-
[show abstract]
[hide abstract]
ABSTRACT: Deficiency of the three essential macronutrients, nitrogen, phosphorus and potassium, leads to large reduction in crop growth and yield. To characterize the molecular genetic basis of adaptation to macronutrient deprivation, we performed microarray analysis of rice root at 6 and 24 h after nitrogen, phosphorus and potassium deficiency treatments. The transcriptome response to nitrogen depletion occurred more rapidly than corresponding responses to phosphorus and potassium deprivation. We identified several genes important for response and adaptation to each nutrient deficiency. Furthermore, we found that signaling via reactive oxygen species is a common feature in response to macronutrient deficiency and signaling via jasmonic acid is associated with potassium depletion response. These results will facilitate deeper understanding of nutrient utilization of plants.
Plant signaling & behavior 04/2013; 8(6).
-
[show abstract]
[hide abstract]
ABSTRACT: Determining the drivers of gene expression patterns is more straightforward in laboratory conditions than in the complex fluctuating environments where organisms typically live. We gathered transcriptome data from the leaves of rice plants in a paddy field along with the corresponding meteorological data and used them to develop statistical models for the endogenous and external influences on gene expression. Our results indicate that the transcriptome dynamics are predominantly governed by endogenous diurnal rhythms, ambient temperature, plant age, and solar radiation. The data revealed diurnal gates for environmental stimuli to influence transcription and pointed to relative influences exerted by circadian and environmental factors on different metabolic genes. The model also generated predictions for the influence of changing temperatures on transcriptome dynamics. We anticipate that our models will help translate the knowledge amassed in laboratories to problems in agriculture and that our approach to deciphering the transcriptome fluctuations in complex environments will be applicable to other organisms.
Cell 12/2012; 151(6):1358-69. · 32.40 Impact Factor
-
Yutaka Sato,
Nobukazu Namiki,
Hinako Takehisa,
Kaori Kamatsuki,
Hiroshi Minami,
Hiroshi Ikawa,
Hajime Ohyanagi,
Kazuhiko Sugimoto,
Jun-Ichi Itoh,
Baltazar A Antonio, Yoshiaki Nagamura
[show abstract]
[hide abstract]
ABSTRACT: Similarity of gene expression across a wide range of biological conditions can be efficiently used in characterization of gene function. We have constructed a rice gene coexpression database, RiceFREND (http://ricefrend.dna.affrc.go.jp/), to identify gene modules with similar expression profiles and provide a platform for more accurate prediction of gene functions. Coexpression analysis of 27 201 genes was performed against 815 microarray data derived from expression profiling of various organs and tissues at different developmental stages, mature organs throughout the growth from transplanting until harvesting in the field and plant hormone treatment conditions, using a single microarray platform. The database is provided with two search options, namely, 'single guide gene search' and 'multiple guide gene search' to efficiently retrieve information on coexpressed genes. A user-friendly web interface facilitates visualization and interpretation of gene coexpression networks in HyperTree, Cytoscape Web and Graphviz formats. In addition, analysis tools for identification of enriched Gene Ontology terms and cis-elements provide clue for better prediction of biological functions associated with the coexpressed genes. These features allow users to clarify gene functions and gene regulatory networks that could lead to a more thorough understanding of many complex agronomic traits.
Nucleic Acids Research 11/2012; · 8.03 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: A wide range of resources on gene expression profiling enhance various strategies in plant molecular biology particularly in characterization of gene function. We have updated our gene expression profile database, RiceXPro (http://ricexpro.dna.affrc.go.jp/), to provide more comprehensive information on the transcriptome of rice encompassing the entire growth cycle and various experimental conditions. The gene expression profiles are currently grouped into three categories, namely, 'field/development' with 572 data corresponding to 12 data sets, 'plant hormone' with 143 data corresponding to 13 data sets and 'cell- and tissue-type' comprising of 38 microarray data. In addition to the interface for retrieving expression information of a gene/genes in each data set, we have incorporated an interface for a global approach in searching an overall view of the gene expression profiles from multiple data sets within each category. Furthermore, we have also added a BLAST search function that enables users to explore expression profile of a gene/genes with similarity to a query sequence. Therefore, the updated version of RiceXPro can be used more efficiently to survey the gene expression signature of rice in sufficient depth and may also provide clues on gene function of other cereal crops.
