Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
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| comprehensive mitochondrial metabolic shift during the critical node of seed ageing in rice. | the critical node (cn) in seed aging in rice (oryza sativa) is the transformation from phase i (p-i) to phase ii (p-ii) of the reverse s-shaped curve (rs-sc). although mitochondrial dysfunction plays a key role in seed ageing, the metabolic shift in the cn remains poorly understood. here, we investigated the mitochondrial regulatory mechanisms during the cn of rice seed ageing. we showed that during the cn of seed ageing, the mitochondrial ultrastructure was impaired, causing oxygen consumption ... | 2016 | 27124767 |
| molecular dissection of oryza sativa salt-induced ring finger protein 1 (ossirp1): possible involvement in the sensitivity response to salinity stress. | ubiquitination-mediated protein degradation via really interesting new gene (ring) e3 ligase plays an important role in plant responses to abiotic stress conditions. many plant studies have found that ring proteins regulate the perception of various abiotic stresses and signal transduction. in this study, oryza sativa salt-induced ring finger protein 1 (ossirp1) gene was selected randomly from 44 oryza sativa ring finger proteins (osrfps) genes highly expressed in rice roots exposed to salinity ... | 2016 | 27118216 |
| soil incorporation of silica-rich rice husk decreases inorganic arsenic in rice grain. | arsenic decreases rice yield, and inorganic grain as threatens human health; thus, strategies to decrease rice as are critically needed. increased plant-available silica (si) can decrease rice as, yet the source of si matters. rice husk, an underutilized and si-rich byproduct of rice production that contains less labile c and an order of magnitude less as than rice straw, may be an economically viable si resource to decrease rice as, yet the impact of rice husk incorporation on as in the rice-so ... | 2016 | 27109244 |
| crl6, a member of the chd protein family, is required for crown root development in rice. | the root system in monocotyledonous plants is largely composed of postembryonic shoot-borne roots named crown roots, which are important for nutrients and water uptake. the molecular mechanism underlying regulation of crown root development is not fully explored. in this study, we characterized a rice (oryza sativa) mutant defective in crown root formation, designated as crown rootless6 (crl6). histological analysis showed that crl6 influences crown root formation by regulating primordial initia ... | 2016 | 27108205 |
| ribosomal protein s6 kinase1 coordinates with tor-raptor2 to regulate thylakoid membrane biosynthesis in rice. | ribosomal protein s6 kinase (s6k) functions as a key component in the target of rapamycin (tor) pathway involved in multiple processes in eukaryotes. the role and regulation of tor-s6k in lipid metabolism remained unknown in plants. here we provide genetic and pharmacological evidence that tor-raptor2-s6k1 is important for thylakoid galactolipid biosynthesis and thylakoid grana modeling in rice (oryza sativa l.). genetic suppression of s6k1 caused pale yellow-green leaves, defective thylakoid gr ... | 2016 | 27102613 |
| proteomic and physiological studies provide insight into photosynthetic response of rice (oryza sativa l.) seedlings to microgravity. | the mechanisms whereby how photosynthesis is regulated and maintained under conditions of microgravity remain incompletely understood. herein, we took a combination of proteomic and physiological approaches to examine the response of rice (oryza sativa l.) seedlings to spaceflight conditions. our results show that both psi fluorescence emission peak and p700 absorbance amplitude are severely decreased in spaceflight seedlings under microgravity. this is consistent with an observed significant re ... | 2016 | 27096703 |
| osbbx14 delays heading date by repressing florigen gene expression under long and short-day conditions in rice. | b-box (bbx) proteins are zinc finger proteins containing b-box domains, which have roles in arabidopsis growth and development. however, little is known concerning rice bbxs. herein, we identified a rice bbx protein, oryza sativa bbx14 (osbbx14). osbbx14 is highly expressed in flag leaf blades. osbbx14 expression shows a diurnal rhythm under photoperiodic conditions and subsequent continuous white light. osbbx14 is located in the nucleus and has transcriptional activation potential. osbbx14-over ... | 2016 | 27095397 |
