Mi Ok Lee

Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice

We analyzed 6,749 lines tagged by the gene trap vector pGA2707. This resulted in the isolation of 3,793 genomic sequences flanking the T-DNA. Among the insertions, 1,846 T-DNAs were integrated into genic regions, and 1,864 were located in intergenic regions. Frequencies were also higher at the beginning and end of the coding regions and upstream near the ATG start codon. The overall GC content at the insertion sites was close to that measured from the entire rice (Oryza sativa) genome. Functional classification of these 1,846 tagged genes showed a distribution similar to that observed for all the genes in the rice chromosomes. This indicates that T-DNA insertion is not biased toward a particular class of genes. There were 764, 327, and 346 T-DNA insertions in chromosomes 1, 4 and 10, respectively. Insertions were not evenly distributed; frequencies were higher at the ends of the chromosomes and lower near the centromere. At certain sites, the frequency was higher than in the surrounding regions. This sequence database will be valuable in identifying knockout mutants for elucidating gene function in rice. This resource is available to the scientific community at http://www.postech.ac.kr/life/pfg/risd.

Arabidopsis Brassinosteroid-Insensitive dwarf12 Mutants Are Semidominant and Defective in a Glycogen Synthase Kinase 3β-Like Kinase

Mutants defective in the biosynthesis or signaling of brassinosteroids (BRs), plant steroid hormones, display dwarfism. Loss-of-function mutants for the gene encoding the plasma membrane-located BR receptor BRI1 are resistant to exogenous application of BRs, and characterization of this protein has contributed significantly to the understanding of BR signaling. We have isolated two new BR-insensitive mutants (dwarf12-1D and dwf12-2D) after screening Arabidopsis ethyl methanesulfonate mutant populations.dwf12 mutants displayed the characteristic morphology of previously reported BR dwarfs including short stature, short round leaves, infertility, and abnormal de-etiolation. In addition,dwf12 mutants exhibited several unique phenotypes, including severe downward curling of the leaves. Genetic analysis indicates that the two mutations are semidominant in that heterozygous plants show a semidwarf phenotype whose height is intermediate between wild-type and homozygous mutant plants. Unlike BR biosynthetic mutants,dwf12 plants were not rescued by high doses of exogenously applied BRs. Like bri1 mutants,dwf12 plants accumulated castasterone and brassinolide, 43- and 15-fold higher, respectively, providing further evidence that DWF12 is a component of the BR signaling pathway that includes BRI1. Map-based cloning of the DWF12 gene revealed thatDWF12 belongs to a member of the glycogen synthase kinase 3β family. Unlike human glycogen synthase kinase 3β, DWF12 lacks the conserved serine-9 residue in the auto-inhibitory N terminus. In addition, dwf12-1D and dwf12-2D encode changes in consecutive glutamate residues in a highly conserved TREE domain. Together with previous reports that both bin2and ucu1 mutants contain mutations in this TREE domain, this provides evidence that the TREE domain is of critical importance for proper function of DWF12/BIN2/UCU1 in BR signal transduction pathways.

Rice Mitogen-Activated Protein Kinase Interactome Analysis Using the Yeast Two-Hybrid System

Mitogen-activated protein kinase (MAPK) cascades support the flow of extracellular signals to intracellular target molecules and ultimately drive a diverse array of physiological functions in cells, tissues, and organisms by interacting with other proteins. Yet, our knowledge of the global physical MAPK interactome in plants remains largely fragmented. Here, we utilized the yeast two-hybrid system and coimmunoprecipitation, pull-down, bimolecular fluorescence complementation, subcellular localization, and kinase assay experiments in the model crop rice (Oryza sativa) to systematically map what is to our knowledge the first plant MAPK-interacting proteins. We identified 80 nonredundant interacting protein pairs (74 nonredundant interactors) for rice MAPKs and elucidated the novel proteome-wide network of MAPK interactors. The established interactome contains four membrane-associated proteins, seven MAP2Ks (for MAPK kinase), four MAPKs, and 59 putative substrates, including 18 transcription factors. Several interactors were also validated by experimental approaches (in vivo and in vitro) and literature survey. Our results highlight the importance of OsMPK1, an ortholog of tobacco (Nicotiana benthamiana) salicyclic acid-induced protein kinase and Arabidopsis (Arabidopsis thaliana) AtMPK6, among the rice MAPKs, as it alone interacts with 41 unique proteins (51.2% of the mapped MAPK interaction network). Additionally, Gene Ontology classification of interacting proteins into 34 functional categories suggested MAPK participation in diverse physiological functions. Together, the results obtained essentially enhance our knowledge of the MAPK-interacting protein network and provide a valuable research resource for developing a nearly complete map of the rice MAPK interactome.

