[Show abstract][Hide abstract] ABSTRACT: Macronutrients are pivotal elements for proper plant growth and development. Although extensive gene expression profiling revealed a large number of genes differentially expressed under various nutrient deprivation, characterization of these genes has never been fully explored especially in rice. Coexpression network analysis is a useful tool to elucidate the functional relationships of genes based on common expression. Therefore, we performed microarray analysis of rice shoot under nitrogen (N), phosphorus (P), and potassium (K) deficiency conditions. Moreover, we conducted a large scale coexpression analysis by integrating the data with previously generated gene expression profiles of organs and tissues at different developmental stages to obtain a global view of gene networks associated with plant response to nutrient deficiency.
We statistically identified 5400 differentially expressed genes under the nutrient deficiency treatments. Subsequent coexpression analysis resulted in the extraction of 6 modules (groups of highly interconnected genes) with distinct gene expression signatures. Three of these modules comprise mostly of downregulated genes under N deficiency associated with distinct functions such as development of immature organs, protein biosynthesis and photosynthesis in chloroplast of green tissues, and fundamental cellular processes in all organs and tissues. Furthermore, we identified one module containing upregulated genes under N and K deficiency conditions, and a number of genes encoding protein kinase, kinase-like domain containing protein and nutrient transporters. This module might be particularly involved in adaptation to nutrient deficiency via phosphorylation-mediated signal transduction and/or post-transcriptional regulation.
Our study demonstrated that large scale coexpression analysis is an efficient approach in characterizing the nutrient response genes based on biological functions and could provide new insights in understanding plant response to nutrient deficiency.
[Show abstract][Hide abstract] ABSTRACT: Post-transcriptional gene regulation by RNA recognition motif (RRM) proteins through binding to cis-elements in the 3′-untranslated region (3′-UTR) is widely used in eukaryotes to complete various biological processes. Rice MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2) is the RRM protein that functions in the transition to meiosis in proper timing. The MEL2 RRM preferentially associated with the U-rich RNA consensus, UUAGUU[U/A][U/G][A/U/G]U, dependently on sequences and proportionally to MEL2 protein amounts in vitro. The consensus sequences were located in the putative looped structures of the RNA ligand. A genome-wide survey revealed a tendency of MEL2-binding consensus appearing in 3′-UTR of rice genes. Of 249 genes that conserved the consensus in their 3′-UTR, 13 genes spatiotemporally co-expressed with MEL2 in meiotic flowers, and included several genes whose function was supposed in meiosis; such as Replication
A and OsMADS3. The proteome analysis revealed that the amounts of small ubiquitin-related modifier-like protein and eukaryotic translation initiation factor3-like protein were dramatically altered in mel2 mutant anthers. Taken together with transcriptome and gene ontology results, we propose that the rice MEL2 is involved in the translational regulation of key meiotic genes on 3′-UTRs to achieve the faithful transition of germ cells to meiosis.
No preview · Article · Aug 2015 · Plant Molecular Biology
[Show abstract][Hide abstract] ABSTRACT: The endosperm of cereal grains represents the most important source of human nutrition. In addition, the endosperm provides many investigatory opportunities for biologists because of the unique processes that occur during its ontogeny, including syncytial development at early stages. Rice endospermless 1 (enl1) develops seeds lacking an endosperm but carrying a functional embryo. The enl1 endosperm produces strikingly enlarged amoeboid nuclei. These abnormal nuclei result from a malfunction in mitotic chromosomal segregation during syncytial endosperm development. The molecular identification of the causal gene revealed that ENL1 encodes an SNF2 helicase family protein that is orthologous to human PICH, which has been implicated in the resolution of persistent DNA catenation during anaphase. ENL1-Venus (enhanced YFP) localizes to the cytoplasm during interphase but moves to the chromosome arms during mitosis. ENL1-Venus is also detected on a thread-like structure that connects separating sister chromosomes. These observations indicate the functional conservation between PICH and ENL1 and confirm the proposed role of PICH. Although ENL1 dysfunction also affects karyokinesis in the root meristem, enl1 plants can grow in a field and set seeds, indicating that its indispensability is tissue-dependent. Notably, despite the wide conservation of ENL1/PICH among eukaryotes, the loss of function of the ENL1 ortholog in Arabidopsis (CHR24) has only marginal effects on endosperm nuclei and results in normal plant development. Our results suggest that ENL1 is endowed with an indispensable role to secure the extremely rapid nuclear cycle during syncytial endosperm development in rice.This article is protected by copyright. All rights reserved.
