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Search Results: 1 - 10 of 4989 matches for " Doil Choi "
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Multiple Classes of Immune-Related Proteases Associated with the Cell Death Response in Pepper Plants
Chungyun Bae, Su-min Kim, Dong Ju Lee, Doil Choi
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0063533
Abstract: Proteases regulate a large number of biological processes in plants, such as metabolism, physiology, growth, and defense. In this study, we carried out virus-induced gene silencing assays with pepper cDNA clones to elucidate the biological roles of protease superfamilies. A total of 153 representative protease genes from pepper cDNA were selected and cloned into a Tobacco rattle virus-ligation independent cloning vector in a loss-of-function study. Silencing of 61 proteases resulted in altered phenotypes, such as the inhibition of shoot growth, abnormal leaf shape, leaf color change, and lethality. Furthermore, the silencing experiments revealed that multiple proteases play a role in cell death and immune response against avirulent and virulent pathogens. Among these 153 proteases, 34 modulated the hypersensitive cell death response caused by infection with an avirulent pathogen, and 16 proteases affected disease symptom development caused by a virulent pathogen. Specifically, we provide experimental evidence for the roles of multiple protease genes in plant development and immune defense following pathogen infection. With these results, we created a broad sketch of each protease function. This information will provide basic information for further understanding the roles of the protease superfamily in plant growth, development, and defense.
Identification of Novel Pepper Genes Involved in Bax- or INF1-Mediated Cell Death Responses by High-Throughput Virus-Induced Gene Silencing
Jeong Hee Lee,Young Cheol Kim,Doil Choi,Jeong Mee Park
International Journal of Molecular Sciences , 2013, DOI: 10.3390/ijms141122782
Abstract: Hot pepper is one of the economically important crops in Asia. A large number of gene sequences, including expressed sequence tag (EST) and genomic sequences are publicly available. However, it is still a daunting task to determine gene function due to difficulties in genetic modification of a pepper plants. Here, we show the application of the virus-induced gene silencing (VIGS) repression for the study of 459 pepper ESTs selected as non-host pathogen-induced cell death responsive genes from pepper microarray experiments in Nicotiana benthamiana. Developmental abnormalities in N. benthamiana plants are observed in the 32 (7%) pepper ESTs-silenced plants. Aberrant morphological phenotypes largely comprised of three groups: stunted, abnormal leaf, and dead. In addition, by employing the combination of VIGS and Agrobacterium-mediated transient assays, we identified novel pepper ESTs that involved in Bax or INF1-mediated cell death responses. Silencing of seven pepper ESTs homologs suppressed Bax or INF1-induced cell death, five of which suppressed both cell death responses in N. benthamiana. The genes represented by these five ESTs encode putative proteins with functions in endoplasmic reticulum (ER) stress and lipid signaling. The genes represented by the other two pepper ESTs showing only Bax-mediated cell death inhibition encode a CCCH-type zinc finger protein containing an ankyrin-repeat domain and a probable calcium-binding protein, CML30-like. Taken together, we effectively isolated novel pepper clones that are involved in hypersensitive response (HR)-like cell death using VIGS, and identified silenced clones that have different responses to Bax and INF1 exposure, indicating separate signaling pathways for Bax- and INF1-mediated cell death.
