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Oryza Sativa (oryza + sativa)
Terms modified by Oryza Sativa Selected AbstractsRemoval of high-abundance proteins for nuclear subproteome studies in rice (Oryza sativa) endospermELECTROPHORESIS, Issue 3 2008Guosheng Li Abstract Endosperm is a highly specialized storage organ with three sets of genomes. It is one of the most economically important organs in plants. Endosperm development involves parental imprinting and endoreduplication. A thorough study of the endosperm proteome, particularly the nuclear proteome, may provide critical insight into the regulation of seed development. Unfortunately, endosperm is extremely rich in starch grains and protein bodies of different sizes, making proteome studies on nonstorage proteins, particularly the low-abundance proteins, very challenging. Here we have developed a chromatographic method to remove large starch grains and an electrophoresis method to recover low-abundance proteins, respectively. Using these methods, we have identified 468 proteins from the nuclear enriched fraction of rice endosperm, including transcription factors, histone modification proteins, kinetochore proteins, centromere/microtubule binding proteins, and transposon proteins. Among the 468 proteins, 208 (44%) are hypothetical proteins, indicating that the endosperm proteome is poorly explored. In addition, analyses of the MS/MS data using BioWorks 3.1 have identified 59 putative acetylated proteins and 40 putative methylated proteins. Our studies have developed a method to remove starch grains and recover low-abundance proteins, respectively. The methods should be applicable to other organisms. [source] High-throughput multiplex microsatellite marker assay for detection and quantification of adulteration in Basmati rice (Oryza sativa)ELECTROPHORESIS, Issue 14 2007Sunil Archak Abstract Basmati rice is a very special type of aromatic rice known world-wide for its extra long grains and pleasant and distinct aroma. Traditional Basmati rice cultivars, confined to Indo-Gangetic regions of the Indian subcontinent, are often reported to be adulterated with crossbred Basmati varieties and long-grain non-Basmati varieties in the export market. At present, there is no commercial scale technology to reliably detect adulteration. We report here a CE-based multiplex microsatellite marker assay for detection as well as quantification of adulteration in Basmati rice samples. The single-tube assay multiplexes eight microsatellite loci to generate variety-specific allele profiles that can detect adulteration from 1% upwards. The protocol also incorporates a quantitative-competitive PCR-based analysis for quantification of adulteration. Accuracy of quantification has been shown to be ±1.5%. The experiments used to develop and validate the methodology are described. [source] Preferential occurrence of diazotrophic endophytes, Azoarcus spp., in wild rice species and land races of Oryza sativa in comparison with modern racesENVIRONMENTAL MICROBIOLOGY, Issue 2 2000Margret Engelhard Several diazotrophic species of Azoarcus spp. occur as endophytes in the pioneer plant Kallar grass. The purpose of this study was to screen Asian wild rice and cultivated Oryza sativa varieties for natural association with these endophytes. Populations of culturable diazotrophs in surface-sterilized roots were characterized by 16S rDNA sequence analysis, and Azoarcus species were identified by genomic fingerprints. A. indigens and Azoarcus sp. group C were detected only rarely, whereas Azoarcus sp. group D occurred frequently in samples of flooded plants: in 75% of wild rice, 80% of land races of O. sativa from Nepal and 33% of modern cultivars from Nepal and Italy. The putatively endophytic populations of diazotrophs differed with the rice genotype. The diversity of cultured diazotrophs was significantly lower in wild rice species than in modern cultivars. In Oryza officinalis (from Nepal) and O. minuta (from the Philippines), Azoarcus sp. group D were the predominant diazotrophic putative endophytes in roots. In contrast, their number was significantly lower in modern cultivars of O. sativa, whereas numbers and diversity of other diazotrophs, such as Azospirillum spp., Klebsiella sp., Sphingomonas paucimobilis, Burkholderia sp. and Azorhizobium caulinodans, were increased. In land races of O. sativa, the diazotrophic diversity was equally high; however, Azoarcus sp. was found in high apparent numbers. Similar differences in populations were also observed in a culture-independent approach comparing a wild rice (O. officinalis) and a modern-type O. sativa plant: in clone libraries of root-associated nitrogenase (nifH,) gene fragments, the diazotrophic diversity was lower in the wild rice species. New lineages of nifH genes were detected, e.g. one deeply branching cluster within the anf (iron) nitrogenases. Our studies demonstrate that the natural host range of Azoarcus spp. extends to rice, wild rice species and old varieties being preferred over modern cultivars. [source] Nanogold-Loaded Sharp-Edged Carbon Bullets as Plant-Gene CarriersADVANCED FUNCTIONAL MATERIALS, Issue 15 2010Periyasamy S. Vijayakumar Abstract The higher DNA delivery efficiency into plants by gold nanoparticles embedded in sharp carbonaceous carriers is demonstrated. These nanogold-embedded carbon matrices are prepared by heat treatment of biogenic intracellular gold nanoparticles. The DNA-delivery efficiency is tested on a model plant, Nicotiana tabacum, and is further extended to the monocot, Oryza sativa, and a hard dicot tree species, Leucaena leucocephala. These materials reveal good dispersion of the transport material, producing a greater number of GUS