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phosphate uptake and allocation - a closer look at arabidopsis thaliana l. and oryza sativa l.this year marks the 20th anniversary of the discovery and characterization of the two arabidopsis pht1 genes encoding the phosphate transporter in arabidopsis thaliana. so far, multiple inorganic phosphate (pi) transporters have been described, and the molecular basis of pi acquisition by plants has been well-characterized. these genes are involved in pi acquisition, allocation, and/or signal transduction. this review summarizes how pi is taken up by the roots and further distributed within two ...201627574525
a rice gene homologous to arabidopsis agd2-like defense1 participates in disease resistance response against infection with magnaporthe oryzae.ald1 (aberrant growth and death2 [agd2]-like defense1) is one of the key defense regulators in arabidopsis thaliana and nicotiana benthamiana. in these model plants, ald1 is responsible for triggering basal defense response and systemic resistance against bacterial infection. as well ald1 is involved in the production of pipecolic acid and an unidentified compound(s) for systemic resistance and priming syndrome, respectively. these previous studies proposed that ald1 is a potential candidate for ...201627493611
alternative splicing of rice wrky62 and wrky76 transcription factor genes in pathogen defense.the wrky family of transcription factors (tfs) functions as transcriptional activators or repressors in various signaling pathways. in this study, we discovered that oswrky62 and oswrky76, two genes of the wrky iia subfamily, undergo constitutive and inducible alternative splicing. the full-length oswrky62.1 and oswrky76.1 proteins formed homocomplexes and heterocomplexes, and the heterocomplex dominates in the nuclei when analyzed in nicotiana benthamiana leaves. transgenic overexpression of os ...201627208272
metabolic and transcriptomic changes induced in host during hypersensitive response mediated resistance in rice against the asian rice gall midge.an incompatible interaction between rice (oryza sativa) and the asian rice gall midge (agm, orseolia oryzae wood-mason), that is usually manifested through a hypersensitive response (hr), represents an intricate relationship between the resistant host and its avirulent pest. we investigated changes in the transcriptome and metabolome of the host (indica rice variety: rp2068-18-3-5, rp), showing hr when attacked by an avirulent gall midge biotype (gmb1), to deduce molecular and biochemical bases ...201626892000
pathogen effectors and plant immunity determine specialization of the blast fungus to rice subspecies.understanding how fungi specialize on their plant host is crucial for developing sustainable disease control. a traditional, centuries-old rice agro-system of the yuanyang terraces was used as a model to show that virulence effectors of the rice blast fungus magnaporthe oryzaeh play a key role in its specialization on locally grown indica or japonica local rice subspecies. our results have indicated that major differences in several components of basal immunity and effector-triggered immunity of ...201628008850
root transcriptome of two contrasting indica rice cultivars uncovers regulators of root development and physiological responses.the huge variation in root system architecture (rsa) among different rice (oryza sativa) cultivars is conferred by their genetic makeup and different growth or climatic conditions. unlike model plant arabidopsis, the molecular basis of such variation in rsa is very poorly understood in rice. cultivars with stable variation are valuable resources for identification of genes involved in rsa and related physiological traits. we have screened for rsa and identified two such indica rice cultivars, ir ...201628000793
two trichome birefringence-like proteins mediate xylan acetylation, which is essential for leaf blight resistance in rice.acetylation is a ubiquitous modification on cell wall polymers, which play a structural role in plant growth and stress defenses. however, the mechanisms for how crop plants accomplish cell wall polymer o-acetylation are largely unknown. here, we report on the isolation and characterization of two trichome birefringence-like (tbl) mutants in rice (oryza sativa), which are affected in xylan o-acetylation. ostbl1 and ostbl2 single mutant and the tbl1 tbl2 double mutant displayed a stunted growth p ...201627864442
effect of methyl salicylate (mesa), an elicitor on growth, physiology and pathology of resistant and susceptible rice varieties.methyl salicylate (mesa) is a volatile organic compound synthesized from salicylic acid (sa) a plant hormone that helps to fight against plant disease. seed treatment with mesa, is an encouraging method to the seed industry to produce more growth and yield. the aim of our study is to find out the growth, development and disease tolerance of rice seed treated with different concentrations of mesa. also the seed treatments were studied to determine whether they directly influenced seedling emergen ...201627725719
two different transcripts of a lammer kinase gene play opposite roles in disease resistance.alternative splicing of genes can increase protein diversity and affect mrna stability. genome-wide transcriptome sequencing has demonstrated that alternative splicing occurs in a large number of intron-containing genes of different species. however, despite the phenomenon having been known for decades, it is largely unknown how the alternatively spliced transcripts function differently. here, we report that two alternatively spliced transcripts of the rice (oryza sativa) lammer kinase gene osdr ...201627621422
identification and linkage analysis of a new rice bacterial blight resistance gene from xm14, a mutant line from ir24.bacterial blight caused by xanthomonas oryzae pv. oryzae (xoo) is a chief factor limiting rice productivity worldwide. xm14, a rice mutant line resistant to xoo, has been obtained by treating ir24, which is susceptible to six philippine xoo races and six japanese xoo races, with n-methyl-n-nitrosourea. xm14 showed resistance to six japanese xoo races. the f2 population from xm14 × ir24 clearly showed 1 resistant : 3 susceptible segregation, suggesting control of resistance by a recessive gene. t ...201627795689
the systemic acquired resistance regulator osnpr1 attenuates growth by repressing auxin signaling through promoting iaa-amido synthase expression.systemic acquired resistance is a long-lasting and broad-spectrum disease resistance to pathogens. our previous study demonstrated that overexpression of nonexpressor of pathogenesis-related genes1 (osnpr1), a master gene for systemic acquired resistance in rice (oryza sativa), greatly enhanced resistance to bacterial blight caused by xanthomonas oryzae pv oryzae however, the growth and development of the osnpr1 overexpression (osnpr1-ox) plants were restrained, and the mechanism remained elusiv ...201627378815
ascribing functions to genes: journey towards genetic improvement of rice via functional genomics.rice, one of the most important cereal crops for mankind, feeds more than half the world population. rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. this humungous resource of sequence data has confronted research fraternity with a herculean challenge as well ...201627252584
both overexpression and suppression of an oryza sativa nb-lrr-like gene oslsr result in autoactivation of immune response and thiamine accumulation.tight and accurate regulation of immunity and thiamine biosynthesis is critical for proper defence mechanisms and several primary metabolic cycles in plants. although thiamine is known to enhance plant defence by priming, the mechanism by which thiamine biosynthesis responds to immune signals remains poorly understood. here we identified a novel rice (oryza sativa l.) nb-lrr gene via an insertion mutation, this mutant confesses a low seed setting phenotype and the corresponding genetic locus was ...201627052628
