Yul-Ho Kim

Map-based Cloning and Characterization of the BPH18 Gene from Wild Rice Conferring Resistance to Brown Planthopper (BPH) Insect Pest

Brown planthopper (BPH) is a phloem sap-sucking insect pest of rice which causes severe yield loss. We cloned the BPH18 gene from the BPH-resistant introgression line derived from the wild rice species Oryza australiensis. Map-based cloning and complementation test revealed that the BPH18 encodes CC-NBS-NBS-LRR protein. BPH18 has two NBS domains, unlike the typical NBS-LRR proteins. The BPH18 promoter::GUS transgenic plants exhibited strong GUS expression in the vascular bundles of the leaf sheath, especially in phloem cells where the BPH attacks. The BPH18 proteins were widely localized to the endo-membranes in a cell, including the endoplasmic reticulum, Golgi apparatus, trans-Golgi network, and prevacuolar compartments, suggesting that BPH18 may recognize the BPH invasion at endo-membranes in phloem cells. Whole genome sequencing of the near-isogenic lines (NILs), NIL-BPH18 and NIL-BPH26, revealed that BPH18 located at the same locus of BPH26. However, these two genes have remarkable sequence differences and the independent NILs showed differential BPH resistance with different expression patterns of plant defense-related genes, indicating that BPH18 and BPH26 are functionally different alleles. These findings would facilitate elucidation of the molecular mechanism of BPH resistance and the identified novel alleles to fast track breeding BPH resistant rice cultivars.

Quadruple 9-mer-based protein binding microarray with DsRed fusion protein

BackgroundThe interaction between a transcription factor and DNA motif (cis-acting element) is an important regulatory step in gene regulation. Comprehensive genome-wide methods have been developed to characterize protein-DNA interactions. Recently, the universal protein binding microarray (PBM) was introduced to determine if a DNA motif interacts with proteins in a genome-wide manner.ResultsWe facilitated the PBM technology using a DsRed fluorescent protein and a concatenated sequence of oligonucleotides. The PBM was designed in such a way that target probes were synthesized as quadruples of all possible 9-mer combinations, permitting unequivocal interpretation of the cis-acting elements. The complimentary DNA strands of the features were synthesized with a primer and DNA polymerase on microarray slides. Proteins were labeled via N-terminal fusion with DsRed fluorescent protein, which circumvents the need for a multi-step incubation. The PBM presented herein confirmed the well-known DNA binding sequences of Cbf1 and CBF1/DREB1B, and it was also applied to elucidate the unidentified cis-acting element of the OsNAC6 rice transcription factor.ConclusionOur method demonstrated PBM can be conveniently performed by adopting: (1) quadruple 9-mers may increase protein-DNA binding interactions in the microarray, and (2) a one-step incubation shortens the wash and hybridization steps. This technology will facilitate greater understanding of genome-wide interactions between proteins and DNA.

Significance of fetal hemoglobin-containing erythroblasts (F blasts) and the F blast/F cell ratio in myelodysplastic syndromes

To investigate the relationship between the fetal hemoglobin-containing erythroblasts (F blasts) and apoptosis in myelodysplastic syndromes (MDS), we immunohistochemically assessed F blasts, F cells, and apoptosis in 137 patients with MDS. A marked increase in the number of F blasts in the bone marrow was identified in 116 of 137 patients (84.7%), and the number of F cells was elevated in 54 patients (39.4%). Among the erythroblasts stained by anti-glycophorin C antibody, the mean percentage of F blasts was 14.63 ± 9.17% in MDS, which was significantly higher than that in non-MDS patients with stress erythropoiesis (4.82 ± 3.35%, P < 0.01), although there were no significant differences in the number of F cells between these groups. In particular, 62 of the 137 MDS patients (45.3%) had an apparent increase in F blasts but no elevation of F cells. The apoptotic rate was significantly higher in the patients with a F blast/F cell (Fb/Fc) ratio ⩾5.0 than in those with a Fb/Fc ratio <1.0 (P < 0.01). The results indicate that F cell precursors are incapable of maturing into functioning end-stage F cells, presumably owing to apoptotic cell death. The measurement of F blasts in the bone marrow is needed for the precise evaluation of fetal-type erythropoiesis in MDS.

