| simple and rapid determination of n(6)-(δ(2)-isopentenyl)adenine, zeatin, and dihydrozeatin in plants using on-line cleanup liquid chromatography coupled with hybrid quadrupole-orbitrap high-resolution mass spectrometry. | a simple and rapid method was developed for the determination of three free cytokinins, namely, n(6)-(δ(2)-isopentenyl)adenine, zeatin, and dihydrozeatin, in plants using turboflow on-line cleanup liquid chromatography combined with hybrid quadrupole-orbitrap high-resolution mass spectrometry. the samples were extracted using acetonitrile, and then the extract was purified on a c18-p column, in which the sample matrix was removed and the analytes were retained. subsequently, the analytes were el ... | 2015 | 25808789 |
| the arabidopsis ca²⁺-dependent protein kinase cpk27 is required for plant response to salt-stress. | ca(2+)-dependent protein kinases (cdpks) play vital roles in plant adaptations to environmental challenges. the precise regulatory mechanism of cdpks in mediating salt stress still remains unclear, although several cdpk members have been identified to be involved in salt stress accumulation in various plants, such as arabidopsis thaliana and oryza sativa. here, we investigated the function of an arabidopsis cdpk, cpk27, in salt stress-signaling. cpk27 is a membrane-localized protein kinase; its ... | 2015 | 25791495 |
| autophagy supports biomass production and nitrogen use efficiency at the vegetative stage in rice. | much of the nitrogen in leaves is distributed to chloroplasts, mainly in photosynthetic proteins. during leaf senescence, chloroplastic proteins, including rubisco, are rapidly degraded, and the released nitrogen is remobilized and reused in newly developing tissues. autophagy facilitates the degradation of intracellular components for nutrient recycling in all eukaryotes, and recent studies have revealed critical roles for autophagy in rubisco degradation and nitrogen remobilization into seeds ... | 2015 | 25786829 |
| an ontology approach to comparative phenomics in plants. | plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. although phenotype comparisons across datasets have long been possible on a small scale, comprehensive queries and analyses that span a broad set of reference species, research disciplines, and knowledg ... | 2015 | 25774204 |
| polyamine oxidase 1 from rice (oryza sativa) is a functional ortholog of arabidopsis polyamine oxidase 5. | polyamine oxidase 1 (ospao1), from rice (oryza sativa), and polyamine oxidase 5 (atpao5), from arabidopsis (arabidopsis thaliana), are enzymes sharing high identity at the amino acid level and with similar characteristics, such as polyamine specificity and ph preference; furthermore, both proteins localize to the cytosol. a loss-of-function arabidopsis mutant, atpao5-2, was hypersensitive to low doses of exogenous thermospermine but this phenotype could be rescued by introduction of the wild-typ ... | 2014 | 25763711 |
| rice acyl-coa-binding proteins osacbp4 and osacbp5 are differentially localized in the endoplasmic reticulum of transgenic arabidopsis. | acyl-coa-binding proteins (acbps) are known to bind and transport acyl-coa esters and phospholipids intracellularly. in our recent paper in the new phytologist, we reported that the six acyl-coa-binding proteins (osacbps) in rice (oryza sativa) are distributed across various subcellular compartments in transgenic arabidopsis (arabidopsis thaliana) such as the cytosol (osacbp1, osacbp2 and osacbp3), the endoplasmic reticulum (er) including the tubules (osacbp4 and osacbp5) and the cisternae (osac ... | 2014 | 25763631 |
| co-ordination of flower development through epigenetic regulation in two model species: rice and arabidopsis. | angiosperms produce flowers for reproduction. flower development is a multistep developmental process, beginning with the initiation of the floral meristems, followed by floral meristem identity specification and maintenance, organ primordia initiation, floral organ identity specification, floral stem cell termination and finally floral organ maturation. during flower development, each of a large number of genes is expressed in a spatiotemporally regulated manner. underlying these molecular and ... | 2015 | 25746984 |
| cell dedifferentiation and organogenesis in vitro require more snrna than does seedling development in arabidopsis thaliana. | small nuclear rna (snrna) is a class of non-coding rnas that processes pre-mrna and rrna. transcription of abundant snrna species is regulated by the snrna activating protein complex (snapc), which is conserved among multicellular organisms including plants. srd2, a putative subunit of snapc in arabidopsis thaliana, is essential for development, and the point mutation srd2-1 causes severe defects in hypocotyl dedifferentiation and de novo meristem formation. based on phenotypic analysis of srd2- ... | 2015 | 25740809 |
| expath: a database of comparative expression analysis inferring metabolic pathways for plants. | in general, the expression of gene alters conditionally to catalyze a specific metabolic pathway. microarray-based datasets have been massively produced to monitor gene expression levels in parallel with numerous experimental treatments. although several studies facilitated the linkage of gene expression data and metabolic pathways, none of them are amassed for plants. moreover, advanced analysis such as pathways enrichment or how genes express under different conditions is not rendered. | 2015 | 25708775 |
| deformed floral organ1 (dfo1) regulates floral organ identity by epigenetically repressing the expression of osmads58 in rice (oryza sativa). | floral organ identity in plants is controlled by floral homeotic a/b/c/d/e-class genes. in arabidopsis thaliana, several epigenetic repressors that regulate these floral organ identity genes have been characterized. however, the roles of epigenetic factors in rice floral development have not been explored in detail. here, we report the identification and functional characterization of a rice epigenetic repressor, deformed floral organ1 (dfo1) gene, which causes abnormal floral morphology when mu ... | 2015 | 25675970 |
| epigenetic regulation of rice flowering and reproduction. | current understanding of the epigenetic regulator roles in plant growth and development has largely derived from studies in the dicotyledonous model plant arabidopsis thaliana. rice (oryza sativa) is one of the most important food crops in the world and has more recently becoming a monocotyledonous model plant in functional genomics research. during the past few years, an increasing number of studies have reported the impact of dna methylation, non-coding rnas and histone modifications on transc ... | 2014 | 25674094 |
| analyses of ca2+ dynamics using a ubiquitin-10 promoter-driven yellow cameleon 3.6 indicator reveal reliable transgene expression and differences in cytoplasmic ca2+ responses in arabidopsis and rice (oryza sativa) roots. | ca(2+) signatures are central to developmental processes and adaptive responses in plants. however, high-resolution studies of ca(2+) dynamics using genetically encoded ca(2+) indicators (gecis) such as yellow cameleon (yc) proteins have so far not been conducted in important model crops such as rice (oryza sativa). we conducted a comparative study of 35s and ubiquitin-10 (ubq10) promoter functionality in arabidopsis thaliana and o. sativa plants expressing the ca(2+) indicator yellow cameleon 3 ... | 2015 | 25641067 |
| genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in brachypodium distachyon. | in eukaryotes, alternative splicing (as) promotes transcriptome and proteome diversity. the extent of genome-wide as changes occurring during a plant-microbe interaction is largely unknown. here, using high-throughput, paired-end rna sequencing, we generated an isoform-level spliceome map of brachypodium distachyon infected with panicum mosaic virus and its satellite virus. overall, we detected ∼44,443 transcripts in b. distachyon, ∼30% more than those annotated in the reference genome. expressi ... | 2015 | 25634987 |
| osjaz9 acts as a transcriptional regulator in jasmonate signaling and modulates salt stress tolerance in rice. | the basic functions of plant-specific tify proteins as transcriptional regulators have been reported in plants. some tify genes are responsive to abiotic stresses, but the functions of these genes in stress tolerance have seldom been reported. osjaz9 is a member of the jaz subfamily which belongs to the tify gene family in rice (oryza sativa). suppression of osjaz9 resulted in reduced salt tolerance. the altered salt tolerance was mainly due to changes in ion (especially k(+)) homeostasis, which ... | 2015 | 25617318 |
| genome-wide survey of the seagrass zostera muelleri suggests modification of the ethylene signalling network. | seagrasses are flowering plants which grow fully submerged in the marine environment. they have evolved a range of adaptations to environmental challenges including light attenuation through water, the physical stress of wave action and tidal currents, high concentrations of salt, oxygen deficiency in marine sediment, and water-borne pollination. although, seagrasses are a key stone species of the costal ecosystems, many questions regarding seagrass biology and evolution remain unanswered. genom ... | 2015 | 25563969 |
| rice phytochrome b (osphyb) negatively regulates dark- and starvation-induced leaf senescence. | light regulates leaf senescence and light deprivation causes large-scale transcriptional reprogramming to dismantle cellular components and remobilize nutrients to sink organs, such as seeds and storage tissue. we recently reported that in arabidopsis (arabidopsis thaliana), phytochrome-interacting factor4 (pif4) and pif5 promote dark-induced senescence and natural senescence by directly activating the expression of typical senescence-associated genes (sags), including oresara1 (ore1) and ethyle ... | 2015 | 27135344 |
| abscisic acid: hidden architect of root system structure. | plants modulate root growth in response to changes in the local environment, guided by intrinsic developmental genetic programs. the hormone abscisic acid (aba) mediates responses to different environmental factors, such as the presence of nitrate in the soil, water stress and salt, shaping the structure of the root system by regulating the production of lateral roots as well as controlling root elongation by modulating cell division and elongation. curiously, aba controls different aspects of r ... | 2015 | 27135341 |
| prediction of plant pre-micrornas and their micrornas in genome-scale sequences using structure-sequence features and support vector machine. | micrornas (mirnas) are a family of non-coding rnas approximately 21 nucleotides in length that play pivotal roles at the post-transcriptional level in animals, plants and viruses. these molecules silence their target genes by degrading transcription or suppressing translation. studies have shown that mirnas are involved in biological responses to a variety of biotic and abiotic stresses. identification of these molecules and their targets can aid the understanding of regulatory processes. recent ... | 2014 | 25547126 |
| molecular phylogenetic study and expression analysis of atp-binding cassette transporter gene family in oryza sativa in response to salt stress. | atp-binding cassette (abc) transporter is a large gene superfamily that utilizes the energy released from atp hydrolysis for transporting myriad of substrates across the biological membranes. although many investigations have been done on the structural and functional analysis of the abc transporters in oryza sativa, much less is known about molecular phylogenetic and global expression pattern of the complete abc family in rice. in this study, we have carried out a comprehensive phylogenetic ana ... | 2015 | 25531538 |
| pectin enhances rice (oryza sativa) root phosphorus remobilization. | plants growing in phosphorus (p)-deficient conditions can either increase their exploration of the environment (hence increasing p uptake) or can solubilize and reutilize p from established tissue sources. however, it is currently unclear if p stored in root cell wall can be reutilized. the present study shows that culture of the rice cultivars 'nipponbare' (nip) and 'kasalath' (kas) in p-deficient conditions results in progressive reductions in root soluble inorganic phosphate (pi). however, ni ... | 2015 | 25528599 |
| regulation of inflorescence architecture by cytokinins. | in flowering plants, the arrangement of flowers on a stem becomes an inflorescence, and a huge variety of inflorescence architecture occurs in nature. inflorescence architecture also affects crop yield. in simple inflorescences, flowers form on a main stem; by contrast, in compound inflorescences, flowers form on branched stems and the branching pattern defines the architecture of the inflorescence. in this review, we highlight recent findings on the regulation of inflorescence architecture by c ... | 2014 | 25505480 |
| plant omics data center: an integrated web repository for interspecies gene expression networks with nlp-based curation. | comprehensive integration of large-scale omics resources such as genomes, transcriptomes and metabolomes will provide deeper insights into broader aspects of molecular biology. for better understanding of plant biology, we aim to construct a next-generation sequencing (ngs)-derived gene expression network (gen) repository for a broad range of plant species. so far we have incorporated information about 745 high-quality mrna sequencing (mrna-seq) samples from eight plant species (arabidopsis thal ... | 2015 | 25505034 |
| plant-pras: a database of physicochemical and structural properties and novel functional regions in plant proteomes. | arabidopsis thaliana is an important model species for studies of plant gene functions. research on arabidopsis has resulted in the generation of high-quality genome sequences, annotations and related post-genomic studies. the amount of annotation, such as gene-coding regions and structures, is steadily growing in the field of plant research. in contrast to the genomics resource of animals and microorganisms, there are still some difficulties with characterization of some gene functions in plant ... | 2015 | 25435546 |
| microrna biogenesis factor drb1 is a phosphorylation target of mitogen activated protein kinase mpk3 in both rice and arabidopsis. | microrna (mirna) biogenesis requires atdrb1 (double-stranded rna binding protein)/hyl1 (hyponastic leaves1) protein for processing and maturation of mirna precursors. the atdrb1/hyl1 protein associates with atdcl1 (dicer-like1) and accurately processes primary-mirnas (pri-mrnas) first to precursor-mirnas (pre-mirnas) and finally to mature mirnas. the dephosphorylation of atdrb1/hyl1 protein is very important for the precise processing of mirna precursors. the monocot model crop plant oryza sativ ... | 2015 | 25417716 |
| higher sterol content regulated by cyp51 with concomitant lower phospholipid content in membranes is a common strategy for aluminium tolerance in several plant species. | several studies have shown that differences in lipid composition and in the lipid biosynthetic pathway affect the aluminium (al) tolerance of plants, but little is known about the molecular mechanisms underlying these differences. phospholipids create a negative charge at the surface of the plasma membrane and enhance al sensitivity as a result of the accumulation of positively charged al(3+) ions. the phospholipids will be balanced by other electrically neutral lipids, such as sterols. in the p ... | 2015 | 25416794 |