SNUGB: a versatile genome browser supporting comparative and functional fungal genomics
Kyongyong Jung, Jongsun Park, Jaeyoung Choi, Bongsoo Park, Seungill Kim, Kyohun Ahn, Jaehyuk Choi, Doil Choi, Seogchan Kang, Yong-Hwan Lee
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-586
Abstract: The Seoul National University Genome Browser (SNUGB) integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets) and 34 plant and animal (38 datasets) species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion.The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site http://genomebrowser.snu.ac.kr/ webcite.As the number of sequenced genomes rapidly increases, search and comparison of sequence features within and between species has become an integral part of most biological inquires. To facilitate uses of the sequenced genomes, numerous bioinformatics tools have been developed; among these, genome browser plays an essential role by providing various means for viewing genome sequences and annotated features (e.g., chromosomal position and context of individual genes, protein/nucleotide sequences, structures of exon/intron, and promoters) via graphical and text interfaces. Widely utilized genome browsers include: (i) Ensembl http://www.ensembl.org/ webcite, which is specialized for mammalian genomics and comparative genomics [1], (ii) UCSC Genome Browser http://genome.ucsc.edu/ webcite, which archives genome sequences of 30 vertebrate and 24 non-vertebrate species [2], (iii) GBrowse http://g
Evolution of ribosomal DNA-derived satellite repeat in tomato genome
Sung-Hwan Jo, Dal-Hoe Koo, Jihyun F Kim, Cheol-Goo Hur, Sanghyeob Lee, Tae-jin Yang, Suk-Yoon Kwon, Doil Choi
BMC Plant Biology , 2009, DOI: 10.1186/1471-2229-9-42
Abstract: FISH analysis revealed that the satellite repeat showing homology with intergenic spacer (IGS) of rDNA present in the tomato genome. By comparing the sequences representing distinct stages in the divergence of rDNA repeat with those of canonical rDNA arrays, the molecular mechanism of the evolution of satellite repeat is described. Comprehensive sequence analysis and phylogenetic analysis demonstrated that a long terminal repeat retrotransposon was interrupted into each copy of the 18S rDNA and polymerized by recombination rather than transposition via an RNA intermediate. The repeat was expanded through doubling the number of IGS into the 25S rRNA gene, and also greatly increasing the copy number of type I subrepeat in the IGS of 25-18S rDNA by segmental duplication. Homogenization to a single type of subrepeat in the satellite repeat was achieved as the result of amplifying copy number of the type I subrepeat but eliminating neighboring sequences including the type II subrepeat and rRNA coding sequence from the array. FISH analysis revealed that the satellite repeats are commonly present in closely-related Solanum species, but vary in their distribution and abundance among species.These results represent that the dynamic satellite repeats were originated from intergenic spacer of rDNA unit in the tomato genome. This result could serve as an example towards understanding the initiation and the expansion of the satellite repeats in complex eukaryotic genome.The large variety of genome sizes found throughout the plant kingdom is mainly attributed to species-specific differences in ploidy and repetitive DNA content [1]. Repetitive DNA can be divided into two categories: interspersed repeats, which are individual repeat units that are distributed around the genome in an apparently random fashion, and tandem repeated DNA, whose repeat units are placed next to each other in an array. Several previous studies have uncovered interspersed repeats, the retrotransposons, whic
Identification of Gene-Specific Polymorphisms and Association with Capsaicin Pathway Metabolites in Capsicum annuum L. Collections
Umesh K. Reddy, Aldo Almeida, Venkata L. Abburi, Suresh Babu Alaparthi, Desiree Unselt, Gerald Hankins, Minkyu Park, Doil Choi, Padma Nimmakayala
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0086393
Abstract: Pepper (Capsicum annuum L.) is an economically important crop with added nutritional value. Production of capsaicin is an important quantitative trait with high environmental variance, so the development of markers regulating capsaicinoid accumulation is important for pepper breeding programs. In this study, we performed association mapping at the gene level to identify single nucleotide polymorphisms (SNPs) associated with capsaicin pathway metabolites in a diverse Capsicum annuum collection during two seasons. The genes Pun1, CCR, KAS and HCT were sequenced and matched with the whole-genome sequence draft of pepper to identify SNP locations and for further characterization. The identified SNPs for each gene underwent candidate gene association mapping. Association mapping results revealed Pun1 as a key regulator of major metabolites in the capsaicin pathway mainly affecting capsaicinoids and precursors for acyl moieties of capsaicinoids. Six different SNPs in the promoter sequence of Pun1 were found associated with capsaicin in plants from both seasons. Our results support that CCR is an important control point for the flux of p-coumaric acid to specific biosynthesis pathways. KAS was found to regulate the major precursors for acyl moieties of capsaicinoids and may play a key role in capsaicinoid production. Candidate gene association mapping of Pun1 suggested that the accumulation of capsaicinoids depends on the expression of Pun1, as revealed by the most important associated SNPs found in the promoter region of Pun1.