Inheritance and Quantitative Trait Loci Analysis of Resistance Genes to Bruchid and Bean Bug in Mungbean ( Vigna radiata L. Wilczek)

Bruchid (Callosobruchus chinenesis L.) and pod sucking bug (Riptortus clavatus Thunberg) are serious insect pests during the reproduction stage and seed storage period of legume crops worldwide. However, few sources of resistance to each of these insects have been identified and characterized, and no genetic studies have been carried out with simultaneous tests of these two insects. In this study, the inheritance of seed resistance to Callosobruchus chinenesis L. and Riptortus clavatus Thunberg was examined in a mungbean cultivar, Jangan mungbean, which was developed by backcrossing with the V2709 resistant donor. The F1, F2, and F3 seed generations were developed from the cross between susceptible and resistant parents, and evaluated for resistance to the two insects. It was found that resistance to bruchid and bean bug was controlled by a single dominant gene in the F1 and F2 seeds. However, the segregation pattern of reciprocal reaction to each insect in F2 seeds showed seeds were susceptible to each insect. These results suggest that the resistance genes in Jangan mungbean to bug and weevil are either different or closely linked with each other. A genetic linkage map 13.7 cM in length with 6 markers was successfully constructed. Two QTLs were identified for bruchid resistance, and a QTL for bean bug resistance was detected. One of the QTLs for resistance to bruchid was shared with the QTL for bean bug. These newly developed closely linked markers will be used for cloning of the resistance genes to bruchid and bean bug in the future.

A pepper MSRB2 gene confers drought tolerance in rice through the protection of chloroplast-targeted genes.

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.

Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica

Ascorbic acid (AsA) maintains redox homeostasis by scavenging reactive oxygen species from prokaryotes to eukaryotes, especially plants. The enzyme monodehydroascorbate reductase (MDHAR) regenerates AsA by catalysing the reduction of monodehydroascorbate, using NADH or NADPH as an electron donor. The detailed recycling mechanism of MDHAR remains unclear due to lack of structural information. Here, we present the crystal structures of MDHAR in the presence of cofactors, nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), and complexed with AsA as well as its analogue, isoascorbic acid (ISD). The overall structure of MDHAR is similar to other iron-sulphur protein reductases, except for a unique long loop of 63–80 residues, which seems to be essential in forming the active site pocket. From the structural analysis and structure-guided point mutations, we found that the Arg320 residue plays a major substrate binding role, and the Tyr349 residue mediates electron transfer from NAD(P)H to bound substrate via FAD. The enzymatic activity of MDHAR favours NADH as an electron donor over NADPH. Our results show, for the first time, structural insights into this preference. The MDHAR-ISD complex structure revealed an alternative binding conformation of ISD, compared with the MDHAR-AsA complex. This implies a broad substrate (antioxidant) specificity and resulting greater protective ability of MDHAR.

FSTVAL: a new web tool to validate bulk flanking sequence tags

BackgroundInformation about a transgene locus is one of the major concerns in transgenic research because expression of the transgene or a gene interrupted by the integration event could be affected. Thus, the flanking sequences obtained from transgenic plants need to be analyzed in terms of genomic context, such as genic and intergenic regions. This process may consist of several steps: 1) elimination of a vector sequence from the flanking sequence, 2) finding the locations in the target genome, and 3) statistics of the integration sites. These steps could be automated for flanking sequences from several dozens of transgenic plants generated in an ordinary targeted gene expression strategy. It would be indispensable in a genome-wide mutagenesis screen using T-DNA or transposons because these projects often generate several thousands of transgenic lines and just as many loci of the transgene among the transgenic plants.ResultsWe present an open access web tool, f lanking s equence t ags val idator (FSTVAL), to manage bulk flanking sequence tags (FSTs). FSTVAL automatically evaluates the FSTs and finds the best mapping positions of the FST against a known genome sequence. The statistics, in terms of genic and intergenic regions, are presented as a table, a distribution map, and a frequency graph along the chromosomes. Currently, 17 plant genome sequences, including Arabidopsis thaliana, Oryza sativa, and Glycine max, are available as reference genomes. We evaluated the utility and accuracy of the tool with 5,144 rice FSTs. The whole process, from uploading the sequences to generating tables of insertions, required a few minutes, with less than 4 clicks in the web environment.ConclusionsRun for 1u2009year and tested over 1,000 times, we have confirmed FSTVAL efficiently handles bulk FSTs. FSTVAL is freely available without login at http://bioinfo.mju.ac.kr/fstval/.

Cobll1 is linked to drug resistance and blastic transformation in chronic myeloid leukemia.