| heat shock factors in carrot: genome-wide identification, classification, and expression profiles response to abiotic stress. | heat shock factors (hsfs) play key roles in the response to abiotic stress in eukaryotes. in this study, 35 dchsfs were identified from carrot (daucus carota l.) based on the carrot genome database. all 35 dchsfs were divided into three classes (a, b, and c) according to the structure and phylogenetic relationships of four different plants, namely, arabidopsis thaliana, vitis vinifera, brassica rapa, and oryza sativa. comparative analysis of algae, gymnosperms, and angiosperms indicated that the ... | 2015 | 25403331 |
| arabidopsis mterf15 is required for mitochondrial nad2 intron 3 splicing and functional complex i activity. | mitochondria play a pivotal role in most eukaryotic cells, as they are responsible for the generation of energy and diverse metabolic intermediates for many cellular events. during endosymbiosis, approximately 99% of the genes encoded by the mitochondrial genome were transferred into the host nucleus, and mitochondria import more than 1000 nuclear-encoded proteins from the cytosol to maintain structural integrity and fundamental functions, including dna replication, mrna transcription and rna me ... | 2014 | 25402171 |
| expression analysis of genes encoding mitogen-activated protein kinases in maize provides a key link between abiotic stress signaling and plant reproduction. | mitogen-activated protein kinases (mapks) play important roles in stress responses and development in plants. maize (zea mays), an important cereal crop, is a model plant species for molecular studies. in the last decade, several mapks have been identified in maize; however, their functions have not been studied extensively. genome-wide identification and expression analysis of maize mapk genes could provide valuable information for understanding their functions. in this study, 20 non-redundant ... | 2015 | 25388988 |
| brassinosteroid regulates cell elongation by modulating gibberellin metabolism in rice. | brassinosteroid (br) and gibberellin (ga) are two predominant hormones regulating plant cell elongation. a defect in either of these leads to reduced plant growth and dwarfism. however, their relationship remains unknown in rice (oryza sativa). here, we demonstrated that br regulates cell elongation by modulating ga metabolism in rice. under physiological conditions, br promotes ga accumulation by regulating the expression of ga metabolic genes to stimulate cell elongation. br greatly induces th ... | 2014 | 25371548 |
| a plausible mechanism, based upon short-root movement, for regulating the number of cortex cell layers in roots. | formation of specialized cells and tissues at defined times and in specific positions is essential for the development of multicellular organisms. often this developmental precision is achieved through intercellular signaling networks, which establish patterns of differential gene expression and ultimately the specification of distinct cell fates. here we address the question of how the short-root (shr) proteins from arabidopsis thaliana (atshr), brachypodium distachyon (bdshr), and oryza sativa ... | 2014 | 25352666 |
| the mir156-spl9-dfr pathway coordinates the relationship between development and abiotic stress tolerance in plants. | young organisms have relatively strong resistance to diseases and adverse conditions. when confronted with adversity, the process of development is delayed in plants. this phenomenon is thought to result from the rebalancing of energy, which helps plants to coordinate the relationship between development and stress tolerance; however, the molecular mechanism underlying this phenomenon remains mysterious. in this study, we found that mir156 integrates environmental signals to ensure timely flower ... | 2014 | 25345491 |
| ethylene-induced inhibition of root growth requires abscisic acid function in rice (oryza sativa l.) seedlings. | ethylene and abscisic acid (aba) have a complicated interplay in many developmental processes. their interaction in rice is largely unclear. here, we characterized a rice ethylene-response mutant mhz4, which exhibited reduced ethylene-response in roots but enhanced ethylene-response in coleoptiles of etiolated seedlings. mhz4 was identified through map-based cloning and encoded a chloroplast-localized membrane protein homologous to arabidopsis thaliana (arabidopsis) aba4, which is responsible fo ... | 2014 | 25330236 |
| the eucalyptus grandis r2r3-myb transcription factor family: evidence for woody growth-related evolution and function. | the r2r3-myb family, one of the largest transcription factor families in higher plants, controls a wide variety of plant-specific processes including, notably, phenylpropanoid metabolism and secondary cell wall formation. we performed a genome-wide analysis of this superfamily in eucalyptus, one of the most planted hardwood trees world-wide. a total of 141 predicted r2r3-myb sequences identified in the eucalyptus grandis genome sequence were subjected to comparative phylogenetic analyses with ar ... | 2015 | 25250741 |
| temperature responses of mesophyll conductance differ greatly between species. | the temperature responses of mesophyll conductance (gm ) were investigated for nine species using carbon isotope techniques combining tunable diode laser spectroscopy and gas exchange measurements. species included the evergreen trees eucalyptus pauciflora and quercus engelmannii; the tropical evergreen tree lophostemon confertus; as well as the herbaceous species nicotiana tabacum, oryza sativa, triticum aestivum, gossypium hirsutum, glycine max and arabidopsis thaliana. responses varied from a ... | 2015 | 25224884 |
| regulation of meiotic gene expression in plants. | with the recent advances in genomics and sequencing technologies, databases of transcriptomes representing many cellular processes have been assembled. meiotic transcriptomes in plants have been studied in arabidopsis thaliana, rice (oryza sativa), wheat (triticum aestivum), petunia (petunia hybrida), sunflower (helianthus annuus), and maize (zea mays). studies in all organisms, but particularly in plants, indicate that a very large number of genes are expressed during meiosis, though relatively ... | 2014 | 25202317 |
| stress induced mapk genes show distinct pattern of codon usage in arabidopsis thaliana, glycine max and oryza sativa. | mitogen activated protein kinase (mapk) genes provide resistance to various biotic and abiotic stresses. codon usage profiling of the genes reveals the characteristic features of the genes like nucleotide composition, gene expressivity, optimal codons etc. the present study is a comparative analysis of codon usage patterns for different mapk genes in three organisms, viz. arabidopsis thaliana, glycine max (soybean) and oryza sativa (rice). the study has revealed a high at content in mapk genes o ... | 2014 | 25187684 |
| mutation of oryza sativa coronatine insensitive 1b (oscoi1b) delays leaf senescence. | jasmonic acid (ja) functions in plant development, including senescence and immunity. arabidopsis thaliana coronatine insensitive 1 encodes a ja receptor and functions in the ja-responsive signaling pathway. the arabidopsis genome harbors a single coi gene, but the rice (oryza sativa) genome harbors three coi homologs, oscoi1a, oscoi1b, and oscoi2. thus, it remains unclear whether each oscoi has distinct, additive, synergistic, or redundant functions in development. here, we use the oscoi1b-1 kn ... | 2015 | 25146897 |