functional analysis of jasmonates in rice through mutant approaches.jasmonic acid, one of the major plant hormones, is, unlike other hormones, a lipid-derived compound that is synthesized from the fatty acid linolenic acid. it has been studied intensively in many plant species including arabidopsis thaliana, in which most of the enzymes participating in its biosynthesis were characterized. in the past 15 years, mutants and transgenic plants affected in the jasmonate pathway became available in rice and facilitate studies on the functions of this hormone in an im ...201627135235
transcriptome-based identification of differently expressed genes from xanthomonas oryzae pv. oryzae strains exhibiting different virulence in rice varieties.xanthomonas oryzae pv. oryzae (xoo) causes bacterial blight (bb) in rice (oryza sativa l.). in this study, we investigated the genome-wide transcription patterns of two xoo strains (kacc10331 and hb1009), which showed different virulence patterns against eight rice cultivars, including irbb21 (carrying xa21). in total, 743 genes showed a significant change (p-value < 0.001 in t-tests) in their mrna expression levels in the hb1009 (k3a race) strain compared with the xoo kacc10331 strain (k1 race) ...201626907259
qtls for resistance to major rice diseases exacerbated by global warming: brown spot, bacterial seedling rot, and bacterial grain rot.in rice (oryza sativa l.), damage from diseases such as brown spot, caused by bipolaris oryzae, and bacterial seedling rot and bacterial grain rot, caused by burkholderia glumae, has increased under global warming because the optimal temperature ranges for growth of these pathogens are relatively high (around 30 °c). therefore, the need for cultivars carrying genes for resistance to these diseases is increasing to ensure sustainable rice production. in contrast to the situation for other importa ...201627178300
oswrky80-oswrky4 module as a positive regulatory circuit in rice resistance against rhizoctonia solani.plant wrky transcription factors play pivotal roles in diverse biological processes but most notably in plant defense response to pathogens. sheath blight represents one of the predominant diseases in rice. however, our knowledge about the functions of wrky proteins in rice defense against sheath blight is rather limited.201627888467
dna microarray and gene ontology enrichment analysis reveals that a mutation in opsx affects virulence and chemotaxis in xanthomonas oryzae pv. oryzae.xanthomonas oryzae pv. oryzae (xoo) causes bacterial leaf blight (blb) in rice (oryza sativa l.). in this study, we investigated the effect of a mutation in opsx (xoo1056), which encodes a saccharide biosynthesis regulatory protein, on the virulence and bacterial chemotaxis of xoo. we performed dna microarray analysis, which showed that 63 of 2,678 genes, including genes related to bacterial motility (flagellar and chemotaxis proteins) were significantly downregulated (<-2 log2 fold changes) by ...201627298594
integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread.plant immune receptors of the class of nucleotide-binding and leucine-rich repeat domain (nlr) proteins can contain additional domains besides canonical nb-arc (nucleotide-binding adaptor shared by apaf-1, r proteins, and ced-4 (nb-arc)) and leucine-rich repeat (lrr) domains. recent research suggests that these additional domains act as integrated decoys recognizing effectors from pathogens. proteins homologous to integrated decoys are suspected to be effector targets and involved in disease or ...201626848538
structure and catalytic mechanism of monodehydroascorbate reductase, mdhar, from oryza sativa l. japonica.ascorbic acid (asa) maintains redox homeostasis by scavenging reactive oxygen species from prokaryotes to eukaryotes, especially plants. the enzyme monodehydroascorbate reductase (mdhar) regenerates asa by catalysing the reduction of monodehydroascorbate, using nadh or nadph as an electron donor. the detailed recycling mechanism of mdhar remains unclear due to lack of structural information. here, we present the crystal structures of mdhar in the presence of cofactors, nicotinamide adenine dinuc ...201627652777
a mutagenic study identifying critical residues for the structure and function of rice manganese transporter osmtp8.1.rice (oryza sativa) mtp8.1 (osmtp8.1) is a tonoplast-localized manganese transporter of the cation diffusion facilitator family. here we present a structure-function analysis of osmtp8.1 based on the site-directed and random mutagenesis and complementation assays in manganese hypersensitive yeast, in combination with three-dimensional (3d) structure modeling based on the crystal structure of the escherichia coli cdf family member, ecyiip. two metal-binding sites are conserved in osmtp8.1 with ec ...201627555514
methane production and oxidation in an anoxic rice soil as influenced by inorganic redox species.the effects of addition of inorganic redox substances (species of no3-, mn4+, fe3+, and so4(2-)) on methane production and oxidation in anoxic rice (oryza sativa l.) soil samples were examined. sulfate was the most inhibitory for methane production followed by fe3+, no3-, and mn4+, in that order. addition of rice straw at a rate of 1% (w/w) as a carbon source to increase the electron donor to the electron acceptor ratio did not completely alleviate the inhibitory effects of redox species on meth ...201611790032
photoperiod shift effects on yield characteristics of rice.edible yield must be maximized for each crop species selected for inclusion in the controlled ecological life-support system (celss) proposed by nasa to support long-term manned space missions. in a greenhouse study aimed at increasing biomass partitioning to rice (oryza sativa l.) grain, plants of the high yielding semi-dwarf rice cultivar ai-nan-tsao were started in pots under 8-h photoperiods at a density of 212 plants m-2. after different periods of time under 8-h photoperiods, pots were swi ...201611540306
sensitivity of wheat and rice to low levels of atmospheric ethylene.ethylene (c2h4) gas is produced throughout the life cycle of plants and can accumulate in closed growth chambers to levels 100 times higher than in outside environments. elevated atmospheric c2h4 can cause a variety of abnormal responses, but the sensitivity to elevated c2h4 is not well characterized. we evaluated the c2h4 sensitivity of wheat (triticum aestivum l.) and rice (oryza sativa l.) in five studies. the first three studies compared the effects of continuous c2h4 levels ranging from 0 t ...201614552359
anaerobic conditions improve germination of a gibberellic acid deficient rice.dwarf plants are useful in research because multiple plants can be grown in a small area. rice (oryza sativa l.) is especially important since its relatively simple genome has recently been sequenced. we are characterizing a gibberellic acid (ga) mutant of rice (japonica cv 'shiokari,' line n-71) that is extremely dwarf (20 cm tall). unfortunately, this ga mutation is associated with poor germination (70%) under aerobic conditions. neither exogenous ga nor a dormancy-breaking heat treatment impr ...201614552358