Nucleic Acids Research 11/2012; · 8.03 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Magnesium (Mg)-mediated alleviation of aluminum (Al) toxicity has been observed in a number of plant species, but the mechanisms underlying the alleviation are still poorly understood. When a putative rice (Oryza sativa) Mg transporter gene, Oryza sativa MAGNESIUM TRANSPORTER1 (OsMGT1), was knocked out, the tolerance to Al, but not to cadmium and lanthanum, was decreased. However, this inhibition could be rescued by addition of 10 μm Mg, but not by the same concentration of barium or strontium. OsMGT1 was expressed in both the roots and shoots in the absence of Al, but the expression only in the roots was rapidly up-regulated by Al. Furthermore, the expression did not respond to low pH and other metals including cadmium and lanthanum, and was regulated by an Al-responsive transcription factor, AL RESISTANCE TRANSCRIPTION FACTOR1. An investigation of subcellular localization showed that OsMGT1 was localized to the plasma membrane. A short-term (30 min) uptake experiment with stable isotope (25)Mg showed that knockout of OsMGT1 resulted in decreased Mg uptake, but that the uptake in the wild type was enhanced by Al. Mg concentration in the cell sap of the root tips was also increased in the wild-type rice, but not in the knockout lines in the presence of Al. A microarray analysis showed that transcripts of genes related to stress were more up- and down-regulated in the knockout lines. Taken together, our results indicate that OsMGT1 is a transporter for Mg uptake in the roots and that up-regulation of this gene is required for conferring Al tolerance in rice by increasing Mg concentration in the cell.
Plant physiology 06/2012; 159(4):1624-33. · 6.53 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Rice (Oryza sativa) is the most aluminum (Al)-tolerant crop among small-grain cereals, but the mechanism underlying its high Al resistance is still not well understood. To understand the mechanisms underlying high Al-tolerance, we performed a comparative genome-wide transcriptional analysis by comparing expression profiling between the Al-tolerance cultivar (Koshihikari) and an Al-sensitive mutant star1 (SENSITIVE TO AL RHIZOTOXICITY 1) in both the root tips and the basal roots. Exposure to 20 µM AlCl(3) for 6 h resulted in up-regulation (higher than 3-fold) of 213 and 2015 genes including 185 common genes in the root tips of wild-type and the mutant, respectively. On the other hand, in the basal root, genes up-regulated by Al were 126 and 2419 including 76 common genes in the wild-type and the mutant, respectively. These results indicate that Al-response genes are not only restricted to the root tips, but also in the basal root region. Analysis with genes up- or down-regulated only in the wild-type reveals that there are other mechanisms for Al-tolerance except for a known transcription factor ART1-regulated one in rice. These mechanisms are related to nitrogen assimilation, secondary metabolite synthesis, cell-wall synthesis and ethylene synthesis. Although the exact roles of these putative tolerance genes remain to be examined, our data provide a platform for further work on Al-tolerance in rice.