foci per unit area. The added advantages of the composite carrier are the lower plasmid and gold requirements. Plant-cell damage with the carbon-supported particles is very minimal and can be gauged from the increased plant regeneration and transformation efficiency compared with that of the commercial micrometer-sized gold particles. This is ascribed to the sharp edges that the carbon supports possess, which lead to better piercing capabilities with minimum damage. [source] Crayfish effects on seeds and seedlings: identification and quantification of damageFRESHWATER BIOLOGY, Issue 4 2005PEDRO M. ANASTÁCIO Summary 1. The red-swamp crayfish (Procambarus clarkii) is an invasive species and an important pest of wet-seeded rice fields (Oryza sativa) in California (U.S.A.) and in Portugal. Our work quantifies rice consumption and non-consumptive destruction and identifies the types of direct damage inflicted by crayfish. 2. The following fractions were quantified in the presence and absence of crayfish and at 3 and 6 days of rice development: (1) non-germinated seeds, (2) damaged seeds, (3) seeds not recovered, (4) intact rooted seedlings, (5) rooted damaged seedlings, (6) uprooted intact seedlings, (7) uprooted damaged seedlings. 3. Coarse particulate organic matter (CPOM) fragments produced during the feeding process were <2% of the material removed by crayfish. 4. Damage occurred with or without uprooting of the plants, but the incidence of uprooting without consumption was low (1.4%). 5. Consumption of recently developed parts of the rice plant was the main cause of damage and the observed effect was stronger on 6-day-old than on 3-day-old seedlings. Seedlings were more affected by crayfish than were seeds. 6. Crayfish affected the majority of seeds and seedlings available although consumption was low: 0.015 g dry weight (DW) rice g,1 wet weight (WW) crayfish per 12 h at 3 days and 0.063 g DW rice g,1 WW crayfish per 12 h at 6 days. 7. Our results are important for the mitigation of crayfish related problems in rice fields and for understanding the mechanisms of crayfish-macrophyte interactions. [source] Response of Photosynthesis and Water Relations of Rice (Oryza sativa) to Elevated Atmospheric Carbon Dioxide in the Subhumid Zone of Sri LankaJOURNAL OF AGRONOMY AND CROP SCIENCE, Issue 2 2003W. A. J. M. De Costa Abstract The objective of the present paper is to determine the response of the physiological parameters related to biomass production and plant water relations in a standard Sri Lankan rice (Oryza sativa) variety (BG-300) to elevated CO2 (i.e. 570 µmol/mol). During two seasons, rice crops were grown under three different experimental treatments; namely, at 570 µmol/mol (i.e. ,elevated') and 370 µmol/mol (,ambient') CO2 within open top chambers, and at ambient CO2 under open field conditions. Leaf net photosynthetic rate in the elevated treatment increased by 22,75 % in comparison to the ambient. However, the ratio between intercellular and ambient CO2 concentrations remained constant across different CO2 treatments and seasons. CO2 enrichment decreased individual leaf stomatal conductance and transpiration rate per unit leaf area, and increased both leaf and canopy temperatures. However, the overall canopy stomatal conductance and daily total canopy transpiration rate of the elevated treatment were approximately the same as those achieved under ambient conditions. This was because of the significantly greater leaf area index and greater leaf,air vapour pressure deficit under CO2 enrichment. The leaf chlorophyll content increased significantly under elevated CO2; however, the efficiency (i.e. photochemical yield) of light energy capture by Photosystem II (i.e. Fv/Fm) in chlorophyll a did not show a significant and consistent variation with CO2 enrichment. [source] Serological detection and immunogold localization of cross-reactive antigens shared by Camellia sinensis and Exobasidium vexansJOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2007B.N. Chakraborty Abstract Aims:, Pathogenicity of Exobasidium vexans, causal agent of blister blight of tea, was studied in 30 commercially cultivated tea varieties by analysing the antigenic patterns of host and pathogen using immunological techniques. Methods and Results:, Whole plant inoculation of tea varieties with E. vexans showed that T-78 and T-17/1/54 were most susceptible and most resistant respectively. Antigen preparations from tea varieties, pathogen, nonpathogen (Fusarium oxysporum) and of nonhosts (Glycine max, Leucaena leucocephala and Oryza sativa) were compared by indirect enzyme-linked immunosorbent assay and dot-immunobinding assay using polyclonal antibodies raised against the pathogen, nonpathogen, susceptible and resistant tea varieties. Cross-reactive antigens (CRA) were found among susceptible varieties and E. vexans isolates but not in resistant varieties, nonhosts or nonpathogen. Indirect staining of antibodies using fluorescein isothiocyanate indicated CRA were concentrated mainly around epidermal and mesophyll cells in compatible host (T-78). This was substantiated by ultrastructural studies using gold-labelled antibodies through transmission electron microscopy which showed specific localization in the chloroplasts and host cytoplasm. Conclusion:, Pathogenicity of E. vexans to different tea varieties is therefore related to the level of antigenic similarity between host and pathogen. Significance and Impact of the Study:, Immunological methods proved to be valuable in screening commercially cultivated tea varieties against E. vexans. [source] The WRKY Gene Family in Rice (Oryza sativa)JOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 6 2007Christian A. Ross Abstract WRKY