74 results on '"Yong Qiang Gu"'
Search Results
2. Haplotype variation of Glu-D1 locus and the origin of Glu-D1d allele conferring superior end-use qualities in common wheat.
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Zhenying Dong, Yushuang Yang, Yiwen Li, Kunpu Zhang, Haijuan Lou, Xueli An, Lingli Dong, Yong Qiang Gu, Olin D Anderson, Xin Liu, Huanju Qin, and Daowen Wang
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Medicine ,Science - Abstract
In higher plants, seed storage proteins (SSPs) are frequently expressed from complex gene families, and allelic variation of SSP genes often affects the quality traits of crops. In common wheat, the Glu-D1 locus, encoding 1Dx and 1Dy SSPs, has multiple alleles. The Glu-D1d allele frequently confers superior end-use qualities to commercial wheat varieties. Here, we studied the haplotype structure of Glu-D1 genomic region and the origin of Glu-D1d. Using seven diagnostic DNA markers, 12 Glu-D1 haplotypes were detected among common wheat, European spelt wheat (T. spelta, a primitive hexaploid relative of common wheat), and Aegilops tauschii (the D genome donor of hexaploid wheat). By comparatively analyzing Glu-D1 haplotypes and their associated 1Dx and 1Dy genes, we deduce that the haplotype carrying Glu-D1d was likely differentiated in the ancestral hexaploid wheat around 10,000 years ago, and was subsequently transmitted to domesticated common wheat and T. spelta. A group of relatively ancient Glu-D1 haplotypes was discovered in Ae. tauschii, which may serve for the evolution of other haplotypes. Moreover, a number of new Glu-D1d variants were found in T. spelta. The main steps in Glu-D1d differentiation are proposed. The implications of our work for enhancing the utility of Glu-D1d in wheat quality improvement and studying the SSP alleles in other crop species are discussed.
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- 2013
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3. Complete chloroplast genome sequences of Mongolia medicine Artemisia frigida and phylogenetic relationships with other plants.
- Author
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Yue Liu, Naxin Huo, Lingli Dong, Yi Wang, Shuixian Zhang, Hugh A Young, Xiaoxiao Feng, and Yong Qiang Gu
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Medicine ,Science - Abstract
BACKGROUND: Artemisia frigida Willd. is an important Mongolian traditional medicinal plant with pharmacological functions of stanch and detumescence. However, there is little sequence and genomic information available for Artemisia frigida, which makes phylogenetic identification, evolutionary studies, and genetic improvement of its value very difficult. We report the complete chloroplast genome sequence of Artemisia frigida based on 454 pyrosequencing. METHODOLOGY/PRINCIPAL FINDINGS: The complete chloroplast genome of Artemisia frigida is 151,076 bp including a large single copy (LSC) region of 82,740 bp, a small single copy (SSC) region of 18,394 bp and a pair of inverted repeats (IRs) of 24,971 bp. The genome contains 114 unique genes and 18 duplicated genes. The chloroplast genome of Artemisia frigida contains a small 3.4 kb inversion within a large 23 kb inversion in the LSC region, a unique feature in Asteraceae. The gene order in the SSC region of Artemisia frigida is inverted compared with the other 6 Asteraceae species with the chloroplast genomes sequenced. This inversion is likely caused by an intramolecular recombination event only occurred in Artemisia frigida. The existence of rich SSR loci in the Artemisia frigida chloroplast genome provides a rare opportunity to study population genetics of this Mongolian medicinal plant. Phylogenetic analysis demonstrates a sister relationship between Artemisia frigida and four other species in Asteraceae, including Ageratina adenophora, Helianthus annuus, Guizotia abyssinica and Lactuca sativa, based on 61 protein-coding sequences. Furthermore, Artemisia frigida was placed in the tribe Anthemideae in the subfamily Asteroideae (Asteraceae) based on ndhF and trnL-F sequence comparisons. CONCLUSION: The chloroplast genome sequence of Artemisia frigida was assembled and analyzed in this study, representing the first plastid genome sequenced in the Anthemideae tribe. This complete chloroplast genome sequence will be useful for molecular ecology and molecular phylogeny studies within Artemisia species and also within the Asteraceae family.
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- 2013
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4. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon.
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Yu Cui, Mi Yeon Lee, Naxin Huo, Jennifer Bragg, Lijie Yan, Cheng Yuan, Cui Li, Sara J Holditch, Jingzhong Xie, Ming-Cheng Luo, Dawei Li, Jialin Yu, Joel Martin, Wendy Schackwitz, Yong Qiang Gu, John P Vogel, Andrew O Jackson, Zhiyong Liu, and David F Garvin
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Medicine ,Science - Abstract
The ND18 strain of Barley stripe mosaic virus (BSMV) infects several lines of Brachypodium distachyon, a recently developed model system for genomics research in cereals. Among the inbred lines tested, Bd3-1 is highly resistant at 20 to 25 °C, whereas Bd21 is susceptible and infection results in an intense mosaic phenotype accompanied by high levels of replicating virus. We generated an F(6:7) recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21 and used the RILs, and an F(2) population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance. The results indicate that resistance segregates as expected for a single dominant gene, which we have designated Barley stripe mosaic virus resistance 1 (Bsr1). We constructed a genetic linkage map of the RIL population using SNP markers to map this gene to within 705 Kb of the distal end of the top of chromosome 3. Additional CAPS and Indel markers were used to fine map Bsr1 to a 23 Kb interval containing five putative genes. Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium. Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits.
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- 2012
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5. PIECE 2.0: an update for the plant gene structure comparison and evolution database.
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Yi Wang 0052, Ling Xu, Roger Thilmony, Frank M. You, Yong Qiang Gu, and Devin Coleman-Derr
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- 2017
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6. Genome-wide association analyses of leaf rust resistance in cultivated emmer wheat
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Dhondup Lhamo, Qun Sun, Qijun Zhang, Xuehui Li, Jason D. Fiedler, Guangmin Xia, Justin D. Faris, Yong-Qiang Gu, Upinder Gill, Xiwen Cai, Maricelis Acevedo, and Steven S. Xu
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Genetics ,General Medicine ,Agronomy and Crop Science ,Biotechnology - Published
- 2023
7. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species.
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Yi Wang 0052, Devin Coleman-Derr, Guoping Chen, and Yong Qiang Gu
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- 2015
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8. NetVenn: an integrated network analysis web platform for gene lists.
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Yi Wang 0052, Roger Thilmony, and Yong Qiang Gu
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- 2014
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9. An Algorithm for Discrimination of Multiple-Fragment Peaks in Capillary Fingerprinting Chromatograms.
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Frank M. You, Ming-Cheng Luo, Yong Qiang Gu, Gerard R. Lazo, Jan Dvorak, and Olin D. Anderson
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- 2008
10. PIECE: a database for plant gene structure comparison and evolution.
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Yi Wang 0052, Frank M. You, Gerard R. Lazo, Ming-Cheng Luo, Roger Thilmony, Sean Gordon, Shahryar F. Kianian, and Yong Qiang Gu
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- 2013
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11. RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development.
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Frank M. You, Humphrey Wanjugi, Naxin Huo, Gerard R. Lazo, Ming-Cheng Luo, Olin D. Anderson, Jan Dvorak, and Yong Qiang Gu
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- 2010
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12. MetaCoMET: a web platform for discovery and visualization of the core microbiome.
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Yi Wang 0052, Ling Xu, Yong Qiang Gu, and Devin Coleman-Derr
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- 2016
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13. GSP: a web-based platform for designing genome-specific primers in polyploids.
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Yi Wang 0052, Vijay K. Tiwari, Nidhi Rawat, Bikram S. Gill, Naxin Huo, Frank M. You, Devin Coleman-Derr, and Yong Qiang Gu
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- 2016
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14. AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants.
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Yi Wang 0052, Roger Thilmony, Yunjun Zhao, Guoping Chen, and Yong Qiang Gu
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- 2014
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15. GenoProfiler: batch processing of high-throughput capillary fingerprinting data.
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Frank M. You, Ming-Cheng Luo, Yong Qiang Gu, Gerard R. Lazo, Karin Deal, Jan Dvorak, and Olin D. Anderson
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- 2007
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16. BatchPrimer3: A high throughput web application for PCR and sequencing primer design.