PLoS ONE 01/2012; 7(10):e48197. · 4.09 Impact Factor
-
Hinako Takehisa,
Yutaka Sato,
Motoko Igarashi,
Tomomi Abiko,
Baltazar A Antonio,
Kaori Kamatsuki,
Hiroshi Minami,
Nobukazu Namiki,
Yoshiaki Inukai,
Mikio Nakazono, Yoshiaki Nagamura
[show abstract]
[hide abstract]
ABSTRACT: The root system is a crucial determinant of plant growth potential because of its important functions, e.g. uptake of water and nutrients, structural support and interaction with symbiotic organisms. Elucidating the molecular mechanism of root development and functions is therefore necessary for improving plant productivity, particularly for crop plants, including rice (Oryza sativa). As an initial step towards developing a comprehensive understanding of the root system, we performed a large-scale transcriptome analysis of the rice root via a combined laser microdissection and microarray approach. The crown root was divided into eight developmental stages along the longitudinal axis and three radial tissue types at two different developmental stages, namely: epidermis, exodermis and sclerenchyma; cortex; and endodermis, pericycle and stele. We analyzed a total of 38 microarray data and identified 22,297 genes corresponding to 17,010 loci that showed sufficient signal intensity as well as developmental- and tissue type-specific transcriptome signatures. Moreover, we clarified gene networks associated with root cap function and lateral root formation, and further revealed antagonistic and synergistic interactions of phytohormones such as auxin, cytokinin, brassinosteroids and ethylene, based on the expression pattern of genes related to phytohormone biosynthesis and signaling. Expression profiling of transporter genes defined not only major sites for uptake and transport of water and nutrients, but also distinct signatures of the radial transport system from the rhizosphere to the xylem vessel for each nutrient. All data can be accessed from our gene expression profile database, RiceXPro (http://ricexpro.dna.affrc.go.jp), thereby providing useful information for understanding the molecular mechanisms involved in root system development of crop plants.
The Plant Journal 09/2011; 69(1):126-40. · 6.16 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: When rice seeds germinate under complete submergence, only the coleoptile elongates efficiently. It has been reported previously that coleoptile elongation is reduced in the rice alcohol dehydrogenase 1 (ADH1)-deficient mutant, reduced adh activity (rad). The aim of this study was to elucidate how expressions of genes responsible for coleoptile elongation are affected by the ADH1 deficiency in the rad mutant under submergence.
To identify genes whose expressions are changed in the rad coleoptile at an early stage in germination (i.e. 1 d after imbibition), coleoptiles of the rad mutant and its wild type (WT) were isolated by laser microdissection, and their mRNA levels were examined with a microarray.
The microarray analysis identified 431 genes whose transcript levels were different between rad and WT. Interestingly, among the down-regulated genes in the rad coleoptile, 17·5 % were cell division-related genes and 5·1 % were cell elongation-related genes. It was found that cell division started at 1 d after imbibition and then gradually ceased, whereas in the WT coleoptile cell elongation started between 1 d and 2 d after imbibition and then continued. However, neither cell division nor cell elongation actively occurred in the rad coleoptile, in which the amounts of ATP were reduced.
These results indicate that cell division, as well as cell elongation, occur during coleoptile elongation in rice under complete submergence, and that the reduced ATP levels caused by the ADH1 deficiency repress both of them, thereby impairing coleoptile elongation in the rad mutant under submerged conditions.
Annals of Botany 08/2011; 108(2):253-61. · 4.03 Impact Factor
-
Takeshi Izawa,
Motohiro Mihara,
Yuji Suzuki,
Meenu Gupta,
Hironori Itoh,
Atsushi J Nagano,
Ritsuko Motoyama,
Yuji Sawada,
Masahiro Yano,
Masami Yokota Hirai,
Amane Makino, Yoshiaki Nagamura
[show abstract]
[hide abstract]
ABSTRACT: The circadian clock controls physiological traits such as flowering time, photosynthesis, and growth in plants under laboratory conditions. Under natural field conditions, however, little is known about the significance of the circadian clock in plants. By time-course transcriptome analyses of rice (Oryza sativa) leaves, using a newly isolated rice circadian clock-related mutant carrying a null mutation in Os-GIGANTEA (Os-GI), we show here that Os-GI controlled 75% (false discovery rate = 0.05) of genes among 27,201 genes tested and was required for strong amplitudes and fine-tuning of the diurnal rhythm phases of global gene expression in the field. However, transcripts involved in primary metabolism were not greatly affected by osgi. Time-course metabolome analyses of leaves revealed no trends of change in primary metabolites in osgi plants, and net photosynthetic rates and grain yields were not affected. By contrast, some transcripts and metabolites in the phenylpropanoid metabolite pathway were consistently affected. Thus, net primary assimilation of rice was still robust in the face of such osgi mutation-related circadian clock defects in the field, unlike the case with defects caused by Arabidopsis thaliana toc1 and ztl mutations in the laboratory.