effect of intermediates on ascorbic acid and oxalate biosynthesis of rice and in relation to its stress resistance.rice (oryza sativa l.) roots were fed with l-ascorbic acid (asa) and its putative precursors to observe asa and oxalate concentrations and the resistance of rice to chilling, water stress, and al toxicity. asa concentration was significantly enhanced in both shoots and roots of rice seedlings by feeding with d-glucose or l-galactono-gamma-lactone. asa or l-galactono-gamma-lactone treatment increased accumulation of oxalate mainly in soluble form, while these treatments decreased electrolyte leak ...201616310370
photon emissions from rice cells elicited by n-acetylchitooligosaccharide are generated through phospholipid signaling in close association with the production of reactive oxygen species.biophotons are ultraweak light emissions from biochemical reactions in a living body. they increase in suspension-cultured rice (oryza sativa l.) cells when elicited by n-acetylchitooligosaccharide. biochemical analyses were undertaken to investigate the relationship between disease response and biophotons in order to clarify the emission mechanism of biophotons caused by this elicitor. photon emissions induced by n-acetylchitohexaose were suppressed when cells were pretreated with the reactive ...201617123826
differential responses of antioxidative system to chilling and drought in four rice cultivars differing in sensitivity.responses of antioxidative defense systems to chilling and drought stresses were comparatively studied in four cultivars of rice (oryza sativa l.) differing in sensitivity, two of them (xiangnuo no. 1 and zimanuo) are tolerant to chilling but sensitive to drought and the other two (xiangzhongxian no. 2 and ir50) are tolerant to drought but sensitive to chilling. the seedlings of rice were transferred into growth chamber for 5 d at 8 degrees c as chilling treatment, or at 28 degrees c as control, ...201617098438
locus prl5 improves lodging resistance of rice by delaying senescence and increasing carbohydrate reaccumulation.we investigated the reason for carbohydrate retention in the stem of rice (oryza sativa l.) at full-ripe stage in a near-isogenic line (nil63) carrying prl5, which confers lodging resistance without yield loss. nil63 showed higher lodging resistance than nipponbare (control) without reduced yield. at heading, the carbohydrate content in the nil63 stem (culm and leaf sheathes) was the same as in nipponbare. at 2 weeks after heading, the carbohydrate content in nil63 was significantly higher than ...201616647265
sequence, expression and tissue localization of a gene encoding a makorin ring zinc-finger protein in germinating rice (oryza sativa l. ssp. japonica) seeds.the makorin (mkrn) ring finger protein gene family encodes proteins (makorins) with a characteristic array of zinc-finger motifs and which are present in a wide array of eukaryotes. in the present study, we analyzed the structure and expression of a putative makorin ring finger protein gene in rice (oryza sativa l. ssp. japonica cv. nipponbare). from the analysis of the genomic (ap003543), mrna (ak120250) and deduced protein (bad61603) sequences of the putative mkrn gene of rice, obtained from g ...201617870591
quantitative trait loci for sucrose, starch, and hexose accumulation before heading in rice.we studied the storage of sucrose, starch, and hexose before heading in rice (oryza sativa l.) plants by quantitative trait locus (qtl) analysis with a population of backcross inbred lines (bils) of japonica cv. nipponbare x indica cv. kasalath. carbohydrates are accumulated in the rice plant before heading and are translated to the panicle after heading. a higher capacity for accumulation is thus a main target for improvement in yield. the form of carbohydrate (sucrose, starch, or hexose) diffe ...201617845859
biochemical and physiological characterization of a tau class glutathione transferase from rice (oryza sativa).the classical phase ii detoxification glutathione transferases (gsts) are key metabolic enzymes that catalyze the conjugation of glutathione to various electrophilic compounds. a tau class gst gene (osgstu17) was cloned from rice, which encodes a protein of 223 amino acid residues with a calculated molecular mass of 25.18 kda. the recombinant osgstu17 formed a homodimer protein and showed gsh-conjugating activity with various xenobiotics. kinetic analysis with respect to nbd-cl as substrate reve ...201619640724
molecular characterization of flavonoid malonyltransferase from oryza sativa.in this study, a flavonoid malonyltransferase (osmat-2) was cloned from oryza sativa, and the recombinant protein osmat-2 was purified via affinity chromatography. osmat-2 utilized a variety of flavonoid glucosides, including flavanone glucosides, flavone glucosides, flavonol glucosides, and isoflavone glucosides as substrates, but did not utilize anthocyanin. as an acyl donor, osmat-2 utilized only malonyl-coa. based on reactions with various quercetin 3-o-sugars, we identified the probable pos ...201619733090
malate exudation by six aerobic rice genotypes varying in zinc uptake efficiency.zinc (zn) uptake by plant roots from soils low in plant-available zn may be increased by zn-mobilizing rhizosphere processes, including exudation of low-molecular-weight organic anions. a rhizotron experiment with a low zn clay soil and a nutrient solution experiment were conducted to test if this occurs in six rice (oryza sativa l.) genotypes varying in tolerance to low zn supply. in both experiments, low zn supply resulted in a marked decrease in biomass production of most genotypes compared w ...201719875787
risk assessment of potentially toxic element pollution in soils and rice (oryza sativa) in a typical area of the yangtze river delta.soil pollution with potentially toxic elements (ptes) resulting from rapid industrial development has caused major concerns. selected ptes and their accumulation and distribution in soils and rice (oryza sativa) collected from changshu, east china, were analyzed to evaluate the potential health risk to the local population. the soils were primarily contaminated with hg, followed by cu, cd, pb, and zn. the concentrations of pb, hg, and cd of 46, 32, and 1 rice samples exceeded their national maxi ...201719344985
sds-dependent proteases induced by aba and its relation to rubisco and rubisco activase contents in rice leaves.protease activities and its relation to the contents of ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) and rubisco activase were investigated in detached leaves of rice (oryza sativa l.) floated on the solutions containing abscisic acid (aba) or benzyladenine (ba). rubisco and rubisco activase contents were decreased during the time course and the decreases were enhanced by aba and suppressed by ba. the decrease in rubisco activase was faster than that in rubisco. sds-dependent protea ...201720829052
methane oxidation in an intensively cropped tropical rice field soil under long-term application of organic and mineral fertilizers.methane (ch4) oxidation is the only known biological sink process for mitigating atmospheric and terrestrial emissions of ch4, a major greenhouse gas. methane oxidation in an alluvial soil planted to rice (oryza sativa l.) under long-term application of organic (compost with a c/n ratio of 21.71), and mineral fertilizers was measured in a field-cum-laboratory incubation study. oxidation rates were quantified in terms of decrease in the concentration of ch4 in the headspace of incubation vessels ...201717940256
accumulation, distribution and transformation of ddt and pcbs by phragmites australis and oryza sativa l.: i. whole plant study.glasshouse experiments were conducted to determine the accumulation, distribution and transformation of o,p'-ddt, p,p'-ddt and pcbs by common reed (phragmites australis) and rice (oryza sativa l.) under hydroponic conditions. the culture solution was spiked with the organic pollutants and samples were collected daily. analysis of the plants at harvest showed that both species had removed ddt and pcbs from the solution. ddt appeared to have accumulated within p. australis by both passive adsorpti ...201716547765