genes encode transcription factors that are involved in the regulation of various biological processes. These zinc-finger proteins, especially those members mediating stress responses, are uniquely expanded in plants. To facilitate the study of the evolutionary history and functions of this supergene family, we performed an exhaustive search for WRKY genes using HMMER and a Hidden Markov Model that was specifically trained for rice. This work resulted in a comprehensive list of WRKY gene models in Oryza sativa L. ssp. indica and L. ssp. japonica. Mapping of these genes to individual chromosomes facilitated elimination of the redundant, leading to the identification of 98 WRKY genes in japonica and 102 in indica rice. These genes were further categorized according to the number and structure of their zinc-finger domains. Based on a phylogenetic tree of the conserved WRKY domains and the graphic display of WRKY loci on corresponding indica and japonica chromosomes, we identified possible WRKY gene duplications within, and losses between the two closely related rice subspecies. Also reviewed are the roles of WRKY genes in disease resistance and responses to salicylic acid and jasmonic acid, seed development and germination mediated by gibberellins, other developmental processes including senescence, and responses to abiotic stresses and abscisic acid in rice and other plants. The signaling pathways mediating WRKY gene expression are also discussed. [source] Accumulation of Defence Response-related and Unique Expressed Sequence Tags during the Incompatible Interaction in the Oryza sativa,Magnaporthe oryzae PathosystemJOURNAL OF PHYTOPATHOLOGY, Issue 7-8 2009Rekha Dixit Abstract Resistance gene-dependent accumulation of expressed sequence tags (ESTs) was studied in a blast resistant, Oryza sativa ssp. indica cv. Tetep after challenge inoculation with an incompatible race of Magnaporthe oryzae. The nucleotide sequence of 287 randomly selected cDNA clones from the rice cDNA library constructed from the RNA isolated after challenge inoculation of the host was obtained and submitted in NCBI Genbank (Accession Nos. DN475717,DN475431). Of these, 184 (63%) ESTs were highly representative of the rice transcriptomes. A set of 178 unique transcripts was identified after assembly of 287 ESTs into unigenes. These unigenes were categorized into 17 functional groups. Analysis of this EST library illustrated a broad functional representation. Twenty-one unigenes were identified as putative homologues of the genes that were up regulated during host,pathogen interaction. Similarity search of 178 unigenes with NCBI database of 14 plants unigenes showed similarity ranging from 29,100%. The unigenes obtained in this study were physically located on the pseudomolecules of rice genome. This information can be used for determining the arrays of genes being expressed during Oryza sativa,M. oryzae interactions, which will be helpful in understanding the molecular basis of disease resistance. [source] Reservoir and Non-reservoir Hosts of Bean-Wilt Pathogen, Fusarium oxysporum f. sp. phaseoliJOURNAL OF PHYTOPATHOLOGY, Issue 7-8 2001O. D. Dhingra Abstract The capacity of Fusarium oxysporum f. sp. phaseoli to multiply in the roots of 12 non-host plant species was determined with the objective of selecting potential candidates for crop rotation and/or green manuring in infested bean fields. The plants were inoculated at the seedling stage by a benomyl-resistant mutant of the pathogen using the root-dip technique and transplanted to natural soil. The number of colony forming units/g dry root tissue (CFU/g) was determined at the full bloom stage. Quantitatively, the root colonization differed greatly among the plant species. The roots and lower stem of Dolichos lablab, Phaseolus lunatus, Mucuna aterrima, Canavalia ensiforme and Vigna unguiculata were the most compatible with the pathogen and those of Sorghum bicolor, Crotalaria juncea, Oryza sativa and Zea mays were least compatible. No disease symptoms developed on any plant species. Chlamydospore germination in the rhizosphere also differed significantly among the plant species. There was no correlation between percentage chlamydospore germination in the rhizosphere and extent of root colonization. Most plant species recommended for green manuring in bean fields allowed extensive root and stem colonization by F. o. f. sp. phaseoli and were considered as reservoir hosts. All three of the gramineous species tested and C. juncea were classed as non-reservoir host, because the pathogen did not colonize the stem and its multiplication in the roots was very low. These plant species appear to be good candidates for long-term field evaluation to determine their usefulness in an integrated management of Fusarium bean-wilt. [source] The origins of weedy riceMOLECULAR ECOLOGY, Issue 21 2007NOLAN C. KANE Abstract Where do weeds come from? How do they evolve from nonweedy ancestors? In this issue of Molecular Ecology, Londo and Schaal examine the origin of weedy rice (Oryza sativa) populations in the USA. Analysing nuclear DNA sequence and microsatellite data, they show the importance of parallel evolution, hybridization, gene flow, and migration in the evolution of these weeds. [source] Origins and population genetics of weedy red rice in the USAMOLECULAR ECOLOGY, Issue 21 2007J. P. LONDO Abstract Weedy red rice (Oryza sativa spontonea) is a persistent and problematic weed of rice culture worldwide. A major hypothesis for the mechanism of production of this weed in South and Southeast Asia is hybridization between cultivated rice (Oryza sativa) and wild rice (Oryza rufipogon). However, weedy red rice can often be found outside the range of O. rufipogon