The Plant Cell 05/2011; 23(5):1741-55. · 8.99 Impact Factor
-
Yoshiaki Nagamura,
Baltazar A Antonio,
Yutaka Sato,
Akio Miyao,
Nobukazu Namiki,
Jun-ichi Yonemaru,
Hiroshi Minami,
Kaori Kamatsuki,
Kan Shimura,
Yuji Shimizu,
Hirohiko Hirochika
[show abstract]
[hide abstract]
ABSTRACT: The Rice TOGO Browser is an online public resource designed to facilitate integration and visualization of mapping data of bacterial artificial chromosome (BAC)/P1-derived artificial chromosome (PAC) clones, genes, restriction fragment length polymorphism (RFLP)/simple sequence repeat (SSR) markers and phenotype data represented as quantitative trait loci (QTLs) onto the genome sequence, and to provide a platform for more efficient utilization of genome information from the point of view of applied genomics as well as functional genomics. Three search options, namely keyword search, region search and trait search, generate various types of data in a user-friendly interface with three distinct viewers, a chromosome viewer, an integrated map viewer and a sequence viewer, thereby providing the opportunity to view the position of genes and/or QTLs at the chromosomal level and to retrieve any sequence information in a user-defined genome region. Furthermore, the gene list, marker list and genome sequence in a specified region delineated by RFLP/SSR markers and any sequences designed as primers can be viewed and downloaded to support forward genetics approaches. An additional feature of this database is the graphical viewer for BLAST search to reveal information not only for regions with significant sequence similarity but also for regions adjacent to those with similarity but with no hits between sequences. An easy to use and intuitive user interface can help a wide range of users in retrieving integrated mapping information including agronomically important traits on the rice genome sequence. The database can be accessed at http://agri-trait.dna.affrc.go.jp/.
Plant and Cell Physiology 02/2011; 52(2):230-7. · 4.70 Impact Factor
-
Yutaka Sato,
Baltazar Antonio,
Nobukazu Namiki,
Ritsuko Motoyama,
Kazuhiko Sugimoto,
Hinako Takehisa,
Hiroshi Minami,
Kaori Kamatsuki,
Makoto Kusaba,
Hirohiko Hirochika, Yoshiaki Nagamura
[show abstract]
[hide abstract]
ABSTRACT: Plant growth depends on synergistic interactions between internal and external signals, and yield potential of crops is a manifestation of how these complex factors interact, particularly at critical stages of development. As an initial step towards developing a systems-level understanding of the biological processes underlying the expression of overall agronomic potential in cereal crops, a high-resolution transcriptome analysis of rice was conducted throughout life cycle of rice grown under natural field conditions.
A wide range of gene expression profiles based on 48 organs and tissues at various developmental stages identified 731 organ/tissue specific genes as well as 215 growth stage-specific expressed genes universally in leaf blade, leaf sheath, and root. Continuous transcriptome profiling of leaf from transplanting until harvesting further elucidated the growth-stage specificity of gene expression and uncovered two major drastic changes in the leaf transcriptional program. The first major change occurred before the panicle differentiation, accompanied by the expression of RFT1, a putative florigen gene in long day conditions, and the downregulation of the precursors of two microRNAs. This transcriptome change was also associated with physiological alterations including phosphate-homeostasis state as evident from the behavior of several key regulators such as miR399. The second major transcriptome change occurred just after flowering, and based on analysis of sterile mutant lines, we further revealed that the formation of strong sink, i.e., a developing grain, is not the major cause but is rather a promoter of this change.
Our study provides not only the genetic basis for functional genomics in rice but also new insight into understanding the critical physiological processes involved in flowering and seed development, that could lead to novel strategies for optimizing crop productivity.