| branching out in roots: uncovering form, function, and regulation. | root branching is critical for plants to secure anchorage and ensure the supply of water, minerals, and nutrients. to date, research on root branching has focused on lateral root development in young seedlings. however, many other programs of postembryonic root organogenesis exist in angiosperms. in cereal crops, the majority of the mature root system is composed of several classes of adventitious roots that include crown roots and brace roots. in this update, we initially describe the diversity ... | 2014 | 25136060 |
| qtl analysis of flowering time and ripening traits suggests an impact of a genomic region on linkage group 1 in vitis. | in the recent past, genetic analyses of grapevine focused mainly on the identification of resistance loci for major diseases such as powdery and downy mildew. currently, breeding programs make intensive use of these results by applying molecular markers linked to the resistance traits. however, modern genetics also allows to address additional agronomic traits that have considerable impact on the selection of grapevine cultivars. in this study, we have used linkage mapping for the identification ... | 2014 | 25112201 |
| the os-akt1 channel is critical for k+ uptake in rice roots and is modulated by the rice cbl1-cipk23 complex. | potassium (k(+)) is one of the essential nutrient elements for plant growth and development. plants absorb k(+) ions from the environment via root cell k(+) channels and/or transporters. in this study, the shaker k(+) channel os-akt1 was characterized for its function in k(+) uptake in rice (oryza sativa) roots, and its regulation by os-cbl1 (calcineurin b-like protein1) and os-cipk23 (cbl-interacting protein kinase23) was investigated. as an inward k(+) channel, os-akt1 could carry out k(+) upt ... | 2014 | 25096783 |
| integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots. | unraveling widespread polyploidy events throughout plant evolution is a necessity for inferring the impacts of whole-genome duplication (wgd) on speciation, functional innovations, and to guide identification of true orthologs in divergent taxa. here, we employed an integrated syntenic and phylogenomic analyses to reveal an ancient wgd that shaped the genomes of all commelinid monocots, including grasses, bromeliads, bananas (musa acuminata), ginger, palms, and other plants of fundamental, agric ... | 2014 | 25082857 |
| polyamine oxidase 1 from rice (oryza sativa) is a functional ortholog of arabidopsis polyamine oxidase 5. | polyamine oxidase 1 (ospao1), from rice (oryza sativa), and polyamine oxidase 5 (atpao5), from arabidopsis (arabidopsis thaliana), are enzymes sharing high identity at the amino acid level and with similar characteristics, such as polyamine specificity and ph preference; furthermore, both proteins localize to the cytosol. a loss-of-function arabidopsis mutant, atpao5-2, was hypersensitive to low doses of exogenous thermospermine but this phenotype could be rescued by introduction of the wild-typ ... | 2014 | 25061821 |
| plant microrna-target interaction identification model based on the integration of prediction tools and support vector machine. | confident identification of microrna-target interactions is significant for studying the function of microrna (mirna). although some computational mirna target prediction methods have been proposed for plants, results of various methods tend to be inconsistent and usually lead to more false positive. to address these issues, we developed an integrated model for identifying plant mirna-target interactions. | 2014 | 25051153 |
| identification of small secreted peptides (ssps) in maize and expression analysis of partial ssp genes in reproductive tissues. | maize 1,491 small secreted peptides were identified, which were classified according to the character of peptide sequences. partial ssp gene expressions in reproductive tissues were determined by qrt-pcr. small secreted peptides (ssps) are important cell-cell communication messengers in plants. most information on plant ssps come from arabidopsis thaliana and oryza sativa, while little is known about the ssps of other grass species such as maize (zea mays). in this study, we identified 1,491 ssp ... | 2014 | 25048445 |
| the splicing fate of plant spo11 genes. | toward the global understanding of plant meiosis, it seems to be essential to decipher why all as yet sequenced plants need or at least encode for two different meiotic spo11 genes. this is in contrast to mammals and fungi, where only one spo11 is present. both spo11 in arabidopsis thaliana are essential for the initiation of double strand breaks (dsbs) during the meiotic prophase. in nearly all eukaryotic organisms dsb induction during prophase i by spo11 leads to meiotic dsb repair, thereby en ... | 2014 | 25018755 |
| compartmentation and dynamics of flavone metabolism in dry and germinated rice seeds. | among secondary metabolites, flavonoids are particularly important for the plant life cycle and could be beneficial for human health. the study of arabidopsis thaliana transparent testa mutants showed that seed flavonoids are important for environmental adaptation, reactive oxygen species homeostasis, dormancy and longevity. compared with arabidopsis and maize (zea mays l.), far less research has been conducted on rice (oryza sativa l.) particularly for cultivars with non-pigmented seeds. in thi ... | 2014 | 25008975 |
| clues to the functions of plant ndpk isoforms. | this review describes the five nucleoside diphosphate kinase (ndpk) genes found in both model plants arabidopsis thaliana (thale cress) and oryza sativa l. (rice). phylogenetic and sequence analyses of these genes allow the definition of four types of ndpk isoforms with different predicted subcellular localization. these predictions are supported by experimental evidence for most ndpk types. data mining also provides evidence for the existence of a novel ndpk type putatively localized in the end ... | 2015 | 24964975 |
| rice acyl-coa-binding proteins osacbp4 and osacbp5 are differentially localized in the endoplasmic reticulum of transgenic arabidopsis. | acyl-coa-binding proteins (acbps) are known to bind and transport acyl-coa esters and phospholipids intracellularly. in our recent paper in the new phytologist, we reported that the 6 acyl-coa-binding proteins (osacbps) in rice (oryza sativa) are distributed across various subcellular compartments in transgenic arabidopsis (arabidopsis thaliana) such as the cytosol (osacbp1, osacbp2 and osacbp3), the endoplasmic reticulum (er) including the tubules (osacbp4 and osacbp5) and the cisternae (osacbp ... | 2014 | 24926784 |
| the receptor-like kinase sit1 mediates salt sensitivity by activating mapk3/6 and regulating ethylene homeostasis in rice. | high salinity causes growth inhibition and shoot bleaching in plants that do not tolerate high salt (glycophytes), including most crops. the molecules affected directly by salt and linking the extracellular stimulus to intracellular responses remain largely unknown. here, we demonstrate that rice (oryza sativa) salt intolerance 1 (sit1), a lectin receptor-like kinase expressed mainly in root epidermal cells, mediates salt sensitivity. nacl rapidly activates sit1, and in the presence of salt, as ... | 2014 | 24907341 |
| the plant glycosyltransferase clone collection for functional genomics. | the glycosyltransferases (gts) are an important and functionally diverse family of enzymes involved in glycan and glycoside biosynthesis. plants have evolved large families of gts which undertake the array of glycosylation reactions that occur during plant development and growth. based on the carbohydrate-active enzymes (cazy) database, the genome of the reference plant arabidopsis thaliana codes for over 450 gts, while the rice genome (oryza sativa) contains over 600 members. collectively, gts ... | 2014 | 24905498 |
