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Mandaokar, Ajin,Thines, Bryan,Shin, Byongchul,Markus Lange, B.,Choi, Goh,Koo, Yeon J.,Yoo, Yung J.,Choi, Yang D.,Choi, Giltsu,Browse, John Blackwell Publishing Ltd 2006 The Plant journal Vol.46 No.6
<P>Summary</P><P>In Arabidopsis, jasmonate is required for stamen and pollen maturation. Mutants deficient in jasmonate synthesis, such as <I>opr3</I>, are male-sterile but become fertile when jasmonate is applied to developing flower buds. We have used ATH1 oligonucleotide arrays to follow gene expression in <I>opr3</I> stamens for 22 h following jasmonate treatment. In these experiments, a total of 821 genes were specifically induced by jasmonate and 480 genes were repressed. Comparisons with data from previous studies indicate that these genes constitute a stamen-specific jasmonate transcriptome, with a large proportion (70%) of the genes expressed in the sporophytic tissue but not in the pollen. Bioinformatics tools allowed us to associate many of the induced genes with metabolic pathways that are probably upregulated during jasmonate-induced maturation. Our pathway analysis led to the identification of specific genes within larger families of homologues that apparently encode stamen-specific isozymes. Extensive additional analysis of our dataset identified 13 transcription factors that may be key regulators of the stamen maturation processes triggered by jasmonate. Two of these transcription factors, MYB21 and MYB24, are the only members of subgroup 19 of the R2R3 family of MYB proteins. A <I>myb21</I> mutant obtained by reverse genetics exhibited shorter anther filaments, delayed anther dehiscence and greatly reduced male fertility. A <I>myb24</I> mutant was phenotypically wild-type, but production of a <I>myb21</I><I>myb24</I> double mutant indicated that introduction of the <I>myb24</I> mutation exacerbated all three aspects of the <I>myb21</I> phenotype. Exogenous jasmonate could not restore fertility to <I>myb21</I> or <I>myb21</I><I>myb24</I> mutant plants. Together with the data from transcriptional profiling, these results indicate that MYB21 and MYB24 are induced by jasmonate and mediate important aspects of the jasmonate response during stamen development.</P>
Decoding of Light Signals by Plant Phytochromes and Their Interacting Proteins
Bae, Gabyong,Choi, Giltsu Annual Reviews 2008 Annual review of plant biology Vol.59 No.-
<P>Phytochromes are red/far-red light photoreceptors that convert the information contained in external light into biological signals. The decoding process starts with the perception of red light, which occurs through photoisomerization of a chromophore located within the phytochrome, leading to structural changes that include the disruption of intramolecular interactions between the N- and C-terminal domains of the phytochrome. This disruption exposes surfaces required for interactions with other proteins. In contrast, the perception of far-red light reverses the photoisomerization, restores the intramolecular interaction, and closes the interacting surfaces. Light information represented by the concentration of opened interacting surfaces is converted into biological signals through the modulating activity of interacting proteins. This review summarizes plant phytochromes, phytochrome-interacting proteins, and signal transmission from phytochromes to their interacting proteins.</P>
Kang, Hyojin,Oh, Eunkyoo,Choi, Giltsu,Lee, Doheon Inderscience 2010 International journal of data mining and bioinform Vol.4 No.5
<P>PIL5 is a member of the basic Helix-Loop-Helix (bHLH) transcription factor superfamily. We previously showed that PIL5 binds to the G-box (CACGTG) motif with high affinity. However, since there are many randomly matched G-box motifs throughout the genome, other factors must account for the in-vivo PIL5 binding specificity. In this study, we investigated if in-vivo PIL5 binding sites can be explained by any other attributes extracted from various sources. Our results showed that PIL5 binding sites can be explained by attributes such as neighbouring motif composition, nucleosome density, DNA methylation and distance from transcription start site in addition to G-box.</P>
Shin, Jieun,Park, Eunae,Choi, Giltsu Blackwell Publishing Ltd 2007 The Plant journal Vol.49 No.6
