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ABSTRACT: In this study, to elucidate the mechanisms of adaptation and tolerance to ionizing radiation in woody plants, we investigated the various biological effects of γ-rays on the Lombardy poplar (Populus nigra L. var. italica Du Roi). We detected abnormal leaf shape and color, fusion, distorted venation, shortened internode, fasciation and increased axillary shoots in γ-irradiated poplar plants. Acute γ-irradiation with a dose of 100Gy greatly reduced the height, stem diameter and biomass of poplar plantlets. After receiving doses of 200 and 300Gy, all the plantlets stopped growing, and then most of them withered after 4-10 weeks of γ-irradiation. Comet assays showed that nuclear DNA in suspension-cultured poplar cells had been damaged by γ-rays. To determine whether DNA repair-related proteins are involved in the response to γ-rays in Lombardy poplars, we cloned the PnRAD51, PnLIG4, PnKU70, PnXRCC4, PnPCNA and PnOGG1 cDNAs and investigated their mRNA expression. The PnRAD51, PnLIG4, PnKU70, PnXRCC4 and PnPCNA mRNAs were increased by γ-rays, but the PnOGG1 mRNA was decreased. Moreover, the expression of PnLIG4, PnKU70 and PnRAD51 was also up-regulated by Zeocin known as a DNA cleavage agent. These observations suggest that the morphogenesis, growth and protective gene expression in Lombardy poplars are severely affected by the DNA damage and unknown cellular events caused by γ-irradiation.
Journal of environmental radioactivity 01/2012; 109:19-28. · 1.47 Impact Factor
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ABSTRACT: LHY/CCA1 genes play a key role in the plant circadian clock system and are highly conserved among plant species. However, the evolutionary process of the LHY/CCA1 gene family remains unclear in angiosperms. To obtain details of the phylogeny of these genes, this study characterized LHY/CCA1 genes in a model woody plant,Populus tree.The evolutionary process of angiosperm LHY/CCA1 genes was elucidated using three approaches: comparison of exon–intron structures, reconstruction of phylogenetic trees and examination of syntenic relationships. In addition, the molecular evolutionary rates and the expression patterns of Populus LHYs were analyzed.Gene duplication events of Populus LHYs and Arabidopsis LHY/CCA1 had occurred independently by different chromosomal duplication events arising in each evolutionary lineage. Populus LHYs were under purifying selection by estimating substitution rates of these genes. Further, Populus LHYs conserved diurnal expressions in leaves and stems but the transcripts of LHY2 were more abundant than those of LHY1 in Populus plants.This study uncovered phylogenetic relationships of the LHY/CCA1 gene family in angiosperms. In addition, the transcript abundance and the evolutionary differences between Populus LHY1 and LHY2 imply that Populus LHY2, rather than LHY1, may have a major role in the Populus clock system.
New Phytologist 01/2009; 181(4):808-19. · 6.64 Impact Factor
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ABSTRACT: Cryptomeria japonica D. Don is one of the most commercially important conifers in Japan. However, the allergic disease caused by its pollen is a severe public health problem in Japan. Since large-scale analysis of expressed sequence tags (ESTs) in the male strobili of C. japonica should help us to clarify the overall expression of genes during the process of pollen development, we constructed a full-length enriched cDNA library that was derived from male strobili at various developmental stages.
We obtained 36,011 expressed sequence tags (ESTs) from either one or both ends of 19,437 clones derived from the cDNA library of C. japonica male strobili at various developmental stages. The 19,437 cDNA clones corresponded to 10,463 transcripts. Approximately 80% of the transcripts resembled ESTs from Pinus and Picea, while approximately 75% had homologs in Arabidopsis. An analysis of homologies between ESTs from C. japonica male strobili and known pollen allergens in the Allergome Database revealed that products of 180 transcripts exhibited significant homology. Approximately 2% of the transcripts appeared to encode transcription factors. We identified twelve genes for MADS-box proteins among these transcription factors. The twelve MADS-box genes were classified as DEF/GLO/GGM13-, AG-, AGL6-, TM3- and TM8-like MIKCC genes and type I MADS-box genes.
Our full-length enriched cDNA library derived from C. japonica male strobili provides information on expression of genes during the development of male reproductive organs. We provided potential allergens in C. japonica. We also provided new information about transcription factors including MADS-box genes expressed in male strobili of C. japonica. Large-scale gene discovery using full-length cDNAs is a valuable tool for studies of gymnosperm species.
