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high-throughput cryopreservation of plant cell cultures for functional genomics.suspension-cultured cell lines from plant species are useful for genetic engineering. however, maintenance of these lines is laborious, involves routine subculturing and hampers wider use of transgenic lines, especially when many lines are required for a high-throughput functional genomics application. cryopreservation of these lines may reduce the need for subculturing. here, we established a simple protocol for cryopreservation of cell lines from five commonly used plant species, arabidopsis t ...201222437846
rapid determination of endogenous cytokinins in plant samples by combination of magnetic solid phase extraction with hydrophilic interaction chromatography-tandem mass spectrometry.a 2-acrylamido-2-methyl-1-propanesulfonic acid-co-ethylene glycol dimethacrylate (fe₃o₄/sio₂/p(amps-co-egdma)) copolymer was prepared and used as a magnetic solid phase extraction (mspe) medium for recovery of endogenous cytokinins (cks) from plant extracts. this magnetic porous polymer was characterized by electron microscopy, nitrogen sorption experiments, elemental analysis and fourier-transformed infrared spectroscopy. it was demonstrated to have high extraction capacity toward cks in plants ...201222401906
osmyb2p-1, an r2r3 myb transcription factor, is involved in the regulation of phosphate-starvation responses and root architecture in rice.an r2r3 myb transcription factor, osmyb2p-1, was identified from microarray data by monitoring the expression profile of rice (oryza sativa ssp. japonica) seedlings exposed to phosphate (pi)-deficient medium. expression of osmyb2p-1 was induced by pi starvation. osmyb2p-1 was localized in the nuclei and exhibited transcriptional activation activity. overexpression of osmyb2p-1 in arabidopsis (arabidopsis thaliana) and rice enhanced tolerance to pi starvation, while suppression of osmyb2p-1 by rn ...201222395576
characterization of genes involved in cytokinin signaling and metabolism from rice.two-component signaling elements play important roles in plants, including a central role in cytokinin signaling. we characterized two-component elements from the monocot rice (oryza sativa) using several complementary approaches. phylogenetic analysis reveals relatively simple orthologous relationships among the histidine kinases in rice and arabidopsis (arabidopsis thaliana). in contrast, the histidine-containing phosphotransfer proteins (oshps) and response regulators (osrrs) display a higher ...201222383541
[progress in cre/lox site-specific recombination system in higher eukaryotes].cre/lox system derived from p1 bacteriaphage can quickly and effectively achieve gene insertion, deletion, replacement, and inversion by means of site-specific recombination. as one of the most important tools for gene targeting at present, cre/lox system has been widely used in arabidopsis thaliana, oryza sativa l., mus musculus, drosophila melanogaster, danio rerio, and other higher eukaryotic organisms. this review roundly described the basic profile of cre/lox system, and its application in ...201222382059
targeted disruption of an orthologue of domains rearranged methylase 2, osdrm2, impairs the growth of rice plants by abnormal dna methylation.recent methylome analyses of the entire arabidopsis thaliana genome using various mutants have provided detailed information about the dna methylation pattern and its function. however, information about dna methylation in other plants is limited, partly because of the lack of mutants. to study dna methylation in rice (oryza sativa) we applied homologous recombination-mediated gene targeting to generate targeted disruptants of osdrm2, a rice orthologue of domains rearranged methylase 1 and 2 (dr ...201222380881
in search of function for hypothetical proteins encoded by genes of sa-ja pathways in oryza sativa by in silico comparison and structural modeling.knowledge of rice genome brings new dimensions to the management of abiotic stresses; however, gene sequences in the rice genome are yet to be assigned structure and function. hydrogen peroxide, salicylates and jasmonates act as signal molecules in plants employing common machinery to manage abiotic stress. the present work is primarily focused to assign a structurefunction relationship by modeling of the hypothetical proteins of sa-ja signaling pathway known in arabidopsis thaliana and compare ...201222359427
large-scale identification of mirtrons in arabidopsis and rice.a new catalog of microrna (mirna) species called mirtrons has been discovered in animals recently, which originate from spliced introns of the gene transcripts. however, only one putative mirtron, osa-mir1429, has been identified in rice (oryza sativa). we employed a high-throughput sequencing (hts) data- and structure-based approach to do a genome-wide search for the mirtron candidate in both arabidopsis (arabidopsis thaliana) and rice. five and eighteen candidates were discovered in the two pl ...201222348048
identification of programmed cell death related genes in bamboo.the event of bamboo flowering and subsequent death of bamboo cells, a rare phenomenon is an interesting model to study gene expression/function in the context of the programmed cell death (pcd) in plant. to identify genes involved in autolytic cell death in bamboo (bambusa arundinacea/bambusa bambos voss), a suppressive subtractive cdna hybridization (ssh) was performed between cdna isolated from control (healthy), as driver and test internodal tissue (45days after setting of seeds), as tester. ...201222326529
comparative phosphoproteomic analysis of microsomal fractions of arabidopsis thaliana and oryza sativa subjected to high salinity.plants respond to salt stress by initiating phosphorylation cascades in their cells. many key phosphorylation events take place at membranes. microsomal fractions from 400 mm salt-treated arabidopsis suspension plants were isolated, followed by trypsin shaving, enrichment using zirconium ion-charged or tio(2) magnetic beads, and tandem mass spectrometry analyses for site mapping. a total of 27 phosphorylation sites from 20 arabidopsis proteins including photosystem ii reaction center protein h p ...201222325874
overexpression of rice cbs domain containing protein improves salinity, oxidative, and heavy metal tolerance in transgenic tobacco.we have recently identified and classified a cystathionine β-synthase domain containing protein family in arabidopsis (arabidopsis thaliana) and rice (oryza sativa l.). based on the microarray and mpss data, we have suggested their involvement in stress tolerance. in this study, we have characterized a rice protein of unknown function, oscbsx4. this gene was found to be upregulated under high salinity, heavy metal, and oxidative stresses at seedling stage. transgenic tobacco plants overexpressin ...201222302312
constitutive activation of transcription factor osbzip46 improves drought tolerance in rice.osbzip46 is one member of the third subfamily of bzip transcription factors in rice (oryza sativa). it has high sequence similarity to aba-responsive element binding factor (abf/areb) transcription factors abi5 and osbzip23, two transcriptional activators positively regulating stress tolerance in arabidopsis (arabidopsis thaliana) and rice, respectively. expression of osbzip46 was strongly induced by drought, heat, hydrogen peroxide, and abscisic acid (aba) treatment; however, it was not induced ...201222301130