| identification of embryo proteins associated with seed germination and seedling establishment in germinating rice seeds. | seed germination is a critical phase in the plant life cycle, but the mechanism of seed germination is still poorly understood. in the present study, rice (oryza sativa l. cv. peiai 64s) seeds were sampled individually when they reached different germination stages, quiescent, germinated sensu stricto, germinated completely and seedling, and were used to study the changes in the embryo proteome. a total of 88 protein spots showed a significant change in abundance during germination in water, and ... | 2016 | 27085178 |
| a positive feedback loop governed by sub1a1 interaction with mitogen-activated protein kinase3 imparts submergence tolerance in rice. | mitogen-activated protein kinase (mapk) signal transduction networks have been extensively explored in plants; however, the connection between mapk signaling cascades and submergence tolerance is currently unknown. the ethylene response factor-like protein sub1a orchestrates a plethora of responses during submergence stress tolerance in rice (oryza sativa). in this study, we report that mpk3 is activated by submergence in a sub1a-dependent manner. mpk3 physically interacts with and phosphorylate ... | 2016 | 27081183 |
| crystal structure of the gras domain of scarecrow-like7 in oryza sativa. | gras proteins belong to a plant-specific protein family with many members and play essential roles in plant growth and development, functioning primarily in transcriptional regulation. proteins in the family are minimally defined as containing the conserved gras domain. here, we determined the structure of the gras domain of os-scl7 from rice (oryza sativa) to 1.82 å. the structure includes cap and core subdomains and elucidates the features of the conserved gras lri, vhiid, lrii, pfyre, and saw ... | 2016 | 27081181 |
| mapping qtls for salt tolerance in rice (oryza sativa l.) by bulked segregant analysis of recombinant inbred lines using 50k snp chip. | soil salinity is a major constraint to rice production in large inland and coastal areas around the world. modern high yielding rice varieties are particularly sensitive to high salt stress. there are salt tolerant landraces and traditional varieties of rice but with limited information on genomic regions (qtls) and genes responsible for their tolerance. here we describe a method for rapid identification of qtls for reproductive stage salt tolerance in rice using bulked segregant analysis (bsa) ... | 2016 | 27077373 |
| two highly similar dead box proteins, osrh2 and osrh34, homologous to eukaryotic initiation factor 4aiii, play roles of the exon junction complex in regulating growth and development in rice. | the exon junction complex (ejc), which contains four core components, eukaryotic initiation factor 4aiii (eif4aiii), mago/nashi (mago), y14/tsunagi/rna-binding protein 8a, and barentsz/metastatic lymph node 51, is formed in both nucleus and cytoplasm, and plays important roles in gene expression. genes encoding core ejc components have been found in plants, including rice. currently, the functional characterizations of mago and y14 homologs have been demonstrated in rice. however, it is still un ... | 2016 | 27071313 |
| biology and management of the mexican rice borer (lepidoptera: crambidae) in rice in the united states. | the mexican rice borer, eoreuma loftini (dyar), is an invasive pest of rice, oryza sativa l., in the gulf coast region of the united states. this pest also damages sugarcane, saccharum spp. hybrids; corn, zea mays l.; and sorghum, sorghum bicolor (l.) moench, and feeds on weedy noncrop grasses. multiple aspects of integrated pest management including use of pheromone traps, manipulation of planting dates, harvest cutting height, stubble management, noncrop host management, soil fertility managem ... | 2016 | 28670487 |
| identification, classification, and expression profiles of heat shock transcription factors in tea plant (camellia sinensis) under temperature stress. | in vascular plants, heat shock transcription factors (hsfs) regulate heat stress response by regulating the expression of heat shock proteins. this study systematically and comprehensively analyzed the hsf family in tea plant [camellia sinensis (l.) o. kuntze]. a total of 16 cshsfs were identified from the transcriptome database of tea plant and analyzed for their phylogenetic relationships, motifs, and physicochemical characteristics. on the basis of the phylogenetic comparison of tea plant wit ... | 2016 | 26431998 |