accumulation, distribution and transformation of ddt and pcbs by phragmites australis and oryza sativa l.: ii. enzyme study.two wetland plant species, phragmites australis and oryza sativa, were grown in a glasshouse under hydroponics conditions. enzyme extracts from different parts of the plants were used to determine the transformation rate of o,p'-ddt, p,p'-ddt and pcbs. the organic pollutants were directly spiked into the enzyme extracts, and samples were collected every 30 min and analyzed with a gc-ecd. root extracts of p. australis readily degraded and transformed ddt and some pcb congeners with a low degree o ...201716547764
effects of the interactions between selenium and phosphorus on the growth and selenium accumulation in rice (oryza sativa).the solution culture, paddy soil culture and the simulation experiments in the laboratory were conducted to clarify the interactions between selenium and phosphorus, and its effects on the growth and selenium accumulation in rice. results revealed that a suitable supply of selenium could promote rice growth and excessive selenium could injure rice plant, causing lower biomass, especially in the roots. the supply of selenite could enhance the selenium contents of rice shoots and roots in solution ...201715499790
dissipation of pentachlorophenol in the aerobic-anaerobic interfaces established by the rhizosphere of rice ( oryza sativa l.) root.phytoremediation is an emerging technology for the detoxification and remediation of organic pollutants such as pentachlorophenol (pcp). to investigate the dissipation behavior of pcp in the aerobic-anaerobic interfaces established by the rhizosphere of rice ( l.) root, a glasshouse experiment was conducted using a specially designed rhizobox. the possible biogeochemical mechanisms were also studied through illustration of the dynamic behavior of important electron acceptors and donors that are ...201722031554
chromium bioaccumulation in rice grown in contaminated soil and irrigated mine wastewater--a case study at south kaliapani chromite mine area, orissa, india.the level of chromium (cr) contamination in soils and irrigated mine wastewater at south kaliapani chromite mine region of orissa, (india) were investigated. chromium bioaccumulation in rice plants (oryza sativa l. cv. khandagiri) irrigated with cr+6 contaminated mine wastewater was analyzed along with its attenuation from mine wastewater. the levels of cr+6 in irrigated mine wastewaters in successive rice grown plots were analyzed on 75 days and 100 days after transplantation of seedlings. tota ...201721598771
in silico analysis of expression data for identification of genes involved in spatial accumulation of calcium in developing seeds of rice.the calcium (ca(2+)) transporters, like ca(2+) channels, ca(2+) atpases, and ca(2+) exchangers, are instrumental for signaling and transport. however, the mechanism by which they orchestrate the accumulation of ca(2+) in grain filling has not yet been investigated. hence the present study was designed to identify the potential calcium transporter genes that may be responsible for the spatial accumulation of calcium during grain filling. in silico expression analyses were performed to identify ca ...201722734689
multinuclear magnetic resonance analysis of two humic acid fractions from lowland rice soils.to determine the effects of intensive cropping of tropical lowland rice (oryza sativa l.) and the associated long-term soil submergence on chemical properties of soil organic matter, we used solid-state 13c and 15n and solution 31p nuclear magnetic resonance (nmr) spectroscopy to analyze the labile mobile humic acid (mha) and the more recalcitrant calcium humate (caha) fractions extracted from a series of soils supporting several long-term field experiments in the philippines. the soils varied m ...201711931429
whole-cell biocatalytic and de novo production of alkanes from free fatty acids in saccharomyces cerevisiae.rapid global industrialization in the past decades has led to extensive utilization of fossil fuels, which resulted in pressing environmental problems due to excessive carbon emission. this prompted increasing interest in developing advanced biofuels with higher energy density to substitute fossil fuels and bio-alkane has gained attention as an ideal drop-in fuel candidate. production of alkanes in bacteria has been widely studied but studies on the utilization of the robust yeast host, saccharo ...201726717118
two h-type thioredoxins interact with the e2 ubiquitin conjugase pho2 to fine-tune phosphate homeostasis in rice.phosphate overaccumulator2 (pho2) encodes a ubiquitin-conjugating e2 enzyme that is a major negative regulator of the inorganic phosphate (pi)-starvation response-signaling pathway. a yeast two-hybrid (y2h) screen in rice (oryza sativa; os) using ospho2 as bait revealed an interaction between ospho2 and two h-type thioredoxins, ostrxh1 and ostrxh4. these interactions were confirmed in vivo using bimolecular fluorescence complementation (bifc) of ospho2 and ostrxh1/h4 in rice protoplasts and by i ...201727895204
resolvase osgen1 mediates dna repair by homologous recombination.yen1/gen1 are canonical holliday junction resolvases that belong to the rad2/xpg family. in eukaryotes, such as budding yeast, mice, worms, and humans, yen1/gen1 work together with mus81-mms4/mus81-eme1 and slx1-slx4/slx1-slx4 in dna repair by homologous recombination to maintain genome stability. in plants, the biological function of yen1/gen1 remains largely unclear. in this study, we characterized the loss of function mutants of osgen1 and ossend1, a pair of paralogs of yen1/gen1 in rice (ory ...201728049740
a β-ketoacyl-coa synthase is involved in rice leaf cuticular wax synthesis and requires a cer2-like protein as a cofactor.cuticular waxes are complex mixtures of very-long-chain fatty acids (vlcfas) and their derivatives, forming a natural barrier on aerial surfaces of terrestrial plants against biotic and abiotic stresses. in vlcfa biosynthesis, β-ketoacyl-coa synthase (kcs) is the key enzyme, catalyzing the first reaction in fatty acid elongation and determining substrate specificity. we isolated a rice (oryza sativa) wax crystal-sparse leaf 4 (wsl4) gene using a map-based cloning strategy. wsl4 is predicted to e ...201727913740
molecular interaction between pho2 and gi in rice.plants are often confronted to nutrient limiting conditions, such as inorganic phosphate (pi) deficiency, resulting in a reduction in growth and yield. pho2, encoding a ubiquitin-conjugating e2 enzyme, is a central component of the pi-starvation response signaling pathway. a yeast-two-hybrid screen using oryza sativa (rice) pho2 as bait, revealed an interaction between ospho2 and osgigantea, a key regulator of flowering time, which was confirmed using bimolecular flourescenec complementation (bi ...201728337762
response of alternative splice isoforms of osrad9 gene from oryza sativa to environmental stress.rad9 protein plays an important role in cell-cycle checkpoint signal transduction in human and yeast cells, but knowledge about rad9 in plants is limited. this study reports that the rad9 gene of rice can generate the transcript products osrad9.1 and osrad9.2 through alternative splicing. osrad9.1, with all nine exons, is the main cell-cycle checkpoint protein involved in the response of rice to genotoxic stresses (ultraviolet radiation and antibiotic stress), environmental stresses (drought, sa ...201728301324