the yabby gene tongari-boushi1 is involved in lateral organ development and maintenance of meristem organization in the rice spikelet.the meristem initiates lateral organs in a regular manner, and proper communication between the meristem and the lateral organs ensures the normal development of plants. here, we show that mutation of the rice (oryza sativa) gene tongari-boushi1 (tob1) results in pleiotropic phenotypes in spikelets, such as the formation of a cone-shaped organ instead of the lemma or palea, the development of two florets in a spikelet, or premature termination of the floret meristem, in addition to reduced growt ...201222286138
making sense of low oxygen sensing.plant-specific group vii ethylene response factor (erf) transcription factors have emerged as pivotal regulators of flooding and low oxygen responses. in rice (oryza sativa), these proteins regulate contrasting strategies of flooding survival. recent studies on arabidopsis thaliana group vii erfs show they are stabilized under hypoxia but destabilized under oxygen-replete conditions via the n-end rule pathway of targeted proteolysis. oxygen-dependent sequestration at the plasma membrane maintain ...201222280796
gradual increase of mir156 regulates temporal expression changes of numerous genes during leaf development in rice.the highly conserved plant microrna, mir156, is an essential regulator for plant development. in arabidopsis (arabidopsis thaliana), mir156 modulates phase changing through its temporal expression in the shoot. in contrast to the gradual decrease over time in the shoot (or whole plant), we found that the mir156 level in rice (oryza sativa) gradually increased from young leaf to old leaf after the juvenile stage. however, the mir156-targeted rice squamosa-promoter binding-like (spl) transcription ...201222271747
regulatory functions of snrk1 in stress-responsive gene expression and in plant growth and development.sucrose-nonfermentation1-related protein kinase1 (snrk1) is an evolutionarily conserved energy sensor protein that regulates gene expression in response to energy depletion in plants. efforts to elucidate the functions and mechanisms of this protein kinase are hampered, however, by inherent growth defects of snrk1-null mutant plants. to overcome these limitations and study snrk1 functions in vivo, we applied a method combining transient expression in leaf mesophyll protoplasts and stable express ...201222232383
comparative genomics of the lipid-body-membrane proteins oleosin, caleosin and steroleosin in magnoliophyte, lycophyte and bryophyte.lipid bodies store oils in the form of triacylglycerols. oleosin, caleosin and steroleosin are unique proteins localized on the surface of lipid bodies in seed plants. this study has identified genes encoding lipid body proteins oleosin, caleosin and steroleosin in the genomes of five plants: arabidopsis thaliana, oryza sativa, populus trichocarpa, selaginella moellendorffii and physcomitrella patens. the protein sequence alignment indicated that each oleosin protein contains a highly-conserved ...201223317702
phylogenetic relationships and selective pressure on gene families related to iron homeostasis in land plants.iron is involved in many metabolic processes, such as respiration and photosynthesis, and therefore an essential element for plant development. comparative analysis of gene copies between crops and lower plant groups can shed light on the evolution of genes important to iron homeostasis. a phylogenetic analysis of five metal homeostasis gene families (nas, nramp, ysl, fro, and irt) selected in monocots, dicots, gymnosperms, and bryophytes was performed. the homologous genes were found using know ...201223231606
uniprotkb amid the turmoil of plant proteomics research.the uniprot knowledgebase (uniprotkb) provides a single, centralized, authoritative resource for protein sequences and functional information. the majority of its records is based on automatic translation of coding sequences (cds) provided by submitters at the time of initial deposition to the nucleotide sequence databases (insdc). this article will give a general overview of the current situation, with some specific illustrations extracted from our annotation of arabidopsis and rice proteomes. ...201223230445
identification of quantitative trait loci for blast resistance in bc₂f₃ and bc₂f5 advanced backcross families of rice.advanced backcross families derived from oryza sativa cv mr219/o. rufipogon irgc105491 were utilized for identification of quantitative trait loci (qtl) for blast resistance using simple sequence repeat markers. two hundred and sixty-one bc(2)f(3) families were used to construct a linkage map, using 87 markers, which covered 2375.2 cm of 12 rice chromosomes, with a mean density of 27.3 cm. the families were evaluated in a greenhouse for resistance to blast disease caused by pathotypes p7.2 and p ...201223079822
mutation in oslms, a gene encoding a protein with two double-stranded rna binding motifs, causes lesion mimic phenotype and early senescence in rice (oryza sativa l.).the rice (oryza sativa l.) lesion mimic and senescence (lms) ems-mutant, identified in a japonica cultivar hitomebore, is characterized by a spontaneous lesion mimic phenotype during its vegetative growth, an accelerated senescence after flowering, and enhanced resistance to rice blast (magnaporthe oryzae). to isolate the oslms gene, we crossed the lms mutant to kasalath (indica), and used mutant f(2) plants to initially map the candidate region to about 322-kb on the long arm of chromosome 2. i ...201222976392
secretome analysis of magnaporthe oryzae using in vitro systems.magnaporthe oryzae is a devastating blast fungal pathogen of rice (oryza sativa l.) that causes dramatic decreases in seed yield and quality. during the early stages of infection by this pathogen, the fungal spore senses the rice leaf surface, germinates, and penetrates the cell via an infectious structure known as an appressorium. during this process, m. oryzae secretes several proteins; however, these proteins are largely unknown mainly due to the lack of a suitable method for isolating secret ...201222539438
in-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches.we report here the molecular and phenotypic features of a library of 31,562 insertion lines generated in the model japonica cultivar nipponbare of rice (oryza sativa l.), called oryza tag line (otl). sixteen thousand eight hundred and fourteen t-dna and 12,410 tos17 discrete insertion sites have been characterized in these lines. we estimate that 8686 predicted gene intervals--i.e. one-fourth to one-fifth of the estimated rice nontransposable element gene complement--are interrupted by sequence- ...201222369597
two phenylalanine ammonia lyase isoforms are involved in the elicitor-induced response of rice to the fungal pathogen magnaporthe oryzae.suspension cultured cells of a blast-resistant rice genotype (oryza sativa l. cv. gigante vercelli) were treated with cell wall hydrolysates prepared from the fungal pathogen magnaporthe oryzae. as a consequence, a complex pattern of phenylalanine ammonia lyase time course specific activity levels was evident. ion-exchange chromatographic fractionation of crude extracts suggested that the early (6 h) and the late (48-72 h after elicitation) increase of activity relied upon the sequential inducti ...201222137607
transcription activator-like (tal) effectors targeting ossweet genes enhance virulence on diverse rice (oryza sativa) varieties when expressed individually in a tal effector-deficient strain of xanthomonas oryzae.genomes of the rice (oryza sativa) xylem and mesophyll pathogens xanthomonas oryzae pv. oryzae (xoo) and pv. oryzicola (xoc) encode numerous secreted transcription factors called transcription activator-like (tal) effectors. in a few studied rice varieties, some of these contribute to virulence by activating corresponding host susceptibility genes. some activate disease resistance genes. the roles of x. oryzae tal effectors in diverse rice backgrounds, however, are poorly understood. xoo tal eff ...201223078195