BMC Genomics 09/2008; 9:383. · 4.07 Impact Factor
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ABSTRACT: Secondary metabolites called norlignans are produced in the xylem of Cryptomeria japonica D. Don. Several norlignans have roles in the defense of sapwood against microbial invasion and in the coloration of heartwood. The biosynthetic pathway of norlignans is largely unknown. Norlignans have been reported to accumulate in the sapwood during the drying of C. japonica logs. To search for genes encoding enzymes that catalyze the synthesis of norlignans, we carried out suppression subtractive hybridization using the fresh sapwood of a felled log and the drying sapwood in which a norlignan, agatharesinol, accumulated. A total of 1050 expressed sequence tags were obtained from the subtracted cDNA library, and these were assembled into 146 contigs and 361 singletons. Of these 507 unique sequences, 263 were functionally classified into 12 categories. "Metabolism" was the largest category, with 23% (61) of classified sequences. Twenty-six sequences that encode 16 enzymes were assigned to "secondary metabolism." Expression analysis of 15 genes related to "secondary metabolism" revealed that 12 of these genes had transcripts that were induced during the sapwood drying process. Of the 12 genes, 10 encoded enzymes that use aromatic compounds as substrates. In addition, 58 sequences representing 22 defense-related proteins were found. Our subtraction library should be a useful source for isolating genes encoding proteins involved in secondary metabolism including norlignan biosynthesis and defense in C. japonica xylem.
Tree Physiology 02/2007; 27(1):1-9. · 2.88 Impact Factor
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Tokihiko Nanjo,
Tetsuya Sakurai,
Yasushi Totoki,
Atsushi Toyoda,
Mitsuru Nishiguchi,
Tomoyuki Kado,
Tomohiro Igasaki,
Norihiro Futamura,
Motoaki Seki,
Yoshiyuki Sakaki,
Kazuo Shinozaki,
Kenji Shinohara
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ABSTRACT: Populus is one of favorable model plants because of its small genome. Structural genomics of Populus has reached a breakpoint as nucleotides of the entire genome have been determined. Reaching the post genome era, functional genomics of Populus is getting more important for well-comprehended plant science. Development of bioresorce serving functional genomics is making rapid progress. Huge efforts have achieved deposits of expressed sequence tags (ESTs) in various plant species consequently accelerating functional analysis of genes. ESTs from full-length cDNA clones are especially powerful for accurate molecular annotation. We promoted collection and annotation of the ESTs from Populus full-length enriched cDNA clones as part of functional genomics of tree species.
We have been collecting the full-length enriched cDNA of the female poplar (Populus nigra var. italica) for years. By sequencing P. nigra full-length (PnFL) cDNA libraries, we generated about 116,000 5'-end or 3'-end ESTs corresponding to 19,841 nonredundant PnFL clones. Population of PnFL cDNA clones represents 44% of the predicted genes in the Populus genome.
Our resource of P. nigra full-length enriched clones is expected to provide valuable tools to gain further insight into genome annotation and functional genomics in Populus.
BMC Genomics 02/2007; 8:448. · 4.07 Impact Factor
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ABSTRACT: Poplar, whose genome is the first to be sequenced among woody plants, is a favorable model for plant biologists to enable them to understand molecular processes of growth, development and responses to environmental stimuli in trees. The sequence will allow the development of a strategy for improving environmental stress tolerance in forest trees. In this study, we have generated a full-length enriched cDNA library from leaves of axenically grown poplar (Populus nigra var. italica) subjected to environmental stress treatments by dehydration, high salinity, chilling, heat, abscisic acid (ABA) and H2O2. We sequenced >30,000 expressed sequence tags (ESTs) from the cDNA library and consequently collected approximately 4,500 non-redundant clones. We further analyzed cDNAs encoding an ERF/AP2-domain transcription factor which is specific in plants and plays an important role under stress. Thirteen candidates containing the ERF/AP2 domain were found within our EST resource. Some of them showed stress-responsive gene expression. We report here the first collection of full-length enriched stress-related ESTs of poplar and discuss environmental stress responses of forest trees in the light of comparative genomics.
