Plant Genomics and Breeding Institute

Seoul, South Korea

Plant Genomics and Breeding Institute

Seoul, South Korea

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Park J.,Plant Genomics and Breeding Institute | Park J.,Mokpo National University | Kim S.-G.,Seoul National University | Woo J.-C.,Max Planck Institute for Chemical Ecology | Park C.-M.,Plant Genomics and Breeding Institute
Plant Physiology | Year: 2011

Seed germination is regulated through elaborately interacting signaling networks that integrate diverse environmental cues into hormonal signaling pathways. Roles of gibberellic acid and abscisic acid in germination have been studied extensively using Arabidopsis (Arabidopsis thaliana) mutants having alterations in seed germination. Auxin has also been implicated in seed germination. However, how auxin influences germination is largely unknown. Here, we demonstrate that auxin is linked via the IAA30 gene with a salt signaling cascade mediated by the NAM-ATAF1/2-CUC2 transcription factor NTM2/ Arabidopsis NAC domain-containing protein 69 (for NAC with Transmembrane Motif1) during seed germination. Germination of the NTM2-deficient ntm2-1 mutant seeds exhibited enhanced resistance to high salinity. However, the salt resistance disappeared in the ntm2-1 mutant overexpressing the IAA30 gene, which was induced by salt in a NTM2-dependent manner. Auxin exhibited no discernible effects on germination under normal growth conditions. Under high salinity, however, whereas exogenous application of auxin further suppressed the germination of control seeds, the auxin effects were reduced in the ntm2-1 mutant. Consistent with the inhibitory effects of auxin on germination, germination of YUCCA 3-overexpressing plants containing elevated levels of active auxin was more severely influenced by salt. These observations indicate that auxin delays seed germination under high salinity through cross talk with the NTM2-mediated salt signaling in Arabidopsis. © 2011 American Society of Plant Biologists.


Lee J.,Konkuk University | Lee J.,Plant Genomics and Breeding Institute | Koh H.-J.,Plant Genomics and Breeding Institute
Proteome Science | Year: 2011

Background: Although a great deal of rice proteomic research has been conducted, there are relatively few studies specifically addressing the rice grain proteome. The existing rice grain proteomic researches have focused on the identification of differentially expressed proteins or monitoring protein expression patterns during grain filling stages.Results: Proteins were extracted from rice grains 10, 20, and 30 days after flowering, as well as from fully mature grains. By merging all of the identified proteins in this study, we identified 4,172 non-redundant proteins with a wide range of molecular weights (from 5.2 kDa to 611 kDa) and pI values (from pH 2.9 to pH 12.6). A Genome Ontology category enrichment analysis for the 4,172 proteins revealed that 52 categories were enriched, including the carbohydrate metabolic process, transport, localization, lipid metabolic process, and secondary metabolic process. The relative abundances of the 1,784 reproducibly identified proteins were compared to detect 484 differentially expressed proteins during rice grain development. Clustering analysis and Genome Ontology category enrichment analysis revealed that proteins involved in the metabolic process were enriched through all stages of development, suggesting that proteome changes occurred even in the desiccation phase. Interestingly, enrichments of proteins involved in protein folding were detected in the desiccation phase and in fully mature grain.Conclusion: This is the first report conducting comprehensive identification of rice grain proteins. With a label free shotgun proteomic approach, we identified large number of rice grain proteins and compared the expression patterns of reproducibly identified proteins during rice grain development. Clustering analysis, Genome Ontology category enrichment analysis, and the analysis of composite expression profiles revealed dynamic changes of metabolisms during rice grain development. Interestingly, we detected that proteins involved in glycolysis, TCA-cycle, lipid metabolism, and proteolysis accumulated at higher levels in fully mature grain compared to grain developing stages, suggesting that the accumulation of these proteins during the desiccation stage may be associated with the preparation of proteins required in germination. © 2011 Lee and Koh; licensee BioMed Central Ltd.