leaving questions on the origin and process behind weedy rice infestations. In the USA, weedy red rice was first documented as early as 1846 and has continued to affect rice production areas. In this study, we attempt to identify the origin and population structure of weedy red rice sampled from the USA using both DNA sequence data from a neutral nuclear locus as well as microsatellite genotype data. Results suggest that two major accessions of weedy rice exist, strawhull and blackhull, and these forms may both hybridize with the cultivated rice of the USA, O. sativa japonica. Using population assignment of multilocus genotype signatures with principal component analysis and structure, an Asian origin is supported for US weedy rice. Additionally, hybridization between strawhull and blackhull varieties was inferred and may present the opportunity for the production of new weedy forms in the future. [source] Cross-species amplification tests and diversity analysis using 56 PCR markers in Dactylis glomerata and Lolium perenneMOLECULAR ECOLOGY RESOURCES, Issue 1 2009I. LITRICO Abstract We report results of cross-species amplification in Dactylis glomerata and Lolium perenne of 12 simple sequence repeats (SSRs) isolated from Lolium multiflorum×Festuca glaucescens, 42 SSRs from Festuca arundinacea and two sequence tagged sites from Oryza sativa. We compared the transferability and diversity between D. glomerata and L. perenne, which are important forage crops. While Nei's gene diversity values were equivalent in both species (from 0.14 to 0.92), the mean number of allele per locus was more important in D. glomerata than in L. perenne (5.45 vs. 4.50). These markers will be used for analysing population structure in grassland populations under agronomic practices. [source] Magnaporthe grisea interactions with the model grass Brachypodium distachyon closely resemble those with rice (Oryza sativa)MOLECULAR PLANT PATHOLOGY, Issue 4 2004ANDREW P. M. ROUTLEDGE SUMMARY Germplasm of Brachypodium distachyon was inoculated with Magnaporthe grisea using either rice- (Guy11) or grass-adapted (FAG1.1.1, PA19w-06, PA31v-01) host-limited forms of the fungus, and interactions with varying degrees of susceptibility and resistance were identified. Ecotype ABR5 was resistant to each M. grisea strain whereas ABR1 was susceptible to all but P31vi-01. Mendelian segregation in ABR1 × ABR5 crosses suggested that a single dominant resistance gene conferred resistance to Guy11. Microscopic analyses revealed that the aetiology of Guy11 fungal development and disease progression in ABR1 closely resembled that of rice infections. In ABR5, Guy11 pathogenesis was first suppressed at 48 h post-inoculation, at the secondary hyphal formation stage and was coincident with cytoplasmic granulation. Resistance to strains PA31v-01 and FAG1.1.1 was associated with a localized cell death with little callose deposition. 3,3-Diaminobenzidine staining indicated the elicitation of cell death in B. distachyon was preceded by oxidative stress in the interacting epidermal cells and the underlying mesophyll cells. Northern blot hybridization using probes for barley genes (PR1, PR5 and PAL) indicated that each was more rapidly expressed in ABR5 challenged with Guy11 although the B. distachyon defence genes BD1 and BD8 were more quickly induced in ABR1. Such data show that B. distachyon is an appropriate host for functional genomic investigations into M. grisea pathology and plant responses. [source] OsNOA1/RIF1 is a functional homolog of AtNOA1/RIF1: implication for a highly conserved plant cGTPase essential for chloroplast functionNEW PHYTOLOGIST, Issue 1 2010Hongjia Liu Summary ,The bacterial protein YqeH is a circularly permuted GTPase with homologs encoded by plant nuclear genomes. The rice homolog OsNOA1/RIF1 is encoded by the single-copy gene Os02g01440. OsNOA1/RIF1 is expressed in different tissues and is light-inducible. The OsNOA1/RIF1-EYFP fusion protein was targeted to chloroplasts in transgenic Arabidopsis plants. In addition, the rice homolog was able to rescue most of the growth phenotypes in an Arabidopsis rif1 mutant. ,Rice (Oryza sativa) OsNOA1/RIF1 RNAi mutant seedlings were chlorotic with reduced pigment contents and lower photosystem II (PSII) efficiency. However, the expressions of the chloroplast-encoded genes rbcL, atpB, psaA and psbA were not affected. By contrast, reduced abundance of the chloroplast 16S rRNA was observed in the mutant. ,Quantitative iTRAQ-LC-MS/MS proteomics investigations revealed proteome changes in the rice mutant consistent with the expected functional role of OsNOA1/RIF1 in chloroplast translation. The RNAi mutant showed significantly decreased expression levels of chloroplast-encoded proteins as well as nuclear-encoded components of chloroplast enzyme complexes. Conversely, upregulation of some classes of nonchloroplastic proteins, such as glycolytic and phenylpropanoid pathway enzymes, was detected. ,Our work provides independent indications that a highly conserved nuclear-encoded cGTPase of likely prokaryotic origin is essential for proper chloroplast ribosome assembly and/or translation in plants. [source] Carbohydrate,ethanol transition in cereal grains under anoxiaNEW PHYTOLOGIST, Issue 3 2001Lorenzo Guglielminetti Summary ,,Cereal grains differ greatly in their reponses to anaerobiosis. Here, the in vivo conversion of carbohydrates to ethanol and CO2 under anoxia is reported for three cereal grains. ,,The conversion of glucose, fructose or sucrose to ethanol under anaerobic conditions was investigated in rice (Oryza sativa), barley (Hordeum vulgare) and wheat (Triticum aestivum) grains; alcohol dehydrogenase (EC 1.1.1.1) and pyruvate decarboxylase (EC 