heavy metals health risk assessment for population via consumption of food crops and fruits in owerri, south eastern, nigeria.this study assessed lead, cadmium, and nickel level in food crops, fruits and soil samples from ohaji and umuagwo and owerri in south eastern nigeria and estimated the potential health risks of metals. samples were washed, oven-dried at 70-80°c for 24 h and powdered. samples were digested with perchloric acid and nitric acid. metals were analysed with unicam atomic absorption spectrophotometer.201222853175
biochemical and physiological responses of rice (oryza sativa l.) as influenced by trichoderma harzianum under drought stress.rice is one of the most important food crops drastically affected by drought in lowland rice ecosystems. in the present study, the impact of drought tolerant isolates of endophytic fungus trichoderma harzianum on rice response to drought was investigated. out of 43 trichoderma isolates studied, only five isolates viz., th 56, th 69, th 75, th 82 and th 89 were selected to be drought tolerant as these were able to colonize well on cow dung at low moisture content of 10-20 percent, though two isol ...201222391125
mutants of saccharomyces cerevisiae and bacillus citri changed the protein content of the nigerian oryza sativa variety "igbimo" during fermentation.effect of mutation on protein production by saccharomyces cerevisiae and bacillus citri, the best protein producing yeast and bacterium isolated during a previous natural fermentation of a nigerian rice ("igbimo"). the two microorganisms were grown to logarithmic phase and mutagenized separately using ethylmethyl sulphonate (ems). the wild-types and variants were inoculated individually into sterile "igbimo" rice. fermentation was allowed to take place at 27°c for 7 days after which protein rele ...201223166568
a tfiiia-type zinc finger protein confers multiple abiotic stress tolerances in transgenic rice (oryza sativa l.).the tfiiia-type zinc finger transcription factors are involved in plant development and abiotic stress responses. most tfiiia-type zinc finger proteins are transcription repressors due to existence of an ear-motif in their amino acid sequences. in this work, we found that zfp182, a tfiiia-type zinc finger protein, forms a homodimer in the nucleus and exhibits trans-activation activity in yeast cells. the deletion analysis indicated that a leu-rich region at c-terminus is required for the trans-a ...201222930448
hint: high-quality protein interactomes and their applications in understanding human disease.a global map of protein-protein interactions in cellular systems provides key insights into the workings of an organism. a repository of well-validated high-quality protein-protein interactions can be used in both large- and small-scale studies to generate and validate a wide range of functional hypotheses.201222846459
distinctive expression patterns and roles of the mirna393/tir1 homolog module in regulating flag leaf inclination and primary and crown root growth in rice (oryza sativa).• microrna (mirna)-mediated regulation of auxin signaling components plays a critical role in plant development. mirna expression and functional diversity contribute to the complexity of regulatory networks of mirna/target modules. • this study functionally characterizes two members of the rice (oryza sativa) mir393 family and their target genes, ostir1 and osafb2 (auxin signaling f-box), the two closest homologs of arabidopsis transport inhibitor response 1 (tir1). • we found that the mir393 fa ...201222846038
arms race co-evolution of magnaporthe oryzae avr-pik and rice pik genes driven by their physical interactions.attack and counter-attack impose strong reciprocal selection on pathogens and hosts, leading to development of arms race evolutionary dynamics. here we show that magnaporthe oryzae avirulence gene avr-pik and the cognate rice resistance (r) gene pik are highly variable, with multiple alleles in which dna replacements cause amino acid changes. there is tight recognition specificity of the avr-pik alleles by the various pik alleles. we found that avr-pik physically binds the n-terminal coiled-coil ...201222805093
rice mitogen-activated protein kinase interactome analysis using the yeast two-hybrid system.mitogen-activated protein kinase (mapk) cascades support the flow of extracellular signals to intracellular target molecules and ultimately drive a diverse array of physiological functions in cells, tissues, and organisms by interacting with other proteins. yet, our knowledge of the global physical mapk interactome in plants remains largely fragmented. here, we utilized the yeast two-hybrid system and coimmunoprecipitation, pull-down, bimolecular fluorescence complementation, subcellular localiz ...201222786887
the rice monovalent cation transporter oshkt2;4: revisited ionic selectivity.the family of plant membrane transporters named hkt (for high-affinity k(+) transporters) can be subdivided into subfamilies 1 and 2, which, respectively, comprise na(+)-selective transporters and transporters able to function as na(+)-k(+) symporters, at least when expressed in yeast (saccharomyces cerevisiae) or xenopus oocytes. surprisingly, a subfamily 2 member from rice (oryza sativa), oshkt2;4, has been proposed to form cation/k(+) channels or transporters permeable to ca(2+) when expresse ...201222773759
the barley est dna replication and repair database (best-drrd) as a tool for the identification of the genes involved in dna replication and repair.the high level of conservation of genes that regulate dna replication and repair indicates that they may serve as a source of information on the origin and evolution of the species and makes them a reliable system for the identification of cross-species homologs. studies that had been conducted to date shed light on the processes of dna replication and repair in bacteria, yeast and mammals. however, there is still much to be learned about the process of dna damage repair in plants.201222697361
a constitutive expressed phosphate transporter, ospht1;1, modulates phosphate uptake and translocation in phosphate-replete rice.a number of phosphate (pi) starvation- or mycorrhiza-regulated pi transporters belonging to the pht1 family have been functionally characterized in several plant species, whereas functions of the pi transporters that are not regulated by changes in pi supply are lacking. in this study, we show that rice (oryza sativa) pht1;1 (ospt1), one of the 13 pht1 pi transporters in rice, was expressed abundantly and constitutively in various cell types of both roots and shoots. ospt1 was able to complement ...201222649273
the role of oscom1 in homologous chromosome synapsis and recombination in rice meiosis.com1/sae2 is a highly conserved gene from yeast to higher eukaryotes. its orthologs, known to cooperate with the mrx complex (mre11/rad50/xrs2), are required for meiotic dna double-strand break (dsb) ends resection and specific mitotic dsb repair events. here, the rice (oryza sativa, 2n = 2x = 24) com1/sae2 homolog was identified through positional cloning, termed oscom1. four independent mutants of oscom1 were isolated and characterized. in oscom1 mutants, synaptonemal complex (sc) formation, h ...201222507309
rice asr1 protein with reactive oxygen species scavenging and chaperone-like activities enhances acquired tolerance to abiotic stresses in saccharomyces cerevisiae.abscisic acid stress ripening (asr1) protein is a small hydrophilic, low molecular weight, and stress-specific plant protein. the gene coding region of asr1 protein, which is induced under high salinity in rice (oryza sativa ilmi), was cloned into a yeast expression vector pvtu260 and transformed into yeast cells. heterologous expression of asr1 protein in transgenic yeast cells improved tolerance to abiotic stresses including hydrogen peroxide (h(2)o(2)), high salinity (nacl), heat shock, menad ...201222382682