Plant and Cell Physiology 01/2005; 45(12):1738-48. · 4.70 Impact Factor
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ABSTRACT: Arginine decarboxylase (ADC) catalyzes the first step of polyamine (PA) biosynthesis to produce putrescine (Put) from arginine (Arg). One of the 2 Arabidopsis ADC genes, AtADC2, is induced in response to salt stress causing the accumulation of free Put. To analyze the roles of stress-inducible AtADC2 gene and endogenous Put in stress tolerance, we isolated a Ds insertion mutant of AtADC2 gene (adc2-1) and characterized its phenotypes under salt stress. In the adc2-1 mutant, free Put content was reduced to about 25% of that in the control plants and did not increase under salt stress. Furthermore, the adc2-1 mutant was more sensitive to salt stress than the control plants. The stress sensitivity of adc2-1 was recovered by the addition of exogenous Put. These results indicate that endogenous Put plays an important role in salt tolerance in Arabidopsis. AtADC2 is a key gene for the production of Put under not only salinity conditions, but also normal conditions.
Biochemical and Biophysical Research Communications 02/2004; 313(2):369-75. · 2.48 Impact Factor
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Youko Oono,
Motoaki Seki, Tokihiko Nanjo,
Mari Narusaka,
Miki Fujita,
Rie Satoh,
Masakazu Satou,
Tetsuya Sakurai,
Junko Ishida,
Kenji Akiyama,
Kei Iida,
Kyonoshin Maruyama,
Shinobu Satoh,
Kazuko Yamaguchi-Shinozaki,
Kazuo Shinozaki
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ABSTRACT: Plants respond and adapt to drought stress in order to survive under stress conditions. Several genes that respond to drought at the transcriptional level have been described, but there are few reports on genes involved in the recovery from dehydration. Analysis of rehydration-inducible genes should help not only to understand the molecular mechanisms of stress responses in higher plants, but also to improve the stress tolerance of crops by gene manipulation. We used a full-length cDNA microarray containing ca. 7000 Arabidopsis full-length cDNAs and identified 152 rehydration-inducible genes. Venn diagram analysis showed relationship of the rehydration-inducible genes to proline-inducible and water-treatment-inducible genes. Among the 152 rehydration-inducible genes, 58 genes contained the ACTCAT sequence involved in proline- and hypoosmolarity-inducible gene expression in their promoter regions, suggesting that ACTCAT sequence is a major cis-acting element involved in rehydration-inducible gene expression, and that some novel cis-acting elements are involved in rehydration-inducible gene expression. Functional analysis of rehydration-inducible and rehydration-repressed genes revealed their functions not only in the release from a stressed status but also in the recovery of growth in plants.
The Plant Journal 07/2003; 34(6):868-87. · 6.16 Impact Factor
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ABSTRACT: The toxicity of proline (Pro) to plant growth has raised questions despite its protective functions in response to environmental stresses. To evaluate Pro toxicity, we isolated an Arabidopsis T-DNA-tagged mutant, pdh, that had a defect in Pro dehydrogenase (AtProDH), which catalyzes the first step of Pro catabolism. The pdh mutant showed hypersensitivity to exogenous application of < or =10 mM L-Pro, at which wild-type plants grew normally. A dose-dependent increase in internal free Pro accumulation was observed in pdh plants during external Pro supply. These results do not just prove the toxicity of Pro, but also suggest that AtProDH is the only enzyme acting as a functional ProDH in Arabidopsis: To further analyze the targets of Pro toxicity, we compared the expression of thousands of genes by pdh plants with that by wild-type plants by cDNA microarray analysis. Most genes were unaffected. Here we demonstrate Pro toxicity by using the pdh mutant and discuss a cause-and-effect action between an excess of free Pro and growth inhibition in Arabidopsis.