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Frank M. You, Naxin Huo, Yong Qiang Gu, Ming-Cheng Luo, Yaqin Ma, Dave Hane, Gerard R. Lazo, Jan Dvorak, and Olin D. Anderson
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- 2008
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17. An enhanced optoelectronic NO2 gas sensors based on direct growth ZnO nanowalls in situ on porous rGO
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Zongyuan Liu, Xinhui Fan, Qi Lijun, Lingmin Yu, Yong qiang Gu, and Fen Guo
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Nanostructure ,Materials science ,Oxide ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,law.invention ,chemistry.chemical_compound ,symbols.namesake ,law ,Materials Chemistry ,Irradiation ,Porosity ,Nanocomposite ,Graphene ,business.industry ,Mechanical Engineering ,Metals and Alloys ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,chemistry ,Mechanics of Materials ,Transmission electron microscopy ,symbols ,Optoelectronics ,0210 nano-technology ,business ,Raman spectroscopy - Abstract
ZnO nanowalls were grown in situ on the surface of porous reduced graphene oxide (PG) films using spray, thermal reduction and facile solution method in this work. The products were characterized by powder X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), Raman spectroscopy. The results showed that the highly developed interconnected 3-D ZnO nanowall networks were anchored homogeneously on the surface of PG films to construct 3D ZnO/PG hybrid nanocomposites. This 3D hybrid nanostructure provided many channels for gas diffusion. The fabricated sensor based on ZnO/PG composites showed good photo sensing response (7.4) to 365 nm UV light and an enhanced gas sensitivity (35.31) to 50 ppm NO2 with irradiation of UV light of 1.2 mW/cm2 in the air at room temperature, which was 2.24 fold higher than that of pure ZnO, and the response-recovery times were (∼37s, and 2s) when exposed to 50 ppm NO2. The optoelectronic gas sensing mechanisms of ZnO/PG composites were proposed in detail to understand the effect of UV irradiation in the NO2 detection process.
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- 2018
18. ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery.
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Frank M. You, Naxin Huo, Yong Qiang Gu, Gerard R. Lazo, Jan Dvorak, and Olin D. Anderson
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- 2009
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19. Synthesis and Characterization of Polythiophene Derivatives with Different Alkyl Substitution Groups
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Yong Qiang Gu, Xiao Long Zhang, Wei Xing Chen, and Chun Yan Luo
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chemistry.chemical_classification ,Materials science ,Band gap ,Mechanical Engineering ,Polymer ,Condensed Matter Physics ,Metathesis ,Fluorescence spectroscopy ,chemistry.chemical_compound ,chemistry ,Mechanics of Materials ,Polymer chemistry ,Polythiophene ,Physical chemistry ,General Materials Science ,Fourier transform infrared spectroscopy ,Absorption (chemistry) ,Glass transition - Abstract
Three kinds of poly (3-alkylthiophene), such as poly (3-butylthiophene) (P3BT), poly (3-hexylthiophene) (P3HT) and poly (3-dodecylthiophene) (P3DDT) were prepared by the Grignard Metathesis Method (GRIM). Their chemical structures are characterized by FTIR,1H-NMR and GPC.1H-NMR result shows that regioregular structure of these polymers is relatively higher. The GPC results show that the molecular weight of the polymers is 8.42×104, 1.06×105and 1.21×104g/mol with molecular weight distributions of 1.41, 2.18 and 1.18, respectively. The DSC result shows that the glass transition temperature of three kinds of polymers is 120.8, 146, 118 °C, respectively. UV absorption spectrum and fluorescence spectroscopy of three polymers in THF solution show that the maximum absorption wavelength is 448 nm, 470 nm, 390 nm, and the maximum emission wavelength is 531, 535, 527 nm with the band gap of 2.06, 1.86, 2.21 eV, respectively.
- Published
- 2015
20. Infrared Spectral Characteristics of Azobenzene Containing Side-Chain Liquid Crystal Polymer
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Xiao Long Zhang, Chun Yan Luo, Wei Xing Chen, Yong Qiang Gu, and Ai Jie Ma
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Materials science ,Infrared ,Mechanical Engineering ,Condensed Matter Physics ,Methacrylate ,chemistry.chemical_compound ,Monomer ,Differential scanning calorimetry ,Azobenzene ,chemistry ,Polymerization ,Mechanics of Materials ,Polymer chemistry ,General Materials Science ,Methyl methacrylate ,Fourier transform infrared spectroscopy - Abstract
In order to study the infrared spectral characteristics of side-chain liquid crystal polymer, an infrared monomer containing a permanent dipole azobenzene group spaced from the methacryloyl moiety by a polymethylene segment was synthesized in three steps starting from 4-cyanoaniline. The monomer was polymerized with a push-pull azobenzene monomer, (-)-menthy1 methacrylate in the presence of azobisisobutyronitrile (AIBN) as the radical initiator. Structurally similar amphiphilic polymers were obtained by polymerization of analogous methacrylates in which the polymethylene spacers was replaced by oligo (oxyethy1ene) segments. The obtained polymer was characterized by Fourier transform infrared spectroscopy (FT-IR), ultraviolet-visible spectro photometry (UV-vis), Hot Stage Polarized Microscopy (HS-POM), Differential Scanning Calorimetry (DSC) and Thermo Gravimetric Analyzer (TGA). Its infrared emissivity at different temperatures was tested by Bruker-V70 infrared analyzer. The results showed that the azobenzene poly (methyl methacrylate) (azo-PMMA) has high glass transition temperature(about 40°C), good thermal stability(divied in 294°C) and low infrared emission under 70%.
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- 2015
21. Study on Damage Identification of Simply Supported-Beam Based on Modal Strain Energy Method
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Yong Qiang Gu and Chun Feng Mao
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Identification (information) ,Modal ,Materials science ,genetic structures ,business.industry ,otorhinolaryngologic diseases ,Modal testing ,General Medicine ,Structural engineering ,business ,psychological phenomena and processes ,Finite element method ,Modal strain energy - Abstract
In present study, ANSYS finite element method was utilized to analyze the modal of simply supported beam and then the study on damage identification was performed based on modal strain energy method. The comparative analysis of results obtained by modal strain energy changes rate method and modal strain energy index demonstrates that modal strain energy index is an effective damage identification parameter.
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- 2014
22. The Preliminary Analysis on Tower Crane by Earthquake Effect
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Chun Feng Mao and Yong Qiang Gu
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Engineering ,business.industry ,Modal analysis ,General Medicine ,Structural engineering ,business ,Boom ,Tower ,Tower crane ,Seismic wave ,Displacement (vector) ,Finite element method ,Preliminary analysis - Abstract
Earthquake damages to the tall and towering structures are usually very serious, but these dangers are often hidden. The paper uses the finite element software ANSYS to set up the overall modeling of the TC6010 tower crane which is produced by a company, and carry on the modal analysis based on it. The paper obtains the data of the displacement and the speed response of the complete machine after exerting the Ninghe Tianjin seismic wave, and has the preliminary analysis to the result. The results show that the tower crane is a low-frequency vibrating system and easy to cause the structure resonance, the crane tower may damage in the boom firstly under the action of seismic wave.
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- 2013
23. Ion Beam Figuring Fabricate Effect with Different Removal Sizes
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Yong Qiang Gu
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Figuring ,Fabrication ,Materials science ,Ion beam ,business.industry ,Mechanical Engineering ,Spectral density ,law.invention ,Lens (optics) ,Interferometry ,Optics ,Mechanics of Materials ,law ,Range (statistics) ,General Materials Science ,Spatial frequency ,business - Abstract
Ion Beam Figure (IBF) is believed to be one of the most effective technics that can fabricate lens with nano or even sub-nano accuracy. For different sizes of IBF removal functions, the correct effects in different spatial frequency range are different. Power Spectral Density (PSD) curve can describe surface errors in full spatial frequency range, so it is a very convenient way to evaluate the quality of lens' surface. In this paper, firstly, the principles of IBF and PSD are introduced briefly; Secondly, IBF removal functions with sizes from 2 mm to 15 mm are generated. A lens with surface error more than PV value 400nm is simulated with different sizes of IBF removal functions by Lucy-Richardson algorithm. Finally, experiments are done by IBF plant. A lens is fabricated by different sizes of removal functions and the fabricate results are tested by interferometer precisely and calculated to PSD curves. By the comparison of these curves, the IBF fabricate effects with different removal sizes are analyzed, which show that the smaller the removal size, the better the removal effect in higher spatial frequency range, but in the meantime, it will take a much longer time. Also the reasons of the difference between theory simulation and actual fabrication result are taken into account, and several influence factors are analyzed. (2013) Trans Tech Publications, Switzerland.