identification of alternatively spliced transcripts of rice phytochelatin synthase 2 gene ospcs2 involved in mitigation of cadmium and arsenic stresses.the ospcs2 exhibits root- and shoot-specific differential ratios of alternatively spliced transcripts in indica rice under cd stress, and plays role in cd and as stress tolerance and accumulation. enzymatic activity of phytochelatin synthase (pcs) in plant produces phytochelatins, which help in sequestration of heavy metal(loid)s inside the cell vacuole to alleviate toxicity. here we report that among the two pcs genes-ospcs1 and ospcs2 in indica rice (oryza sativa) cultivar, the ospcs2 produces ...201728283922
characterization and ectopic expression of cowri1, an ap2/erebp domain-containing transcription factor from coconut (cocos nucifera l.) endosperm, changes the seeds oil content in transgenic arabidopsis thaliana and rice (oryza sativa l.).coconut (cocos nucifera l.) is a key tropical crop and a member of the monocotyledonous family arecaceae (palmaceae). few genes and related metabolic processes involved in coconut endosperm development have been investigated. in this study, a new member of the wri1 gene family was isolated from coconut endosperm and was named cowri1. its transcriptional activities and interactions with the acetyl-coa carboxylase (bccp2) promoter of cowri1 were confirmed by the yeast two-hybrid and yeast one-hybr ...201728179911
homologous u-box e3 ubiquitin ligases ospub2 and ospub3 are involved in the positive regulation of low temperature stress response in rice (oryza sativa l.).rice u-box e3 ub ligases (ospubs) are implicated in biotic stress responses. however, their cellular roles in response to abiotic stress are poorly understood. in this study, we performed functional analyses of two homologous ospub2 and ospub3 in response to cold stress (4°c). ospub2 was up-regulated by high salinity, drought, and cold, whereas ospub3 was constitutively expressed. a subcellular localization assay revealed that ospub2 and ospub3 were localized to the exocyst positive organelle (e ...201728163713
fine mapping of rymv3: a new resistance gene to rice yellow mottle virus from oryza glaberrima.a new resistance gene against rice yellow mottle virus was identified and mapped in a 15-kb interval. the best candidate is a cc-nbs-lrr gene. rice yellow mottle virus (rymv) disease is a serious constraint to the cultivation of rice in africa and selection for resistance is considered to be the most effective management strategy. the aim of this study was to characterize the resistance of tog5307, a highly resistant accession belonging to the african cultivated rice species (oryza glaberrima), ...201728144699
genome inside genome: ngs based identification and assembly of endophytic sphingopyxis granuli and pseudomonas aeruginosa genomes from rice genomic reads.the interactions between crop plants and the endophytic bacteria colonizing them are poorly understood and experimental methods were found to be inadequate to meet the complexities associated with the interaction. moreover, research on endophytic bacteria was focused at host plant species level and not at cultivar level which is essential for understanding the role played by them on the productivity of specific crop genotype. high throughput genomics offers valuable tools for identification, cha ...201728192179
reconstruction of the astaxanthin biosynthesis pathway in rice endosperm reveals a metabolic bottleneck at the level of endogenous β-carotene hydroxylase activity.astaxanthin is a high-value ketocarotenoid rarely found in plants. it is derived from β-carotene by the 3-hydroxylation and 4-ketolation of both ionone end groups, in reactions catalyzed by β-carotene hydroxylase and β-carotene ketolase, respectively. we investigated the feasibility of introducing an extended carotenoid biosynthesis pathway into rice endosperm to achieve the production of astaxanthin. this allowed us to identify potential metabolic bottlenecks that have thus far prevented the ac ...201727567632
jasmonic acid-mediated defense suppresses brassinosteroid-mediated susceptibility to rice black streaked dwarf virus infection in rice.plant hormones play a vital role in plant immune responses. however, in contrast to the relative wealth of information on hormone-mediated immunity in dicot plants, little information is available on monocot-virus defense systems. we used a high-throughput-sequencing approach to compare the global gene expression of rice black-streaked dwarf virus (rbsdv)-infected rice plants with that of healthy plants. exogenous hormone applications and transgenic rice were used to test rbsdv infectivity and p ...201727976810
meloidogyne graminicola: a major threat to rice agriculture.superkingdom eukaryota; kingdom metazoa; phylum nematoda; class chromadorea; order tylenchida; suborder tylenchina; infraorder tylenchomorpha; superfamily tylenchoidea; family meloidogynidae; subfamily meloidogyninae; genus meloidogyne.201726950515
transcriptomic and histological responses of african rice (oryza glaberrima) to meloidogyne graminicola provide new insights into root-knot nematode resistance in monocots.the root-knot nematode meloidogyne graminicola is responsible for production losses in rice ( oryza sativa ) in asia and latin america. the accession tog5681 of african rice, o. glaberrima , presents improved resistance to several biotic and abiotic factors, including nematodes. the aim of this study was to assess the cytological and molecular mechanisms underlying nematode resistance in this accession.201728334204
production of bp178, a derivative of the synthetic antibacterial peptide bp100, in the rice seed endosperm.bp178 peptide is a synthetic bp100-magainin derivative possessing strong inhibitory activity against plant pathogenic bacteria, offering a great potential for future applications in plant protection and other fields. here we report the production and recovery of a bioactive bp178 peptide using rice seeds as biofactories.201728292258
human leukemia inhibitory factor produced by the expresstec method from rice (oryza sativa l.) is active in human neural stem cells and mouse induced pluripotent stem cells.stem cell-based therapy has the potential to treat an array of human diseases. however, to study the therapeutic potential and safety of these cells, a scalable cell culture medium is needed that is free of human or bovine-derived serum proteins. thus, cost-effective recombinant serum proteins and cytokines are needed to produce such mediums. one such cytokine, leukemia inhibitory factor (lif), has been shown to be a critical paracrine factor that maintains stem cell pluripotency in murine embry ...201724776984
activation of a calcium-dependent protein kinase involved in the azospirillum growth promotion in rice.rice seedlings (oryza sativa) inoculated with the plant growth-promoting rhizobacteria azospirillum brasilense ft326 showed an enhanced development of the root system 3 days after inoculation. later on, a remarkable enlargement of shoots was also evident. an increase in the ca(2+)-dependent histone kinase activity was also detected as a result of inoculation. the biochemical characterization and western-blot analysis of the kinase strongly supports the hypothesis that it belongs to a member of t ...201728044270
an activity-staining method on filtration paper enables high-throughput screening of temperature-sensitive and inactive mutations of rice α-amylase for improvement of rice grain quality.α-amylase is a starch-hydrolyzing enzyme (ec 3.2.1.1) indispensable for germination of cereal seeds, but it is also expressed during the ripening stage. previous studies demonstrated that the enzyme is activated in developing rice seeds under extremely hot weather and triggers a loss of grain quality by hindering the accumulation of storage starch in the endosperm. since inactive or, preferably, heat-labile α-amylases are preferable for breeding premium rice, we developed a method for rapid scre ...201728339688