BMC Plant Biology 01/2011; 11:10. · 3.45 Impact Factor
-
Koichiro Aya,
Go Suzuki,
Keita Suwabe,
Tokunori Hobo,
Hirokazu Takahashi,
Katsuhiro Shiono,
Kentaro Yano,
Nobuhiro Tsutsumi,
Mikio Nakazono, Yoshiaki Nagamura,
Makoto Matsuoka,
Masao Watanabe
[show abstract]
[hide abstract]
ABSTRACT: Co-expression networks systematically constructed from large-scale transcriptome data reflect the interactions and functions of genes with similar expression patterns and are a powerful tool for the comprehensive understanding of biological events and mining of novel genes. In Arabidopsis (a model dicot plant), high-resolution co-expression networks have been constructed from very large microarray datasets and these are publicly available as online information resources. However, the available transcriptome data of rice (a model monocot plant) have been limited so far, making it difficult for rice researchers to achieve reliable co-expression analysis. In this study, we performed co-expression network analysis by using combined 44 K agilent microarray datasets of rice, which consisted of 33 laser microdissection (LM)-microarray datasets of anthers, and 143 spatiotemporal transcriptome datasets deposited in RicexPro. The entire data of the rice co-expression network, which was generated from the 176 microarray datasets by the Pearson correlation coefficient (PCC) method with the mutual rank (MR)-based cut-off, contained 24,258 genes and 60,441 genes pairs. Using these datasets, we constructed high-resolution co-expression subnetworks of two specific biological events in the anther, "meiosis" and "pollen wall synthesis". The meiosis network contained many known or putative meiotic genes, including genes related to meiosis initiation and recombination. In the pollen wall synthesis network, several candidate genes involved in the sporopollenin biosynthesis pathway were efficiently identified. Hence, these two subnetworks are important demonstrations of the efficiency of co-expression network analysis in rice. Our co-expression analysis included the separated transcriptomes of pollen and tapetum cells in the anther, which are able to provide precise information on transcriptional regulation during male gametophyte development in rice. The co-expression network data presented here is a useful resource for rice researchers to elucidate important and complex biological events.
PLoS ONE 01/2011; 6(10):e26162. · 4.09 Impact Factor
-
Nucleic Acids Research. 01/2011; 39:1141-1148.
-
[show abstract]
[hide abstract]
ABSTRACT: Elucidating the function of all predicted genes in rice remains as the ultimate goal in cereal genomics in order to ensure the development of improved varieties that will sustain an expanding world population. We constructed a gene expression database (RiceXPro, URL: http://ricexpro.dna.affrc.go.jp/) to provide an overview of the transcriptional changes throughout the growth of the rice plant in the field. RiceXPro contains two data sets corresponding to spatiotemporal gene expression profiles of various organs and tissues, and continuous gene expression profiles of leaf from transplanting to harvesting. A user-friendly web interface enables the extraction of specific gene expression profiles by keyword and chromosome search, and basic data analysis, thereby providing useful information as to the organ/tissue and developmental stage specificity of expression of a particular gene. Analysis tools such as t-test, calculation of fold change and degree of correlation facilitate the comparison of expression profiles between two random samples and the prediction of function of uncharacterized genes. As a repository of expression data encompassing growth in the field, this database can provide baseline information of genes that underlie various agronomically important traits in rice.
Nucleic Acids Research 11/2010; 39(Database issue):D1141-8. · 8.03 Impact Factor
-
Imene Rajhi,
Takaki Yamauchi,
Hirokazu Takahashi,
Shunsaku Nishiuchi,
Katsuhiro Shiono,
Ryosuke Watanabe,
Ahmed Mliki, Yoshiaki Nagamura,
Nobuhiro Tsutsumi,
Naoko K Nishizawa,
Mikio Nakazono
[show abstract]
[hide abstract]
ABSTRACT: • To adapt to waterlogging in soil, some gramineous plants, such as maize (Zea mays), form lysigenous aerenchyma in the root cortex. Ethylene, which is accumulated during waterlogging, promotes aerenchyma formation. However, the molecular mechanism of aerenchyma formation is not understood. • The aim of this study was to identify aerenchyma formation-associated genes expressed in maize roots as a basis for understanding the molecular mechanism of aerenchyma formation. Maize plants were grown under waterlogged conditions, with or without pretreatment with an ethylene perception inhibitor 1-methylcyclopropene (1-MCP), or under aerobic conditions. Cortical cells were isolated by laser microdissection and their mRNA levels were examined with a microarray. • The microarray analysis revealed 575 genes in the cortical cells, whose expression was either up-regulated or down-regulated under waterlogged conditions and whose induction or repression was suppressed by pretreatment with 1-MCP. • The differentially expressed genes included genes related to the generation or scavenging of reactive oxygen species, Ca(2+) signaling, and cell wall loosening and degradation. The results of this study should lead to a better understanding of the mechanism of root lysigenous aerenchyma formation.