| identification and functional characterization of bidirectional gene pairs and their intergenic regions in maize. | bidirectional gene pairs exist as a specific form of gene organization in microorganisms and mammals as well as in model plant species, such as arabidopsis and rice. little is known about bidirectional gene pairs in maize, which has a large genome and is one of the most important grain crops. | 2014 | 24886269 |
| learning from nature: the use of non-model species to identify novel acclimations to flooding stress. | excess water in the form of waterlogged soil or deeper submergence (generically termed 'flooding') influences plant growth, survival and species distribution in many natural ecosystems. it also has a negative impact on crop growth and yield since many agricultural species are flooding intolerant. the often devastating effect of flooding on plant performance is related to its interference with gas exchange between the plant and its environment. this results in energy deficiency and carbohydrate s ... | 2014 | 24876298 |
| cytochrome p450 93g1 is a flavone synthase ii that channels flavanones to the biosynthesis of tricin o-linked conjugates in rice. | flavones are a major class of flavonoids with a wide range of physiological functions in plants. they are constitutively accumulated as c-glycosides and o-linked conjugates in vegetative tissues of grasses. it has long been presumed that the two structural modifications of flavones occur through independent metabolic routes. previously, we reported that cytochrome p450 93g2 (cyp93g2) functions as a flavanone 2-hydroxylase (f2h) that provides 2-hydroxyflavanones for c-glycosylation in rice (oryza ... | 2014 | 24843076 |
| mutation in xyloglucan 6-xylosytransferase results in abnormal root hair development in oryza sativa. | root hairs are important for nutrient uptake, anchorage, and plant-microbe interactions. from a population of rice (oryza sativa) mutagenized by ethyl methanesulfonate (ems), a short root hair2 (srh2) mutant was identified. in hydroponic culture, srh2 seedlings were significantly reduced in root hair length. bubble-like extrusions and irregular epidermal cells were observed at the tips of srh2 root hairs when grown under acidic conditions, suggesting the possible reduction of the tensile strengt ... | 2014 | 24834920 |
| phylogenetic analyses provide the first insights into the evolution of ovate family proteins in land plants. | the ovate gene encodes a nuclear-localized regulatory protein belonging to a distinct family of plant-specific proteins known as the ovate family proteins (ofps). ovate was first identified as a key regulator of fruit shape in tomato, with nonsense mutants displaying pear-shaped fruits. however, the role of ofps in plant development has been poorly characterized. | 2014 | 24812252 |
| comparative functional analysis of wheat (triticum aestivum) zinc finger-containing glycine-rich rna-binding proteins in response to abiotic stresses. | although the functional roles of zinc finger-containing glycine-rich rna-binding proteins (rzs) have been characterized in several plant species, including arabidopsis thaliana and rice (oryza sativa), the physiological functions of rzs in wheat (triticum aestivum) remain largely unknown. here, the functional roles of the three wheat rz family members, named tarz1, tarz2, and tarz3, were investigated using transgenic arabidopsis plants under various abiotic stress conditions. expression of tarzs ... | 2014 | 24800811 |
| ran1 is involved in plant cold resistance and development in rice (oryza sativa). | of the diverse abiotic stresses, low temperature is one of the major limiting factors that lead to a series of morphological, physiological, biochemical, and molecular changes in plants. ran, an evolutionarily conserved small g-protein family, has been shown to be essential for the nuclear translocation of proteins. it also mediates the regulation of cell cycle progression in mammalian cells. however, little is known about ran function in rice (oryza sativa). we report here that ran gene osran1 ... | 2014 | 24790113 |
| genome-wide identification, evolution, and expression analysis of rna-binding glycine-rich protein family in maize. | the rna-binding glycine-rich protein (rb-grp) family is characterized by the presence of a glycine-rich domain arranged in (gly)n-x repeats and an rna-recognition motif (rrm). rb-grps participate in varied physiological and biochemical processes especially in the stress response of plants. in this study, a total of 23 rb-grps distributed on 10 chromosomes were identified in maize (zea mays l.), and they were divided into four subgroups according to their conserved domain architecture. five pairs ... | 2014 | 24783971 |
| identification and characterization of aba receptors in oryza sativa. | abscisic acid (aba) is an essential phytohormone that regulates plant stress responses. aba receptors in arabidopsis thaliana (atpyls) have been extensively investigated by structural, biochemical, and in vivo studies. in contrast, relatively little is known about the aba signal transduction cascade in rice. besides, the diversities of atpyls manifest that the information accumulated in arabidopsis cannot be simply adapted to rice. thus, studies on rice aba receptors are compulsory. by taking a ... | 2014 | 24743650 |
| subcellular localization of rice acyl-coa-binding proteins (acbps) indicates that osacbp6::gfp is targeted to the peroxisomes. | acyl-coa-binding proteins (acbps) show conservation at the acyl-coa-binding (acb) domain which facilitates binding to acyl-coa esters. in arabidopsis thaliana, six acbps participate in development and stress responses. rice (oryza sativa) also contains six genes encoding acbps. we investigated differences in subcellular localization between monocot rice and eudicot a. thaliana acbps. the subcellular localization of the six osacbps was achieved via transient expression of green fluorescence prote ... | 2014 | 24738983 |
| characterization of the β-1,3-glucanase gene in peanut (arachis hypogaea l.) by cloning and genetic transformation. | plant β-1,3-glucanases are commonly involved in disease resistance. this report describes the cloning and genetic transformation of a β-1,3-glucanase gene from peanut. the gene was isolated from both the genomic dna and cdna of peanut variety huayu20 by polymerase chain reaction (pcr) and reverse transcription pcr (rt-pcr), respectively. the dna sequence contained 1471 bp including two exons and one intron, and the coding sequence contained 1047 bp that coded for a 348-amino acid protein with a ... | 2014 | 24668677 |
| molecular control of seasonal flowering in rice, arabidopsis and temperate cereals. | rice (oryza sativa) and arabidopsis thaliana have been widely used as model systems to understand how plants control flowering time in response to photoperiod and cold exposure. extensive research has resulted in the isolation of several regulatory genes involved in flowering and for them to be organized into a molecular network responsive to environmental cues. when plants are exposed to favourable conditions, the network activates expression of florigenic proteins that are transported to the s ... | 2014 | 24651369 |
| study on folate binding domain of dihydrofolate reductase in different plant species and human beings. | data base (ncbi and tigr) searches are made to retrieve protein sequences of different plant species namely medicago truncatula, pisum sativum, ricinus communis, arabidopsis thaliana, vitis vinifera, glycine max, daucus carota, oryza sativa japonica group, arabidopsis lyrata subsp. lyrata, brachypodium distachyon, oryza sativa indica group, zea mays and careful alignment of derived sequences shows 95% or higher identity. similarly, dhfr sequence of human being is also retrieved from ncbi. a phyl ... | 2014 | 24616563 |