crystal structure of rice importin-α and structural basis of its interaction with plant-specific nuclear localization signals.in the classical nucleocytoplasmic import pathway, nuclear localization signals (nlss) in cargo proteins are recognized by the import receptor importin-α. importin-α has two separate nls binding sites (the major and the minor site), both of which recognize positively charged amino acid clusters in nlss. little is known about the molecular basis of the unique features of the classical nuclear import pathway in plants. we determined the crystal structure of rice (oryza sativa) importin-α1a at 2-å ...201223250448
inhibition of a basal transcription factor 3-like gene osj10gbtf3 in rice results in significant plant miniaturization and typical pollen abortion.btf3, which was originally recognized as a basal transcription factor, has been known to be involved in transcription initiation, translational regulation and protein localization in many eukaryotic organisms. however, its function remains largely unknown in plant species. in the present study, we analyzed a btf3-related sequence in oryza sativa l. subsp. japonica, which shares the conserved domain of a nascent polypeptide-associated complex with human btf3, and was referred to as osj10gbtf3. th ...201223147221
glutathione reductase from oryza sativa increases acquired tolerance to abiotic stresses in a genetically modified saccharomyces cerevisiae strain.glutathione reductase (gr, e.c. 1.6.4.2) is an important enzyme that reduces glutathione disulfide (gssg) to a sulfydryl form (gsh) in the presence of an nadph-dependent system. this is a critical antioxidant mechanism. owing to the significance of gr, this enzyme has been examined in a number of animals, plants, and microbes. we performed a study to evaluate the molecular properties of gr (osgr) from rice (oryza sativa). to determine whether heterologous expression of osgr can reduce the delete ...201223124348
oslea3-2, an abiotic stress induced gene of rice plays a key role in salt and drought tolerance.late embryogenesis abundant (lea) proteins are involved in tolerance to drought, cold and high salinity in many different organisms. in this report, a lea protein producing full-length gene oslea3-2 was identified in rice (oryza sativa) using the rapid amplification of cdna ends (race) method. oslea3-2 was found to be only expressed in the embryo and can be induced by abiotic stresses. the coding protein localizes to the nucleus and overexpression of oslea3-2 in yeast improved growth performance ...201223024799
ysl16 is a phloem-localized transporter of the copper-nicotianamine complex that is responsible for copper distribution in rice.cu is an essential element for plant growth, but the molecular mechanisms of its distribution and redistribution within the plants are unknown. here, we report that yellow stripe-like16 (ysl16) is involved in cu distribution and redistribution in rice (oryza sativa). rice ysl16 was expressed in the roots, leaves, and unelongated nodes at the vegetative growth stage and highly expressed in the upper nodes at the reproductive stage. ysl16 was expressed at the phloem of nodes and vascular tissues o ...201223012434
functional analysis of oshsbp1 and oshsbp2 revealed their involvement in the heat shock response in rice (oryza sativa l.).the heat shock response (hsr) induces the production of heat shock proteins (hsps) through the activation of heat shock factors (hsf). hsf binding protein (hsbp) is reported to modulate the function of hsf by binding to their trimer and hence to regulate hsr. this report describes the role of oshsbp1 and oshsbp2 in the regulation of the hsr and seed development of rice. both genes expressed ubiquitously in all tissues under normal growth conditions while their expression levels were significantl ...201222996677
regeneration of transgenic rice with bacterial ipt gene driven by senescence specific (sag12) promoter by particle bombardment.transgenic rice plants were generated using particle bombardment to introduce the agrobacterium cytokinin biosynthesis gene driven by arabidopsis (arabidopsis thaliana) senescence specific promoter (sag12) for delaying leaf senescence. using two plasmids we co-transformed one week old embryogenic calli derived from mature japonica rice (oryza sativa) variety chin guang. the selectable marker hygromycin phosphotransferase (hph) gene and the reporter gene b-ß-glucuronidase (uida), both under the c ...201224575232
alteration of leaf metabolism in bt-transgenic rice (oryza sativa l.) and its wild type under insecticide stress.insecticide is always used to control the damage from pests, while the potential influence on plants is rarely known. time-course metabolic changes of wild and bacillus thuringiensis (bt) transgenic rice (oryza sativa l.) plants after insecticide treatment were investigated by using gas chromatography-mass spectrometry (gc-ms). a combined statistical strategy of 2-way anova and multivariate analyses (principal component analysis and hierarchal cluster analysis) was performed to find the stress-a ...201222768924
eukaryotic genomes may exhibit up to 10 generic classes of gene promoters.the main function of gene promoters appears to be the integration of different gene products in their biological pathways in order to maintain homeostasis. generally, promoters have been classified in two major classes, namely tata and cpg. nevertheless, many genes using the same combinatorial formation of transcription factors have different gene expression patterns. accordingly, we tried to ask ourselves some fundamental questions: why certain genes have an overall predisposition for higher ge ...201223020586
extracellular membrane vesicles and phytopathogenicity of acholeplasma laidlawii pg8.for the first time, the phytopathogenicity of extracellular vesicles of acholeplasma laidlawii pg8 (a ubiquitous mycoplasma that is one of the five common species of cell culture contaminants and is a causative agent for phytomycoplasmoses) in oryza sativa l. plants was studied. data on the ability of extracellular vesicles of acholeplasma laidlawii pg8 to penetrate from the nutrient medium into overground parts of oryza sativa l. through the root system and to cause alterations in ultrastructur ...201223251100
genetic organization of the hrp gene cluster in acidovorax avenae strain n1141 and a novel effector protein that elicits immune responses in rice (oryza sativa l.).the immune system of plants consists of two main arms, pathogen-associated molecular pattern (pamp)-triggered immunity (pti) and effector-triggered immunity (eti). the multiple effectors that trigger eti are translocated into plant cells by the type iii secretion system (t3ss) of pathogenic bacteria. the rice-avirulent n1141 strain of acidovorax avenae causes eti in rice, including hypersensitive response (hr) cell death. sequence analysis indicated that the n1141 genome contains the hrp gene cl ...201222232252
evaluation of four phloem-specific promoters in vegetative tissues of transgenic citrus plants.'mexican' lime (citrus aurantifolia swingle) was transformed with constructs that contained chimeric promoter-gus gene fusions of phloem-specific rolc promoter of agrobacterium rhizogenes, arabidopsis thaliana sucrose-h(+) symporter (atsuc2) gene promoter of arabidopsis thaliana, rice tungro bacilliform virus (rtbv) promoter and sucrose synthase l (rss1) gene promoter of oryza sativa (rice). histochemical β-glucuronidase (gus) analysis revealed vascular-specific expression of the gus protein in ...201222228816