New Phytologist 11/2010; 190(2):351-68. · 6.64 Impact Factor
-
Susumu Oda,
Fumi Kaneko,
Kentaro Yano,
Tomoaki Fujioka,
Hiromi Masuko,
Jong-In Park,
Shunsuke Kikuchi,
Kazuki Hamada,
Makoto Endo,
Kuniaki Nagano, Yoshiaki Nagamura,
Makiko Kawagishi-Kobayashi,
Keita Suwabe,
Go Suzuki,
Masao Watanabe
[show abstract]
[hide abstract]
ABSTRACT: Cool temperature conditions are known to lead to pollen sterility in rice. Pollen sterility is an agriculturally important phenomenon because it imparts a large influence directly on rice yield. However, cool temperature stress tolerance varies among rice cultivars and avoidance of cool temperature stress is difficult by practical method of agriculture. In this study using two rice cultivars, Hitomebore (high tolerance) and Sasanishiki (low tolerance), we analyzed morphological features and gene expression profiles, under cool temperature stress, in anther development of rice. Hitomebore was given cool temperature stress (19 degrees C) at flowering stage, and showed 87.3% seed fertility. Meanwhile, the seed fertility decreased to 41.7% in the case of Sasanishiki. A transverse section of Hitomebore anther revealed that the degradation of the tapetum started at the uninucleate microspore stage, and the tapetum had completely vanished at mature stage. The tapetum provides nutrients for pollen development, and its degradation occurs at a late stage in pollen development. In contrast, degradation of the tapetum did not occur at the uninucleate microspore stage in Sasanishiki, and the tapetum was clearly intact at mature stage, suggesting that tapetum degradation is critical for accurate pollen development and cool temperature tolerance correlated with the degree of tapetum degeneration. In gene expression analysis of anther, 356 genes that showed different expression levels between two cultivars at cool temperatures were found. These genes will lead to understanding the mechanism of cool temperature stress response in rice pollen development and the identification of genes involved in accurate tapetum degradation.
Genes & Genetic Systems 04/2010; 85(2):107-20. · 0.95 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Laser microdissection (LM) combined with microarray analysis or next-generation sequencing of cDNA is a powerful tool for understanding molecular events in individual cell types of plants as well as animals. Obtaining high quality RNA is essential for this approach. For plant tissues, paraffin-embedded sections better preserve cell structure than do frozen sections. However, the conventional method for preparing paraffin sections is a lengthy process involving embedding the tissue and floating and drying the sections, during which time RNA degradation occurs. Here, we describe a method for preparing serial sections that greatly reduces RNA degradation: we reduced (1) the embedding time from 4-6 days to about 5 h by using a recently developed microwave method; (2) the time of floating sections from ~10 min to less than 5 min, (3) the drying time from ~12 to 1 h; and (4) the drying temperature from 42 to 4°C. With this method, we were able to isolate higher integrity RNA from many kinds of plant tissues than is typically obtained by the conventional paraffin preparation method. The improvement in RNA quality and yield removes a major obstacle to the widespread use of LM with high-throughput technologies for plants.