| rice fertilization-independent endosperm1 regulates seed size under heat stress by controlling early endosperm development. | although heat stress reduces seed size in rice (oryza sativa), little is known about the molecular mechanisms underlying the observed reduction in seed size and yield. to elucidate the mechanistic basis of heat sensitivity and reduced seed size, we imposed a moderate (34°c) and a high (42°c) heat stress treatment on developing rice seeds during the postfertilization stage. both stress treatments reduced the final seed size. at a cellular level, the moderate heat stress resulted in precocious end ... | 2014 | 24590858 |
| two rice authentic histidine phosphotransfer proteins, osahp1 and osahp2, mediate cytokinin signaling and stress responses in rice. | cytokinin plays an important role in plant development and stress tolerance. studies of arabidopsis (arabidopsis thaliana) have demonstrated that cytokinin acts through a two-component system that includes a histidine (his) kinase, a his phosphotransfer protein (hp), and a response regulator. phylogenetic analyses have revealed the conservation of his kinases but lineage-specific expansion of hps and response regulators in rice (oryza sativa). however, whether the functions of rice hps have dive ... | 2014 | 24578505 |
| genomic analysis of nac transcription factors in banana (musa acuminata) and definition of nac orthologous groups for monocots and dicots. | identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding. a comprehensive understanding of the gene families associated with drought tolerance is therefore highly relevant. nac transcription factors form a large plant-specific gene family involved in the regulation of tissue development and responses to biotic and abiotic stresses. the main goal of this study was to set up a framework of orthologous groups determined by an expert sequence compar ... | 2014 | 24570169 |
| evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes. | the structure of eukaryotic genes evolves extensively by intron loss or gain. previous studies have revealed two models for gene structure evolution through the loss of introns: rna-based gene conversion, dubbed the fink model and retroposition model. however, retrogenes that experienced both intron loss and intron-retaining events have been ignored; evolutionary processes responsible for the variation in complex exon-intron structure were unknown. we detected hundreds of retroduplication-derive ... | 2014 | 24520158 |
| a positive feedback loop between heat shock protein101 and heat stress-associated 32-kd protein modulates long-term acquired thermotolerance illustrating diverse heat stress responses in rice varieties. | heat stress is an important factor that has a negative impact on rice (oryza sativa) production. to alleviate this problem, it is necessary to extensively understand the genetic basis of heat tolerance and adaptability to heat stress in rice. here, we report the molecular mechanism underlying heat acclimation memory that confers long-term acquired thermotolerance (lat) in this monocot plant. our results showed that a positive feedback loop formed by two heat-inducible genes, heat shock protein10 ... | 2014 | 24520156 |
| integrated analysis of the effects of cold and dehydration on rice metabolites, phytohormones, and gene transcripts. | correlations between gene expression and metabolite/phytohormone levels under abiotic stress conditions have been reported for arabidopsis (arabidopsis thaliana). however, little is known about these correlations in rice (oryza sativa 'nipponbare'), despite its importance as a model monocot. we performed an integrated analysis to clarify the relationships among cold- and dehydration-responsive metabolites, phytohormones, and gene transcription in rice. an integrated analysis of metabolites and g ... | 2014 | 24515831 |
| origins and evolution of wuschel-related homeobox protein family in plant kingdom. | wuschel-related homeobox (wox) is a large group of transcription factors specifically found in plants. wox members contain the conserved homeodomain essential for plant development by regulating cell division and differentiation. however, the evolutionary relationship of wox members in plant kingdom remains to be elucidated. in this study, we searched 350 wox members from 50 species in plant kingdom. linkage analysis of wox protein sequences demonstrated that amino acid residues 141-145 and 153- ... | 2014 | 24511289 |
| molecular control of grass inflorescence development. | the grass family is one of the largest families in angiosperms and has evolved a characteristic inflorescence morphology, with complex branches and specialized spikelets. the origin and development of the highly divergent inflorescence architecture in grasses have recently received much attention. increasing evidence has revealed that numerous factors, such as transcription factors and plant hormones, play key roles in determining reproductive meristem fate and inflorescence patterning in grasse ... | 2014 | 24471834 |
| a selection strategy in plant transformation based on antisense oligodeoxynucleotide inhibition. | antisense oligodeoxynucleotide (asodn) inhibition was developed in the 1970s, and since then has been widely used in animal research. however, in plant biology, the method has had limited application because plant cell walls significantly block efficient uptake of asodn to plant cells. recently, we have found that asodn uptake is enhanced in a sugar solution. the method has promise for many applications, such as a rapid alternative to time-consuming transgenic studies, and high potential for stu ... | 2014 | 24438514 |
| trithorax group protein oryza sativa trithorax1 controls flowering time in rice via interaction with early heading date3. | trithorax group proteins are chromatin-remodeling factors that activate target gene expression by antagonistically functioning against the polycomb group. in arabidopsis (arabidopsis thaliana), arabidopsis trithorax protein1 (atx1) regulates flowering time and floral organ identity. here, we observed that suppression of oryza sativa trithorax1 (ostrx1), an ortholog of atx1, delayed flowering time in rice (oryza sativa). because the delay occurred only under long-day conditions, we evaluated the ... | 2014 | 24420930 |
| a novel rice cytochrome p450 gene, cyp72a31, confers tolerance to acetolactate synthase-inhibiting herbicides in rice and arabidopsis. | target-site and non-target-site herbicide tolerance are caused by the prevention of herbicide binding to the target enzyme and the reduction to a nonlethal dose of herbicide reaching the target enzyme, respectively. there is little information on the molecular mechanisms involved in non-target-site herbicide tolerance, although it poses the greater threat in the evolution of herbicide-resistant weeds and could potentially be useful for the production of herbicide-tolerant crops because it is oft ... | 2014 | 24406793 |
| della activity is required for successful pollen development in the columbia ecotype of arabidopsis. | excessive gibberellin (ga) signalling, mediated through the della proteins, has a negative impact on plant fertility. loss of della activity in the monocot rice (oryza sativa) causes complete male sterility, but not in the dicot model arabidopsis (arabidopsis thaliana) ecotype landsberg erecta (ler), in which della function has been studied most extensively, leading to the assumption that della activity is not essential for arabidopsis pollen development. a novel della fertility phenotype was id ... | 2014 | 24400898 |