<P>Summary</P><P>Phytochromes are red/far-red light receptors that regulate various light responses by initiating the transcriptional cascades responsible for changing the expression patterns of 10–30% of the entire plant transcriptome. Several transcription factors that are thought to participate in this process have been identified, but the functional relationships among them have not yet been fully elucidated. Here we investigated the functional relationship between two such transcription factors, PIF3 and HY5, and their effects on anthocyanin biosynthesis. Our results revealed that PIF3 and HY5 do not regulate each other at either the transcriptional or the protein levels in continuous light conditions, suggesting that they are not directly linked within phytochrome-mediated signaling. We found that both PIF3 and HY5 positively regulate anthocyanin biosynthesis by activating the transcription of the same anthocyanin biosynthetic genes, but the positive effects of PIF3 required functional HY5. Chromatin immunoprecipitation analyses indicated that both PIF3 and HY5 regulate anthocyanin biosynthetic gene expression by directly binding to different regions of the gene promoters <I>in vivo</I>. Additional experiments revealed that PIF3 bound the promoters regardless of light and HY5. Collectively, these data show that PIF3 and HY5 regulate anthocyanin biosynthesis by simultaneously binding anthocyanin biosynthetic gene promoters at separate sequence elements.</P>
Kwon, Chang Seob,Lee, Daeyoup,Choi, Giltsu,Chung, Won-Il Blackwell Publishing Ltd 2009 The Plant journal Vol.60 No.1
<P>Summary</P><P>Trimethylation of histone H3 at lysine 27 (H3K27me3) is a histone marker that is present in inactive gene loci in both plants and animals. Transcription of some of the genes with H3K27me3 should be induced by internal or external cues, yet the dynamic fate of H3K27me3 in these genes during transcriptional regulation is poorly understood in plants. Here we show that H3K27me3 in two cold-responsive genes, <I>COR15A</I> and <I>ATGOLS3</I>, decreases gradually in Arabidopsis during exposure to cold temperatures. We found that removal of H3K27me3 can occur by both histone occupancy-dependent and -independent mechanisms. Upon cold exposure, histone H3 levels decreased in the promoter regions of <I>COR15A</I> and <I>ATGOLS3</I> but not in their transcribed regions. When we returned cold-exposed plants to normal growth conditions, transcription of <I>COR15A</I> and <I>ATGOLS3</I> was completely repressed to the initial level before cold exposure in 1 day. In contrast, plants still maintained the cold-triggered decrease in H3K27me3 at <I>COR15A</I> and <I>ATGOLS3</I>, but this decrease did not enhance transcriptional induction of the two genes upon re-exposure to cold. Taken together, these results indicate that gene activation is not inhibited by H3K27me3 itself but rather leads to removal of H3K27me3, and that H3K27me3 can be inherited at a quantitative level, thereby serving as a memory marker for recent transcriptional activity in Arabidopsis.</P>
Moon, Hae-Jeong,Lee, Bo-Young,Choi, Giltsu,Shin, Dong-Jin,D. Theertha Prasad,Lee, Ok-Sun,Kwak, Sang-Soo,Kim, Doh-Hoon,Nam, Jae-Sung,Bahk, Jeong-Dong,Hong, Jong-Chan,Lee, Sang-Yeol,Cho, Moo-Je,Lim, Cha Plant molecular biology and biotechnology research 2003 Plant molecular biology and biotechnology research Vol.2003 No.-
NDP kinases (NDPKs) are multifunctional proteins that regulate a variety of eukaryotic cellular activities, including cell proliferation, development, and differentiation. However, much less is known about the functional significance of NDPKs in plants. We show here that NDPK is associated with H_(2)O_(2)-mediated mitogen-activated protein kinase signaling in plants. H_(2)O_(2)stress strongly induces the expression of the NDPK2 gene in Arabidopsis thaliana (AtNDPK2). Proteins from transgenic plants overexpressing AtNDPK2 showed high levels of autophosphorylation and NDPK activity, and they have lower levels of reactive oxygen species (ROS) than wild-type plants. Mutants lacking AtNDPK2 had higher levels of ROS than wild type. H_(2)O_(2) treatment induced the phosphorylation of two endogenous proteins whose molecular weights suggested they are AtMPK3 and AtMPK6, two H_(2)O_(2)-activated A. thaliana mitogen-activated protein kinses. In the absence of H_(2)O_(2) treatment, phosphorylation of these proteins was slightly elevated in plants overexpressing AtNDPK2 but markedly decreased in the AtNDPK2 deletion mutant. Yeast two-hybrid and in vitro protein pull-down assays revealed that AtNDPK2 specifically interacts with AtMPK3 and AtMPK6. Furthermore, AtNDPK2 also enhances the myelin basic protein phosphorylation activity of AtMPK3 in vitro. Finally, constitutive overexpression of AtNDPK2 in Arabidopsis plants conferred an enhanced tolerance to multiple environmental stresses that elicit ROS accumulation in situ. Thus, AtNDPK2 appears to play a previously uncharacterized regulatory role in H_(2)O_(2)-mediated MAPK signaling in plants.