development of an inducible male-sterility system in rice through pollen-specific expression of l-ornithinase (arge) gene of e. coli.in the present investigation, an inducible male-sterility system has been developed in the rice. in order to introduce inducible male-sterility, the coding region of l-ornithinase (arge) gene of e. coli was fused to the oryza sativa indica pollen allergen (osipa) promoter sequence which is known to function specifically in the pollen grains. transgenic plants were obtained with arge gene and the transgenic status of plants was confirmed by pcr and southern blot analyses. rt-pcr analysis confirme ...201728167027
the oshapl1-dth8-hd1 complex functions as the transcription regulator to repress heading date in rice.heading date is an important agronomic trait related to crop yield. many genes related to heading date have already been identified in rice (oryza sativa), and a complicated, preliminary regulatory genetic network has also already been established, but the protein regulatory network is poorly understood. we have identified a novel heading date regulator, heme activator protein like 1 (oshapl1), which inhibits flowering under long-day conditions. oshapl1 is a nuclear-localized protein that is hig ...201728043949
osasr5 enhances drought tolerance through a stomatal closure pathway associated with aba and h2 o2 signalling in rice.drought is one of the major abiotic stresses that directly implicate plant growth and crop productivity. although many genes in response to drought stress have been identified, genetic improvement to drought resistance especially in food crops is showing relatively slow progress worldwide. here, we reported the isolation of abscisic acid, stress and ripening (asr) genes from upland rice variety, irat109 (oryza sativa l. ssp. japonica), and demonstrated that overexpression of osasr5 enhanced osmo ...201727420922
cd immobilization and reduced tissue cd accumulation of rice (oryza sativa wuyun-23) in the presence of heavy metal-resistant bacteria.two metal-resistant bacillus megaterium h3 and neorhizobium huautlense t1-17 were investigated for their immobilization of cd in solution and tissue cd accumulation of rice (oryza sativa wuyun-23) in the cd-contaminated soil. strains h3 and t1-17 decreased 79-96% of water-soluble cd in solution and increased grain biomass in the high cd-contaminated soil. inoculation with h3 and t1-17 significantly decreased the root (ranging from 25% to 58%), above-ground tissue (ranging from 13% to 34%), and p ...201728011421
identification of phenolic compounds that suppress the virulence of xanthomonas oryzae on rice via the type iii secretion system.the targeting of bacterial type iii secretion systems (t3sss), which are critical virulence factors in most gram-negative pathogens, is regarded as an alternative strategy for the development of novel anti-microbial drugs. xanthomonas oryzae pv. oryzae (xoo) and x. oryzae pv. oryzicola (xoc) are two of the most important bacterial pathogens on rice, which cause leaf blight and leaf streak diseases, respectively. to identify potential anti-virulence drugs against these two pathogens, we screened ...201727084974
oscul3a negatively regulates cell death and immunity by degrading osnpr1 in rice.cullin3-based ring e3 ubiquitin ligases (crl3), composed of cullin3 (cul3), rbx1, and btb proteins, are involved in plant immunity, but the function of cul3 in the process is largely unknown. here, we show that rice (oryza sativa) oscul3a is important for the regulation of cell death and immunity. the rice lesion mimic mutant oscul3a displays a significant increase in the accumulation of flg22- and chitin-induced reactive oxygen species, and in pathogenesis-related gene expression as well as res ...201728100706
rice leaf transcriptional profiling suggests a functional interplay between xanthomonas oryzae pv. oryzae lipopolysaccharide and extracellular polysaccharide in modulation of defense responses during infection.treatment of rice leaves with isolated xanthomonas oryzae pv. oryzae lipopolysaccharide (lps) induces the production of callose deposits, reactive oxygen species, and enhanced resistance against subsequent bacterial infection. expression profiling of x. oryzae pv. oryzae lps-treated rice (oryza sativa subsp. indica) leaves showed that genes involved in the biosynthetic pathways for lignins, phenylpropanoids, chorismate, phenylalanine, salicylic acid, and ethylene, as well as a number of pathogen ...201727918246
genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm.bacterial blight, which is caused by xanthomonas oryzae pv. oryzae (xoo), is one of the most devastating rice diseases worldwide. the development and use of disease-resistant cultivars have been the most effective strategy to control bacterial blight. identifying the genes mediating bacterial blight resistance is a prerequisite for breeding cultivars with broad-spectrum and durable resistance. we herein describe a genome-wide association study involving 172 diverse oryza sativa ssp. indica acces ...201728355306
genome-wide association analysis tracks bacterial leaf blight resistance loci in rice diverse germplasm.a range of resistance loci against different races of xanthomonas oryzae pv. oryzae (xoo), the pathogen causing bacterial blight (bb) disease of rice, have been discovered and characterized. several have been deployed in modern varieties, however, due to rapid evolution of xoo, a number have already become ineffective. the continuous "arms race" between xoo and rice makes it imperative to discover new resistance loci to enable durable deployment of multiple resistance genes in modern breeding li ...201728321828
characterization of a disease susceptibility locus for exploring an efficient way to improve rice resistance against bacterial blight.bacterial blight caused by xanthomonas oryzae pv. oryzae (xoo) is the most harmful bacterial disease of rice worldwide. previously, we characterized major disease resistance (mr) gene xa25, which confers race-specific resistance to xoo strain pxo339. the xa25 is a recessive allele of the sweet13 locus, but sweet13's interaction with pxo339 and how efficiently using this locus for rice breeding still need to be defined. here we show that the sweet13 allele from rice zhenshan 97 is a susceptibilit ...201728251460
novel interaction between ccr4 and caf1 in rice ccr4-not deadenylase complex.rice is an important crop in the world. however, little is known about rice mrna deadenylation, which is an important regulation step of gene expression at the post-transcriptional level. the ccr4-not1 complex contains two key components, ccr4 and caf1, which are the main cytoplasmic deadenylases in eukaryotic cells. in yeast and humans, ccr4 can interact with caf1 via its n-terminal lrr domain. however, no ccr4 protein containing n-terminal lrr motifs have been found in plants. in this manuscri ...201727714489
identification of 4-mercapto-4-methylpentan-2-one as the characteristic aroma of sake made from low-glutelin rice.the grassy characteristic aroma perceived in brewed sake made from low-glutelin rice (oryza sativa l. mizuhonoka) was examined by gas chromatography-olfactometry and gas chromatography-mass spectrometry. by comparing the odor properties and kovats retention indices to those of standard compounds, 4-mercapto-4-methylpentan-2-one (4mmp) was found to contribute to the characteristic aroma. sake brewing using mizuhonoka, low-glutelin rice, and gin-ohmi (a control) revealed that 4mmp concentrations i ...201727773607