| plantdhs: a database for dnase i hypersensitive sites in plants. | gene expression is regulated by orchestrated binding of regulatory proteins to promoters and other cis-regulatory dna elements (cres). several plant databases have been developed for mapping promoters or dna motifs associated with promoters. however, there is a lack of databases that allow investigation for all cres. here we present plantdhs (http://plantdhs.org), a plant dnase i hypersensitive site (dhs) database that integrates histone modification, rna sequencing, nucleosome positioning/occup ... | 2016 | 26400163 |
| callose synthesis during reproductive development in monocotyledonous and dicotyledonous plants. | callose, a linear β-1,3-glucan molecule, plays important roles in a variety of processes in angiosperms, including development and the response to biotic and abiotic stress. despite the importance of callose deposition, our understanding of the roles of callose in rice reproductive development and the regulation of callose biosynthesis is limited. glucan synthase-like genes encode callose synthases (gsls), which function in the production of callose at diverse sites in plants. studies have shown ... | 2016 | 26451709 |
| uniprotkb/swiss-prot, the manually annotated section of the uniprot knowledgebase: how to use the entry view. | the universal protein resource (uniprot, http://www.uniprot.org ) consortium is an initiative of the sib swiss institute of bioinformatics (sib), the european bioinformatics institute (ebi) and the protein information resource (pir) to provide the scientific community with a central resource for protein sequences and functional information. the uniprot consortium maintains the uniprot knowledgebase (uniprotkb), updated every 4 weeks, and several supplementary databases including the uniprot refe ... | 2016 | 26519399 |
| detection and isolation of plant-associated bacteria scavenging atmospheric molecular hydrogen. | high-affinity hydrogen (h2 )-oxidizing bacteria possessing group 5 [nife]-hydrogenase genes are important contributors to atmospheric h2 uptake in soil environments. although previous studies reported the occurrence of a significant h2 uptake activity in vegetation, there has been no report on the identification and diversity of the responsible microorganisms. here, we show the existence of plant-associated bacteria with the ability to consume atmospheric h2 that may be a potential energy source ... | 2016 | 26636257 |
| selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome. | whereas de novo assemblies of rna-seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies. here we present a detailed comparison of 99 transcriptome assemblies, generated with 6 de novo assemblers including clc, trinity, soap, oases, abyss and nextgene. controlled analyses of de novo assemblies for arabidopsis thaliana and oryza sativa transcriptomes provide new insights into the strength ... | 2016 | 26731733 |
| osbri1 activates br signaling by preventing binding between the tpr and kinase domains of osbsk3 via phosphorylation. | many plant receptor kinases transduce signals through receptor-like cytoplasmic kinases (rlcks); however, the molecular mechanisms that create an effective on-off switch are unknown. the receptor kinase br insensitive1 (bri1) transduces brassinosteroid (br) signal by phosphorylating members of the br-signaling kinase (bsk) family of rlcks, which contain a kinase domain and a c-terminal tetratricopeptide repeat (tpr) domain. here, we show that the br signaling function of bsks is conserved in ara ... | 2016 | 26697897 |
| a chemical genetic strategy identify the phostin, a synthetic molecule that triggers phosphate starvation responses in arabidopsis thaliana. | plants display numerous strategies to cope with phosphate (pi)-deficiency. despite multiple genetic studies, the molecular mechanisms of low-pi-signalling remain unknown. to validate the interest of chemical genetics to investigate this pathway we discovered and analysed the effects of phostin (psn), a drug mimicking pi-starvation in arabidopsis. we assessed the effects of psn and structural analogues on the induction of pi-deficiency responses in mutants and wild-type and followed their accumul ... | 2016 | 26243630 |
| deciphering the roles of acyl-coa-binding proteins in plant cells. | lipid trafficking is vital for metabolite exchange and signal communications between organelles and endomembranes. acyl-coa-binding proteins (acbps) are involved in the intracellular transport, protection, and pool formation of acyl-coa esters, which are important intermediates and regulators in lipid metabolism and cellular signaling. in this review, we highlight recent advances in our understanding of plant acbp families from a cellular and developmental perspective. plant acbps have been exte ... | 2016 | 26340904 |