- Published
- 2013
24. Analysis on Tower Crane under Wind Load by ANSYS
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Wen Feng Wang, Shao Dong Guo, and Yong Qiang Gu
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Engineering ,business.industry ,Modal analysis ,Wind wave ,General Medicine ,Structural engineering ,business ,Tower crane ,Tower ,Boom ,Finite element method ,Displacement (vector) ,Wind engineering - Abstract
With high-rise construction increasing in city, it demands more and higher-performance tower cranes. Damages by wind to the tall and towering structures are usually very serious, but these dangers are often hidden.The paper uses the finite element software ANSYS to set up the overall modeling of the TC6010 tower crane which is produced by a company, and carry on the FEM analysis effected by wind based on it . The paper obtains the data of the displacement response of the complete machine after exerting the wind wave, and has the preliminary analysis to the result. The results show that the tower crane is a low-frequency vibrating system and easy to cause the structure resonance, the crane tower may damage in the boom firstly under the action of wind load.
- Published
- 2012
25. PIECE: a database for plant gene structure comparison and evolution
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Ming-Cheng Luo, Yi Wang, Frank M. You, Yong Qiang Gu, Sean P. Gordon, Gerard R. Lazo, Roger Thilmony, and Shahryar F. Kianian
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0106 biological sciences ,Sequence alignment ,Biology ,computer.software_genre ,Genes, Plant ,01 natural sciences ,Genome ,Evolution, Molecular ,03 medical and health sciences ,Phylogenetics ,Databases, Genetic ,Genetics ,Gene family ,Gene ,Phylogeny ,030304 developmental biology ,Plant Proteins ,2. Zero hunger ,Comparative genomics ,0303 health sciences ,Internet ,Phylogenetic tree ,Database ,food and beverages ,Articles ,Exons ,15. Life on land ,Introns ,Multigene Family ,computer ,Sequence Alignment ,Orthologous Gene ,Genome, Plant ,010606 plant biology & botany - Abstract
Gene families often show degrees of differences in terms of exon–intron structures depending on their distinct evolutionary histories. Comparative analysis of gene structures is important for understanding their evolutionary and functional relationships within plant species. Here, we present a comparative genomics database named PIECE (http://wheat.pw.usda.gov/piece) for Plant Intron and Exon Comparison and Evolution studies. The database contains all the annotated genes extracted from 25 sequenced plant genomes. These genes were classified based on Pfam motifs. Phylogenetic trees were pre-constructed for each gene category. PIECE provides a user-friendly interface for different types of searches and a graphical viewer for displaying a gene structure pattern diagram linked to the resulting bootstrapped dendrogram for each gene family. The gene structure evolution of orthologous gene groups was determined using the GLOOME, Exalign and GECA software programs that can be accessed within the database. PIECE also provides a web server version of the software, GSDraw, for drawing schematic diagrams of gene structures. PIECE is a powerful tool for comparing gene sequences and provides valuable insights into the evolution of gene structure in plant genomes.
- Published
- 2012
26. Dynamic evolution of resistance gene analogs in the orthologous genomic regions of powdery mildew resistance gene MlIW170 in Triticum dicoccoides and Aegilops tauschii
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Ping Lu, Qiuhong Wu, Yong-Qiang Gu, Naxin Huo, Shuhong Ouyang, Zhenzhong Wang, Deyun Zhang, Yongxing Chen, Jingzhong Xie, Yu Cui, Dong Zhang, Ming-Cheng Luo, Jan Dvorak, Zhiyong Liu, Yan Zhang, Qixin Sun, Jie Zhu, Ziji Liu, and Yong Liang
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Genetic Markers ,DNA, Plant ,Genotype ,Genetic Linkage ,Blumeria graminis ,Locus (genetics) ,Genes, Plant ,Genome ,Chromosomes, Plant ,Evolution, Molecular ,Ascomycota ,Gene duplication ,Genetics ,Aegilops tauschii ,Gene ,Phylogeny ,Triticum ,Disease Resistance ,Plant Diseases ,biology ,food and beverages ,General Medicine ,biology.organism_classification ,Physical Chromosome Mapping ,Ploidy ,Agronomy and Crop Science ,Powdery mildew ,Biotechnology - Abstract
Rapid evolution of powdery mildew resistance gene MlIW170 orthologous genomic regions in wheat subgenomes. Wheat is one of the most important staple grain crops in the world and also an excellent model for plant ploidy evolution research with different ploidy levels from diploid to hexaploid. Powdery mildew disease caused by Blumeria graminis f.sp. tritici can result in significant loss in both grain yield and quality in wheat. In this study, the wheat powdery mildew resistance gene MlIW170 locus located at the Triticum dicoccoides chromosome 2B short arm was further characterized by constructing and sequencing a BAC-based physical map contig covering a 0.3 cM genetic distance region (880 kb) and developing additional markers to delineate the resistance gene within a 0.16 cM genetic interval (372 kb). Comparative analyses of the T. dicoccoides 2BS region with the orthologous Aegilops tauschii 2DS region showed great gene colinearity, including the structure organization of both types of RGA1/2-like and RPS2-like resistance genes. Comparative analyses with the orthologous regions from Brachypodium and rice genomes revealed considerable dynamic evolutionary changes that have re-shaped this MlIW170 region in the wheat genome, resulting in a high number of non-syntenic genes including resistance-related genes. This result might reflect the rapid evolution in R-gene regions. Phylogenetic analysis on these resistance-related gene sequences indicated the duplication of these genes in the MlIW170 region, occurred before the separation of the wheat B and D genomes.
- Published
- 2015
27. Subtractive cDNA Libraries Identify Differentially Expressed Genes in Dormant and Growing Buds of Leafy Spurge (Euphorbia esula)
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Rodney G. Lym, Ying Jia, Yong-Qiang Gu, David P. Horvath, Wun S. Chao, and James V. Anderson
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Euphorbia esula ,Plant Science ,Biology ,Euphorbia ,Gene Expression Regulation, Plant ,Gene expression ,Genetics ,Cluster Analysis ,RNA, Messenger ,Leafy ,Gene ,Gene Library ,Reverse Transcriptase Polymerase Chain Reaction ,cDNA library ,Gene Expression Profiling ,Nucleic Acid Hybridization ,RNA ,Genomics ,General Medicine ,biology.organism_classification ,Suppression subtractive hybridization ,Dormancy ,Seasons ,Agronomy and Crop Science ,Plant Shoots - Abstract
Two subtractive cDNA libraries were developed to study genes associated with bud dormancy (reverse library) and initiation of shoot growth (forward library) in leafy spurge. To identify unique sequences represented in each library, 15744 clones were screened to reduce the level of redundancy within both libraries. A total of 516 unique sequences were obtained from 2304 minimally redundant clones. Radioactive probes developed from RNAs extracted from crown buds of either intact (para-dormant control) or a series of growth-induced (2 h, 2, and 4 d after decapitation) plants were used to identify differentially expressed genes by macroarray analysis. Semi-quantitative RT-PCR was used to confirm results obtained by macroarray analysis and to determine the expression profiles for other transcripts identified within the subtractive libraries. Selected clones were also used to examine gene expression in crown buds after growth induction and/or during normal seasonal growth. In this study, four distinct patterns of gene expression were observed during the transition from para-dormancy to growth-induction. Many of the differentially regulated genes identified have unknown or hypothetical functions while others are known to play important roles in molecular functions. Gene ontology analysis identified a greater proportion of genes involved with catalytic activity in the forward library while the reverse library had a greater proportion of genes involved in DNA/RNA binding.