functional characterization of endophytic fungal community associated with oryza sativa l. and zea mays l.in a natural ecosystem, the plant is in a symbiotic relationship with beneficial endophytes contributing huge impact on its host plant. therefore, exploring beneficial endophytes and understanding its interaction is a prospective area of research. the present work aims to characterize the fungal endophytic communities associated with healthy maize and rice plants and to study the deterministic factors influencing plant growth and biocontrol properties against phytopathogens, viz, pythium ultimum ...201728303127
molecular, structural, and phylogenetic analyses of taxus chinensis jazs.taxus spp. are ancient gymnosperms that produce a unique secondary metabolite, namely, taxol, an anticancer drug. jaz proteins are key regulators of the ja signaling pathway, which control taxol biosynthesis. however, the jaz proteins of taxus spp. are poorly studied. in this work, nine jaz genes from taxus chinensis were identified using our previous transcriptome data and named as tcjaz1-tcjaz9. of these nine tcjaz proteins, eight contain jas and tify domains, and the jas domain of tcjaz6 is i ...201728390989
overexpression of an arabidopsis thaliana galactinol synthase gene improves drought tolerance in transgenic rice and increased grain yield in the field.drought stress has often caused significant decreases in crop production which could be associated with global warming. enhancing drought tolerance without a grain yield penalty has been a great challenge in crop improvement. here, we report the arabidopsis thaliana galactinol synthase 2 gene (atgols2) was able to confer drought tolerance and increase grain yield in two different rice (oryza sativa) genotypes under dry field conditions. the developed ubi:atgols2 transgenic lines also had higher ...201728378532
genome-wide analysis and expression profiling of the grf gene family in oilseed rape (brassica napus l.).growth regulating-factors (grfs) are plant-specific transcription factors that help regulate plant growth and development. genome-wide identification and evolutionary analyses of grf gene families have been performed in arabidopsis thaliana, zea mays, oryza sativa, and brassica rapa, but a comprehensive analysis of the grf gene family in oilseed rape (brassica napus) has not yet been reported. in the current study, we identified 35 members of the bngrf family in b. napus. we analyzed the chromos ...201728363779
dynamic regulation of auxin response during rice development revealed by newly established hormone biosensor markers.the hormone auxin is critical for many plant developmental processes. unlike the model eudicot plant arabidopsis (arabidopsis thaliana), auxin distribution and signaling in rice tissues has not been systematically investigated due to the absence of suitable auxin response reporters. in this study we observed the conservation of auxin signaling components between arabidopsis and model monocot crop rice (oryza sativa), and generated complementary types of auxin biosensor constructs, one derived fr ...201728326089
osnla1, a ring-type ubiquitin ligase, maintains phosphate homeostasis in oryza sativa via degradation of phosphate transporters.inorganic phosphate (pi) transporters (pts) play vital roles in pi uptake and translocation in plants. under pi sufficient conditions, pts are degraded to prevent excess pi accumulation. the mechanisms targeting pts for degradation are not fully elucidated. in this study, we found that the oryza sativa (rice) ortholog of arabidopsis thaliana nitrogen limitation adaptation (nla), osnla1 protein, a ring-type e3 ubiquitin-ligase, was predominantly localized in the plasma membrane, and could interac ...201728229491
analysis of plant udp-arabinopyranose mutase (uam): role of divalent metals and structure prediction.udp-arabinopyranose mutase (uam) is a plant enzyme which interconverts udp-arabinopyranose (udp-arap; a six-membered sugar) to udp-arabinofuranose (udp-araf; a five-membered sugar). plant mutases belong to a small gene family called reversibly glycosylated proteins (rgps). so far, uam has been identified in oryza sativa (rice), arabidopsis thaliana and hordeum vulgare (barley). the enzyme requires divalent metal ions for catalytic activity. here, the divalent metal ion dependency of uams from o. ...201728192204
identification of symmetrical rna editing events in the mitochondria of salvia miltiorrhiza by strand-specific rna sequencing.salvia miltiorrhiza is one of the most widely-used medicinal plants. here, we systematically analyzed the rna editing events in its mitochondria. we developed a pipeline using reditools to predict rna editing events from stand-specific rna-seq data. the predictions were validated using reverse transcription, rt-pcr amplification and sanger sequencing experiments. putative sequences motifs were characterized. comparative analyses were carried out between s. miltiorrhiza, arabidopsis thaliana and ...201728186130
origin and diversification of leucine-rich repeat receptor-like protein kinase (lrr-rlk) genes in plants.leucine-rich repeat receptor-like protein kinases (lrr-rlks) are the largest group of receptor-like kinases in plants and play crucial roles in development and stress responses. the evolutionary relationships among lrr-rlk genes have been investigated in flowering plants; however, no comprehensive studies have been performed for these genes in more ancestral groups. the subfamily classification of lrr-rlk genes in plants, the evolutionary history and driving force for the evolution of each lrr-r ...201728173747
phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules.molecular evolutionary studies correlate genomic and phylogenetic information with the emergence of new traits of organisms. these traits are, however, the consequence of dynamic gene networks composed of functional modules, which might not be captured by genomic analyses. here, we established a method that combines large-scale genomic and phylogenetic data with gene co-expression networks to extensively study the evolutionary make-up of modules in the moss physcomitrella patens, and in the angi ...201728161902
the rla1/smos1 transcription factor functions with osbzr1 to regulate brassinosteroid signaling and rice architecture.brassinosteroids (brs) are plant-specific steroid hormones that control plant growth and development. recent studies have identified key components of the br signaling pathway in arabidopsis thaliana and in rice (oryza sativa); however, the mechanism of br signaling in rice, especially downstream of gsk3/shaggy-like kinase (gsk2), remains unclear. here, we identified a br-insensitive rice mutant, reduced leaf angle1 (rla1), and cloned the corresponding gene. rla1 was identical to the previously ...201728100707
the calcium-dependent protein kinase (cdpk) and cdpk-related kinase gene families in hevea brasiliensis-comparison with five other plant species in structure, evolution, and expression.calcium-dependent protein kinases (cdpks or cpks) play important roles in various physiological processes of plants, including growth and development, stress responses and hormone signaling. although the cdpk gene family has been characterized in several model plants, little is known about this gene family in hevea brasiliensis (the para rubber tree). here, we characterize the entire h. brasiliensis cdpk and cdpk-related kinase (crk) gene families comprising 30 cdpk genes (hbcpk1 to 30) and nine ...201728097084
tracheophytes contain conserved orthologs of a basic helix-loop-helix transcription factor that modulate root hair specific genes.root hair specific (rhs) genes, which contain the root hair-specific cis-element (rhe) in their regulatory regions, function in root hair morphogenesis. here, we demonstrate that an arabidopsis thaliana basic helix-loop-helix transcription factor, root hair defectve six-like4 (rsl4), directly binds to the rhe in vitro and in vivo, upregulates rhs genes, and stimulates root hair formation in arabidopsis. orthologs of rsl4 from a eudicot (poplar [populus trichocarpa]), a monocot (rice [oryza sativ ...201728087829