population diversity of rice stripe virus-derived sirnas in three different hosts and rnai-based antiviral immunity in laodelphgax striatellus.small rna-mediated gene silencing plays evolutionarily conserved roles in gene regulation and defense against invasive nucleic acids. virus-derived small interfering rnas (vsirnas) are one of the key elements involved in rna silencing-based antiviral activities in plant and insect. vsirnas produced after viruses infecting hosts from a single kingdom (i.e., plant or animal) are well described. in contrast, vsirnas derived from viruses capable of infecting both plants and their insect vectors have ...201223029445
improving the nutritive value of rice seeds: elevation of cysteine and methionine contents in rice plants by ectopic expression of a bacterial serine acetyltransferase.with the aim of increasing the cysteine level in rice (oryza sativa l.) and thus improving its nutritional quality, transgenic rice plants were generated expressing an escherichia coli serine acetyltransferase isoform (ecsat), the enzyme synthesizing o-acetylserine, the precursor of cysteine. the gene was fused to the transit peptide of the arabidopsis rubisco and driven by a ubiquitin promoter to target the enzyme to plastids. twenty-two transgenic plants were examined for transgene protein exp ...201223048130
crystal structures of rice (oryza sativa) glyceraldehyde-3-phosphate dehydrogenase complexes with nad and sulfate suggest involvement of phe37 in nad binding for catalysis.cytosolic oryza sativa glyceraldehyde-3-phosphate dehydrogenase (osgapdh), the enzyme involved in the ubiquitous glycolysis, catalyzes the oxidative phosphorylation of glyceraldehyde-3-phosphate to 1,3-biphosphoglycerate (bpg) using nicotinamide adenine dinucleotide (nad) as an electron acceptor. we report crystal structures of osgapdh in three conditions of nad-free, nad-bound and sulfate-soaked forms to discuss the molecular determinants for coenzyme specificity. the structure of osgapdh showe ...201222903596
strain-dependent effects of inoculation of lactobacillus plantarum subsp. plantarum on fermentation quality of paddy rice (oryza sativa l. subsp. japonica) silage.paddy rice has been of particular interest as a forage crop in japan. in this study, the isolated strains to1000, to1001, to1002, and to1003 were characterized by phenotypic and genotypic approaches. these strains were identified as lactobacillus plantarum subsp. plantarum by species-specific pcr. phenotypic characteristics varied among different strains of the same subspecies, and the strains represented unique and diverse phenotypes related to fermentation factors, such as carbohydrate assimil ...201223003205
kinetic and phylogenetic analysis of plant polyamine uptake transporters.the rice gene polyamine uptake transporter1 (put1) was originally identified based on its homology to the polyamine uptake transporters lmpot1 and tcpat12 in leishmania major and trypanosoma cruzi, respectively. here we show that five additional transporters from rice and arabidopsis that cluster in the same clade as put1 all function as high affinity spermidine uptake transporters. yeast expression assays of these genes confirmed that uptake of spermidine was minimally affected by 166 fold or g ...201222711282
transcriptional reprogramming by root knot and migratory nematode infection in rice.rice is one of the most important staple crops worldwide, but its yield is compromised by different pathogens, including plant-parasitic nematodes. in this study we have characterized specific and general responses of rice (oryza sativa) roots challenged with two endoparasitic nematodes with very different modes of action. local transcriptional changes in rice roots upon root knot (meloidogyne graminicola) and root rot nematode (rrn, hirschmanniella oryzae) infection were studied at two time poi ...201222985291
an efficient and high-throughput protocol for agrobacterium-mediated transformation based on phosphomannose isomerase positive selection in japonica rice (oryza sativa l.).a number of agrobacterium-mediated rice transformation systems have been developed and widely used in numerous laboratories and research institutes. however, those systems generally employ antibiotics like kanamycin and hygromycin, or herbicide as selectable agents, and are used for the small-scale experiments. to address high-throughput production of transgenic rice plants via agrobacterium-mediated transformation, and to eliminate public concern on antibiotic markers, we developed a comprehens ...201222610504
identification and cloning of the cu/zn superoxide dismutase gene from halophyte plant aeluropus littoralis.reactive oxygen species (ros) derived from molecular oxygen under biotic and abiotic stress such as salinity which have deleterious effects on cell metabolism. the toxic effect of ros counteract by enzymatic as well as non-enzymatic antioxidant system. superoxide dismutase (sod) has a potential role for elimination of ros. halophytes respond to salt stress at different levels and can be a model for increasing salt tolerance in crop plants. thus salt tolerance gene isolation and cloning of gene a ...201222567863
purification, crystallization and preliminary x-ray analysis of osareb8 from rice, a member of the areb/abf family of bzip transcription factors, in complex with its cognate dna.the areb/abf family of bzip transcription factors play a key role in drought stress response and tolerance during the vegetative stage in plants. to reveal the dna-recognition mechanism of the areb/abf family of proteins, the bzip domain of osareb8, an areb/abf-family protein from oryza sativa, was expressed in escherichia coli, purified and crystallized with its cognate dna. crystals of the osareb8-dna complex were obtained by the sitting-drop vapour-diffusion method at 277 k with a reservoir s ...201222505428
characterization of glycine-rich rna-binding proteins in brassica napus under stress conditions.although the functional roles of glycine-rich rna-binding proteins (grps) during stress adaptation have been extensively evaluated in arabidopsis thaliana and rice (oryza sativa), the stress-responsive roles of a majority of grps have not been characterized in other plant species including rapeseed (brassica napus). here, the characteristic features and stress-responsive expression patterns of grps in b. napus (bngrps) were investigated. the genome of b. napus contains seven closely related bngr ...201222462633
molecular characterization and functional analysis by heterologous expression in e. coli under diverse abiotic stresses for oslea5, the atypical hydrophobic lea protein from oryza sativa l.in this study, we report the molecular characterization and functional analysis of oslea5 gene, which belongs to the atypical late embryogenesis abundant (lea) group 5c from oryza sativa l. the cdna of oslea5 contains a 456 bp orf encoding a polypeptide of 151 amino acids with a calculated molecular mass of 16.5 kda and a theoretical pi of 5.07. the oslea5 polypeptide is rich in leu (10%), ser (8.6%), and asp (8.6%), while cys, trp, and gln residue contents are very low, which are 2, 1.3, and 1. ...201222127413
experimental infection of fusarium proliferatum in oryza sativa plants; fumonisin b1 production and survival rate in grains.fusarium proliferatum is a plant pathogenic fungus associated with crops such as asparagus and corn, and it possesses the ability to produce a range of mycotoxins, including fumonisins. in asia, rice (oryza sativa) is a staple cereal and is occasionally colonized by this fungus without obvious physiological changes. f. proliferatum is closely related to gibberella fujikuroi (anamorph f. fujikuroi) responsible for bakanae disease in rice; however there are few reports of f. proliferatum as a rice ...201222534354