- Published
- 2006
28. AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants
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Yunjun Zhao, Roger Thilmony, Yong Qiang Gu, Guoping Chen, and Yi Wang
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Interface (Java) ,Systems biology ,Arabidopsis ,computer.software_genre ,Interactome ,General Biochemistry, Genetics and Molecular Biology ,law.invention ,Annotation ,User-Computer Interface ,law ,Arabidopsis thaliana ,Protein Interaction Maps ,Databases, Protein ,Internet ,Database ,biology ,Arabidopsis Proteins ,Plants ,biology.organism_classification ,Up-Regulation ,Graph (abstract data type) ,Venn diagram ,Original Article ,General Agricultural and Biological Sciences ,computer ,Information Systems ,Abscisic Acid - Abstract
Systems biology analysis of protein modules is important for understanding the functional relationships between proteins in the interactome. Here, we present a comprehensive database named AIM for Arabidopsis (Arabidopsis thaliana) interactome modules. The database contains almost 250 000 modules that were generated using multiple analysis methods and integration of microarray expression data. All the modules in AIM are well annotated using multiple gene function knowledge databases. AIM provides a user-friendly interface for different types of searches and offers a powerful graphical viewer for displaying module networks linked to the enrichment annotation terms. Both interactive Venn diagram and power graph viewer are integrated into the database for easy comparison of modules. In addition, predicted interologs from other plant species (homologous proteins from different species that share a conserved interaction module) are available for each Arabidopsis module. AIM is a powerful systems biology platform for obtaining valuable insights into the function of proteins in Arabidopsis and other plants using the modules of the Arabidopsis interactome. Database URL: http://probes.pw.usda.gov/AIM
- Published
- 2014
29. Tomato Transcription Factors Pti4, Pti5, and Pti6 Activate Defense Responses When Expressed in Arabidopsis
- Author
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Gregory B. Martin, Mary C. Wildermuth, Suma Chakravarthy, Caimei Yang, Yong-Qiang Gu, Yu Han, Xiaohua He, and Ying-Tsu Loh
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Transcriptional Activation ,Arabidopsis ,Receptors, Cell Surface ,Cyclopentanes ,Plant Science ,Protein Serine-Threonine Kinases ,Plant disease resistance ,Defensins ,chemistry.chemical_compound ,Ascomycota ,Solanum lycopersicum ,Gene Expression Regulation, Plant ,Pseudomonas ,Botany ,Plant defense against herbivory ,Pseudomonas syringae ,Oxylipins ,Gene ,Transcription factor ,Plant Diseases ,Plant Proteins ,Cell Nucleus ,biology ,Arabidopsis Proteins ,Jasmonic acid ,fungi ,Nuclear Proteins ,food and beverages ,Promoter ,Cell Biology ,Ethylenes ,biology.organism_classification ,Immunity, Innate ,Cell biology ,DNA-Binding Proteins ,chemistry ,Mutation ,Salicylic Acid ,Research Article ,Transcription Factors - Abstract
The Pti4, Pti5, and Pti6 proteins from tomato were identified based on their interaction with the product of the Pto disease resistance gene, a Ser-Thr protein kinase. They belong to the ethylene-response factor (ERF) family of plantunique transcription factors and bind specifically to the GCC-box cis element present in the promoters of many pathogenesis-related ( PR ) genes. Here, we show that these tomato ERFs are localized to the nucleus and function in vivo as transcription activators that regulate the expression of GCC box‐containing PR genes. Expression of Pti4 , Pti5 , or Pti 6 in Arabidopsis activated the expression of the salicylic acid‐regulated genes PR1 and PR2 . Expression of jasmonic acid‐ and ethylene-regulated genes, such as PR3 , PR4 , PDF1.2 , and Thi2.1 , was affected differently by each of the three tomato ERFs, with Arabidopsis -Pti4 plants having very high levels of PDF1.2 transcripts. Exogenous application of salicylic acid to Arabidopsis- Pti4 plants suppressed the increased expression of PDF1.2 but further stimulated PR1 expression. Arabidopsis plants expressing Pti4 displayed increased resistance to the fungal pathogen Erysiphe orontii and increased tolerance to the bacterial pathogen Pseudomonas syringae pv tomato . These results indicate that Pti4, Pti5, and Pti6 activate the expression of a wide array of PR genes and play important and distinct roles in plant defense.
- Published
- 2002
30. Identification of residues critical for activity of the wound-induced leucine aminopeptidase (LAP-A) of tomato
- Author
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Linda L. Walling and Yong-Qiang Gu
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chemistry.chemical_classification ,biology ,digestive, oral, and skin physiology ,Mutant ,Exopeptidase ,Random hexamer ,equipment and supplies ,Biochemistry ,Fusion protein ,Aminopeptidase ,Enzyme ,chemistry ,biology.protein ,Enzyme kinetics ,Leucine ,human activities - Abstract
The importance of two putative Zn2+-binding (Asp347, Glu429) and two catalytic (Arg431, Lys354) residues in the tomato leucine aminopeptidase (LAP-A) function was tested. The impact of substitutions at these positions, corresponding to the bovine LAP residues Asp255, Glu334, Arg336, and Lys262, was evaluated in His6–LAP-A fusion proteins expressed in Escherichia coli. Sixty-five percent of the mutant His6–LAP-A proteins were unstable or had complete or partial defects in hexamer assembly or stability. The activity of hexameric His6–LAP-As on Xaa-Leu and Leu-Xaa dipeptides was tested. Most substitutions of Lys354 (a catalytic residue) resulted in His6–LAP-As that cleaved dipeptides at slower rates. The Glu429 mutants (a Zn2+-binding residue) had more diverse phenotypes. Some mutations abolished activity and others retained partial or complete activity. The E429D His6–LAP-A enzyme had Km and kcat values similar to the wild-type His6–LAP-A. One catalytic (Arg431) and one Zn-binding (Asp347) residue were essential for His6–LAP-A activity, as most R431 and D347 mutant His6–LAP-As did not hydrolyze dipeptides. The R431K His6–LAP-A that retained the positive charge had partial activity as reflected in the 4.8-fold decrease in kcat. Surprisingly, while the D347E mutant (that retained a negative charge at position 347) was inactive, the D347R mutant that introduced a positive charge retained partial activity. A model to explain these data is proposed.
- Published
- 2002
31. Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer (Triticum dicoccoides)
- Author
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Qixin Sun, Tsomin Yang, Dong Zhang, Jingzhong Xie, Hua Sun, Xiaojie Zhao, Li-li Wang, Yong-Qiang Gu, Ming-Cheng Luo, Jaroslav Doležel, Ping Lu, Shuhong Ouyang, Zhenzhong Wang, Zhiyong Liu, Jun Han, Qiuhong Wu, Yong Liang, Wei Song, Naxin Huo, Rudi Appels, Hong-Qing Ling, Gabriel Keeble-Gagnère, Yongxing Chen, Yu Cui, and Deyun Zhang
- Subjects
lcsh:Medicine ,Blumeria graminis ,Locus (genetics) ,Crops ,Plant Science ,Biology ,Genes, Plant ,Plant Genetics ,Polyploidy ,chemistry.chemical_compound ,Gene mapping ,Ascomycota ,Molecular marker ,Plant Genomics ,Genetics ,lcsh:Science ,Triticum ,Disease Resistance ,Plant Diseases ,Multidisciplinary ,Wheat diseases ,lcsh:R ,food and beverages ,Chromosome Mapping ,Biology and Life Sciences ,Crop Diseases ,Computational Biology ,Agriculture ,Genomics ,Comparative Genomics ,biology.organism_classification ,Triticum urartu ,chemistry ,Wheat ,lcsh:Q ,Brachypodium ,Plant Biotechnology ,Structural Genomics ,Powdery mildew ,Research Article ,Cereal Crops ,Biotechnology - Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases in the world. In this study, a single dominant powdery mildew resistance gene MlIW172 was identified in the IW172 wild emmer accession and mapped to the distal region of chromosome arm 7AL (bin7AL-16-0.86-0.90) via molecular marker analysis. MlIW172 was closely linked with the RFLP probe Xpsr680-derived STS marker Xmag2185 and the EST markers BE405531 and BE637476. This suggested that MlIW172 might be allelic to the Pm1 locus or a new locus closely linked to Pm1. By screening genomic BAC library of durum wheat cv. Langdon and 7AL-specific BAC library of hexaploid wheat cv. Chinese Spring, and after analyzing genome scaffolds of Triticum urartu containing the marker sequences, additional markers were developed to construct a fine genetic linkage map on the MlIW172 locus region and to delineate the resistance gene within a 0.48 cM interval. Comparative genetics analyses using ESTs and RFLP probe sequences flanking the MlIW172 region against other grass species revealed a general co-linearity in this region with the orthologous genomic regions of rice chromosome 6, Brachypodium chromosome 1, and sorghum chromosome 10. However, orthologous resistance gene-like RGA sequences were only present in wheat and Brachypodium. The BAC contigs and sequence scaffolds that we have developed provide a framework for the physical mapping and map-based cloning of MlIW172.