Flooding stress-induced glycine-rich RNA-binding protein from Nicotiana tabacum.

A cDNA clone for a transcript preferentially expressed during an early phase of flooding was isolated from Nicotiana tabacum. Nucleotide sequencing of the cDNA clone identified an open reading frame that has high homology to the previously reported glycine-rich RNA-binding proteins. The open reading frame consists of 157 amino acids with an N-terminal RNA-recognition motif and a C-terminal glycine-rich domain, and thus the cDNA clone was designated as Nicotiana tabaccum glycine-rich RNA-binding protein-1 (NtGRP1). Expression of NtGRP1 was upregulated under flooding stress and also increased, but at much lower levels, under conditions of cold, drought, heat, high salt content, and abscisic acid treatment. RNA homopolymer-binding assay showed that NtGRP1 binds to all the RNA homopolymers tested with a higher affinity to poly r(G) and poly r(A) than to poly r(U) and poly r(C). Nucleic acid-binding assays showed that NtGRP1 binds to ssDNA, dsDNA, and mRNA. NtGRP1 suppressed expression of the fire luciferase gene in vitro, and the suppression of luciferase gene expression could be rescued by addition of oligonucleotides. Collectively, the data suggest NtGRP1 as a negative modulator of gene expression by binding to DNA or RNA in bulk that could be advantageous for plants in a stress condition like flooding.

Molecular Cloning and Functional Analysis of Rice (Oryza sativa L.) OsNDR1 on Defense Signaling Pathway

A novel rice (Oryza sativa L.) gene, homologous to Arabidopsis pathogenesis-related NDR1 gene, was cloned from cDNA library prepared from 30 min Magnaporthe grisea -treated rice seedling leaves, and named as OsNDR1. OsNDR1 encoded a 220-aminoacid polypeptide and was highly similar to the Arabidopsis AtNDR1 protein. OsNDR1 is a plasma membrane (PM)-localized protein, and presumes through sequence analysis and protein localization experiment. Overexpression of OsNDR1 promotes the expression of PBZ1 that is essential for the activation of defense/stressrelated gene. The OsNDR1 promoter did not respond significantly to treatments with either SA, PBZ, or ETP. Exogenously applied BTH induces the same set of SAR genes as biological induction, providing further evidence for BTH as a signal. Presumably, BTH is bound by a receptor and the binding triggers a signal transduction cascade that has an ultimate effect on transcription factors that regulate SAR gene expression. Thus OsNDR1 may act as a transducer of pathogen signals and/or interact with the pathogen and is indeed another important step in clarifying the component participating in the defense response pathways in rice.

Heat-inducible C3HC4 type RING zinc finger protein gene from Capsicum annuum enhances growth of transgenic tobacco.

Capsicum annuum RING Zinc Finger Protein 1 (CaRZFP1) gene is a novel C3HC4-type RING zinc finger protein gene which was previously isolated from a cDNA library for hot pepper plants treated of heat-shock. The CaRZFP1 was inducible to diverse environmental stresses in hot pepper plants. We introduced the CaRZFP1 into the Wisconsin 38 cultivar of tobacco (Nicotiana tabacum) by Agrobacterium mediated transformation under the control of the CaMV 35S promoter. Expression of the transgene in the transformed tobacco plants was demonstrated by RNA blot analyses. There appeared no adverse effect of over-expression of the transgene on overall growth and development of transformants. The genetic analysis of tested T1 lines showed that the transgene segregated in a Mendelian fashion. Transgenic tobacco lines that expressed the CaRZFP1 gene were compared with several different empty vector lines and they exhibited enhanced growth; they have larger primary root, more lateral root, larger hypocotyls and bigger leaf size, resulting in heavier fresh weight. Enhanced growth of transgenic lines accompanied with longer vegetative growth that resulted in bigger plants with higher number of leaves. Microarray analysis revealed the up-regulation of some growth related genes in the transgenic plants which were verified by specific oligomer RNA blot analyses. These results indicate that CaRZFP1 activates and up-regulates some growth related proteins and thereby effectively promoting plant growth.