| a transcriptome-wide study on the microrna- and the argonaute 1-enriched small rna-mediated regulatory networks involved in plant leaf senescence. | leaf senescence is an important physiological process during the plant life cycle. however, systemic studies on the impact of micrornas (mirnas) on the expression of senescence-associated genes (sags) are lacking. besides, whether other argonaute 1 (ago1)-enriched small rnas (srnas) play regulatory roles in leaf senescence remains unclear. in this study, a total of 5,123 and 1,399 ago1-enriched srnas, excluding mirnas, were identified in arabidopsis thaliana and rice (oryza sativa), respectively ... | 2016 | 26206233 |
| plantapa: a portal for visualization and analysis of alternative polyadenylation in plants. | alternative polyadenylation (apa) is an important layer of gene regulation that produces mrnas that have different 3' ends and/or encode diverse protein isoforms. up to 70% of annotated genes in plants undergo apa. increasing numbers of poly(a) sites collected in various plant species demand new methods and tools to access and mine these data. we have created an open-access web service called plantapa (http://bmi.xmu.edu.cn/plantapa) to visualize and analyze genome-wide poly(a) sites in plants. ... | 2016 | 27446120 |
| origin and functional prediction of pollen allergens in plants. | pollen allergies have long been a major pandemic health problem for human. however, the evolutionary events and biological function of pollen allergens in plants remain largely unknown. here, we report the genome-wide prediction of pollen allergens and their biological function in the dicotyledonous model plant arabidopsis (arabidopsis thaliana) and the monocotyledonous model plant rice (oryza sativa). in total, 145 and 107 pollen allergens were predicted from rice and arabidopsis, respectively. ... | 2016 | 27436829 |
| knock out of the phosphate 2 gene tapho2-a1 improves phosphorus uptake and grain yield under low phosphorus conditions in common wheat. | mir399 and its target phosphate2 (pho2) play pivotal roles in phosphate signaling in plants. loss of function mutation in pho2 leads to excessive pi accumulation in shoots and growth retardation in diploid plants like arabidopsis thaliana and rice (oryza sativa). here we isolated three pho2 homologous genes tapho2-a1, -b1 and -d1 from hexaploid wheat (triticum aestivum). these tapho2 genes all contained mir399-binding sites and were able to be degraded by tae-mir399. tapho2-d1 was expressed much ... | 2016 | 27416927 |
| heterologous expression of a rice mir395 gene in nicotiana tabacum impairs sulfate homeostasis. | sulfur participates in many important mechanisms and pathways of plant development. the most common source of sulfur in soil -so4(2-)- is absorbed into root tissue and distributed into aerial part through vasculature system, where it is reduced into sulfite and finally sulfide within the subcellular organs such as chloroplasts and mitochondria and used for cysteine and methionine biosynthesis. micrornas are involved in many regulation pathways by repressing the expression of their target genes. ... | 2016 | 27350219 |
| overexpression of rice glutaredoxin osgrx_c7 and osgrx_c2.1 reduces intracellular arsenic accumulation and increases tolerance in arabidopsis thaliana. | glutaredoxins (grxs) are a family of small multifunctional proteins involved in various cellular functions, including redox regulation and protection under oxidative stress. despite the high number of grx genes in plant genomes (48 grxs in rice), the biological functions and physiological roles of most of them remain unknown. here, the functional characterization of the two arsenic-responsive rice grx family proteins, osgrx_c7 and osgrx_c2.1 are reported. over-expression of osgrx_c7 and osgrx_c2 ... | 2016 | 27313586 |
| genome-wide identification and analysis of the myb transcription factor superfamily in solanum lycopersicum. | myb proteins constitute one of the largest transcription factor families in the plant kingdom, members of which perform a variety of functions in plant biological processes. however, there are only very limited reports on the characterization of myb transcription factors in tomato (solanum lycopersicum). in our study, a total of 127 myb genes have been identified in the tomato genome. a complete overview of these myb genes is presented, including the phylogeny, gene structures, protein motifs, c ... | 2016 | 27279646 |