evolution and structural diversification of nictaba-like lectin genes in food crops with a focus on soybean (glycine max).the nictaba family groups all proteins that show homology to nictaba, the tobacco lectin. so far, nictaba and an arabidopsis thaliana homologue have been shown to be implicated in the plant stress response. the availability of more than 50 sequenced plant genomes provided the opportunity for a genome-wide identification of nictaba-like genes in 15 species, representing members of the fabaceae, poaceae, solanaceae, musaceae, arecaceae, malvaceae and rubiaceae. additionally, phylogenetic relations ...201728087663
genome-wide identification, characterisation and expression profiles of calcium-dependent protein kinase genes in barley (hordeum vulgare l.).in plant cells, calcium-dependent protein kinases (cdpks) are important sensors of ca(2+) flux resulting from various environmental stresses like cold, drought or salt stress. previous genome sequence analysis and comparative studies in arabidopsis (arabidopsis thaliana l.) and rice (oryza sativa l.) defined a multi-gene family of cdpks. here, we identified and characterised the cdpk gene complement of the model plant, barley (hordeum vulgare l.). comparative analysis encompassed phylogeny recon ...201727447459
three zinc-finger rna-binding proteins in cabbage (brassica rapa) play diverse roles in seed germination and plant growth under normal and abiotic stress conditions.despite the increasing understanding of the stress-responsive roles of zinc-finger rna-binding proteins (rzs) in several plant species, such as arabidopsis thaliana, wheat (triticum aestivum) and rice (oryza sativa), the functions of rzs in cabbage (brassica rapa) have not yet been elucidated. in this study, the functional roles of the three rz family members present in the cabbage genome, designated as brrz1, brrz2 and brrz3, were investigated in transgenic arabidopsis under normal and environm ...201727528428
rsl class i genes positively regulate root hair development in oryza sativa.root hairs are filamentous protuberances from superficial cells of plant roots that are critical for nutrient uptake. genes encoding root hair defective-six like (rsl) class i basic helix-loop-helix proteins are expressed in future root hair cells (trichoblasts) of the arabidopsis thaliana root where they positively regulate root hair cell development. we characterized the function of class i genes in oryza sativa root development. we show that there are three rsl class i genes in o. sativa and ...201727716929
genome-wide identification and characterization of trna-derived rna fragments in land plants.the manuscript by alves et al. entitled "genome-wide identification and characterization of trna-derived rna fragments in land plants" describes the identification and characterization of trnaderived srna fragments in plants. by combining bioinformatic analysis and genetic and molecular approaches, we show that trf biogenesis does not rely on canonical microrna/sirna processing machinery (i.e., independent of dicer-like proteins). moreover, we provide evidences that the arabidopsis s-like ribonu ...201727681945
northern blotting techniques for small rnas.cells have evolved intricate rna-directed mechanisms that destroy viruses, silence transposons, and regulate gene expression. these nucleic acid surveillance and gene silencing mechanisms rely upon the selective base-pairing of ~19-25 nt small rnas to complementary rna targets. this chapter describes northern blot hybridization techniques for the detection of such small rnas. blots spiked with synthetic standards are used to illustrate the detection specificity and sensitivity of dna oligonucleo ...201727770364
the rice receptor-like kinases dwarf and runtish spikelet1 and 2 repress cell death and affect sugar utilization during reproductive development.cell-to-cell communication precisely controls the creation of new organs during reproductive growth. however, the sensor molecules that mediate developmental signals in monocot plants are poorly understood. here, we report that dwarf and runtish spikelet1 (drus1) and drus2, two closely related receptor-like kinases (rlks), redundantly control reproductive growth and development in rice (oryza sativa). a drus1-1 drus2 double knockout mutant, but not either single mutant, showed extreme dwarfism a ...201728082384
a nuclear-localized rice glyoxalase i enzyme, osglyi-8, functions in the detoxification of methylglyoxal in the nucleus.the cellular levels of methylglyoxal (mg), a toxic byproduct of glycolysis, rise under various abiotic stresses in plants. detoxification of mg is primarily through the glyoxalase pathway. the first enzyme of the pathway, glyoxalase i (glyi), is a cytosolic metalloenzyme requiring either ni(2+) or zn(2+) for its activity. plants possess multiple glyi genes, of which only some have been partially characterized; hence, the precise molecular mechanism, subcellular localization and physiological rel ...201727797431
design of an optimal promoter involved in the heat-induced transcriptional pathway in arabidopsis, soybean, rice and maize.interactions between heat shock (hs) factors (hsfs) and heat shock response elements (hses) are important during the heat shock response (hsr) of flora and fauna. moreover, plant hsfs that are involved in heat stress are also involved in abiotic stresses such as dehydration and cold as well as development, cell differentiation and proliferation. because the specific combination of hsfs and hses involved in plants under heat stress remains unclear, the mechanism of their interaction has not yet b ...201727862521
analysis of ribosome-associated mrnas in rice reveals the importance of transcript size and gc content in translation.gene expression is controlled at transcriptional and post-transcriptional levels including decoding of messenger rna (mrna) into polypeptides via ribosome-mediated translation. translational regulation has been intensively studied in the model dicot plant arabidopsis thaliana, and in this study, we assessed the translational status [proportion of steady-state mrna associated with ribosomes] of mrnas by translating ribosome affinity purification followed by mrna-sequencing (trap-seq) in rice (ory ...201727852012
identification of brassinosteroid genes in brachypodium distachyon.brassinosteroids (brs) are steroidal phytohormones that are involved in diverse physiological processes and affect many important traits, such as plant stature, stress tolerance, leaf angle, fertility, and grain filling. br signaling and biosynthetic pathways have been studied in various plants, such as the model dicot arabidopsis thaliana; however, relatively little is known about these pathways in monocots.201728061864
constitutive expression of a plant ferredoxin-like protein (pflp) enhances capacity of photosynthetic carbon assimilation in rice (oryza sativa).the plant ferredoxin-like protein (pflp) gene, cloned from sweet peppers predicted as an electron carrier in photosynthesis, shows high homology to the fd-i sequence of arabidopsis thaliana, lycopersicon esculentum, oryza sativa and spinacia oleracea. most of pflp related studies focused on anti-pathogenic effects, while less understanding for the effects in photosynthesis with physiological aspects, such as photosynthesis rate, and levels of carbohydrate metabolites. this project focuses on the ...201728054169
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