molecular and culture-dependent analyses revealed similarities in the endophytic bacterial community composition of leaves from three rice (oryza sativa) varieties.the endophytic bacterial communities of the three most important rice varieties cultivated in uruguay were compared by a multiphasic approach. leaves of mature plants grown in field experiments for two consecutive crop seasons were studied. no significant differences were found in the heterotrophic bacterial density for the three varieties. pantoea ananatis and pseudomonas syringae constituted 51% of the total of the isolates. these species were always present regardless of the variety or the se ...201222375835
lack of the golgi phosphate transporter pht4;6 causes strong developmental defects, constitutively activated disease resistance mechanisms and altered intracellular phosphate compartmentation in arabidopsis.the golgi-located phosphate exporter pht4;6 has been described as involved in salt tolerance but further analysis on the physiological impact of pht4;6 remained elusive. here we show that pht4;6-gfp is targeted to the trans-golgi compartment and that loss of function of this carrier protein has a dramatic impact on plant growth and development. knockout mutants of pht4;6 exhibit a dwarf phenotype that is complemented by the homologous gene from rice (oryza sativa). interestingly, pht4;6 mutants ...201222788523
mechanisms of oryza sativa (poaceae) resistance to tagosodes orizicolus (homoptera: delphacidae) under greenhouse condition in venezuela.tagosodes orizicolus is one of the main plagues of rice in tropical america causing two types of damages, the direct one, feeding and oviposition effect, and an indirect one, by the transmission of the "rice hoja blanca virus". during 2006-2007 we carried out research under greenhouse conditions at fundaci6n danac, venezuela, in order to determine the mechanisms of antixenosis, antibiosis and tolerance to t. orizicolus, which could be acting in commercial varieties and advanced lines of the rice ...201222458212
rna silencing suppressor pns11 of rice gall dwarf virus induces virus-like symptoms in transgenic rice.transgenic rice (oryza sativa) plants expressing the pns11 protein of rice gall dwarf virus (rgdv) displayed multiple abnormal phenotypes, some of which were highly reminiscent of the symptoms observed in rgdv-infected rice. further analysis indicated that the apparent alterations in plant growth and morphology were correlated with the expression levels of microrna160, microrna162, microrna167, microrna168, and the microrna target osarf8. especially, the striking dwarfing phenotype depended on t ...201222592958
identification of novel oryza sativa mirnas in deep sequencing-based small rna libraries of rice infected with rice stripe virus.micrornas (mirnas) play essential regulatory roles in the development of eukaryotes. methods based on deep-sequencing have provided a powerful high-throughput strategy for identifying novel mirnas and have previously been used to identify over 100 novel mirnas from rice. most of these reports are related to studies of rice development, tissue differentiation, or abiotic stress, but novel rice mirnas related to viral infection have rarely been identified. in previous work, we constructed and pyro ...201223071571
rnai-directed down-regulation of rsv results in increased resistance in rice (oryza sativa l.).rice stripe disease (rsd), caused by rice stripe virus (rsv), is a serious disease in temperate rice-growing areas. we have created an rnai construct containing coat protein gene (cp) and disease specific protein gene (sp) sequences from rsv. the rnai construct was transformed into two susceptible japonica varieties, suyunuo and guanglingxiangjing, to develop resistance against rsd. the homozygous progeny of rice plants in the t(5) and t(7) generations containing rnai constructs, after self-fert ...201222261864
historical contingencies modulate the adaptability of rice yellow mottle virus.the rymv1-2 and rymv1-3 alleles of the rymv1 resistance to rice yellow mottle virus (rymv), coded by an eif(iso)4g1 gene, occur in a few cultivars of the asiatic (oryza sativa) and african (o. glaberrima) rice species, respectively. the most salient feature of the resistance breaking (rb) process is the converse genetic barrier to rymv1-2 and rymv1-3 resistance breakdown. this specificity is modulated by the amino acid (glutamic acid vs. threonine) at codon 49 of the viral protein genome-linked ...201222291591
Transcriptional profiling in cadmium-treated rice seedling roots using suppressive subtractive hybridization.Cadmium (Cd), a non-essential metal, is a kind of toxic heavy metal to life, which can accumulate in rice tissues including seeds, thus posing a risk to human health through food chain. To investigate the molecular mechanisms of rice response to Cd exposure, suppression subtractive hybridization and mirror orientation selection were used to compare gene expression profiles in seedling roots of Cd-exposed and control (unexposed) rice plants (Oryza sativa L., Nipponbare). Approximately 1700 positi ...201221855360
Accumulation and phytotoxicity of microcystin-LR in rice (Oryza sativa).Irrigation with eutrophic water containing microcystins-LR (MC-LR) poses a potential risk to crops. However, the accumulation of MC-LR in rice grains and the mechanism of MC-LR-induced inhibition in rice roots are not understood. In this study, we detected the accumulation of MC-LR in rice grains collected from Taihu Lake region. MC-LR could accumulate in rice grains, but the risk evaluation suggested that MC-LR levels in rice grains from Taihu Lake region may not pose a threat to human health c ...201222036264
StackTIS: A stacked generalization approach for effective prediction of translation initiation sites.The prediction of the translation initiation site in an mRNA or cDNA sequence is an essential step in gene prediction and an open research problem in bioinformatics. Although recent approaches perform well, more effective and reliable methodologies are solicited. We developed an adaptable data mining method, called StackTIS, which is modular and consists of three prediction components that are combined into a meta-classification system, using stacked generalization, in a highly effective framewo ...201222079568
the rice transcription factor idef1 directly binds to iron and other divalent metals for sensing cellular iron status.iron is essential for most living organisms and its availability often determines survival and proliferation. the oryza sativa (rice) transcription factor idef1 plays a crucial role in regulating iron deficiency-induced genes involved in iron homeostasis. in the present report, we found characteristic histidine-asparagine repeat and proline-rich regions in idef1 and its homolog in hordeum vulgare (barley), hvidef1. an immobilized metal ion affinity chromatography assay revealed that idef1 and hv ...201221880076
molecular basis underlying the s5-dependent reproductive isolation and compatibility of indica/japonica rice hybrids.the s5 locus regulates spikelet fertility of indica/japonica hybrid rice. there are three alleles at the s5 locus, including an indica allele (s5i), a japonica allele (s5j), and a wide-compatibility allele (s5n). this study analyzed the molecular basis for s5-dependent reproductive isolation and compatibility of indica/japonica rice hybrids. three s5 alleles were expressed at extremely low levels, and only in the ovary. s5n was more similar to s5i in both rna and protein expression profiles. the ...201222218926