- Published
- 2014
32. Overexpression, purification and biochemical characterization of the wound-induced leucine aminopeptidase of tomato
- Author
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Frances M. Holzer, Yong-Qiang Gu, and Linda L. Walling
- Subjects
Hot Temperature ,Macromolecular Substances ,Swine ,Proteolysis ,Biochemistry ,Aminopeptidase ,Gene Expression Regulation, Enzymologic ,Inclusion bodies ,Substrate Specificity ,Leucyl Aminopeptidase ,chemistry.chemical_compound ,Amastatin ,Solanum lycopersicum ,Gene Expression Regulation, Plant ,Leucine ,Escherichia coli ,medicine ,Animals ,Protease Inhibitors ,Cloning, Molecular ,chemistry.chemical_classification ,Manganese ,medicine.diagnostic_test ,biology ,Activator (genetics) ,digestive, oral, and skin physiology ,Exopeptidase ,equipment and supplies ,Molecular biology ,Anti-Bacterial Agents ,Molecular Weight ,Plant Leaves ,Kinetics ,Enzyme ,chemistry ,biology.protein ,Peptides ,human activities - Abstract
Wounding of tomato leaves results in the accumulation of an exoprotease called leucine aminopeptidase (LAP-A). While the expression of LapA genes are well characterized, the specificity of the LAP-A enzyme has not been studied. The LAP-A preprotein and mature polypeptide were overexpressed in Escherichia coli. PreLAP-A was not processed and was inactive accumulating in inclusion bodies. In contrast, 55-kDa mature LAP-A subunits assembled into an active, 357-kDa enzyme in E. coli. LAP-A from E. coli cultures was purified to apparent homogeneity and characterized relative to its animal (porcine LAP) and prokaryotic (E. coli PepA) homologues. Similar to the porcine and E. coli enzymes, the tomato LAP-A had high temperature and pH optima. Mn2+ was a strong activator for all three enzymes, while chelators, zinc ion, and the slow-binding aminopeptidase inhibitors (amastatin and bestatin) strongly inhibited activities of all three LAPs. The substrate specificities of porcine, E. coli and tomato LAPs were determined using amino-acid-p-nitroanilide and -beta-naphthylamide substrates. The tomato LAP-A preferentially hydrolyzed substrates with N-terminal Leu, Met and Arg residues. LAP-A had substantially lower levels of activity on other chromogenic substrates. Several differences in substrate specificities for the animal, plant and prokaryotic enzymes were noted.
- Published
- 1999
33. Leucine Aminopeptidase RNAs, Proteins, and Activities Increase in Response to Water Deficit, Salinity, and the Wound Signals Systemin, Methyl Jasmonate, and Abscisic Acid1
- Author
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Elizabeth A. Bray, Véronique Pautot, Linda L. Walling, Wun S. Chao, and Yong Qiang Gu
- Subjects
0106 biological sciences ,0303 health sciences ,Methyl jasmonate ,Physiology ,fungi ,food and beverages ,Plant Science ,Systemin ,Biology ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Biochemistry ,chemistry ,Gene expression ,Genetics ,Pseudomonas syringae ,Octadecanoid pathway ,Leucyl aminopeptidase ,Abscisic acid ,Salicylic acid ,Research Article ,030304 developmental biology ,010606 plant biology & botany - Abstract
LapARNAs, proteins, and activities increased in response to systemin, methyl jasmonate, abscisic acid (ABA), ethylene, water deficit, and salinity in tomato (Lycopersicon esculentum). Salicylic acid inhibited wound-induced increases of LapA RNAs. Experiments using the ABA-deficient flacca mutant indicated that ABA was essential for wound and systemin induction ofLapA, and ABA and systemin acted synergistically to induce LapA gene expression. In contrast,pin2 (proteinase inhibitor 2) was not dependent on exogenous ABA. Whereas both LapA and le4(L. esculentumdehydrin) were up-regulated by increases in ABA, salinity, and water deficit, only LapAwas regulated by octadecanoid pathway signals. Comparison ofLapA expression with that of thePR-1 (pathogenesis-related 1) andGluB (basic β-1,3-glucanase) genes indicated that these PR protein genes were modulated by a systemin-independent jasmonic acid-signaling pathway. These studies showed that at least four signaling pathways were utilized during tomato wound and defense responses. Analysis of the expression of aLapA1:GUS gene in transgenic plants indicated that theLapA1 promoter was active during floral and fruit development and was used during vegetative growth only in response to wounding, Pseudomonas syringae pv tomatoinfection, or wound signals. This comprehensive understanding of the regulation of LapA genes indicated that this regulatory program is distinct from the wound-induced pin2, ABA-responsive le4, and PR protein genes.
- Published
- 1999
34. Molecular mechanisms involved in bacterial speck disease resistance of tomato
- Author
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Yong–Qiang Gu and Gregory B. Martin
- Subjects
Hypersensitive response ,Genetics ,Transduction (genetics) ,Kinase ,Pseudomonas syringae ,R gene ,Signal transduction ,Plant disease resistance ,Biology ,General Agricultural and Biological Sciences ,Gene ,Article ,General Biochemistry, Genetics and Molecular Biology - Abstract
An important recent advance in the field of plant–microbe interactions has been the cloning of genes that confer resistance to specific viruses, bacteria, fungi or nematodes. Disease resistance (R) genes encode proteins with predicted structural motifs consistent with them having roles in signal recognition and transduction. The future challenge is to understand howRgene products specifically perceive defence–eliciting signals from the pathogen and transduce those signals to pathways that lead to the activation of plant defence responses. In tomatoes, the Pto kinase (product of thePto Rgene) confers resistance to strains of the bacterial speck pathogen,Pseudomonas syringaepv.tomato, that carry the corresponding avirulence geneavrPto. Resistance to bacterial speck disease is initiated by a mechanism involving the physical interaction of the Pto kinase and the AvrPto protein. This recognition event initiates signalling events that lead to defence responses including an oxidative burst, the hypersensitive response and expression of pathogenesis–related genes. Pto–interacting (Pti) proteins have been identified that appear to act downstream of the Pto kinase and our current studies are directed at elucidating the roles of these components.
- Published
- 1998
35. Genetic association of OPR genes with resistance to Hessian fly in hexaploid wheat
- Author
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Brett F. Carver, Chor-Tee Tan, Ming-Shun Chen, Yong-Qiang Gu, and Liuling Yan
- Subjects
Oxidoreductases Acting on CH-CH Group Donors ,Population ,Lipoxygenase ,Quantitative Trait Loci ,Locus (genetics) ,Hessian fly resistance ,Insect resistance pathway ,Quantitative trait locus ,Polyploidy ,Inbred strain ,Gene mapping ,Species Specificity ,Botany ,Genetics ,Animals ,12-oxophytodienoic acid reductase (OPR) ,Allele ,education ,Gene ,Mayetiola destructor ,Triticum ,education.field_of_study ,biology ,Diptera ,fungi ,Quantitative trait loci (QTL) ,food and beverages ,Chromosome Mapping ,biology.organism_classification ,lipoxygenase (LOX) ,Wheat ,Hybridization, Genetic ,Biotechnology ,Research Article - Abstract
BackgroundHessian fly (Mayetiola destructor) is one of the most destructive pests of wheat. The genes encoding 12-oxo-phytodienoic acid reductase (OPR) and lipoxygenase (LOX) play critical roles in insect resistance pathways in higher plants, but little is known about genes controlling resistance to Hessian fly in wheat.ResultsIn this study, 154 F6:8recombinant inbred lines (RILs) generated from a cross between two cultivars, ‘Jagger’ and ‘2174’ of hexaploid wheat (2n = 6 × =42; AABBDD), were used to map genes associated with resistance to Hessian fly. Two QTLs were identified. The first one was a major QTL on chromosome 1A (QHf.osu-1A), which explained 70% of the total phenotypic variation. The resistant allele at this locus in cultivar 2174 could be orthologous to one or more of the previously mapped resistance genes (H9,H10,H11,H16, andH17) in tetraploid wheat. The second QTL was a minor QTL on chromosome 2A (QHf.osu-2A), which accounted for 18% of the total phenotypic variation. The resistant allele at this locus in 2174 is collinear to anYr17-containing-fragment translocated from chromosome 2N ofTriticum ventricosum(2n = 4 × =28; DDNN) in Jagger. Genetic mapping results showed that twoOPRgenes,TaOPR1-AandTaOPR2-A, were tightly associated withQHf.osu-1AandQHf.osu-2A,respectively. AnotherOPRgene and threeLOXgenes were mapped but not associated with Hessian fly resistance in the segregating population.ConclusionsThis study has located two major QTLs/genes in bread wheat that can be directly used in wheat breeding programs and has also provided insights for the genetic association and disassociation of Hessian fly resistance withOPRandLOXgenes in wheat.