| stress-inducible expression of atdreb1a transcription factor greatly improves drought stress tolerance in transgenic indica rice. | the cultivation of rice (oryza sativa l.), a major food crop, requires ample water (30 % of the fresh water available worldwide), and its productivity is greatly affected by drought, the most significant environmental factor. much research has focussed on identifying quantitative trait loci, stress-regulated genes and transcription factors that will contribute towards the development of climate-resilient/tolerant crop plants in general and rice in particular. the transcription factor dreb1a, ide ... | 2014 | 24398893 |
| profiling micrornas and their targets in an important fleshy fruit: tomato (solanum lycopersicum). | tomato (solanum lycopersicum) is an important and the most useful plant based diet. it is widely used for its antioxidant property. presently, only two digits, tomato micrornas (mirnas) are reported in mirbase: a mirna database. this study is aimed to profile and characterize more mirnas and their targets in tomato. a comprehensive comparative genomic approach is applied and a total of 109 new mirnas belonging to 106 families are identified and characterized from the tomato expressed sequence ta ... | 2014 | 24315821 |
| dissection of two major components of the post-zygotic hybridization barrier in rice endosperm. | a post-zygotic hybridization barrier is often observed in the endosperm of seeds produced by interspecific or interploidy crosses. in arabidopsis thaliana, for example, hybrid endosperm from both types of cross shows altered timing of cellularization and an altered rate of nuclear divisions. therefore, it has been proposed that interspecific and interploidy crosses share common molecular mechanisms for establishment of an effective species barrier. however, these two types of hybridization barri ... | 2013 | 24286595 |
| introns targeted by plant micrornas: a possible novel mechanism of gene regulation. | in plant cells, most micrornas (mirnas) perform cleavages of target mature mrnas in the cytoplasm. a recent report of a mirna pathway involved in dna methylation in the rice nucleus raises the possibility that plant mirnas could cleave intron-containing pre-mrnas (the precursor of messenger rnas) located in the nucleus. | 2013 | 24280590 |
| wikipathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. | next-generation sequencing and 'omics' platforms are used extensively in plant biology research to unravel new genomes and study their interactions with abiotic and biotic agents in the growth environment. despite the availability of a large and growing number of genomic data sets, there are only limited resources providing highly-curated and up-to-date metabolic and regulatory networks for plant pathways. | 2013 | 24280312 |
| development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient rice. | cis-acting elements are essential genomic sequences that control gene expression. in higher eukaryotes, a series of cis-elements function cooperatively. however, further studies are required to examine the co-regulation of multiple cis-elements on a promoter. the aim of this study was to propose a model of cis-element networks that cooperatively regulate gene expression in rice under iron (fe) deficiency. | 2013 | 24279975 |
| the distribution of different classes of nuclear localization signals (nlss) in diverse organisms and the utilization of the minor nls-binding site inplantnuclear import factor importin-α. | the specific recognition between the import receptor importin-α and the nuclear localization signals (nlss) is crucial to ensure the selective transport of cargoes into the nucleus. nlss contain 1 or 2 clusters of positively charged amino acids, which usually bind to the major (monopartite nlss) or both minor and major nls-binding sites (bipartite nlss). in our recent study, we determined the structure of importin-α1a from rice (oryza sativa), and made 2 observations that suggest an increased ut ... | 2013 | 24270630 |
| molecular characterization of two glutathione peroxidase genes of panax ginseng and their expression analysis against environmental stresses. | glutathione peroxidases (gpxs) are a group of enzymes that protect cells against oxidative damage generated by reactive oxygen species (ros). gpx catalyzes the reduction of hydrogen peroxide (h2o2) or organic hydroperoxides to water or alcohols by reduced glutathione. the presence of gpxs in plants has been reported by several groups, but the roles of individual members of this family in a single plant species have not been studied. two gpx cdnas were isolated and characterized from the embryoge ... | 2014 | 24269671 |
| expression of arabidopsis glycine-rich rna-binding protein atgrp2 or atgrp7 improves grain yield of rice (oryza sativa) under drought stress conditions. | although posttranscriptional regulation of rna metabolism is increasingly recognized as a key regulatory process in plant response to environmental stresses, reports demonstrating the importance of rna metabolism control in crop improvement under adverse environmental stresses are severely limited. to investigate the potential use of rna-binding proteins (rbps) in developing stress-tolerant transgenic crops, we generated transgenic rice plants (oryza sativa) that express arabidopsis thaliana gly ... | 2014 | 24268168 |
| an in vitro system for the rapid functional characterization of genes involved in carotenoid biosynthesis and accumulation. | we have developed an assay based on rice embryogenic callus for rapid functional characterization of metabolic genes. we validated the assay using a selection of well-characterized genes with known functions in the carotenoid biosynthesis pathway, allowing rapid visual screening of callus phenotypes based on tissue color. we then used the system to identify the functions of two uncharacterized genes: a chemically synthesized β-carotene ketolase gene optimized for maize codon usage, and a wild-ty ... | 2014 | 24267591 |
| genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots. | transcription initiation, essential to gene expression regulation, involves recruitment of basal transcription factors to the core promoter elements (cpes). the distribution of currently known cpes across plant genomes is largely unknown. this is the first large scale genome-wide report on the computational prediction of cpes across eight plant genomes to help better understand the transcription initiation complex assembly. the distribution of thirteen known cpes across four monocots (brachypodi ... | 2013 | 24205361 |
| high-throughput analysis of rice genes by means of the heterologous full-length cdna overexpressor (fox)-hunting system. | mutant populations are indispensable tools for investigating plant gene functions. gain-of-function technology is one of the approaches used for the systematic production of mutant resources and activation tagging is a well-established method to generate gain-of-function mutants in plants. as an alternative approach for the systematic generation of a gain-of-function mutant population, we developed the full-length cdna overexpressor (fox)-hunting system in which full-length cdnas (fl-cdnas) are ... | 2013 | 24166434 |
| overexpression of a partial fragment of the salt-responsive gene osnuc1 enhances salt adaptation in transgenic arabidopsis thaliana and rice (oryza sativa l.) during salt stress. | the rice (oryza sativa l.) nucleolin gene, osnuc1, transcripts were expressed in rice leaves, flowers, seeds and roots but differentially expressed within and between two pairs of salt-sensitive and salt-resistant rice lines when subjected to salt stress. salt-resistant lines exhibited higher osnuc1 transcript expression levels than salt-sensitive lines during 0.5% (w/v) nacl salt stress for 6d. two sizes of osnuc1 full-length cdna were found in the rice genome database and northern blot analysi ... | 2013 | 24157209 |