Kim H.-J.,Plant Genomics and Breeding Institute | Han J.-H.,Kangwon National University | Kim K.S.,Kangwon National University | Lee Y.-H.,Plant Genomics and Breeding Institute
Fungal Genetics and Biology | Year: 2014

The ascomycete fungus Magnaporthe oryzae is an economically important pathogen that causes rice blast disease worldwide. Accumulating evidence indicates that the fungal velvet genes are key regulators of a number of cellular processes, including development, pathogenicity and secondary metabolism, in many species of fungi. In this study, we identified and functionally characterized four genes (. MoVOSA, MoVELB, MoVEA, and MoVELC) from the genome of the fungal pathogen M. oryzae. These genes were homologous to the velvet gene family of Aspergillus nidulans. Deletions of MoVEA, MoVELB, and MoVELC resulted in a significant decrease in conidiation, indicating their roles as positive regulators thereof. The MoVELC gene was involved in development of conidial morphology, while MoVELB and MoVEA appeared necessary for conidial germination, MoVEA further being indispensable for appressorial development and modulation of reactive oxygen species in disease development. Deletion of MoVELC affected the cell wall integrity of appressoria, resulting in failure to penetrate host cells. Unexpectedly, MoVOSA appeared dispensable for the development and pathogenicity of M. oryzae, even though its homologs play specific roles in other fungal species. Taken together, our data demonstrate that the velvet genes are linked to M. oryzae infection-related development and pathogenicity, and the findings provide a framework for comparative studies of the conserved velvet gene family across a range of fungal taxa, which may provide new insight into fungal development and pathogenicity. © 2014 Elsevier Inc.


Niu Y.,Chinese Academy of Sciences | Luo H.,Chinese Academy of Sciences | Sun C.,Chinese Academy of Sciences | Yang T.-J.,Plant Genomics and Breeding Institute | And 4 more authors.
Gene | Year: 2014

Panax notoginseng (Burk) F. H. Chen, an economically significant medicinal plant with hemostatic and health tonic activities, has been used in Traditional Chinese Medicine (TCM) for more than 3000. years. Triterpene saponins are responsible for most of the pharmacological activities of P. notoginseng. Here, we cloned five cDNA sequences encoding the key enzymes involved in triterpene saponin biosynthesis, namely, PnFPS, PnSS, PnSE1, PnSE2, and PnDS, and analyzed the conserved domains and phylogenetics of their corresponding proteins. Their organ-specific expression patterns in four-year-old P. notoginseng were detected by real-time PCR, showing that they were all most highly expressed in flowers. In addition, four of the genes, excluding PnSE2, were upregulated in leaves following stimulation with methyl jasmonate. This study is the first comprehensive analysis of the expression patterns of pivotal genes for triterpene saponin biosynthesis in P. notoginseng and provides a basis to further elucidate the molecular mechanism for the biosynthesis of these medically important compounds. © 2013 Elsevier B.V.


Han S.-H.,Plant Genomics and Breeding Institute | Sakuraba Y.,Plant Genomics and Breeding Institute | Koh H.-J.,Plant Genomics and Breeding Institute | Paek N.-C.,Plant Genomics and Breeding Institute
Molecules and Cells | Year: 2012

In field conditions, the zebra2 (z2) mutant in rice (Oryza sativa) produces leaves with transverse pale-green/yellow stripes. It was recently reported that ZEBRA2 encodes carotenoid isomerase (CRTISO) and that low levels of lutein, an essential carotenoid for non-photochemical quenching, cause leaf variegation in z2 mutants. However, we found that the z2 mutant phenotype was completely suppressed by growth under continuous light (CL; permissive) conditions, with concentrations of chlorophyll, carotenoids and chloroplast proteins at normal levels in z2 mutants under CL. In addition, three types of reactive oxygen species (ROS; superoxide [O 2], hydrogen peroxide [H 2O 2], and singlet oxygen [ 1O 2]) accumulated to high levels in z2 mutants grown under short-day conditions (SD; alternate 10-h light/14-h dark; restrictive), but do not accumulate under CL conditions. However, the levels of lutein and zeaxanthin in z2 leaves were much lower than normal in both permissive CL and restrictive SD growth conditions, indicating that deficiency of these two carotenoids is not responsible for the leaf variegation phenotype. We found that the CRTISO substrate tetra-cis-lycopene accumulated during the dark periods under SD, but not under CL conditions. Its accumulation was also positively correlated with 1O 2 levels generated during the light period, which consequently altered the expression of 1O 2-responsive and cell death-related genes in the variegated z2 leaves. Taking these results together, we propose that the z2 leaf variegation can be largely attributed to photoperiodic accumulation of tetra-cis-lycopene and generation of excessive 1O 2 under natural day-night conditions. © 2012 KSMCB.


