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de los Reyes, Benildo G,Mohanty, Bijayalaxmi,Yun, Song Joong,Park, Myoung-Ryoul,Lee, Dong-Yup Springer US 2015 Rice Vol.8 No.-
<P>Dissecting the upstream regulatory architecture of rice genes and their cognate regulator proteins is at the core of network biology and its applications to comparative functional genomics. With the rapidly advancing comparative genomics resources in the genus <I>Oryza</I>, a reference genome annotation that defines the various cis-elements and trans-acting factors that interface each gene locus with various intrinsic and extrinsic signals for growth, development, reproduction and adaptation must be established to facilitate the understanding of phenotypic variation in the context of regulatory networks. Such information is also important to establish the foundation for mining non-coding sequence variation that defines novel alleles and epialleles across the enormous phenotypic diversity represented in rice germplasm. This review presents a synthesis of the state of knowledge and consensus trends regarding the various cis-acting and trans-acting components that define spatio-temporal regulation of rice genes based on representative examples from both foundational studies in other model and non-model plants, and more recent studies in rice. The goal is to summarize the baseline for systematic upstream sequence annotation of the rapidly advancing genome sequence resources in <I>Oryza</I> in preparation for genus-wide functional genomics. Perspectives on the potential applications of such information for gene discovery, network engineering and genomics-enabled rice breeding are also discussed.</P>
Myoung Ryoul Park,So-Hyeon Baek,Benildo G. de los Reyes,Karl H. Hasenstein,Song Joong Yun 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07
Phosphorus (P) is an important structural component and plays critical roles in the process of energy transfer and signal transduction. Effect of low P on carbohydrate metabolism was investigated at the transcription level via transcriptome analysis using the rice 60K oligonucleotide DNA microarrays. Two-week-old rice seedlings were grown under a low (32 μM) or high (320 μM) P condition for two weeks and leaves from the seedlings were used for transcriptome analysis. Expression of genes involved in carbohydrate metabolic pathways (eg. glycolysis, sucrose degradation and starch synthesis and degradation) was most significantly affected under low P. Under low P, most genes involved in glycolysis were intensively down-regulated, genes of starch biosynthesis and degradation pathway were up- or down-regulated, and many genes involved in sucrose biosynthesis were intensively up-regulated. In leaves under low P, glucose and pyruvate levels decreased, but sucrose and starch levels increased. These results suggest that carbohydrate metabolism is adjusted primarily through comprehensive transcriptional modulation of genes involved in the carbohydrate metabolic super-pathway.
Mohanty, Bijayalaxmi,Takahashi, Hirokazu,de los Reyes, Benildo G.,Wijaya, Edward,Nakazono, Mikio,Lee, Dong-Yup Springer US 2016 Rice Vol.9 No.1
<P><B>Background</B></P><P>Rice is the only crop that germinates and elongates the coleoptile under complete submergence. It has been shown that <I>alcohol dehydrogenase 1 (ADH1)-</I>deficient mutant of rice with <I>reduced alcohol dehydrogenase activity</I> (<I>rad</I>) and reduced ATP level, is viable with much reduced coleoptile elongation under such condition. To understand the altered transcriptional regulatory mechanism of this mutant, we aimed to establish possible relationships between gene expression and <I>cis</I>-regulatory information content.</P><P><B>Findings</B></P><P>We performed promoter analysis of the publicly available differentially expressed genes in <I>ADH1</I> mutant. Our results revealed that a crosstalk between a number of key transcription factors (TFs) and different phytohormones altered transcriptional regulation leading to the survival of the mutant. Amongst the key TFs identified, we suggest potential involvement of MYB, bZIP, ARF and ERF as transcriptional activators and WRKY, ABI4 and MYC as transcriptional repressors of coleoptile elongation to maintain metabolite levels for the cell viability. Out of the repressors, WRKY TF is most likely playing a major role in the alteration of the physiological implications associated with the cell survival.</P><P><B>Conclusions</B></P><P>Overall, our analysis provides a possible transcriptional regulatory mechanism underlying the survival of the <I>rad</I> mutant under complete submergence in an energy crisis condition and develops hypotheses for further experimental validation.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12284-016-0124-3) contains supplementary material, which is available to authorized users.</P>
( Dong Geun Choi ),( Nam Hee Yoo ),( Chang Yeon Yu ),( Benildo De Los Reyes ),( Song Joong Yun ) 생화학분자생물학회 2004 BMB Reports Vol.37 No.5
All members of R. glutinosa show the unique characteristic of intrinsic tolerance to paraquat (PQ). Antioxidant enzymes have been proposed to be the primary mechanism of PQ resistance in several plant species. Therefore, the antioxidant enzyme systems of R. glutinosa were evaluated by comparatively analyzing cellular antioxidant enzyme levels, and their responses of oxidative stresses and hormones. The levels of ascorbate peroxidase (APX), glutathione reductase (GR), non-specific peroxidase (PDX), and superoxide dismutase (SOD) were 7.3-, 4.9-, 2.7- and 1.6-fold higher in PQ-tolerant R. glutinosa than in PQ-susceptible soybeans. However, the activity of catalase (CAT) was about 12-fold higher in the soybeans. The activities of antioxidant enzymes reduced after PQ treatment in the two species, with the exception of PDX and SOD in R. glutinosa, which increased by about 40%. Interestingly, the activities of APX, SOD and PDX in R. glutinosa, relative to those in soybeans, were further increased by 49, 67 and 93% after PQ treatment. The considerably higher intrinsic levels, and increases in the relative activities of antioxidant enzymes in R. glutinosa under oxidative stress support the possible role of these enzymes in the PQ tolerance of R. glutinosa. However, the relatively lower levels of SOD versus PQ tolerance, and the mixed responses of antioxidant enzymes to stresses and hormones, suggest a possible alternative mechanism(s) for PQ tolerance in R. glutinosa.