| rice db: an oryza information portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and arabidopsis. | omics research in oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. we present rice db, an oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. rice db has been designed to integrate the direct comparison of rice with arabidopsis (arabidopsis thaliana), based on orthology or 'expressology', thus u ... | 2013 | 24147765 |
| how unique is the low oxygen response? an analysis of the anaerobic response during germination and comparison with abiotic stress in rice and arabidopsis. | plants face a variety of environmental stresses and have evolved molecular mechanisms to survive these challenges. one of these stresses is low oxygen conditions, which can occur under flooding conditions. rice (oryza sativa) is somewhat unique for its ability to tolerate and even germinate under low to no oxygen conditions. in this study, we examined global transcriptomic responses over the course of germination and in response to low oxygen and other abiotic stress in rice and arabidopsis (ara ... | 2013 | 24101922 |
| can a late bloomer become an early bird? tools for flowering time adjustment. | the transition from the vegetative to reproductive stage followed by inflorescence is a critical step in plant life; therefore, studies of the genes that influence flowering time have always been of great interest to scientists. flowering is a process controlled by many genes interacting mutually in a genetic network, and several hypothesis and models of flowering have been suggested so far. plants in temperate climatic conditions must respond mainly to changes in the day length (photoperiod) an ... | 2014 | 24091290 |
| maize lazy1 mediates shoot gravitropism and inflorescence development through regulating auxin transport, auxin signaling, and light response. | auxin is a plant hormone that plays key roles in both shoot gravitropism and inflorescence development. however, these two processes appear to be parallel and to be regulated by distinct players. here, we report that the maize (zea mays) prostrate stem1 mutant, which is allelic to the classic mutant lazy plant1 (la1), displays prostrate growth with reduced shoot gravitropism and defective inflorescence development. map-based cloning identified maize zmla1 as the functional ortholog of lazy1 in r ... | 2013 | 24089437 |
| survey of genes involved in rice secondary cell wall formation through a co-expression network. | the plant secondary cell wall is the major source of lignocellulosic biomass, a renewable energy resource that can be used for bioethanol production. to comprehensively identify transcription factors (tfs), glycosyltransferase (gt) and glycosyl hydrolase (gh) involved in secondary cell wall formation in rice (oryza sativa), co-expression network analysis was performed using 68 microarray data points for different rice tissues and stages. in addition to rice genes encoding orthologs of arabidopsi ... | 2013 | 24089433 |
| root transcript profiling of two rorippa species reveals gene clusters associated with extreme submergence tolerance. | complete submergence represses photosynthesis and aerobic respiration, causing rapid mortality in most terrestrial plants. however, some plants have evolved traits allowing them to survive prolonged flooding, such as species of the genus rorippa, close relatives of arabidopsis (arabidopsis thaliana). we studied plant survival, changes in carbohydrate and metabolite concentrations, and transcriptome responses to submergence of two species, rorippa sylvestris and rorippa amphibia. we exploited the ... | 2013 | 24077074 |
| roles of pollen-specific boron efflux transporter, osbor4, in the rice fertilization process. | arabidopsis thaliana bor1 was the first boron (b) transporter identified in living systems. there are four atbor1-like genes, osbor1, 2, 3 and 4, present in the rice genome. we characterized the activity, expression and physiological function of osbor4. osbor4 is an active efflux transporter of b. quantitative pcr analysis and osbor4 promoter-green fluorescent protein (gfp) fusion revealed that osbor4 was both highly and specifically expressed in pollen. we obtained five tos17 insertion mutants ... | 2013 | 24068795 |
| nitrogen-dependent regulation of de novo cytokinin biosynthesis in rice: the role of glutamine metabolism as an additional signal. | cytokinin activity in plants is closely related to nitrogen availability, and an arabidopsis gene for adenosine phosphate-isopentenyltransferase (ipt), ipt3, is regulated by inorganic nitrogen sources in a nitrate-specific manner. in this study, we have identified another regulatory system of cytokinin de novo biosynthesis in response to nitrogen status. in rice, osipt4, osipt5, osipt7 and osipt8 were up-regulated in response to exogenously applied nitrate and ammonium, with accompanying accumul ... | 2013 | 24058148 |
| the ubiquitin receptor da1 interacts with the e3 ubiquitin ligase da2 to regulate seed and organ size in arabidopsis. | seed size in higher plants is determined by the coordinated growth of the embryo, endosperm, and maternal tissue. several factors that act maternally to regulate seed size have been identified, such as auxin response factor2, apetala2, kluh, and da1, but the genetic and molecular mechanisms of these factors in seed size control are almost totally unknown. we previously demonstrated that the ubiquitin receptor da1 acts synergistically with the e3 ubiquitin ligase enhancer1 of da1 (eod1)/big broth ... | 2013 | 24045020 |
| selective acquisition and retention of genomic sequences by pack-mutator-like elements based on guanine-cytosine content and the breadth of expression. | the process of gene duplication followed by sequence and functional divergence is important for the generation of new genes. pack-mules, nonautonomous mutator-like elements (mules) that carry genic sequence(s), are potentially involved in generating new open reading frames and regulating parental gene expression. these elements are identified in many plant genomes and are most abundant in rice (oryza sativa). despite the abundance of pack-mules, the mechanism by which parental genes are captured ... | 2013 | 24028844 |
| subfunctionalization of sigma factors during the evolution of land plants based on mutant analysis of liverwort (marchantia polymorpha l.) mpsig1. | sigma factor is a subunit of plastid-encoded rna polymerase that regulates the transcription of plastid-encoded genes by recognizing a set of promoters. sigma factors have increased in copy number and have diversified during the evolution of land plants, but details of this process remain unknown. liverworts represent the basal group of embryophytes and are expected to retain the ancestral features of land plants. in liverwort (marchantia polymorpha l.), we isolated and characterized a t-dna-tag ... | 2013 | 24025801 |
| perturbation of brachypodium distachyon cellulose synthase a4 or 7 results in abnormal cell walls. | cellulose is an integral component of the plant cell wall and accounts for approximately forty percent of total plant biomass but understanding its mechanism of synthesis remains elusive. cellulose synthase a (cesa) proteins function as catalytic subunits of a rosette-shaped complex that synthesizes cellulose at the plasma membrane. arabidopsis thaliana and rice (oryza sativa) secondary wall cesa loss-of-function mutants have weak stems and irregular or thin cell walls. | 2013 | 24024469 |