| comprehensive analyses of the annexin gene family in wheat. | annexins are an evolutionarily conserved multigene family of calcium-dependent phospholipid binding proteins that play important roles in stress resistance and plant development. they have been relatively well characterized in model plants arabidopsis (arabidopsis thaliana) and rice (oryza sativa), but nothing has been reported in hexaploid bread wheat (triticum aestivum) and barely (hordeum vulgare), which are the two most economically important plants. | 2016 | 27236332 |
| overexpression of wheat gene tamor improves root system architecture and grain yield in oryza sativa. | improved root architecture is an effective strategy to increase crop yield. we demonstrate that overexpression of transcription factor gene more root (tamor) from wheat (triticum aestivum l.) results in more roots and higher grain yield in rice (oryza sativa). tamor, encoding a plant-specific transcription factor belonging to the asymmetric leaves2/lateral organ boundaries (as2/lob) protein family, is highly conserved in wheat and its wild relatives. in this study, tissue expression patterns ind ... | 2016 | 27229732 |
| metabolism of l-arabinose in plants. | l-arabinose (l-ara) is a plant-specific sugar accounting for 5-10 % of cell wall saccharides in arabidopsis (arabidopsis thaliana) and rice (oryza sativa). l-ara occurs in pectic arabinan, rhamnogalacturonan ii, arabinoxylan, arabinogalactan-protein (agp), and extensin in the cell walls, as well as in glycosylated signaling peptides like clavata3 and small glycoconjugates such as quercetin 3-o-arabinoside. this review focuses on recent advances towards understanding the generation of l-ara and t ... | 2016 | 27220955 |
| members of btb gene family of scaffold proteins suppress nitrate uptake and nitrogen use efficiency. | development of crops with improved nitrogen use efficiency (nue) is essential for sustainable agriculture. however, achieving this goal has proven difficult since nue is a complex trait encompassing physiological and developmental processes. we thought to tackle this problem by taking a systems biology approach to identify candidate target genes. first, we used a supervised machine-learning algorithm to predict a nue gene network in arabidopsis (arabidopsis thaliana). second, we identified bt2, ... | 2016 | 27208309 |
| albino leaf1 that encodes the sole octotricopeptide repeat protein is responsible for chloroplast development. | chloroplast, the photosynthetic organelle in plants, plays a crucial role in plant development and growth through manipulating the capacity of photosynthesis. however, the regulatory mechanism of chloroplast development still remains elusive. here, we characterized a mutant with defective chloroplasts in rice (oryza sativa), termed albino leaf1 (al1), which exhibits a distinct albino phenotype in leaves, eventually leading to al1 seedling lethality. electronic microscopy observation demonstrated ... | 2016 | 27208287 |
| genome-wide characterization of soybean p 1b -atpases gene family provides functional implications in cadmium responses. | the p1b-atpase subfamily is an important group involved in transporting heavy metals and has been extensively studied in model plants, such as arabidopsis thaliana and oryza sativa. emerging evidence indicates that one homolog in glycine max is also involved in cadmium (cd) stress, but the gene family has not been fully investigated in soybean. | 2016 | 27207280 |
| isomir bank: a research resource for tracking isomirs. | : next-generation sequencing (ngs) technology has revealed that micrornas (mirnas) are capable of exhibiting frequent differences from their corresponding mature reference sequences, generating multiple variants: the isoforms of mirnas (isomirs). these isomirs mainly originate via the imprecise and alternative cleavage during the pre-mirna processing and post-transcriptional modifications that influence mirna stability, their sub-cellular localization and target selection. although several tools ... | 2016 | 27153728 |
| genome-wide identification and characterization of novel lncrnas in populus under nitrogen deficiency. | long non-coding rnas (lncrnas) have been identified as important regulatory factors of gene expression in eukaryotic species, such as homo sapiens, arabidopsis thaliana, and oryza sativa. however, the systematic identification of potential lncrnas in trees is comparatively rare. in particular, the characteristics, expression, and regulatory roles of lncrnas in trees under nutrient stress remain largely unknown. a genome-wide strategy was used in this investigation to identify and characterize no ... | 2016 | 27138920 |