4.1.1.1) activities were also analysed under aerobic and anaerobic incubation. ,,Our data suggest that rice grains are able to produce ethanol under anoxia for the whole period of anoxic treatment, whereas barley and wheat grains can produce this terminal product of fermentation only during the first days of anaerobiosis. The level of enzymes involved in the fermentation pathway increases strongly under anoxic conditions in all three cereals. ,,Conversion of hexose to CO2 is nearly unaffected by anoxia in wheat, barley and rice, whereas only rice grains are able to degrade and utilize sucrose efficiently under anoxia. By contrast, wheat and barley do not utilize sucrose efficiently under anaerobic conditions. [source] Designing herbicide formulation characteristics to maximize efficacy and minimize rice injury in paddy environmentsPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 6 2001Steven A Cryer Abstract Mathematical descriptors, coupled with experimental observations, are used to quantify differential uptake of an experimental herbicide in Japonica and Indica rice (Oryza sativa, non-target) and barnyardgrass (Echinochloa crus-galli, target). Partitioning, degradation, plant uptake and metabolism are described using mass-balance conservation equations in the form of kinetic approximations. Estimated environmental concentrations, governed by the pesticide formulation, are described using superimposed analytical solutions for the one-dimensional diffusion equation in spherical coordinates and by a finite difference representation of the two-dimensional diffusion equation in Cartesian coordinates. Formulation attributes from granules include active ingredient release rates, particle sizes, pesticide loading, and granule spacing. The diffusion model for pesticide transport is coupled with the compartment model to follow the fate and transport of a pesticide from its initial application location to various environmental matrices of interest. Formulation effects, partitioning and degradation in the various environmental matrices, differential plant uptake and metabolism, and dose-response information for plants are accounted for. This novel model provides a mechanism for selecting formulation delivery systems that optimize specific attributes (such as weed control or the therapeutic index) for risk-assessment procedures. In this report we describe how this methodology was used to explore the factors affecting herbicide efficacy and to define an optimal release rate for a granule formulation. © 2001 Society of Chemical Industry [source] The rice Mybleu transcription factor increases tolerance to oxygen deprivation in Arabidopsis plantsPHYSIOLOGIA PLANTARUM, Issue 1 2007Monica Mattana Mybleu is a natural incomplete transcription factor of rice (Oryza sativa), consisting of a partial Myb repeat followed by a short leucine zipper. We previously showed its localization to the apical region of rice roots and coleoptiles. Specifically, in coleoptiles, Mybleu is expressed under both aerobic and anaerobic conditions, whereas in roots, it is expressed only under aerobic conditions. Mybleu is able to dimerize with canonical leucine zippers and to activate transcription selectively. To investigate Mybleu function in vivo, we transformed Arabidopsis thaliana and evaluated several morphological, physiological and biochemical parameters. In agreement with a hypothesized role of Mybleu in cell elongation in the differentiation zone, we found that the constitutive expression of this transcription factor in Arabidopsis induced elongation in the primary roots and in the internodal region of the floral stem; we also observed a modification of the root apex morphology in transformed lines. Based on the high expression of Mybleu in anaerobic rice coleoptiles, we studied the role of this transcription factor in transgenic plants grown under low-oxygen conditions. We found that overexpression of this transcription factor increased tolerance to oxygen deficit. In transgenic plants, this effect may depend both on the maintenance of a higher metabolism during stress and on the higher expression levels of certain genes involved in the anaerobic response. [source] A CDPK type protein kinase is involved in rice SPS light modulationPHYSIOLOGIA PLANTARUM, Issue 2 2002Gabriela C. Pagnussat A protein kinase activity that can phosphorylate and inactivate rice (Oryza sativa) sucrose-phosphate synthase (SPS; UDP-glucose: d -fructose-6-phosphate-2-glucosyl transferase, EC 2.4.1.14) was measured in extracts prepared from leaves exposed to light-dark transitions. Enzyme activity present in extracts from dark leaves was about 5-fold higher than the activity in extracts from leaves that had been collected in the light. The protein kinase (named R-SPSK) was purified about 100-fold from dark leaves and its biochemical properties were studied. The micromolar dependence of Ca2+ exhibited by R-SPSK, and its response to calmodulin antagonists was similar to the properties associated with members of the plant Calcium-Dependent Protein Kinase (CDPK) family. Two modulators of SPS activity, Pi and Glc-6-P, were examined for an effect on R-SPSK. While Glc-6-P did not affect R-SPSK activity, Pi drastically increased the kinase activity. Taken together, these data provide evidence that SPS may be regulated by a CDPK type protein-kinase whose activity is modulated by light-dark transitions and stimulated by Pi, the negative effector of SPS activity. [source] Expression of Oryza sativa MAP kinase gene is developmentally regulated and stress-responsivePHYSIOLOGIA PLANTARUM, Issue 4 2002Hao-Jen Huang Mitogen-activated protein kinase (MAPK) pathways are modules involved in the transduction of extracellular signals to