Goh J.,Plant Genomics and Breeding Institute | Kim K.S.,Plant Genomics and Breeding Institute | Park J.,Plant Genomics and Breeding Institute | Jeon J.,Plant Genomics and Breeding Institute | And 2 more authors.
Fungal Genetics and Biology | Year: 2011

Rice blast, caused by the pathogen Magnaporthe oryzae, is a serious hindrance to rice production and has emerged as an important model for the characterization of molecular mechanisms relevant to pathogenic development in plants. Similar to other pathogenic fungi, conidiation plays a central role in initiation of M. oryzae infection and spread over a large area. However, relatively little is known regarding the molecular mechanisms that underlie conidiation in M. oryzae. To better characterize these mechanisms, we identified a conidiation-defective mutant, ATMT0225B6 (MoCDC15T-DNA), in which a T-DNA insertion disrupted a gene that encodes a homolog of fission yeast cdc15, and generated a second strain containing a disruption in the same allele (ΔMoCDC15T-DNA). The cdc15 gene has been shown to act as a coordinator of the cell cycle in yeast. Functional analysis of the MoCDC15T-DNA and ΔMoCDC15T-DNA mutants revealed that MoCDC15 is required for conidiation, preinfection development and pathogenicity in M. oryzae. Conidia from these mutants were viable, but failed to adhere to hydrophobic surface, a crucial step required for subsequent pathogenic development. All phenotypic defects observed in mutants were rescued in a strain complemented with wild type MoCDC15. Together, these data indicate that MoCDC15 functions as a coordinator of several biological processes important for pathogenic development in M. oryzae. © 2011 Elsevier Inc.


Sakuraba Y.,Plant Genomics and Breeding Institute | Kim Y.-S.,Plant Genomics and Breeding Institute | Yoo S.-C.,Plant Genomics and Breeding Institute | Hortensteiner S.,University of Zürich | Paek N.-C.,Plant Genomics and Breeding Institute
Biochemical and Biophysical Research Communications | Year: 2013

During natural or dark-induced senescence, chlorophyll degradation causes leaf yellowing. Recent evidence indicates that chlorophyll catabolic enzymes (CCEs) interact with the photosynthetic apparatus; for example, five CCEs (NYC1, NOL, PPH, PAO and RCCR) interact with LHCII. STAY-GREEN (SGR) and CCEs interact with one another in senescing chloroplasts; this interaction may allow metabolic channeling of potentially phototoxic chlorophyll breakdown intermediates. 7-Hydroxymethyl chlorophyll a reductase (HCAR) also acts as a CCE, but HCAR functions during leaf senescence remain unclear. Here we show that in Arabidopsis, HCAR-overexpressing plants exhibited accelerated leaf yellowing and, conversely, hcar mutants stayed green during dark-induced senescence. Moreover, HCAR interacted with LHCII in in vivo pull-down assays, and with SGR, NYC1, NOL and RCCR in yeast two-hybrid assays, indicating that HCAR is a component of the proposed SGR-CCE-LHCII complex, which acts in chlorophyll breakdown. Notably, HCAR and NOL are expressed throughout leaf development and are drastically down-regulated during dark-induced senescence, in contrast with SGR, NYC1, PPH and PAO, which are up-regulated during dark-induced senescence. Moreover, HCAR and NOL are highly up-regulated during greening of etiolated seedlings, strongly suggesting a major role for NOL and HCAR in the chlorophyll cycle during vegetative stages, possibly in chlorophyll turnover. © 2012 Elsevier Inc.