c-terminal residues of oryza sativa gun4 are required for the activation of the chlh subunit of magnesium chelatase in chlorophyll synthesis.oryza sativa gun4 together with the magnesium chelatase subunits chli, chld, and chlh have been heterologously expressed and purified to reconstitute magnesium chelatase activity in vitro. maximum magnesium chelatase activity requires pre-activation of oschlh with osgun4, mg(2+) and protoporphyrin-ix. osgun4 and oschlh preincubated without protoporphyrin-ix yields magnesium chelatase activity similar to assays without osgun4, suggesting formation of a dead-end complex. either 9 or 10 c-terminal ...201222226678
a systems approach for identifying resistance factors to rice stripe virus.rice stripe virus (rsv) causes disease that can severely affect the productivity of rice (oryza sativa). several rsv resistant cultivars have been developed. however, host factors conferring rsv resistance in these cultivars are still elusive. here, we present a systems approach for identifying potential rice resistance factors. we developed two near isogenic rsv resistant (nil22) and susceptible (nil37) lines and performed gene expression profiling of the two lines in rsv infected and uninfecte ...201222217248
biochemical identification of the osmkk6-osmpk3 signaling pathway for chilling stress tolerance in rice.mitogen-activated protein kinase (mapk) pathways have been implicated in stress signaling in plants. in this study, we performed yeast two-hybrid screening to identify partner mapks for osmkk6, a rice mapk kinase, and revealed specific interactions of osmkk6 with osmpk3 and osmpk6. osmpk3 and osmpk6 each co-immunoprecipitated osmkk6, and both were directly phosphorylated by osmkk6 in vitro. a mbp kinase assay of the immunoprecipitation complex indicated that osmpk3 and osmpk6 were activated in r ...201222248149
Molecular characterization of a rice metal tolerance protein, OsMTP1.Rice (Oryza sativa L. 'Nipponbare') cDNA subtractive suppression hybridization (SSH) libraries constructed using cadmium (Cd)-treated seedling roots were screened to isolate Cd-responsive genes. A cDNA clone, encoding the rice homolog of Metal Tolerance Protein (OsMTP1), was induced by Cd treatment. Plant MTPs belong to cation diffusion facilitator (CDF) protein family, which are widespread in bacteria, fungi, plants, and animals. OsMTP1 heterologous expression in yeast mutants showed that OsMTP ...201221892614
impact of mine waste dumps on growth and biomass of economically important crops.the present study aimed to investigate the effect of magnesite and bauxite waste dumps on growth and biochemical parameters of some edible and economically important plants such as vigna radiata, v. mungo, v. unguiculata, eleusine coracana, cajanus cajan, pennisetum glaucum, macrotyloma uniflorum, oryza sativa, sorghum bicolour, sesamum indicum, ricinus communis, brassica juncea, gossypium hirsutum and jatropha curcas. the growth rate of all the crops was observed in the range of 75 to 100% in m ...201223741803
observations on the foliar nematode, aphelenchoides besseyi, infecting tuberose and rice in india.the foliar nematode aphelenchoides besseyi causes white tip disease in rice (oryza sativa l.) and floral malady in tuberose (polianthes tuberosa l.). this nematode is widely distributed in the rice fields of many states of india, including west bengal (wb), andhra pradesh (ap), madhya pradesh (mp) and gujarat (gt). in order to generate information on intraspecific variations of a. besseyi as well as to confirm the identity of the nematode species infecting these important crops, morphological ob ...201223482906
antitumor effects of dietary black and brown rice brans in tumor-bearing mice: relationship to composition.feeding a diet supplemented with 10% (w/w) black and brown rice brans inhibited growth of transplanted tumors in mice.201223281142
transcription factor atbzip60 regulates expression of ca(2+)-dependent protein kinase genes in transgenic cells.the arabidopsis thaliana bzip60 (atbzip60) transcription factor regulates stress signaling. however, its molecular mechanism remains to be elucidated. in this investigation, cell suspension cultures of two different plant species rice (oryza sativa l.) and white pine (pinus strobes l.) were transformed using agrobacterium tumefaciens strain lba4404 harboring pbi-atzip60. integration of the atbzip60 gene into the genome of rice and white pine has been confirmed by polymerase chain reaction (pcr), ...201223275191
antimicrobial activity and mechanism of action of a novel cationic α-helical dodecapeptide, a partial sequence of cyanate lyase from rice.cl(14-25), a dodecapeptide, that is a partial region near n-terminus of cyanate lyase (cl, ec 4.3.99.1) from rice (oryza sativa l. japonica), contains three arginine and two lysine residues. it was a novel cationic α-helical antimicrobial peptide. the antimicrobial activity of cl(14-25) against porphyromonas gingivalis, a periodontal pathogen, was quantitatively evaluated by a chemiluminescence method that measures atp derived from viable cells. the 50% growth-inhibitory concentration of cl(14-2 ...201223270672
plant secondary metabolite profiling evidences strain-dependent effect in the azospirillum-oryza sativa association.azospirillum is a plant growth-promoting rhizobacterium (pgpr) able to enhance growth and yield of cereals such as rice, maize and wheat. the growth-promoting ability of some azospirillum strains appears to be highly specific to certain plant species and cultivars. in order to ascertain the specificity of the associative symbiosis between rice and azospirillum, the physiological response of two rice cultivars, nipponbare and cigalon, inoculated with two rice-associated azospirillum was analyzed ...201223266268
transcriptional regulations of the genes of starch metabolism and physiological changes in response to salt stress rice (oryza sativa l.) seedlings.the aim of this investigation was to compare the transcriptional expression of starch metabolism, involving genes and physiological characters, in seedlings of two contrasting salt-tolerant rice genotypes, in response to salt-stress. the soluble sugar content in rice seedlings of both salt-tolerant and salt-sensitive genotypes was enriched, relating to starch degradation, in plants subjected to 200 mm nacl. in the salt-tolerant cultivar pokkali, a major source of carbon may be that derived from ...201223814434
evaluations of allelopathic effect of echinochloa colona weed on rice (oryza sativa l. 'vandana').echinochloa colona (l.) link is a very problematic weed in up land and medium land rice causing significant reduction in yield. in the present investigation, laboratory and field experiments were conducted to evaluate the nature of interaction e. colona on germination and growth of the up land rice cultivar 'vandana'. the effects of decomposing and decomposed aqueous leachates (1-10% w/v) obtained from the dried biomass of 20, 30, 40 and 60 days old ecolona plants were studied on rice using petr ...201223734454
profiling of selected indigenous rice (oryza sativa l.) landraces of rarh bengal in relation to osmotic stress tolerance.a total of ten rare indigenous rice landraces of west bengal were screened for germination potential and seedling growth under varying concentrations of sodium chloride (nacl) and polyethylene glycol (peg) solutions as osmotic stress inducing agents. among the studied rice landraces kelas and bhut moori showed highest degree of tolerance to induced osmotic stresses. proline content of the studied lines was also determined. genetic relationship among the studied rice landraces was assessed with 2 ...201223573049
osarf12, a transcription activator on auxin response gene, regulates root elongation and affects iron accumulation in rice (oryza sativa).• auxin has an important role in maintaining optimal root system architecture (rsa) that can cope with growth reductions of crops caused by water or nutrient shortages. however, the mechanism of controlling rsa remains largely unclear. here, we found a limiting factor of rsa--osarf12--an auxin response factor whose knockout led to decreased primary root length in rice (oryza sativa). • osarf12 as a transcription activator can facilitate the expression of the auxin response element dr5::gfp, and ...201221973088