Plant and Cell Physiology 05/2003; 44(5):541-8. · 4.70 Impact Factor
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Motoaki Seki,
Junko Ishida,
Mari Narusaka,
Miki Fujita, Tokihiko Nanjo,
Taishi Umezawa,
Asako Kamiya,
Maiko Nakajima,
Akiko Enju,
Tetsuya Sakurai,
Masakazu Satou,
Kenji Akiyama,
Kazuko Yamaguchi-Shinozaki,
Piero Carninci,
Jun Kawai,
Yoshihide Hayashizaki,
Kazuo Shinozaki
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ABSTRACT: Full-length cDNAs are essential for functional analysis of plant genes. Recently, cDNA microarray analysis has been developed for quantitative analysis of global and simultaneous analysis of expression profiles. Microarray technology is a powerful tool for identifying genes induced by environmental stimuli or stress and for analyzing their expression profiles in response to environmental signals. We prepared an Arabidopsis full-length cDNA microarray containing around 7,000 independent full-length cDNA groups and analyzed the expression profiles of genes. The transcripts of 245, 299, 54 and 213 genes increased after abscisic acid (ABA), drought-, cold-, and salt-stress treatments, respectively, with inducibilities more than fivefold compared with those of control genes [corrected]. The cDNA microarray analysis showed that many ABA-inducible genes were induced after drought- and high-salinity-stress treatments, and that there is more crosstalk between drought and ABA responses than between ABA and cold responses. Among the ABA-inducible genes identified, we identified 22 transcription factor genes, suggesting that many transcriptional regulatory mechanisms exist in the ABA signal transduction pathways.
Functional and Integrative Genomics 12/2002; 2(6):282-91. · 2.84 Impact Factor
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Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 10/2002; 47(12 Suppl):1684-9.
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Motoaki Seki,
Mari Narusaka,
Junko Ishida, Tokihiko Nanjo,
Miki Fujita,
Youko Oono,
Asako Kamiya,
Maiko Nakajima,
Akiko Enju,
Tetsuya Sakurai,
Masakazu Satou,
Kenji Akiyama,
Teruaki Taji,
Kazuko Yamaguchi-Shinozaki,
Piero Carninci,
Jun Kawai,
Yoshihide Hayashizaki,
Kazuo Shinozaki
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ABSTRACT: Full-length cDNAs are essential for functional analysis of plant genes in the post-sequencing era of the Arabidopsis genome. Recently, cDNA microarray analysis has been developed for quantitative analysis of global and simultaneous analysis of expression profiles. We have prepared a full-length cDNA microarray containing approximately 7000 independent, full-length cDNA groups to analyse the expression profiles of genes under drought, cold (low temperature) and high-salinity stress conditions over time. The transcripts of 53, 277 and 194 genes increased after cold, drought and high-salinity treatments, respectively, more than fivefold compared with the control genes. We also identified many highly drought-, cold- or high-salinity- stress-inducible genes. However, we observed strong relationships in the expression of these stress-responsive genes based on Venn diagram analysis, and found 22 stress-inducible genes that responded to all three stresses. Several gene groups showing different expression profiles were identified by analysis of their expression patterns during stress-responsive gene induction. The cold-inducible genes were classified into at least two gene groups from their expression profiles. DREB1A was included in a group whose expression peaked at 2 h after cold treatment. Among the drought, cold or high-salinity stress-inducible genes identified, we found 40 transcription factor genes (corresponding to approximately 11% of all stress-inducible genes identified), suggesting that various transcriptional regulatory mechanisms function in the drought, cold or high-salinity stress signal transduction pathways.
The Plant Journal 09/2002; 31(3):279-92. · 6.16 Impact Factor
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ABSTRACT: Many organisms, including higher plants, accumulate free proline (Pro) in response to osmotic stress. Although various studies have focused on the ability of Pro as a compatible osmolyte involved in osmotolerance, its specific role throughout plant growth is still unclear. It has been reported that Pro is synthesized from Glu catalyzed by a key enzyme, Δ1-pyrroline-5-carboxylate synthetase (P5CS), in plants. To elucidate essential roles of Pro, we generated antisense transgenic Arabidopsis plants with a P5CS cDNA. Several transgenics accumulated Pro at a significantly lower level than wild-type plants, providing direct evidence for a key role of P5CS in Pro production in Arabidopsis. These antisense transgenics showed morphological alterations in leaves and a defect in elongation of inflorescences. Furthermore, transgenic leaves were hypersensitive to osmotic stress. Microscopic analysis of transgenic leaves, in which the mutated phenotype clearly occurred, showed morphological abnormalities of epidermal and parenchymatous cells and retardation of differentiation of vascular systems. These phenotypes were suppressed by exogenous L-Pro but not by D-Pro or other Pro analogues. In addition, Pro deficiency did not broadly affect all proteins but specifically affected structural proteins of cell walls in the antisense transgenic plants. These results indicate that Pro is not just an osmoregulator in stressed plants but has a unique function involved in osmotolerance as well as in morphogenesis as a major constituent of cell wall structural proteins in plants.
The Plant Journal 01/2002; 18(2):185 - 193. · 6.16 Impact Factor