intracellular targets in all eukaryotes. In plants, there is evidence for MAPKs playing a role in the signalling of abiotic stresses, pathogens, plant hormones, and cell cycle cues. The large number and divergence of plant MAPKs indicates that this ancient mechanism of signal transduction is extensively used in plants. However, there have been no reports of classical MAPK module in rice. In this report, we have isolated a MAPK from rice (Oryza sativa) termed OsMAPK2. The cloned cDNA is 1457 nucleotides long and the deduced amino acid sequence comprised 369 amino acid residues. Sequence analysis revealed that the predicted amino acid sequence is 72% identical to tobacco wound-induced protein kinase (WIPK). Southern analysis suggested a single OsMAPK2 gene in rice. Analysis at the mRNA level has shown that OsMAPK2 is expressed in all plant organs and high relative amounts of OsMAPK2 were detected in the mature panicles in comparison with in the immature panicles. In suspension-cultured cells, the OsMAPK2 mRNA transcript increased markedly upon temperature downshift from 26°C to 4°C and sucrose starvation. In contrast, the OsMAPK2 mRNA level rapidly declined in rice cell challenged by high temperature. A similarly rapid response of OsMAPK2 was observed in stress-treated seedlings, demonstrating that response of the MAPK pathway occurs also in intact plants. These results suggest that this OsMAPK2 may function in the stress-signalling pathway as well as panicle development in rice. [source] Rice sucrose-phosphate synthase: Identification of an isoform specific for heterotrophic tissues with distinct metabolite regulation from the mature leaf enzymePHYSIOLOGIA PLANTARUM, Issue 4 2000Gabriela C. Pagnussat Immunohistological analyses for rice (Oryza sativa) sucrose-phosphate synthase (SPS, UDP-glucose d -fructose-6-phosphate-2-glucosyltransferase, EC 2.4.1.14) show that the protein is differently localized in photosynthetic and etiolated leaves. Very little is known about SPS regulation in heterotrophic tissues; therefore, we studied the biochemical properties of the enzyme from etiolated seedlings and embryo. Two SPS forms (SPS-1 and SPS-2) were partially purified from etiolated seedlings. The effects of Glc-6-P (activator) and Pi (inhibitor) on SPS activities allowed us to differentiate the two forms. SPS-1 showed high sensitivity to Pi which also strongly decreased enzyme activation by Glc-6-P. SPS-2 was highly activated by Glc-6-P and showed low sensitivity to Pi. In vitro alkaline phosphatase treatment suggested that SPS-1 could be regulated as leaf SPS in darkness and that SPS-2 is present in a dephosphorylated state or is not regulated by protein phosphorylation. The relative MM value (116 kDa) estimated for both SPS forms in SDS-PAGE is identical to the rice leaf SPS polypeptide. Taken together, these data led us to conclude that SPS-2 is an enzyme form only present in non-photosynthetic tissues. [source] A bidirectional gene trap construct suitable for T-DNA and Ds -mediated insertional mutagenesis in rice (Oryza sativa L.)PLANT BIOTECHNOLOGY JOURNAL, Issue 5 2004Andrew L. Eamens Summary A construct suitable for genome-wide transfer-DNA (T-DNA) and subsequent transposon-based (Ds) gene trapping has been developed for use in rice (Oryza sativa). This T-DNA/Ds construct contains: Ds terminal sequences immediately inside T-DNA borders for subsequent Ds mobilization; promoterless green fluorescent protein (sgfpS65T) and ,-glucuronidase (uidA) reporter genes, each fused to an intron (from Arabidopsis GPA1 gene) to enable bidirectional gene trapping by T-DNA or Ds; an ampicillin resistance gene (bla) and a bacterial origin of replication (ori) to serve as the plasmid rescue system; an intron-containing hygromycin phosphotransferase gene (hph) as a selectable marker or Ds tracer; and an intron-containing barnase gene in the binary vector backbone (VB) to select against transformants carrying unwanted VB sequences. More than a threefold increase over previously reported reporter gene-based gene trapping efficiencies was observed in primary T-DNA/Ds transformant rice lines, returning an overall reporter gene expression frequency of 23%. Of the plant organs tested, 3.3,7.4% expressed either reporter at varying degrees of organ or tissue specificity. Approximately 70% of the right border (RB) flanking sequence tags (FSTs) retained 1,6 bp of the RB repeat and 30% of the left border (LB) FSTs retained 5,23 bp of the LB repeat. The remaining FSTs carried deletions of 2,84 bp inside the RB or 1,97 bp inside the LB. Transposition of Ds from the original T-DNA was evident in T-DNA/Ds callus lines super-transformed with a transposase gene (Ac) construct, as indicated by gene trap reporter activity and rescue of new FSTs in the resulting double transformant lines. [source] Association mapping of straighthead disorder induced by arsenic in Oryza sativaPLANT BREEDING, Issue 6 2009H. A. Agrama Abstract Straighthead is a physiological disorder in rice (Oryza sativa L.) resulting in sterile florets, poorly developed panicles and yield loss. Because of its sporadic nature and unidentified causes for the disorder, molecular marker assisted selection is essential for resistance improvement in breeding programmes. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association mapping to identify genetic regions associated with straighthead disorder using 547 accessions of germplasm from the USDA rice core collection. Straighthead was evaluated in arsenic treated soil and genotyping was conducted with 75 molecular markers covering the entire rice genome about every 25 cM. A mixed-linear model approach combining the principal component assignments with kinship estimates proved to be particularly promising for association mapping. The extent of linkage disequilibrium was described among the markers. Six markers were found to be significantly associated with straighthead, explaining 35% of the total phenotypic variation. However, only two SSR markers, RM413 and RM277 on chromosome 5 and 12, respectively, have a significant association with low rating indicating straighthead resistance. Confirmation of the marker-straighthead association using segregating populations is necessary before marker-assisted selection can be applied. [source] Chromosomal localization of five mutant genes in rice, Oryza sativa, using primary trisomicsPLANT BREEDING, Issue 1 2000A. C. Sanchez Abstract The chromosomal locations of five mutant genes in rice were determined by crossing the marker stocks with the 12 primary trisomics. Genetic segregation of each gene was studied in the F2 or backcross populations. Out of the 60 possible cross combinations, 43 F2 or BC1 populations were studied. Segregation data indicated that spl11 was located on chromosome 12 while wp2 and eg2(t) were located on chromosome 6. The genes v12(t) and Bc6 were located on chromosomes 8 and 9, respectively, which are sparsely populated with genetic markers. [source] Loss of cytosolic fructose-1,6-bisphosphatase limits photosynthetic sucrose synthesis and causes severe growth retardations in rice (Oryza sativa)PLANT CELL & ENVIRONMENT, Issue 12 2008SANG-KYU LEE ABSTRACT During photosynthesis, triose-phosphates (trioseP) exported from the chloroplast to the cytosol are converted to sucrose via cytosolic fructose-1,6-bisphosphatase (cFBPase). Expression analysis in rice suggests that OscFBP1 plays a major role in the cytosolic conversion of trioseP to sucrose in leaves during the day. The isolated OscFBP1 mutants exhibited markedly decreased photosynthetic rates and severe growth retardation with reduced chlorophyll content, which results in plant death. Analysis of primary carbon metabolites revealed both significantly reduced levels of sucrose, glucose, fructose and starch in leaves of these mutants, and a high accumulation of sucrose to starch in leaves of rice plants. In the oscfbp1 mutants, products of glycolysis and the TCA cycle were significantly increased. A partitioning experiment of 14C-labelled photoassimilates revealed altered carbon distributions including a slight increase in the insoluble fraction representing transitory starch, a significant decrease in the neutral fraction corresponding to soluble sugars and a high accumulation of phosphorylated intermediates and carboxylic acid fractions in the oscfbp1 mutants. These results indicate that the impaired synthesis of sucrose in rice cannot be sufficiently compensated for by the transitory starch-mediated pathways that have been found to facilitate plant growth in the equivalent Arabidopsis mutants. [source] A new precipitation technique provides evidence for the permeability of Casparian bands to ions in young roots of corn (Zea mays L.) and rice (Oryza sativa L.)PLANT CELL & ENVIRONMENT, Issue 11 2005KOSALA RANATHUNGE ABSTRACT Using an insoluble inorganic salt precipitation technique, the permeability of cell walls and especially of endodermal Casparian bands (CBs) for ions was tested in young roots of corn (Zea mays) and rice (Oryza sativa). The test was based on suction of either 100 µm CuSO4 or 200 µm K4[Fe(CN)6] into the root from its medium using a pump (excised roots) or transpirational stream (intact seedlings), and subsequent perfusion of xylem of those root segments with the opposite salt component, which resulted in precipitation of insoluble brown crystals of copper ferrocyanide. Under suction, Cu2+ could cross the endodermis apoplastically in both plant species (although at low rates) developing brown salt precipitates in cell walls of early metaxylem and in the region between CBs and functioning metaxylem vessels. Hence, at least Cu2+ did cross the endodermis dragged along with the water. The results suggested that CBs were not perfect barriers to apoplastic ion fluxes. In contrast, ferrocyanide ions failed to cross the mature endodermis of both corn and rice at detectable amounts. The concentration limit of apoplastic copper was 0.8 µm at a perfusion with 200 µm K4[Fe(CN)6]. Asymmetric development of precipitates suggested that the cation, Cu2+, moved faster than the anion, [Fe(CN)6]4,, through cell walls including CBs. Using Chara cell wall preparations (,ghosts') as a model system, it was observed that, different from Cu2+, ferrocyanide ions remained inside wall-tubes suggesting a substantially lower permeability of the latter which agreed with the finding of an asymmetric development of precipitates. In both corn and rice roots, there was a significant apoplastic flux of ions in regions where laterals penetrated the endodermis. Overall, the results show that the permeability of CBs to ions is not zero. CBs do not represent a perfect barrier for ions, as is usually thought. The permeability of CBs may vary depending on growth conditions which are known to affect the intensity of formation of bands. [source] Rejuvenating rice proteomics: Facts, challenges, and visionsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 20 2006Ganesh Kumar Agrawal Dr. Abstract Proteomics is progressing at an unprecedented pace, as can be exemplified by the progress in model organisms such as yeast, bacteria, and mammals. Proteomics research in plants, however, has not progressed at the same pace. Unscrambling of the genome sequences of the dicotyledoneous Arabidopsis thaliana,(L.) and monocotyledoneous rice (Oryza sativa,L.) plant species, respectively, has made them accessible reference organisms to study plant proteomics. Study of