Full-text · Article · Oct 2014 · The Plant Journal
[Show abstract][Hide abstract] ABSTRACT: The recent whole-genome sequencing of soybean (Glycine max) revealed that soybean experienced whole-genome duplications 59 million and 13 million years ago, and it has an octoploid-like
genome in spite of its diploid nature. We analyzed a natural green-cotyledon mutant line, Tenshin-daiseitou. The physiological
analysis revealed that Tenshin-daiseitou shows a non-functional stay-green phenotype in senescent leaves, which is similar
to that of the mutant of Mendel’s green-cotyledon gene I, the ortholog of SGR in pea. The identification of gene mutations and genetic segregation analysis suggested that defects in GmSGR1 and GmSGR2 were responsible for the green-cotyledon/stay-green phenotype of Tenshin-daiseitou, which was confirmed by RNA interference
(RNAi) transgenic soybean experiments using GmSGR genes. The characterized green-cotyledon double mutant d1d2 was found to have the same mutations, suggesting that GmSGR1 and GmSGR2 are D1 and D2. Among the examined d1d2 strains, the d1d2 strain K144a showed a lower Chl a/b ratio in mature seeds than other strains but not in senescent leaves, suggesting a seed-specific genetic factor of the Chl
composition in K144a. Analysis of the soybean genome sequence revealed four genomic regions with microsynteny to the Arabidopsis
SGR1 region, which included the GmSGR1 and GmSGR2 regions. The other two regions contained GmSGR3a/GmSGR3b and GmSGR4, respectively, which might be pseudogenes or genes with a function that is unrelated to Chl degradation during seed maturation
and leaf senescence. These GmSGR genes were thought to be produced by the two whole-genome duplications, and they provide a good example of such whole-genome
duplication events in the evolution of the soybean genome.
No preview · Article · Aug 2014 · Plant and Cell Physiology
[Show abstract][Hide abstract] ABSTRACT: The plant secondary cell wall is the major source of lignocellulosic biomass, a renewable energy resource which can be used for bioethanol production. To comprehensively identify transcription factors (TFs), glycosyltransferase (GT), and glycosyl hydrolase (GH) involved in secondary cell wall formation in rice (Oryza sativa), co-expression network analysis was performed using 68 microarray data points for different rice tissues and stages. In addition to rice genes encoding orthologs of Arabidopsis thaliana TFs known to regulate secondary cell wall formation, the network analysis suggested many novel TF genes likely to be involved in cell wall formation. In the accompanying paper (Hirano et al.), several of these TFs are shown to be involved in rice secondary cell wall formation.Based on a comparison of the rice and Arabidopsis networks, TFs were classified as common to both species or specific to each plant species, suggesting that in addition to a common transcriptional regulatory mechanism of cell wall formation, the two plants may also use species-specific groups of TFs during secondary wall formation. Similarly, genes encoding GT and GH were also classified as genes showing species-common or species-specific expression patterns. In addition, genes for primary or secondary cell wall formation were also suggested.The list of rice TF, GT, and GH genes provides an opportunity to unveil the regulation of secondary cell wall formation in grasses, leading to optimization of the cell wall for biofuel production.