Journal of Plant Research 03/2010; 123(6):807-13. · 1.75 Impact Factor
-
Sudha K Nair,
Ning Wang,
Yerlan Turuspekov,
Mohammad Pourkheirandish,
Suphawat Sinsuwongwat,
Guoxiong Chen,
Mohammad Sameri,
Akemi Tagiri,
Ichiro Honda,
Yoshiaki Watanabe,
Hiroyuki Kanamori,
Thomas Wicker,
Nils Stein, Yoshiaki Nagamura,
Takashi Matsumoto,
Takao Komatsuda
[show abstract]
[hide abstract]
ABSTRACT: The cleistogamous flower sheds its pollen before opening, forcing plants with this habit to be almost entirely autogamous. Cleistogamy also provides a means of escape from cereal head blight infection and minimizes pollen-mediated gene flow. The lodicule in cleistogamous barley is atrophied. We have isolated cleistogamy 1 (Cly1) by positional cloning and show that it encodes a transcription factor containing two AP2 domains and a putative microRNA miR172 targeting site, which is an ortholog of Arabidopsis thaliana AP2. The expression of Cly1 was concentrated within the lodicule primordia. We established a perfect association between a synonymous nucleotide substitution at the miR172 targeting site and cleistogamy. Cleavage of mRNA directed by miR172 was detectable only in a noncleistogamous background. We conclude that the miR172-derived down-regulation of Cly1 promotes the development of the lodicules, thereby ensuring noncleistogamy, although the single nucleotide change at the miR172 targeting site results in the failure of the lodicules to develop properly, producing the cleistogamous phenotype.
Proceedings of the National Academy of Sciences 12/2009; 107(1):490-5. · 9.68 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: For systematic and genome-wide analyses of rice gene functions, we took advantage of the full-length cDNA overexpresser (FOX) gene-hunting system and generated >12 000 independent FOX-rice lines from >25 000 rice calli treated with the rice-FOX Agrobacterium library. We found two FOX-rice lines generating green calli on a callus-inducing medium containing 2,4-D, on which wild-type rice calli became ivory yellow. In both lines, OsGLK1 cDNA encoding a GARP transcription factor was ectopically overexpressed. Using rice expression-microarray and northern blot analyses, we found that a large number of nucleus-encoded genes involved in chloroplast functions were highly expressed and transcripts of plastid-encoded genes, psaA, psbA and rbcL, increased in the OsGLK1-FOX calli. Transmission electron microscopy showed the existence of differentiated chloroplasts with grana stacks in OsGLK1-FOX calli cells. However, in darkness, OsGLK1-FOX calli did not show a green color or develop grana stacks. Furthermore, we found developed chloroplasts in vascular bundle and bundle sheath cells of coleoptiles and leaves from OsGLK1-FOX seedlings. The OsGLK1-FOX calli exhibited high photosynthetic activity and were able to grow on sucrose-depleted media, indicating that developed chloroplasts in OsGLK1-FOX rice calli are functional and active. We also observed that the endogenous OsGLK1 mRNA level increased synchronously with the greening of wild-type calli after transfer to plantlet regeneration medium. These results strongly suggest that OsGLK1 regulates chloroplast development under the control of light and phytohormones, and that it is a key regulator of chloroplast development.
Plant and Cell Physiology 10/2009; 50(11):1933-49. · 4.70 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Aluminum (Al) toxicity is the major limiting factor of crop production on acid soils, but some plant species have evolved ways of detoxifying Al. Here, we report a C2H2-type zinc finger transcription factor ART1 (for Al resistance transcription factor 1), which specifically regulates the expression of genes related to Al tolerance in rice (Oryza sativa). ART1 is constitutively expressed in the root, and the expression level is not affected by Al treatment. ART1 is localized in the nucleus of all root cells. A yeast one-hybrid assay showed that ART1 has a transcriptional activation potential and interacts with the promoter region of STAR1, an important factor in rice Al tolerance. Microarray analysis revealed 31 downstream transcripts regulated by ART1, including STAR1 and 2 and a couple of homologs of Al tolerance genes in other plants. Some of these genes were implicated in both internal and external detoxification of Al at different cellular levels. Our findings shed light on comprehensively understanding how plants detoxify aluminum to survive in an acidic environment.
The Plant Cell 10/2009; 21(10):3339-49. · 8.99 Impact Factor