Small Heat Shock Proteins Can Release Light Dependence of Tobacco Seed during Germination

Ectopically expressed and heat shock-induced proteins trigger light-independent seed germination in tobacco. Small heat shock proteins (sHSPs) function as ATP-independent molecular chaperones, and although the production and function of sHSPs have often been described under heat stress, the expression and function of sHSPs in fundamental developmental processes, such as pollen and seed development, have also been confirmed. Seed germination involves the breaking of dormancy and the resumption of embryo growth that accompany global changes in transcription, translation, and metabolism. In many plants, germination is triggered simply by imbibition of water; however, different seeds require different conditions in addition to water. For small-seeded plants, like Arabidopsis (Arabidopsis thaliana), lettuce (Lactuca sativa), tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum), light is an important regulator of seed germination. The facts that sHSPs accumulate during seed development, sHSPs interact with various client proteins, and seed germination accompanies synthesis and/or activation of diverse proteins led us to investigate the role of sHSPs in seed germination, especially in the context of light dependence. In this study, we have built transgenic tobacco plants that ectopically express sHSP, and the effect was germination of the seeds in the dark. Administering heat shock to the seeds also resulted in the alleviation of light dependence during seed germination. Subcellular localization of ectopically expressed sHSP was mainly observed in the cytoplasm, whereas heat shock-induced sHSPs were transported to the nucleus. We hypothesize that ectopically expressed sHSPs in the cytoplasm led the status of cytoplasmic proteins involved in seed germination to function during germination without additional stimulus and that heat shock can be another signal that induces seed germination.

Gene expression profile forNicotiana tabacum in the early phase of flooding stress

Although flooding can often severely damage crop yields, few studies of this stress have been made at the genetic level. To identify the genes that probably function in plants at the onset of flooding stress, we constructed a cDNA library representing tobacco plants that experienced short-term stress, i.e., 2 to 4 h of submergence while under illumination. Differential screening of that library produced 73 cDNA clones that showed preferential hybridization with the probe prepared from these stressed plants. The cDNA inserts were isolated from the vector by restriction digest and subjected to reverse northern analysis, which confirmed preferential expression of 41 genes. The remainder either had no significant increase in expression under flooding stress or exhibited no identifiable signal. We then performed northern blot analyses for some selected genes to provide supporting evidence that strongly paralleled our results from the reverse-northern evaluation. Photosynthesis-related genes were the major group, followed by those for well-known glycolysis enzymes and fermentation enzymes. Other genes include those for hydrolytic enzymes and components of the ethylene synthesis pathway. Although many others also were induced, their functions could not be characterized here.

Tobacco class I cytosolic small heat shock proteins are under transcriptional and translational regulations in expression and heterocomplex prevails under the high‐temperature stress condition in vitro

Seven genomic clones of tobacco (Nicotiana tabacum W38) cytosolic class I small heat shock proteins (sHSPs), probably representing all members in the class, were isolated and found to have 66 to 92% homology between their nucleotide sequences. Even though all seven sHSP genes showed heat shock-responsive accumulation of their transcripts and proteins, each member showed discrepancies in abundance and timing of expression upon high-temperature stress. This was mainly the result of transcriptional regulation during mild stress conditions and transcriptional and translational regulation during strong stress conditions. Open reading frames (ORFs) of these genomic clones were expressed in Escherichia coli and the sHSPs were purified from E. coli. The purified tobacco sHSPs rendered citrate synthase and luciferase soluble under high temperatures. At room temperature, non-denaturing pore exclusion polyacrylamide gel electrophoresis on three sHSPs demonstrated that the sHSPs spontaneously formed homo-oligomeric complexes of 200 ∼ 240 kDa. However, under elevated temperatures, hetero-oligomeric complexes between the sHSPs gradually prevailed. Atomic force microscopy showed that the hetero-oligomer of NtHSP18.2/NtHSP18.3 formed a stable oligomeric particle similar to that of the NtHSP18.2 homo-oligomer. These hetero-oligomers positively influenced the revival of thermally inactivated luciferase. Amino acid residues mainly in the N-terminus are suggested for the exchange of the component sHSPs and the formation of dominant hetero-oligomers under high temperatures.

Submergence-inducible and circadian rhythmic basic helix―loop―helix protein gene in Nicotiana tabacum

Submergence stress leads to diverse changes in transcription and translation of genes involved in developmental and physiological metabolisms of plants. The basic helix-loop-helix (bHLH) protein family is one of the largest transcriptional factor families in plants, and has been shown to play pivotal roles in diverse biological responses. However, there has been no report on bHLH protein related to submergence stress response. In this study, a novel bHLH gene, NtbHLH, was isolated from tobacco (Nicotiana tabacum) by differential screening of a submergence-stress-induced cDNA library. NtbHLH cDNA is 1027bp in length, with an open reading frame (ORF) of 702 nucleotides encoding 233 amino acid residues that contain the bHLH domain. RNA-blot analyses showed that transcription of NtbHLH was induced by submergence stress, while cold, heat shock, and drought decreased its expression. The gene expression was down-regulated by gibberellins, but ABA and ethylene seemed not to affect it. It was also apparent that NtbHLH expression follows circadian rhythmicity. The electrophoretic mobility shift and chemical cross-linking assays showed that NtbHLH specifically binds to G-box and forms homo-dimers.