hdt701, a histone h4 deacetylase, negatively regulates plant innate immunity by modulating histone h4 acetylation of defense-related genes in rice.histone acetylation and deacetylation play an important role in the modification of chromatin structure and regulation of gene expression in eukaryotes. chromatin acetylation status is modulated antagonistically by histone acetyltransferases and histone deacetylases (hdacs). in this study, we characterized the function of histone deacetylase701 (hdt701), a member of the plant-specific hd2 subfamily of hdacs, in rice (oryza sativa) innate immunity. transcription of hdt701 is increased in the comp ...201222968716
lysin motif-containing proteins lyp4 and lyp6 play dual roles in peptidoglycan and chitin perception in rice innate immunity.plant innate immunity relies on successful detection of microbe-associated molecular patterns (mamps) of invading microbes via pattern recognition receptors (prrs) at the plant cell surface. here, we report two homologous rice (oryza sativa) lysin motif-containing proteins, lyp4 and lyp6, as dual functional prrs sensing bacterial peptidoglycan (pgn) and fungal chitin. live cell imaging and microsomal fractionation consistently revealed the plasma membrane localization of these proteins in rice c ...201222872757
lyk4, a lysin motif receptor-like kinase, is important for chitin signaling and plant innate immunity in arabidopsis.chitin is commonly found in fungal cell walls and is one of the well-studied microbe/pathogen-associated molecular patterns. previous studies showed that lysin motif (lysm)-containing proteins are essential for plant recognition of chitin, leading to the activation of plant innate immunity. in arabidopsis (arabidopsis thaliana), the lyk1/cerk1 (for lysm-containing receptor-like kinase1/chitin elicitor receptor kinase1) was shown to be essential for chitin recognition, whereas in rice (oryza sati ...201222744984
brassinosteroid action in flowering plants: a darwinian perspective.the year 2012 marks the 150th anniversary of the publication of charles darwin's first botanical book, on the fertilization of orchids (1862), wherein he described pollen grains and outlined his evolutionary principles with respect to plant research. five decades later, the growth-promoting effect of extracts of orchid pollen on coleoptile elongation was documented. these studies led to the discovery of a new class of phytohormones, the brassinosteroids (brs) that were isolated from rapeseed (br ...201222547659
silencing coi1 in rice increases susceptibility to chewing insects and impairs inducible defense.the jasmonic acid (ja) pathway plays a key role in plant defense responses against herbivorous insects. coronatine insensitive1 (coi1) is an f-box protein essential for all jasmonate responses. however, the precise defense function of coi1 in monocotyledonous plants, especially in rice (oryza sativa l.) is largely unknown. we silenced oscoi1 in rice plants via rna interference (rnai) to determine the role of oscoi1 in rice defense against rice leaf folder (lf) cnaphalocrocis medinalis, a chewing ...201222558386
brassinosteroids antagonize gibberellin- and salicylate-mediated root immunity in rice.brassinosteroids (brs) are a unique class of plant steroid hormones that orchestrate myriad growth and developmental processes. although brs have long been known to protect plants from a suite of biotic and abiotic stresses, our understanding of the underlying molecular mechanisms is still rudimentary. aiming to further decipher the molecular logic of br-modulated immunity, we have examined the dynamics and impact of brs during infection of rice (oryza sativa) with the root oomycete pythium gram ...201222353574
comparative transcriptome profiling of the early response to magnaporthe oryzae in durable resistant vs susceptible rice (oryza sativa l.) genotypes.durable resistance to blast, the most significant fungal disease of rice, represents an agronomically relevant character. gigante vercelli (gv) and vialone nano (vn) are two old temperate japonica italian rice cultivars with contrasting response to blast infection: gv displays durable and broad resistance while vn is highly susceptible. rna-seq was used to dissect the early molecular processes deployed during the resistance response of gv at 24 h after blast inoculation. differential gene expres ...201223251593
simultaneous rna-seq analysis of a mixed transcriptome of rice and blast fungus interaction.a filamentous fungus, magnaporthe oryzae, is a causal agent of rice blast disease, which is one of the most serious diseases affecting cultivated rice, oryza sativa. however, the molecular mechanisms underlying both rice defense and fungal attack are not yet fully understood. extensive past studies have characterized many infection-responsive genes in the pathogen and host plant, separately. to understand the plant-pathogen interaction comprehensively, it is valuable to monitor the gene expressi ...201223139845
the mechanism of phloem loading in rice (oryza sativa).carbohydrates, mainly sucrose, that are synthesized in source organs are transported to sink organs to support growth and development. phloem loading of sucrose is a crucial step that drives long-distance transport by elevating hydrostatic pressure in the phloem. three phloem loading strategies have been identified, two active mechanisms, apoplastic loading via sucrose transporters and symplastic polymer trapping, and one passive mechanism. the first two active loading mechanisms require metabol ...201222453778
dynamic nucleotide-binding site and leucine-rich repeat-encoding genes in the grass family.the proper use of resistance genes (r genes) requires a comprehensive understanding of their genomics and evolution. we analyzed genes encoding nucleotide-binding sites and leucine-rich repeats in the genomes of rice (oryza sativa), maize (zea mays), sorghum (sorghum bicolor), and brachypodium distachyon. frequent deletions and translocations of r genes generated prevalent presence/absence polymorphism between different accessions/species. the deletions were caused by unequal crossover, homologo ...201222422941
loss of cellulose synthase-like f6 function affects mixed-linkage glucan deposition, cell wall mechanical properties, and defense responses in vegetative tissues of rice.mixed-linkage glucan (mlg) is a cell wall polysaccharide containing a backbone of unbranched (1,3)- and (1,4)-linked β-glucosyl residues. based on its occurrence in plants and chemical characteristics, mlg has primarily been associated with the regulation of cell wall expansion due to its high and transient accumulation in young, expanding tissues. the cellulose synthase-like f (cslf) subfamily of glycosyltransferases has previously been implicated in mediating the biosynthesis of this polymer. ...201222388489
characterization of cyp76m5-8 indicates metabolic plasticity within a plant biosynthetic gene cluster.recent reports have revealed genomic clustering of enzymatic genes for particular biosynthetic pathways in plant specialized/secondary metabolism. rice (oryza sativa) carries two such clusters for production of antimicrobial diterpenoid phytoalexins, with the cluster on chromosome 2 containing four closely related/homologous members of the cytochrome p450 cyp76m subfamily (cyp76m5-8). notably, the underlying evolutionary expansion of these cyp appears to have occurred after assembly of the ances ...201222215681
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