| analysis of cis-acting regulatory elements of respiratory burst oxidase homolog (rboh) gene families in arabidopsis and rice provides clues for their diverse functions. | nadph oxidase (nox) is a critical enzyme in the production of reactive oxygen species (ros). it catalyzes the production of apoplastic superoxide (o2(-)), that regulates a wide array of biological functions in different organisms. plant noxes are homologs of catalytic subunit of mammalian nadph oxidase and are well-known as respiratory burst oxidase homologs (rbohs). in recent years, there has been growing interest to study plant noxes due to their versatile roles in plant systems. in the presen ... | 2016 | 27111707 |
| identification of reference genes for quantitative expression analysis using large-scale rna-seq data of arabidopsis thaliana and model crop plants. | in quantitative gene expression analysis, normalization using a reference gene as an internal control is frequently performed for appropriate interpretation of the results. efforts have been devoted to exploring superior novel reference genes using microarray transcriptomic data and to evaluating commonly used reference genes by targeting analysis. however, because the number of specifically detectable genes is totally dependent on probe design in the microarray analysis, exploration using micro ... | 2016 | 27040147 |
| acyl-coa-binding proteins (acbps) in plant development. | acyl-coa-binding proteins (acbps) play a pivotal role in fatty acid metabolism because they can transport medium- and long-chain acyl-coa esters. in eukaryotic cells, acbps are involved in intracellular trafficking of acyl-coa esters and formation of a cytosolic acyl-coa pool. in addition to these ubiquitous functions, more specific non-redundant roles of plant acbp subclasses are implicated by the existence of multigene families with variable molecular masses, ligand specificities, functional d ... | 2016 | 27023243 |
| role of lipid metabolism in plant pollen exine development. | pollen plays important roles in the life cycle of angiosperms plants. it acts as not only a biological protector of male sperms but also a communicator between the male and the female reproductive organs, facilitating pollination and fertilization. pollen is produced within the anther, and covered by the specialized outer envelope, pollen wall. although the morphology of pollen varies among different plant species, the pollen wall is mainly comprised of three layers: the pollen coat, the outer e ... | 2016 | 27023241 |
| sumo proteases: uncovering the roles of desumoylation in plants. | plants have evolved to cope with changing environmental conditions. one way plants achieve this is through post-translational modification of target proteins by ubiquitination and sumoylation. these post-translational modifiers (pms) can alter stability, protein-protein interactions, and the overall fate of the protein. both of these systems have remarkable similarities in terms of the process leading to attachment of the pm to its substrate : having to undertake activation, conjugation, and fin ... | 2016 | 27012284 |
| transferring an optimized tap-toolbox for the isolation of protein complexes to a portfolio of rice tissues. | proteins are the cell's functional entities. rather than operating independently, they interact with other proteins. capturing in vivo protein complexes is therefore crucial to gain understanding of the function of a protein in a cellular context. affinity purification coupled to mass spectrometry has proven to yield a wealth of information about protein complex constitutions for a broad range of organisms. for oryza sativa, the technique has been initiated in callus and shoots, but has not been ... | 2016 | 27003905 |
| [the application of genome editing in identification of plant gene function and crop breeding]. | plant genome can be modified via current biotechnology with high specificity and excellent efficiency. zinc finger nucleases (zfn), transcription activator-like effector nucleases (talen) and clustered regularly interspaced short palindromic repeats (crispr)/crispr-associated 9 (cas9) system are the key engineered nucleases used in the genome editing. genome editing techniques enable gene targeted mutagenesis, gene knock-out, gene insertion or replacement at the target sites during the endogenou ... | 2016 | 27001477 |
