Sung-Han Park

Expression analysis of rice VQ genes in response to biotic and abiotic stresses

WRKY transcription factors are encoded by a large gene superfamily with a broad range of roles in plants. Proteins containing a short VQ (FxxxVQxLTG) motif have been recently shown to interact with WRKY transcription factors, implying that AtVQ proteins are important in the plant defense responses in Arabidopsis, either as positive or negative cofactors of WRKY transcription factors. Thirty-nine Oryza sativa genes containing the VQ motif (OsVQs) were identified and the genome structures of OsVQ proteins were characterized through genome-wide analysis in rice. Also, phylogenetic tree analysis was performed with the VQ domain of Arabidopsis and rice. The expression patterns of these OsVQ genes in plants under several stress treatments were assessed, specifically, following infection with the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo), treatment with abscisic acid (ABA), or exposure to drought. The cellular localization of a few OsVQ proteins was examined using rice protoplast system. Based on our results, we suggest that OsVQ proteins function as important co-regulators during the plant defense response to biotic and abiotic stresses.

Multi-Layered Screening Method Identification of Flavonoid-Specific Genes, using Transgenic Rice

ABSTRACT We used microarray analysis to identify 6 730 genes potentially related to flavonoid biosynthesis by comparing their expression between high- and low-flavonoid cultivars at three stages of seed development. The genes included 167 transcription factors, 104 pathway-network genes, and 1 207 potential orthologs with flavonoid-related functions. We compared the transcription factors, pathway genes, and orthologs and identified seven conserved hypothetical genes that are involved in flavonoid biosynthesis. We then verified the seven genes experimentally by reverse transcription-polymerase chain reaction. These conserved genes most likely play regulatory roles either in rice-flavonoid production or flavonoid signaling during seed development. Our study illustrates the effectiveness of microarray analysis followed by multi-layered screening for the identification of flavonoid-related genes in rice.

Analysis of germinating seed stage expressed sequence tags in Oryza sativa L.

Abstract Seed germination is the important stage to ex-press many genes for regulation of energy metabolism, starch degradation and cell division from seed dormancy state. For the functional analysis of seed germination mech-anisms, we were analyzed the rice cDNA clones ( Oryza sativa cultivar Ilpum ) obtained from seed imbibition during 48 hours. Total number of 18,101 Expressed Sequence Tags (ESTs) were clustered using SeqMan program. Among them, 8,836 clones were identified as unique clones. We identified the chitinase gene specifically expressed in seed germination and amylase gene involved to starch degradation from the full length cDNA analysis, and several genes were registered to NCBI GeneBank. To analyzed the commonly expressed genes between inmature seed and germinated seed, 25,668 inmature ESTs and 18,101 germinated ESTs were clustered using SeqMan program and identified 2,514 clones as com-monly expressed unigene. Among them, alpha-glubulin and alcohol dehydrogenase I were supposed to LEA genes only expressed in the immature and germinated seed stages.For the clustering of orthologous group genes, we further analyzed the 8,836 EST clones from germinating seeds using NCBI clusters of orthologous groups database. Among the clones, 5,076 clones were categorized into information storage and processing, cellular processes and signaling, metabolism and poorly characterized genes, proportioning 783 (14.29%), 1,484 (27%), 1,363 (24.8%) and 1,869 (34%) clones to the previous four categories, respectively.

A putative cold shock protein-encoding gene isolated from Arthrobacter sp. A2-5 confers cold stress tolerance in yeast and plants

A putative cold shock protein gene, designated as ArCspA, was isolated from Arthrobacter sp. A2-5 extracted from soil at the South Pole. The ArCspA gene is 873 nucleotide bp long and includes a 207-bp short open reading frame (ORF) with 49.3–92% amino acid identity to peptide sequences of other bacterial cold shock proteins. Northern blot analysis revealed that ArCspA was highly expressed at low temperatures. Bio-functional analysis using ArCspA-overexpressed transgenic Saccharomyces cerevisiae showed that ArCspA conferred cold tolerance on yeast at low temperatures (15°C). We then developed an ArCspA-overexpressed transgenic tobacco line to determine whether ArCspA is also functional in plants. After cold treatment at −25°C for 90 min followed by recovery for 4 weeks at 25°C, 17 transgenic lines survived at a high rate (60.0%), whereas under the same treatment conditions, wild-type plants did not survive. We also found that progeny of transgenic tobacco plants subjected to freezing stress at −20°C had significantly higher seed germination ability than wild-type plants. These results clearly indicate that the ArCspA protein plays an important role in cold tolerance in both yeast and plants.

An integrated database to enhance the identification of SNP markers for rice.

The National Academy of Agricultural Science (NAAS) has developed a web-based marker database to provide information about SNP markers in rice. The database consists of three major functional categories: map viewing, marker searching and gene annotation. It provides 12,829 SNP markers information including gene location information on 12 chromosomes in rice. The annotation of SNP marker provides information such as marker name, EST number, gene definition and general marker information. Users are assisted in tracing any new structures of the chromosomes and gene positional functions using specific SNP markers. Availability The database is available for free at http://nabic.niab.go.kr/SNP/