The Hot Pepper (Capsicum annuum) MicroRNA Transcriptome Reveals Novel and Conserved Targets: A Foundation for Understanding MicroRNA Functional Roles in Hot Pepper
Dong-Gyu Hwang, June Hyun Park, Jae Yun Lim, Donghyun Kim, Yourim Choi, Soyoung Kim, Gregory Reeves, Seon-In Yeom, Jeong-Soo Lee, Minkyu Park, Seungill Kim, Ik-Young Choi, Doil Choi, Chanseok Shin
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0064238
Abstract: MicroRNAs (miRNAs) are a class of non-coding RNAs approximately 21 nt in length which play important roles in regulating gene expression in plants. Although many miRNA studies have focused on a few model plants, miRNAs and their target genes remain largely unknown in hot pepper (Capsicum annuum), one of the most important crops cultivated worldwide. Here, we employed high-throughput sequencing technology to identify miRNAs in pepper extensively from 10 different libraries, including leaf, stem, root, flower, and six developmental stage fruits. Based on a bioinformatics pipeline, we successfully identified 29 and 35 families of conserved and novel miRNAs, respectively. Northern blot analysis was used to validate further the expression of representative miRNAs and to analyze their tissue-specific or developmental stage-specific expression patterns. Moreover, we computationally predicted miRNA targets, many of which were experimentally confirmed using 5′ rapid amplification of cDNA ends analysis. One of the validated novel targets of miR-396 was a domain rearranged methyltransferase, the major de novo methylation enzyme, involved in RNA-directed DNA methylation in plants. This work provides the first reliable draft of the pepper miRNA transcriptome. It offers an expanded picture of pepper miRNAs in relation to other plants, providing a basis for understanding the functional roles of miRNAs in pepper.
Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome
Hyun-Jin Kim, Kwang-Hyun Baek, Seung-Won Lee, JungEun Kim, Bong-Woo Lee, Hye-Sun Cho, Woo Taek Kim, Doil Choi, Cheol-Goo Hur
BMC Plant Biology , 2008, DOI: 10.1186/1471-2229-8-101
Abstract: We built the Pepper EST database to mine the complexity of chili pepper ESTs. The database was built on 122,582 sequenced ESTs and 116,412 refined ESTs from 21 pepper EST libraries. The ESTs were clustered and assembled into virtual consensus cDNAs and the cDNAs were assigned to metabolic pathway, Gene Ontology (GO), and MIPS Functional Catalogue (FunCat). The Pepper EST database is designed to provide a workbench for (i) identifying unigenes in pepper plants, (ii) analyzing expression patterns in different developmental tissues and under conditions of stress, and (iii) comparing the ESTs with those of other members of the Solanaceae family. The Pepper EST database is freely available at http://genepool.kribb.re.kr/pepper/ webcite.The Pepper EST database is expected to provide a high-quality resource, which will contribute to gaining a systemic understanding of plant diseases and facilitate genetics-based population studies. The database is also expected to contribute to analysis of gene synteny as part of the chili pepper sequencing project by mapping ESTs to the genome.Pepper is a member of the family Solanaceae, which is one of the largest families in the plant kingdom and includes more than 3,000 species [1]. The Solanaceae family includes important crops, such as pepper, tomato, tobacco, potato, and eggplant and has been highly cultivated over the years for human nutrition and health. Capsicum species are consumed worldwide and are valued because of their unique color, pungency, and aroma. Capsicum peppers include C. annuum, C. chinense, C. baccatum, C. frutescens, and C. pubescens and are cultivated in different parts of the world. Of these, the varieties of the chili pepper plant species C. annuum, having a modest-sized diploid genome (2n = 24), are the most heavily consumed due to their nutritional value and spicy taste [2]. The chemical that is primarily responsible for the pungency of C. annuum has been identified as capsaicin [3], which elicits numerous b
Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements
Minkyu Park, SungHwan Jo, Jin-Kyung Kwon, Jongsun Park, Jong Hwa Ahn, Seungill Kim, Yong-Hwan Lee, Tae-Jin Yang, Cheol-Goo Hur, Byoung-Cheorl Kang, Byung-Dong Kim, Doil Choi
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-85