No preview · Article · Oct 2013 · Plant and Cell Physiology
[Show abstract][Hide abstract] ABSTRACT: Through co-expression network analysis, we identified 123 rice transcription factors (TFs) as candidate rice secondary cell wall regulators (Hirano et al., the accompanying paper). To validate whether these TFs are associated with secondary cell wall formation, six TF genes belonging to either the MYB, NAC or homeodomain containing TF families were over-expressed or down-regulated in rice. With the exception of OsMYB58/63-RNAi plants, all transgenic plants showed phenotypes possibly related to secondary cell wall alteration, such as dwarfism, narrow and dark green leaves, and also altered rice cinnamyl alcohol dehydrogenase 2 (OsCAD2) gene expression and lignin content. These results suggest that many of the 123 candidate secondary cell wall regulating TFs are likely to function in rice secondary cell wall formation.Further analyses were performed for the OsMYB55/61 and OsBLH6 TFs, one representing TF in which the Arabidopsis ortholog is known to participate in lignin biosynthesis (AtMYB61) and one for which no previous involvement in cell wall formation has been reported even in Arabidopsis (BLH6). OsMYB55/61 and OsBLH6-GFP fusion proteins localized to the nucleus of onion epidermal cells. Moreover, expression of a reporter gene driven by the OsCAD2 promoter was enhanced in rice calli when OsMYB55/61 or OsBLH6 were transiently expressed, demonstrating that they function in secondary cell wall formation. These results show the validity of identifying potential rice secondary cell wall TFs through the rice co-expression network analysis.
No preview · Article · Oct 2013 · Plant and Cell Physiology
[Show abstract][Hide abstract] ABSTRACT: Small RNAs, such as small interfering RNAs (siRNAs) or microRNAs (miRNAs), regulate gene expression at transcriptional and posttranscriptional levels in eukaryotes. miRNAs are processed from duplexes formed on single-stranded RNA. They regulate expression of their target gene either by cleaving mRNA or supressing translation. In general, the primary miRNA transcripts are synthesized by RNA polymerase II and processed similarly to mRNAs. MIRNA genes are usually located in transcriptionally active euchromatic regions. In contrast, siRNAs are processed from duplexes made of two RNA molecules. One of them is often derived from a transposable element (TE) or from repetitive sequences that reside in heterochromatic regions. The other strand is synthesized by the RNA-dependent RNA polymerase on the first strand as a template. siRNAs establish epigenetic marks in parasitic DNA such as TEs, thus they usually act in cis. The rice miRNA miR820, encoded by CACTA TEs (five copies, located on different chromosomes), reduces the expression of the de novo DNA methyltransferase gene OsDRM2. Because miR820 is derived from silent TEs, in which the heterochromatic histone modifications are enriched, the mechanism of MIR820 transcription could be expected to differ from typical miRNAs. Here we show that the primary transcript of MIR820 is mainly derived from the CACTA TE copy on chromosome 7 (MIR820b). Histone modification and DNA methylation status around MIR820b differed from that of the other four loci. These unique epigenetic modifications in MIR820b were only found around the miR820 coding region. We conclude that MIR820b transcription may depend on the unique epigenetic modifications, which in turn may be established by the action of miR820 in cis. This suggests a dual function of miR820 in cis and in trans.
[Show abstract][Hide abstract] ABSTRACT: miR820 is a small RNA species (22 and 24 nucleotides), produced from transcripts originated from a region inside CACTA DNA transposons in rice. Because MIR820 is a transposon gene, its expression may depend on the transposon copy number. Here, we investigated the copy number of MIR820 and its expression levels in various cultivars and wild species of rice. We found no correlation between copy number and expression level, suggesting that MIR820 transcription is regulated not by the copy dosage but by the epigenetic state of each copy.
[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.
[Show abstract][Hide abstract] ABSTRACT: The shoot epidermis of land plants serves as a crucial interface between plants and the atmosphere: pavement cells protect plants from desiccation and other environmental stresses, while stomata facilitate gas exchange and transpiration. Advances have been made in our understanding of stomatal patterning and differentiation, and a set of Ômaster regulatoryÕ transcription factors of stomatal development have been identified. However, they are limited to specifying stomatal differentiation within the epidermis. Here, we report the identification of an Arabidopsis homeodomain-leucine zipper IV (HD-ZIP IV) protein, HOMEODOMAIN GLABROUS2 (HDG2), as a key epidermal component promoting stomatal differentiation. HDG2 is highly enriched in meristemoids, which are transient-amplifying populations of stomatal-cell lineages. Ectopic expression of HDG2 confers differentiation of stomata in internal mesophyll tissues and occasional multiple epidermal layers. Conversely, a loss-of-function hdg2 mutation delays stomatal differentiation and, rarely but consistently, results in aberrant stomata. A closely related HD-ZIP IV gene, Arabidopsis thaliana MERISTEM LAYER1 (AtML1), shares overlapping function with HDG2: AtML1 overexpression also triggers ectopic stomatal differentiation in the mesophyll layer and atml1 mutation enhances the stomatal differentiation defects of hdg2. Consistently, HDG2 and AtML1 bind the same DNA elements, and activate transcription in yeast. Furthermore, HDG2 transactivates expression of genes that regulate stomatal development in planta. Our study highlights the similarities and uniqueness of these two HD-ZIP IV genes in the specification of protodermal identity and stomatal differentiation beyond predetermined tissue layers.