these two reference plants is expected to unravel the mystery of plant biology. Rice, a critically important food crop on the earth, has been termed a "cornerstone" and the "Rosetta stone" for functional genomics of cereal crops. Here, we look at the progress in unraveling rice proteomes and present the facts, challenges, and vision. The text is divided into two major parts: the first part presents the facts and the second part discusses the challenges and vision. The facts include the technology and its use in developing proteomes, which have been critically and constructively reviewed. The challenges and vision deal with the establishment of technologies to exhaustively investigate the protein components of a proteome, to generate high-resolution gel-based reference maps, and to give rice proteomics a functional dimension by studying PTMs and isolation of multiprotein complexes. Finally, we direct a vision on rice proteomics. This is our third review in series on rice proteomics, which aims to stimulate an objective discussion among rice researchers and to understand the necessity and impact of unraveling rice proteomes to their full potential. [source] Proteome analysis of rice uppermost internodes at the milky stagePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 11 2006Pingfang Yang Abstract Uppermost internodes, which connect the part between the ear and lower stem, form an important pathway transporting mineral nutrition from roots and photosynthates from leaves (especially the flag leaf) to the ear. The milky stage is the first stage of seed ripening. The uppermost internodes of rice at the milky stage are critical for seed quality and yield. Total soluble proteins of the uppermost internodes of rice (Oryza sativa,L. ssp.,indica) at the milky stage were analyzed using proteomic methods. Using 2-DE, 762,reproducible protein spots were detected. Among them, 132,abundant proteins were analyzed using MALDI-TOF-MS. Searching in the National Center for Biotechnology Information database, we could identify 98,proteins, which represent 80,gene products. These proteins belong to 11,functional groups with energy production-associated proteins in the first place. The large accumulation of proteins involved in metabolism, signaling, and stress resistance indicated that the uppermost internodes of rice have a high physiological and stress-resistant activity. In addition, our results will also enrich the database of the rice proteome. [source] Rice cellulose synthase-like D4 is essential for normal cell-wall biosynthesis and plant growthTHE PLANT JOURNAL, Issue 6 2009Ming Li Summary Cellulose synthase-like (CSL) proteins of glycosyltransferase family 2 (GT2) are believed to be involved in the biosynthesis of cell-wall polymers. The CSL D sub-family (CSLD) is common to all plants, but the functions of CSLDs remain to be elucidated. We report here an in-depth characterization of a narrow leaf and dwarf1 (nd1) rice mutant that shows significant reduction in plant growth due to retarded cell division. Map-based cloning revealed that ND1 encodes OsCSLD4, one of five members of the CSLD sub-family in rice. OsCSLD4 is mainly expressed in tissues undergoing rapid growth. Expression of OsCSLD4 fluorescently tagged at the C- or N-terminus in rice protoplast cells or Nicotiana benthamiana leaves showed that the protein is located in the endoplasmic reticulum or Golgi vesicles. Golgi localization was verified using phenotype-rescued transgenic plants expressing OsCSLD4,GUS under the control of its own promoter. Two phenotype-altered tissues, culms and root tips, were used to investigate the specific wall defects. Immunological studies and monosaccharide compositional and glycosyl linkage analyses explored several wall compositional effects caused by disruption of OsCSLD4, including alterations in the structure of arabinoxylan and the content of cellulose and homogalacturonan, which are distinct in the monocot grass species Oryza sativa (rice). The inconsistent alterations in the two tissues and the observable structural defects in primary walls indicate that OsCSLD4 plays important roles in cell-wall formation and plant growth. [source] OsRecQ1, a QDE-3 homologue in rice, is required for RNA silencing induced by particle bombardment for inverted repeat DNA, but not for double-stranded RNATHE PLANT JOURNAL, Issue 2 2008Hui Chen Summary Based on the nucleotide sequence of QDE-3 in Neurospora crassa, which is involved in RNA silencing, rice (Oryza sativa) mutant lines disrupted by the insertion of the rice retrotransposonTos17 were selected. Homozygous individuals from the M1 and M2 generations were screened and used for further analyses. The expression of the gene was not detected in leaves or calli of the mutant lines, in contrast to the wild type (WT). Induction of RNA silencing by particle bombardment was performed to investigate any effects of the OsRecQ1 gene on RNA silencing with silencing inducers of the GFP (green fluorescence protein)/GUS (, -glucuronidase) gene in the mutant lines. The results showed that OsRecQ1 is required for RNA silencing induced by particle bombardment for inverted-repeat DNA, but not for double-stranded RNA (dsRNA). The levels of transcripts from inverted-repeat DNA were much lower in the mutant lines than those in the WT. Furthermore, no effects were observed in the accumulation of endogenous microRNAs (miR171 and miR156) and the production of the short interspersed nuclear element retroelement by small interfering RNA. On the basis of these results, we propose that OsRecQ1 may participate in the process that allows inverted repeat DNA to be transcribed into dsRNA, which can trigger RNA silencing. [source] | ||||||||||||||||||||||||||||