- Published
- 2013
36. A Complex Array of Proteins Related to the Multimeric Leucine Aminopeptidase of Tomato
- Author
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Frances M. Holzer, Véronique Pautot, Yong-Qiang Gu, and Linda L. Walling
- Subjects
0106 biological sciences ,Physiology ,Plant Science ,01 natural sciences ,Aminopeptidase ,Lycopersicon ,03 medical and health sciences ,Genetics ,Pseudomonas syringae ,Leucyl aminopeptidase ,Polyacrylamide gel electrophoresis ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,biology ,digestive, oral, and skin physiology ,food and beverages ,Exopeptidase ,equipment and supplies ,biology.organism_classification ,Fusion protein ,Biochemistry ,Polyclonal antibodies ,biology.protein ,human activities ,Research Article ,010606 plant biology & botany - Abstract
Leucine aminopeptidase (LAP) mRNAs are induced in response to mechanical wounding, pathogen infection, and insect infestation (V. Pautot, F.M. Holzer, B. Reisch, L.L. Walling [1993] Proc Natl Acad Sci USA 90: 9906-9910). Polyclonal antibodies to a glutathione S-transferase-LAP fusion protein and affinity-purified antibodies recognizing LAP antigenic determinants detected four classes of polypeptides in tomato (Lycopersicon esculentum) leaves. All four classes had multiple polypeptides in two-dimensional polyacrylamide gel electrophoresis immunoblots. Although antigenically related to the wound-induced tomato LAP proteins, the 77- and 66-kD LAP-like proteins accumulated in both healthy and wounded leaves. Two classes of 55-kD polypeptides with distinctive isoelectric points were designated as plant LAPs; only the acidic LAP proteins accumulated to high levels after mechanical wounding or Pseudomonas syringae pv tomato infection of tomato leaves. The temporal accumulation of LAP mRNAs was correlated with the increase in acidic LAP protein subunits. A slow-migrating LAP activity was detected using a native gel assay after wounding. The molecular mass of the native wound-induced LAP enzyme was 353 kD. The 55-kD acidic LAP proteins were associated with induced LAP activity, whereas the neutral LAPs and the LAP-like proteins were not associated with this exopeptidase. A second, fast-migrating aminopeptidase was detected in both healthy and wounded tomato leaves. Cell fractionation experiments revealed that wound-induced LAP is a soluble enzyme.
- Published
- 1996
37. Correction of full spatial frequency errors with ion beam figuring
- Author
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Yong-qiang Gu
- Subjects
Figuring ,Physics ,White light interferometry ,business.industry ,Spectral density ,law.invention ,Lens (optics) ,Interferometry ,Optics ,law ,Astronomical interferometer ,Spatial frequency ,Photolithography ,business - Abstract
For Lens that will be used in photo lithography systems, not only Low Spatial Frequency (LSF) errors, but also Middle and High Spatial Frequency (M/HSF) errors should be corrected to very low level. Ion Beam Figuring (IBF) is believed to be one of the most effective ways that can fabricate lens to especially high surface accuracy; In fact, it has also certain effects on removing errors in higher spatial frequency range. Firstly, the principle of IBF was introduced; Then, Power Spectral Density (PSD) is introduced, which is used to evaluate IBF’s corrective effects on errors in different spatial frequency ranges; Finally, by the use of IBF machine, a convex lens with diameter 90mm was fabricated, and its surface error was improved from PVr value15nm to less than 10nm, measured by Fizeau phase shift interferometer precisely. Also, M/HSF errors were measured before and after IBF fabrication, by White Light Interferometer and Atom Force Microscope separately. The initial and final Power Spectrum Density (PSD) curves of the lens were generated and compared with each other, which shows that IBF technic has really good ability to remove LSF errors, and can also reduce M/HSF errors greatly in the meantime. The results help to evaluate the corrective effects of IBF technic on errors in the full spatial frequency range.
- Published
- 2012
38. Application of optical tweezers in the research of molecular interaction between lymphocyte function associated antigen-1 and its monoclonal antibody
- Author
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Hao Dong, Chen, Kui Kui, Ge, Yin Mei, Li, Jian Guang, Wu, Yong Qiang, Gu, Hai Ming, Wei, and Zhi Gang, Tian
- Subjects
Killer Cells, Natural ,Optical Tweezers ,Antibodies, Monoclonal ,Humans ,Cells, Cultured ,Lymphocyte Function-Associated Antigen-1 ,Microspheres - Abstract
Lymphocyte function associated antigen-1 (CD11a/CD18, LFA-1) plays an important role in the structure of the immunological synapse and is required for efficient lysis of cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells. To study the activation mode of LFA-1 on the NK cell surface, optical tweezers were used in the work. As an emerging technology, optical tweezers are widely used to manipulate microscopic objects and measure the forces of molecular interactions in the field of biological research. In our study, a new platform was constructed to study the single molecular behavior of receptor on cell surface using optical tweezers. Based on the platform, the interaction between an NK cell and a polystyrene microsphere coated with anti-LFA-1 antibody was observed. The result confirmed that the adhesion forces between an NK cell and a polystyrene bead were time-dependent. According to our findings, we propose that anti-LFA-1 antibody may cause the clustering of LFA-1 on NK cell surface.
- Published
- 2007
39. Silencing of subfamily I of protein phosphatase 2A catalytic subunits results in activation of plant defense responses and localized cell death
- Author
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Xiaohua He, Gregory B. Martin, Jeffrey C. Anderson, Olga del Pozo, Yong-Qiang Gu, and Xiaoyan Tang
- Subjects
Hypersensitive response ,Subfamily ,Protein subunit ,Molecular Sequence Data ,Arabidopsis ,Plant Science ,Biology ,Polymerase Chain Reaction ,Solanum lycopersicum ,Tobacco ,Genetics ,Pseudomonas syringae ,Phosphoprotein Phosphatases ,Protein phosphorylation ,Amino Acid Sequence ,Gene Silencing ,Protein Phosphatase 2 ,Phosphorylation ,Pathogenesis-related protein ,DNA Primers ,Plant Diseases ,Plant Proteins ,Base Sequence ,Effector ,Arabidopsis Proteins ,fungi ,food and beverages ,Cell Biology ,Protein phosphatase 2 ,Cell biology ,Plant Leaves ,Protein Subunits ,Biochemistry - Abstract
The central importance of protein phosphorylation in plant defense responses has been demonstrated by the isolation of several disease-resistance genes that encode protein kinases. In addition, there are many reports of changes in protein phosphorylation accompanying plant responses to pathogens. In contrast, little is known about the role of protein dephosphorylation in regulating plant defenses. We report that expression of the LePP2Ac1 gene, which encodes a catalytic subunit of the heterotrimeric protein phosphatase 2A (PP2Ac), is rapidly induced in resistant tomato leaves upon inoculation with an avirulent strain of Pseudomonas syringae pv. tomato. By analysis of PP2Ac gene sequences from several plant species, we found that PP2Ac genes cluster into two subfamilies, with LePP2Ac1 belonging to subfamily I. Virus-induced gene silencing (VIGS) in Nicotiana benthamiana was used to suppress expression of genes from subfamily I and not from subfamily II. The PP2Ac-silenced plants had greatly decreased PP2A activity, constitutively expressed pathogenesis-related (PR) genes, and developed localized cell death in stems and leaves. In addition, the plants were more resistant to a virulent strain of P. syringae pv. tabaci and showed an accelerated hypersensitive response (HR) to effector proteins from both P. syringae and the fungal pathogen, Cladosporium fulvum. Thus, catalytic subunits of PP2Ac subfamily I act as negative regulators of plant defense responses likely by de-sensitizing protein phosphorylation cascades.