Choi, Dong-Geun,Yoo, Nam-Hee,Yu, Chang-Yeon,De Los Reyes, Benildo,Yun, Song-Joong Korean Society for Biochemistry and Molecular Biol 2004 Journal of biochemistry and molecular biology Vol.37 No.5
All members of R. glutinosa show the unique characteristic of intrinsic tolerance to paraquat (PQ). Antioxidant enzymes have been proposed to be the primary mechanism of PQ resistance in several plant species. Therefore, the antioxidant enzyme systems of R. glutinosa were evaluated by comparatively analyzing cellular antioxidant enzyme levels, and their responses of oxidative stresses and hormones. The levels of ascorbate peroxidase (APX), glutathione reductase (GR), non-specific peroxidase (POX), and superoxide dismutase (SOD) were 7.3-, 4.9-, 2.7- and 1.6-fold higher in PQ-tolerant R. glutinosa than in PQ-susceptible soybeans. However, the activity of catalase (CAT) was about 12-fold higher in the soybeans. The activities of antioxidant enzymes reduced after PQ treatment in the two species, with the exception of POX and SOD in R. glutinosa, which increased by about 40%. Interestingly, the activities of APX, SOD and POX in R. glutinosa, relative to those in soybeans, were further increased by 49, 67 and 93% after PQ treatment. The considerably higher intrinsic levels, and increases in the relative activities of antioxidant enzymes in R. glutinosa under oxidative stress support the possible role of these enzymes in the PQ tolerance of R. glutinosa. However, the relatively lower levels of SOD versus PQ tolerance, and the mixed responses of antioxidant enzymes to stresses and hormones, suggest a possible alternative mechanism(s) for PQ tolerance in R. glutinosa.
Park, Myoung Ryoul,Baek, So-Hyeon,de los Reyes, Benildo G.,Yun, Song Joong,Hasenstein, Karl H. Elsevier 2012 Journal of plant physiology Vol.169 No.2
<P><B>Abstract</B></P><P>Phosphorus (P) is a structural component of nucleic acids and phospholipids and plays important roles in plant growth and development. P accumulation was significantly reduced (about 35%) in rice leaves from plants grown under low (32μM) P compared to 320μMP grown plants. Genome response to low P was examined using the rice 60K oligonucleotide DNA microarrays. At the threshold significance of |log<SUB>2</SUB>| fold>2.0, 21,033 genes (about 33.7% of all genes on the microarray) were affected by P deficiency. Among all genes on the microarray, 4271 genes were sorted into 51 metabolic pathways. Low P affected 1494 (35.0%) genes and the largest category of genes was related to sucrose degradation to ethanol and lactate pathway. To survey the role of P in rice, 25 pathways were selected based on number of affected genes. Among these pathways, cytosolic glycolysis contained the least number of upregulated but most down-regulated genes. Low P decreased glucose, pyruvate and chlorophyll, and genes related to carbon metabolism and chlorophyllide <I>a</I> biosynthesis. However, sucrose and starch levels increased. These results indicate that P nutrition affects diverse metabolic pathways mostly related to glucose, pyruvate, sucrose, starch, and chlorophyll <I>a</I>.</P>
윤성중,Eun Ae Cho,Chong Ae Lee,Young Soo Kim,So Hyeon Baek,Benildo G. de los Reyes 한국분자세포생물학회 2005 Molecules and cells Vol.19 No.1
A cDNA encoding γ-tocopherol methyltransferase (γ-TMT) from Arabidopsis thaliana was overexpressed in lettuce (Latuca sativa L.) to improve the tocopherol composition. Seven lines of lettuce (T0) containing the γ-TMT transgene were produced by Agrobacteriummediated transformation. The inheritance and expression of the transgene were confirmed by DNA and RNA gel blot analyses as well as quantification of tocopherols and γ-TMT activities. The ratio of α-/γ- tocopherol content (TR) varied from 0.6 to 1.2 in nontransformed plants, while the T0 plants had ratios of 0.8 to 320. The ratio ranged from 0.4 to 544 in 41 T1 progenies of the T0 transgenic line gTM3, and the phenotypic segregation indicated monogenic inheritance of the transgene (i.e., 3:1 = dominant:wild-type classes). There was a tight relationship between the TR phenotype and γ-TMT activity, and enzyme activities were affected by the copy number and transcript levels of the transgene. The TR phenotype was stably expressed in T2 progenies of T1 plants. The results from this study indicated that a stable inheritance and expression of Arabidopsis γ-TMT transgene in lettuce results in a higher enzyme activity and the conversion of the γ-tocopherol pool to α-tocopherol in transgenic lettuce.