryza sativa L. ssp. japonica） Rho family of the small GTPases, is a pivotal gene involved in rice photoperiod fertility conversion of photoperiod sensitive genic male sterile rice which influences the rice fertility via controlling the pollen tube growth. Using OsRacD as bait, two GDP dissociation inhibitor genes designated as OsRhoGDI1 and OsRhoGDI2 were screened by yeast two-hybrid system. To further study the regulation mechanism of OsRhoGDIs, and also the relationships between OsRhoGDIs and OsRacD, the upstream regulation sequences of OsRhoGDI1 and OsRhoGDI2 were cloned by PCR, and the cis-elements in the promoters were predicted using internet tools in this study. The results showed that there were several kinds of response elements, such as phytohormone response elements, lightregulated elements and adversity induced elements in the promoters of OsRhoGDIs, some of which were similar. Comparing with the promoter of OsRacD, several pollen tube germination related elements were found. On one hand, the expression and regulation mechanism of OsRhoGDIs were complex, they may be regulated by several signaling pathways commonly, and the regulation mechanisms were similar to some extent. On the other hand, it was suggested that the fertility of photoperiod sensitive genic male sterile rice may be controlled by the cooperative expression of OsRhoGDIs and OsRacD.

关键词： rice OsRhoGDIs Rho OsRacD cis-acting elements

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Analysis on Sequence and elements of Cucumisin Promoter

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Agricultural Biotechnology 2017年第2期6卷 19-21,44页

作者： Siming HOU Lingyun LIU Xiaohong YANG Department of Life Science and Technology Kunming University

Abstract Leaves of melon were collected and extracted by the CTAB method for total DNA which was used for PCR amplification, obtaining the gene sequence of cucumisin promoter. The sequence results were processed and analyzed with DNAman, DNAstar and other softwares, and bioinformatic element analysis was performed with PlantCARE and PLACE. The analysis results showed that the cucumisin promoter shared 100%, 99% and 99% homology with AY055805, LN713264 and LN681897, respectively. The promoter sequence contains a variety of c/s-acting elements common in fruit promoters of higher plants such as TATA-Box and CAAT-Box, and light-responsive elements, some of which involved in ABA and VP1 responsiveness and salicylic acid responsiveness. This study provides a scien- tific basis for further research on genetic engineering of fruits.

关键词： Fruit promoter Sequence analysis Melon gene Bioinformatics analysis cis-acting elements

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Global Identification and Characterization of Pathogen-Inducible Rice promoters

Global Identification and Characterization of Pathogen-Induc...

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中国植物病理学会2015年学术年会

作者： KONG Wei-wen CHENG Jia LI Bin School of Horticulture and Plant Protection Yangzhou University

Pathogen-inducible plant promoters（PIPs） are able to respond to pathogens after infection,which are usually activated by pathogens only at the time point after *** could have applications as molecular markers,and for engineering crops with increased disease *** study obtained 62 pathogen-inducible plant promoters sequences from 14 species through literatures and public *** potential cis-acting elements of the above PIPs were identified using Plant CARE and PLACE *** candidate rice PIPs,which contain potential pathogen-inducible AS-1,G-box,H-box and GCC-box cis-acting elements,were screened from rice promoterome *** a result,total 417 candidate rice PIPs were *** genes under the control of potential rice PIPs were annotated by searching NCBI COG database with their sequences as *** the candidate genes,55.26%are function-unknown;13.16%may involve in metabolism;9.57%may function in the cellular processes and signaling;8.61%are poorly characterized;8.37%may play roles in the information storage and processing;and 5.02%may act as dual *** validate the 417 candidate rice PIPs,several microarray data of infected rice by pathogens were downloaded from public database and *** results indicated that changes with highly significance（p ＜ 0.01） were observed in transcriptional level from 128 candidate genes controlled by *** the genes,92 genes were upregulated,and 63 genes were down-regulated in the microarray *** a control,20 rice genes controlled by non-PIPs（out of the PIPs） were randomly selected from 12 rice chromosomes（one or two genes selected from each chromosome） and their expression were analyzed based on the above microarray *** total 139 microarray treatments,5 gene-events were observed whose expressions varied on the significant *** false positive rate is 3.60%（5/139）.The results of this study would underlie the elucidation of mechanisms by which rice PIPs regulate g

关键词： Rice Pathogen-inducible promoters cis-acting elements Regulation of gene expression Microarray data analysis

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