- Published
- 2004
40. Identification of residues critical for activity of the wound-induced leucine aminopeptidase (LAP-A) of tomato
- Author
-
Yong-Qiang, Gu and Linda L, Walling
- Subjects
Kinetics ,Leucyl Aminopeptidase ,Solanum lycopersicum ,Sequence Homology, Amino Acid ,Hydrolysis ,Molecular Sequence Data ,Mutagenesis, Site-Directed ,Animals ,Cattle ,Amino Acid Sequence ,Protein Structure, Quaternary ,DNA Primers - Abstract
The importance of two putative Zn2+-binding (Asp347, Glu429) and two catalytic (Arg431, Lys354) residues in the tomato leucine aminopeptidase (LAP-A) function was tested. The impact of substitutions at these positions, corresponding to the bovine LAP residues Asp255, Glu334, Arg336, and Lys262, was evaluated in His6-LAP-A fusion proteins expressed in Escherichia coli. Sixty-five percent of the mutant His6-LAP-A proteins were unstable or had complete or partial defects in hexamer assembly or stability. The activity of hexameric His6-LAP-As on Xaa-Leu and Leu-Xaa dipeptides was tested. Most substitutions of Lys354 (a catalytic residue) resulted in His6-LAP-As that cleaved dipeptides at slower rates. The Glu429 mutants (a Zn2+-binding residue) had more diverse phenotypes. Some mutations abolished activity and others retained partial or complete activity. The E429D His6-LAP-A enzyme had Km and kcat values similar to the wild-type His6-LAP-A. One catalytic (Arg431) and one Zn-binding (Asp347) residue were essential for His6-LAP-A activity, as most R431 and D347 mutant His6-LAP-As did not hydrolyze dipeptides. The R431K His6-LAP-A that retained the positive charge had partial activity as reflected in the 4.8-fold decrease in kcat. Surprisingly, while the D347E mutant (that retained a negative charge at position 347) was inactive, the D347R mutant that introduced a positive charge retained partial activity. A model to explain these data is proposed.
- Published
- 2002
41. Pti4 is induced by ethylene and salicylic acid, and its product is phosphorylated by the Pto kinase
- Author
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Venkatappa K. Thara, Caimei Yang, Yong-Qiang Gu, Gregory B. Martin, and Jianmin Zhou
- Subjects
Plant Science ,Biology ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Gene expression ,RNA, Messenger ,Cycloheximide ,Phosphorylation ,Protein kinase A ,Transcription factor ,Gene ,Plant Proteins ,Regulation of gene expression ,Protein Synthesis Inhibitors ,Kinase ,Promoter ,Cell Biology ,Ethylenes ,Molecular biology ,DNA-Binding Proteins ,Biochemistry ,chemistry ,Salicylic Acid ,Protein Kinases ,Salicylic acid ,Protein Binding ,Transcription Factors ,Research Article - Abstract
The tomato Pti4 gene encodes a transcription factor that was identified on the basis of its specific interaction with the product of the Pto disease resistance gene in a yeast two-hybrid system. We show here that the Pti4 protein specifically binds the GCC-box cis element, which is present in the promoter region of many pathogenesis-related (PR) genes. Expression of the Pti4 gene in tomato leaves was rapidly induced by ethylene and by infection with Pseudomonas syringae pv tomato, and this induction preceded expression of GCC-box-containing PR genes. Although salicylic acid also induced Pti4 gene expression, it did not induce GCC-box PR genes. Rather, salicylic acid antagonized ethylene-mediated expression of GCC-box PR genes. We demonstrate that the Pti4 protein is specifically phosphorylated by the Pto kinase and that this phosphorylation enhances binding of Pti4 to the GCC box. In addition, induced overexpression of Pto and Pti4 in tomato leaves resulted in a concomitant increase in GCC-box PR genes. Our results support a model in which phosphorylation of the Pti4 protein by the Pto kinase enhances the ability of Pti4 to activate expression of GCC-box PR genes in tomato.
- Published
- 2000
42. Leucine aminopeptidase RNAs, proteins, and activities increase in response to water deficit, salinity, and the wound signals systemin, methyl jasmonate, and abscisic acid
- Author
-
Chao, W.S., Yong-Qiang Gu,, Pautot, Veronique, Bray, E.A., Walling, L.L., ProdInra, Migration, Laboratoire de biologie cellulaire et moléculaire, and Institut National de la Recherche Agronomique (INRA)
- Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics ,PRIVATION D'EAU ,ABA ,[SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics ,REPONSE DE LA PLANTE ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 1999
43. Study on the roughness evolution of optical surfaces during ion beam sputtering.
- Author
-
Xiao Liang, Xiang Wang, Yong-Qiang Gu, Jin-Jin Zheng, Huai-Jiang Yang, and Yong-Xin Sui
- Subjects
ION beams ,PARTICLE beams ,ALGORITHMS ,OPTICAL engineering ,OPTICAL amplifiers - Abstract
Ion beam machining technology has been extensively adopted to obtain an ultraprecision surface in ultraviolet lithography optics. However, there exist complex mechanisms leading the surface to evolve complicated topographies and increasing roughness. We build a kinetic model integrating with the typical sputter theory and a bond-counting Monte Carlo algorithm based on the compound materials to investigate the surface roughness evolution during ion beam sputtering. The influences of primary sputter, reflection, secondary sputter, geometrical shadowing, redeposition, and thermal diffusion were all taken into consideration to compose a dynamic evolution process. In calculation, using this model the surface first possesses a period of smoothing and then goes into a roughening stage, where the roughness follows the regular power law. Quantitative analyses of surface roughness derived from calculations are also examined and compared with experiments. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
44. Localization and post-translational processing of the wound-induced leucine aminopeptidase proteins of tomato
- Author
-
Linda L. Walling, Wun S. Chao, and Yong-Qiang Gu
- Subjects
Untranslated region ,DNA, Complementary ,Insecta ,DNA, Plant ,Molecular Sequence Data ,Biochemistry ,Aminopeptidase ,Leucyl Aminopeptidase ,Solanum lycopersicum ,Complementary DNA ,Animals ,Electrophoresis, Gel, Two-Dimensional ,Amino Acid Sequence ,Deoxyribonucleases, Type II Site-Specific ,Molecular Biology ,Furin ,Gene ,Plant Diseases ,chemistry.chemical_classification ,biology ,Base Sequence ,digestive, oral, and skin physiology ,Cell Biology ,equipment and supplies ,Molecular biology ,Amino acid ,Blot ,chemistry ,Enzyme Induction ,Protein Biosynthesis ,biology.protein ,Leucine ,human activities ,Protein Processing, Post-Translational - Abstract
Leucine aminopeptidase (LAP) is induced by wounding and bacterial pathogen infection in tomato. DNA blot analysis of XbaI-digested lambdalap genomic clones demonstrated that LapA1 and LapA2 cDNAs were encoded by two different LapA genes in the tomato genome. The coding and untranslated regions of LapA1 and LapA2 mRNAs shared more than 93% identity. The deduced amino acid sequences of LapA cDNA clones and in vitro translation of LapA1 mRNA indicated that LAP-A was synthesized as a 60-kDa precursor protein. The processing of a 60-kDa preLAP-A into the mature 55-kDa LAP-A was demonstrated in vivo by expression of the full-length LapA1 cDNA in insect cells. Sequencing of a single LAP-A form isolated from a two-dimensional polyacrylamide gel indicated that LAP-A proteins had two different N termini that were separated by two residues. The LAP-A presequence had features similar to chloroplast transit peptides. Comparison of LAP-A levels in chloroplast and total protein extracts from methyl jasmonate-treated leaves indicated that a small proportion of the LAP-A proteins was detected in the plastids. Inspection of the LAP-A presequence indicated the presence of a dibasic protease (Kex2/furin) processing site motif 6-8 residues upstream from the LAP-A N termini. Its potential role in LAP-A precursor biogenesis is discussed.