Drug resistance to BCR-ABL1 tyrosine kinase inhibitor (TKI) and disease progression to blast crisis (BC) are major clinical problems in chronic myeloid leukemia (CML); however, underlying mechanisms governing this process remain to be elucidated. Here, we report Cordon-bleu protein-like 1 (Cobll1) as a distinct molecular marker associated with drug resistance as well as progression to BC. In detail, Cobll1 increases IKKγ stability, leading to NF-κB activation and reduction of nilotinib-dependent apoptosis, suggesting Cobll1-mediated NF-κB could be involved in drug resistance. Recently, NF-κB signalling has been highlighted as a core mechanism for chronic phase (CP)-BC progression, stem cell survival and tyrosine kinase inhibitor resistance. We also demonstrated that high expression of Cobll1 confers drug resistance to tyrosine kinase inhibitors in CML cell line as well as patient samples. The analysis of large sets of primary CML samples (n=90) shows that Cobll1 expression is dramatically increased in BC but not in CP, which is correlated with a poor survival rate (P=0.002). Moreover, our studies show that Cobll1 is highly expressed in CD34+ primitive stem cell populations, and the zebrafish paralog Cobll1b is important for normal hematopoiesis during embryonic development. Based on these results, we propose that Cobll1 is a novel biomarker and potential therapeutic target for CML-BC.

Effect of Light Quality on the Expression of Glycoalkaloid Biosynthetic Genes Contributing to Steroidal Glycoalkaloid Accumulation in Potato

Light quality and intensity have severe impact on Steroidal glycoalkaloid (SGA) biosynthesis, causing the quality degradation of potato by greening and accelerating SGA-induced toxicity. In this study, Atlantic and Haryoung cultivars responded differently when exposed to seven light qualities viz., purple, red, blue, green, yellow, UV and fluorescent lights. Haryoung tuber exhibited a 44xa0% lesser SGA accumulation in yellow light compared to fluorescent light. Further screening of selected light sources by investigating the expression pattern of key genes and SGA contents, showed lower transcript levels of key genes in yellow light which in-turn reflected in the least amount of SGA accumulation with a 22xa0% lesser SGA levels in yellow light compared to fluorescent light. This suppression in the SGA accumulation suggests that yellow light can be used as an alternative light source instead of fluorescent light which would help in minimizing the quality degradation and SGA- induced toxicity.ResumenLa calidad e intensidad de la luz tienen un impacto severo en la biosíntesis de un glicoalcaloide esteroidal (SGA), que causa la degradación de la calidad de la papa por verdeo y por aceleración de la toxicidad inducida por SGA. En este estudio, las variedades Atlantic y Haryoung respondieron de manera diferente cuando se expusieron a siete calidades de luz, por ejemplo, morado, rojo, azul, verde, amarillo, UV y fluorescente. El tubérculo de Haryoung exhibió una acumulación de 44xa0% menos de SGA en luz amarilla, en comparación con la fluorescente. Pruebas posteriores de fuentes selectas de luz, mediante la investigación del patrón de expresión de genes clave y los contenidos de SGA, mostraron niveles más bajos de transcripción de los genes clave en luz amarilla, que a su vez se reflejó en la menor cantidad de acumulación de SGA con 22xa0% menos niveles de SGA en luz amarilla comparada con la fluorescente. Esta supresión en la acumulación de SGA sugiere que la luz amarilla pudiera usarse como una fuente alternativa de luz en vez de la fluorescente, lo cual pudiera ayudar en minimizar la degradación de la calidad y la toxicidad inducida por SGA.

Genistein production in rice seed via transformation with soybean IFS genes

To produce genistein in rice, the isoflavone synthase (IFS) genes, SpdIFS1 and SpdIFS2 were cloned from the Korean soybean cultivar, Sinpaldalkong II as it has a higher genistein content than other soybean varieties. SpdIFS1 and SpdIFS2 show a 99.6% and 98.2% identity at the nucleotide level and 99.4% and 97.9% identity at the amino acid level, respectively, with IFS1 and IFS2 from soybean (GenBank accession Nos. AF195798 and AF195819). Plant expression vectors were constructed harboring SpdIFS1 or SpdIFS2 under the control of a rice globulin promoter that directs seed specific expression, and used to transform two rice varieties, Heugnam, a black rice, and Nakdong, a normal rice cultivar without anthocyanin pigment. Because naringenin, the substrate of SpdIFS1 and SpdIFS2, is on the anthocyanin biosynthesis pathway, the relative production rate of genistein was compared between SpdIFS-expressing transgenic Heugnam and Nakdong. Southern blot analysis of eight of the resulting transgenic rice plants revealed that the T0 plants had one to three copies of the SpdIFS1 or SpdIFS2 gene. The highest level of genistein content found in rice seeds was 103 μg/g. These levels were about 30-fold higher in our transgenic rice lines than the genistein aglycon content of a non-leguminous IFS-expressing transgenic tobacco petal, equaling about 12% of total genistein content of Sinpaldalkong II. There were no significant differences found between the genistein content in Heugnam and Nakdong transgenic rice plants.