[Show abstract][Hide abstract] ABSTRACT: Leaf shape is one of the key determinants of plant architecture. Leaf shape also affects the amount of sunlight captured and influences photosynthetic efficiency; thus, it is an important agronomic trait in crop plants. Understanding the molecular mechanisms governing leaf shape is a central issue of plant developmental biology and agrobiotechnology. In this paper, we characterized the narrow-leaf phenotype of FL90, a linkage tester line of rice (Oryza sativa). Microscopic and scanning electron micrograph analyses of FL90 leaves revealed defects in the development of marginal regions and a reduction in the number of longitudinal veins. The narrow-leaf phenotype of FL90 shows a two-factor recessive inheritance and is caused by the loss of function of two WUSCHEL-related homeobox genes, NAL2 and NAL3 (NAL2/3), which are duplicate genes orthologous to maize NS1 and NS2 and to Arabidopsis PRS. The overexpression of NAL2/3 in transgenic rice plants results in wider leaves containing increased numbers of veins, suggesting that NAL2/3 expression regulates leaf width. Thus, NAL2/3 can be used to modulate leaf shape and improve agronomic yield in crop plants.
No preview · Article · Feb 2013 · Plant and Cell Physiology
[Show abstract][Hide abstract] ABSTRACT: Inflorescence structures result from the activities of meristems, which coordinate both the renewal of stem cells in the center and organ formation at the periphery. The fate of a meristem is specified at its initiation and changes as the plant develops. During rice inflorescence development, newly formed meristems acquire a branch meristem (BM) identity, and can generate further meristems or terminate as spikelets. Thus, the form of rice inflorescence is determined by a reiterative pattern of decisions made at the meristems. In the dominant gain-of-function mutant tawawa1-D, the activity of the inflorescence meristem (IM) is extended and spikelet specification is delayed, resulting in prolonged branch formation and increased numbers of spikelets. In contrast, reductions in TAWAWA1 (TAW1) activity cause precocious IM abortion and spikelet formation, resulting in the generation of small inflorescences. TAW1 encodes a nuclear protein of unknown function and shows high levels of expression in the shoot apical meristem, the IM, and the BMs. TAW1 expression disappears from incipient spikelet meristems (SMs). We also demonstrate that members of the SHORT VEGETATIVE PHASE subfamily of MADS-box genes function downstream of TAW1. We thus propose that TAW1 is a unique regulator of meristem activity in rice and regulates inflorescence development through the promotion of IM activity and suppression of the phase change to SM identity.
Preview · Article · Dec 2012 · Proceedings of the National Academy of Sciences
[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.
[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.
Preview · Article · Nov 2012 · Nucleic Acids Research
[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.
Preview · Article · Nov 2012 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: Structures and sequences of the five copies of miR820 in Nipponbare rice. (A) Schematic representations of the structures of the five copies of CACTA transposons carrying miR820. (B) Stem-loop structures of the five copies of pre-miR820 in Nipponbare, predicted by the mfold program. The miR820 sequences are designated by red rectangles. (C) Sequence alignment of members of the miR820 family, miR820a–e, in Nipponbare rice. Dots indicate identical nucleotides.
[Show abstract][Hide abstract] ABSTRACT: Multiple sequence alignment of the five copies of pre-miR820 in the Nipponbare genome. Sequence alignment was made using ClustalX at default settings. The blue lines, red box, and black box indicate the regions corresponding to the stem-loop structure, miR820, and miR820*, respectively.