- Published
- 1996
45. Lily cofactor-independent phosphoglycerate mutase: purification, partial sequencing, and immunolocalization
- Author
-
Guang-Yuh Jauh, Yong Qiang Gu, Linda L. Walling, Elizabeth M. Lord, and J L Wang
- Subjects
DNA, Complementary ,Immunoelectron microscopy ,Molecular Sequence Data ,Plant Science ,Cross Reactions ,Zea mays ,Phosphoglycerate mutase ,Complementary DNA ,Plant Cells ,Sequence Homology, Nucleic Acid ,Genetics ,Humans ,Amino Acid Sequence ,Vitronectin ,Cloning, Molecular ,Polyacrylamide gel electrophoresis ,Phosphoglycerate Mutase ,Lilium ,biology ,Base Sequence ,Sequence Homology, Amino Acid ,Histocytochemistry ,Immunogold labelling ,Plants ,biology.organism_classification ,Molecular biology ,Recombinant Proteins ,Cytosol ,Microscopy, Electron ,Biochemistry ,Cytoplasm - Abstract
A cofactor-independent phosphoglycerate mutase (PGAM-i) was isolated to homogeneity from monocotyledonous Lilium longiflorum Thunb. Two-dimensional (2D) polyacrylamide gel electrophoresis resolved three PGAM-i forms. This enzyme was originally identified by cross-reactivity to antibodies affinity-purified from 2D gels using human vitronectin (VN). Antibody produced against a denatured protein spot from a 2D gel did not recognize VN protein, but partial protein and DNA sequencing showed similarity of the former protein to maize PGAM-i. Immunoblots from roots, styles, leaves, and anthers showed the presence of PGAM-i in all tissues examined; it was isolated predominantly from the soluble cell fraction, with some present in the insoluble cell fraction. Immunoelectron microscopy demonstrated its localization in the cytoplasm and plastids in root cells near the apical meristem. In addition, immunogold labeling detected signals from the nucleus. The immunohistochemical localization of the enzyme in the nucleus, as well as in the cytosol and plastids, indicates that lily PGAM-i might have multiple functions in the cell.
- Published
- 1996
46. Plant Aminopeptidases: Occurrence, Function and Characterization
- Author
-
Yong-Qiang Gu and Linda L. Walling
- Subjects
Dipeptidase ,chemistry.chemical_classification ,Enzyme ,Biochemistry ,biology ,Chemistry ,biology.protein ,Peptide bond ,Tripeptide ,Exopeptidase ,Carboxypeptidase ,Tripeptidyl peptidase ,Function (biology) - Abstract
Peptidases have a central role in the degradation of proteins by hydrolyzing peptide bonds. Based on the reaction catalyzed, these enzymes can be classified as endopeptidases, aminopeptidases or carboxypeptidases. Relative to the endoproteases and carboxypeptidases, the three types of exopeptidases that act at free N-termini of proteins or peptides are less well characterized. Aminopeptidases, dipeptidyl peptidases and tripeptidyl peptidases cleave peptides or proteins and liberate single amino acid residues, dipeptides or tripeptides, respectively. Dipeptidases and tripeptidases are aminopeptidases that preferentially act on dipeptides and tripeptides. While all three classes of N-terminal exopeptidases have been described in animals, only aminopeptidases have been described in plants.
- Published
- 1996
47. Two classes of proteins and mRNAs in Lilium longiflorum L. indentified by human vitronectin probes
- Author
-
Co-Shine Wang, Yong Qiang Gu, Linda L. Walling, Carl F. Ware, and Elizabeth M. Lord
- Subjects
Gene isoform ,Physiology ,Plant Science ,Cross Reactions ,Antibodies ,Complementary DNA ,Genetics ,Animals ,Humans ,RNA, Messenger ,Vitronectin ,Amino Acids ,Cell adhesion ,Glycoproteins ,Plant Proteins ,Antiserum ,Gel electrophoresis ,Messenger RNA ,Lilium ,biology ,Plants ,biology.organism_classification ,Molecular biology ,Biochemistry ,biology.protein ,Rabbits ,Soybeans ,DNA Probes ,Research Article - Abstract
Vitronectin (VN) is a substrate adhesion molecule, an extracellular matrix glycoprotein that facilitates cell adhesion and cell movement in animals. We have reported the cross-reactivity of a 55-kD protein in plants with rabbit anti-human VN antibodies and the presence of VN-like sequences in plant genomes using a human VN cDNA probe. We have extended these studies by using human VN riboprobes to detect VN-like mRNAs in lily (Lilium longiflorum L.) and soybean. In both species, two mRNAs were detected. We have also identified a new cross-reactive protein (41 kD) using a different preparation of human VN antiserum. In lily roots five 41-kD isoforms were observed, whereas only three of these isoforms accumulated in leaves. Monospecific antibodies prepared against the plant proteins cross-reacted with the human VN protein and vice versa. We have purified the 41-kD protein using two-dimensional gel electrophoresis, and amino acid composition analysis indicates that it is similar in composition to human VN.
- Published
- 1994
48. Pti4 Is Induced by Ethylene and Salicylic Acid, and Its Product Is Phosphorylated by the Pto Kinase
- Author
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Yong-Qiang Gu, Caimei Yang, Venkatappa K. Thara, Jianmin Zhou, and Gregory B. Martin
- Subjects
Cell Biology ,Plant Science - Published
- 2000
49. Genetic association of OPR genes with resistance to Hessian fly in hexaploid wheat.
- Author
-
Chor Tee Tan, Carver, Brett F., Ming-Shun Chen, Yong-Qiang Gu, and Liuling Yan
- Subjects
GENETICS ,WHEAT ,LOCUS (Genetics) ,CULTIVARS ,GENE mapping - Abstract
Background: Hessian fly (Mayetiola destructor) is one of the most destructive pests of wheat. The genes encoding 12-oxo-phytodienoic acid reductase (OPR) and lipoxygenase (LOX) play critical roles in insect resistance pathways in higher plants, but little is known about genes controlling resistance to Hessian fly in wheat. Results: In this study, 154 F6:8 recombinant inbred lines (RILs) generated from a cross between two cultivars, 'Jagger' and '2174' of hexaploid wheat (2n = 6 × =42; AABBDD), were used to map genes associated with resistance to Hessian fly. Two QTLs were identified. The first one was a major QTL on chromosome 1A (QHf.osu-1A), which explained 70% of the total phenotypic variation. The resistant allele at this locus in cultivar 2174 could be orthologous to one or more of the previously mapped resistance genes (H9, H10, H11, H16, and H17) in tetraploid wheat. The second QTL was a minor QTL on chromosome 2A (QHf.osu-2A), which accounted for 18% of the total phenotypic variation. The resistant allele at this locus in 2174 is collinear to an Yr17-containing-fragment translocated from chromosome 2N of Triticum ventricosum (2n = 4 × =28; DDNN) in Jagger. Genetic mapping results showed that two OPR genes, TaOPR1-A and TaOPR2-A, were tightly associated with QHf.osu-1A and QHf.osu-2A, respectively. Another OPR gene and three LOX genes were mapped but not associated with Hessian fly resistance in the segregating population. Conclusions: This study has located two major QTLs/genes in bread wheat that can be directly used in wheat breeding programs and has also provided insights for the genetic association and disassociation of Hessian fly resistance with OPR and LOX genes in wheat. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
50. Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat.
- Author
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Wanjugi, Humphrey, Coleman-Derr, Devin, Huo, Naxin, Kianian, Shahryar F., Ming-Cheng Luo, Jiajie Wu, Anderson, Olin, and Yong Qiang Gu
- Subjects
WHEAT ,TRANSPOSONS ,GENOMES ,DNA ,CHROMOSOMES - Abstract
Copyright of Genome is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2009
- Full Text
- View/download PDF
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