Abstract: For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila) were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation.Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.The Solanaceae is an unusually divergent family consisting of approximately 90 genera and 3,000-4,000 species [1]. Members of the Solanaceae have evolved into extremely divergent forms, ranging from trees to annual herbs, and they occupy diverse habitats ranging from deserts to aquatic areas [1]. Such hyper-diversity in one family makes it useful to study plant adaptation and diversification. Despite this diversity, all Solanaceous species evolved during the last 40 million years [2]. Furthermore, almost all members share the same chromosome number (x = 12) [2].To date, diversity within the Solanaceae has been studied by comparative genome analyses using common genetic markers. As a result, we know that the Solanaceae genomes have undergone relatively small numbers of chromosomal rearrangements (e.g., about 5 rearrangements between potato and tomato and about 30 rearrangements between pepper and tomato), maintaining well-conserved gene content and order [3-8]. The conservation of the Solanaceae
Spectral Density Scaling of Fluctuating Interfaces
Hyun-Joo Kim,Doil Jung
Physics , 2012, DOI: 10.1142/S0217984913501972
Abstract: Covariance matrix of heights measured relative to the average height of a growing self-affine surface in the steady state are investigated in the framework of random matrix theory. We show that the spectral density of the covariance matrix scales as $\rho(\lambda) \sim \lambda^{-\nu}$ deviating from the prediction of random matrix theory and has a scaling form, $\rho(\lambda, L) = \lambda^{-\nu} f(\lambda / L^{\phi})$ for the lateral system size $L$, where the scaling function $f(x)$ approaches a constant for $x \ll 1$ and zero for $x \gg 1$. The obtained values of exponents by numerical simulations are $\nu \approx 1.73$ and $\phi \approx 1.40$ for the Edward-Wilkinson class and $\nu \approx 1.64$ and $\phi \approx 1.79$ for the Kardar-Parisi-Zhang class, respectively. The distribution of the largest eigenvalues follows a scaling form as $\rho(\lambda_{max}, L) = 1/L^b f_{max} ((\lambda_{max} -L^a)/L^b)$, which is different from the Tracy-Widom distribution of random matrix theory while the exponents $a$ and $b$ are given by the same values for the two different classes.
A Pepper MSRB2 Gene Confers Drought Tolerance in Rice through the Protection of Chloroplast-Targeted Genes
Joung Sug Kim, Hyang-Mi Park, Songhwa Chae, Tae-Ho Lee, Duk-Ju Hwang, Sung-Dug Oh, Jong-Sug Park, Dae-Geun Song, Cheol-Ho Pan, Doil Choi, Yul-Ho Kim, Baek Hie Nahm, Yeon-Ki Kim
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0090588
Abstract: Background The perturbation of the steady state of reactive oxygen species (ROS) due to biotic and abiotic stresses in a plant could lead to protein denaturation through the modification of amino acid residues, including the oxidation of methionine residues. Methionine sulfoxide reductases (MSRs) catalyze the reduction of methionine sulfoxide back to the methionine residue. To assess the role of this enzyme, we generated transgenic rice using a pepper CaMSRB2 gene under the control of the rice Rab21 (responsive to ABA protein 21) promoter with/without a selection marker, the bar gene. Results A drought resistance test on transgenic plants showed that CaMSRB2 confers drought tolerance to rice, as evidenced by less oxidative stress symptoms and a strengthened PSII quantum yield under stress conditions, and increased survival rate and chlorophyll index after the re-watering. The results from immunoblotting using a methionine sulfoxide antibody and nano-LC-MS/MS spectrometry suggest that porphobilinogen deaminase (PBGD), which is involved in chlorophyll synthesis, is a putative target of CaMSRB2. The oxidized methionine content of PBGD expressed in E. coli increased in the presence of H2O2, and the Met-95 and Met-227 residues of PBGD were reduced by CaMSRB2 in the presence of dithiothreitol (DTT). An expression profiling analysis of the overexpression lines also suggested that photosystems are less severely affected by drought stress. Conclusions Our results indicate that CaMSRB2 might play an important functional role in chloroplasts for conferring drought stress tolerance in rice.
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