Cho K.,John Innes Center | O'Neill C.M.,John Innes Center | Kwon S.,South Korean National Institute of Animal Science | Yang T.,Plant Genomics and Breeding Institute | And 3 more authors.
Plant Journal | Year: 2010

We conducted a sequence-level comparative analyses, at the scale of complete bacterial artificial chromosome (BAC) clones, between the genome of the most economically important Brassica species, Brassica napus (oilseed rape), and those of Brassica rapa, the genome of which is currently being sequenced, and Arabidopsis thaliana. We constructed a new B. napus BAC library and identified and sequenced clones that contain homoeologous regions of the genome including stearoyl-ACP desaturase-encoding genes. We sequenced the orthologous region of the genome of B. rapa and conducted comparative analyses between the Brassica sequences and those of the orthologous region of the genome of A. thaliana. The proportion of genes conserved (∼56%) is lower than has been reported previously between A. thaliana and Brassica (∼66%). The gene models for sets of conserved genes were used to determine the extent of nucleotide conservation of coding regions. This was found to be 84.2 ± 3.9% and 85.8 ± 3.7% between the B. napus A and C genomes, respectively, and that of A. thaliana, which is consistent with previous results for other Brassica species, and 97.5 ± 3.1% between the B. napus A genome and B. rapa, and 93.1 ± 4.9% between the B. napus C genome and B. rapa. The divergence of the B. napus genes from the A genome and the B. rapa genes was greater than anticipated and indicates that the A genome ancestor of the B. napus cultivar studied was relatively distantly related to the cultivar of B. rapa selected for genome sequencing. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.


Hwang I.,Sunchon National University | Jung H.-J.,Sunchon National University | Park J.-I.,Sunchon National University | Yang T.-J.,Plant Genomics and Breeding Institute | Nou I.-S.,Sunchon National University
Genomics | Year: 2014

Plant bZIP transcription factors play crucial roles in biological processes. In this study, 136 putative bZIP transcription members were identified in Brassica rapa. The bZIP family can be divided into nine groups according to the specific amino acid rich domain in B. rapa and Arabidopsis thaliana. To screen the cold stress responsive BrbZIP genes, we evaluated whether the transcription patterns of the BrbZIP genes were enhanced by cold treatment in the inbred lines, Chiifu and Kenshin, by microarray data analysis and qRT-PCR. The expression level of six genes increased significantly in Kenshin, but these genes were unchanged in Chiifu. These findings suggest that the six genes that encoded proteins containing N-rich regions might be involved in cold stress response. The results presented herein provide valuable information regarding the molecular basis of the bZIP transcription factors and their potential function in regulation growth and development, particularly in cold stress response. © 2014 Elsevier Inc.


Goh J.,Plant Genomics and Breeding Institute | Jeon J.,Plant Genomics and Breeding Institute | Kim K.S.,Plant Genomics and Breeding Institute | Kim K.S.,Kangwon National University | And 3 more authors.
PLoS ONE | Year: 2011

In eukaryotes, microbodies called peroxisomes play important roles in cellular activities during the life cycle. Previous studies indicate that peroxisomal functions are important for plant infection in many phytopathogenic fungi, but detailed relationships between fungal pathogenicity and peroxisomal function still remain unclear. Here we report the importance of peroxisomal protein import through PTS2 (Peroxisomal Targeting Signal 2) in fungal development and pathogenicity of Magnaporthe oryzae. Using an Agrobacterium tumefaciens-mediated transformation library, a pathogenicity-defective mutant was isolated from M. oryzae and identified as a T-DNA insert in the PTS2 receptor gene, MoPEX7. Gene disruption of MoPEX7 abolished peroxisomal localization of a thiolase (MoTHL1) containing PTS2, supporting its role in the peroxisomal protein import machinery. ΔMopex7 showed significantly reduced mycelial growth on media containing short-chain fatty acids as a sole carbon source. ΔMopex7 produced fewer conidiophores and conidia, but conidial germination was normal. Conidia of ΔMopex7 were able to develop appressoria, but failed to cause disease in plant cells, except after wound inoculation. Appressoria formed by ΔMopex7 showed a defect in turgor generation due to a delay in lipid degradation and increased cell wall porosity during maturation. Taken together, our results suggest that the MoPEX7-mediated peroxisomal matrix protein import system is required for fungal development and pathogenicity M. oryzae. © 2011 Goh et al.

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