| molecular evolution and gene expression differences within the hd-zip transcription factor family of zea mays l. | homeodomain-leucine zipper (hd-zip) transcription factors regulate developmental processes and stress responses in plants, and they vary widely in gene number and family structure. in this study, 55 predicted maize hd-zip genes were systematically analyzed with respect to their phylogenetic relationships, molecular evolution, and gene expression in order to understand the functional diversification within the family. phylogenetic analysis of hd-zip proteins from zea mays, oryza sativa, arabidops ... | 2016 | 26979310 |
| ectopic expression of a cytochrome p450 monooxygenase gene ptcyp714a3 from populus trichocarpa reduces shoot growth and improves tolerance to salt stress in transgenic rice. | in arabidopsis thaliana and oryza sativa, the cytochrome p450 (cyp) 714 protein family represents a unique group of cyp monooxygenase, which functions as a shoot-specific regulator in plant development through gibberellin deactivation. here, we report the functional characterizations of ptcyp714a3, an oscyp714d1/eui homologue from populus trichocarpa. ptcyp714a3 was ubiquitously expressed with the highest transcript level in cambium-phloem tissues, and was greatly induced by salt and osmotic str ... | 2016 | 26970512 |
| overexpression of the rice akt1 potassium channel affects potassium nutrition and rice drought tolerance. | potassium (k(+)) is the most important cationic nutrient for all living organisms and has roles in most aspects of plant physiology. to assess the impact of one of the main k(+) uptake components, the k(+) inward rectifying channel akt1, we characterized both loss of function and overexpression of osakt1 in rice. in many conditions, akt1 expression correlated with k(+) uptake and tissue k(+) levels. no salinity-related growth phenotype was observed for either loss or gain of function mutants. ho ... | 2016 | 26969743 |
| transcriptomes of plant gametophytes have a higher proportion of rapidly evolving and young genes than sporophytes. | reproductive traits in plants tend to evolve rapidly due to various causes that include plant-pollinator coevolution and pollen competition, but the genomic basis of reproductive trait evolution is still largely unknown. to characterize evolutionary patterns of genome wide gene expression in reproductive tissues in the gametophyte and to compare them to developmental stages of the sporophyte, we analyzed evolutionary conservation and genetic diversity of protein-coding genes using microarray-bas ... | 2016 | 26956888 |
| characterization of a small acyl-coa-binding protein (acbp) from helianthus annuus l. and its binding affinities. | acyl-coa-binding proteins (acbps) bind to acyl-coa esters and promote their interaction with other proteins, lipids and cell structures. small class i acbps have been identified in different plants, such as arabidopsis thaliana (atacbp6), brassica napus (bnacbp) and oryza sativa (osacbp1, osacbp2, osacbp3), and they are capable of binding to different acyl-coa esters and phospholipids. here we characterize haacbp6, a class i acbp expressed in sunflower (helianthus annuus) tissues, studying the s ... | 2016 | 26938582 |
| genome-wide identification and evolutionary analyses of the pp2c gene family with their expression profiling in response to multiple stresses in brachypodium distachyon. | the type-2c protein phosphatases (pp2cs), negatively regulating aba responses and mapk cascade pathways, play important roles in stress signal transduction in plants. brachypodium distachyon is a new model plant for exploring the functional genomics of temperate grasses, cereals and biofuel crops. to date, genome-wide identification and analysis of the pp2c gene family in b. distachyon have not been investigated. | 2016 | 26935448 |
| three-dimensional imaging of plant organs using a simple and rapid transparency technique. | clearing techniques eliminate factors that interfere with microscopic observation, including light scattering and absorption by pigments and cytoplasmic components. the techniques allow fluorescence-based detailed analyses of materials and characterization of the three-dimensional structure of organs. we describe a simple and rapid clearing and imaging method, termed 'tomei' (transparent plant organ method for imaging), which enables microscopic observation of intact plant organs. this method in ... | 2016 | 26928932 |
| computational identification and comparative analysis of mirna precursors in three palm species. | in the present study, mirna precursors in the genomes of three palm species were identified. analyzes of sequence conservation and biological function of their putative targets contribute to understand the roles of mirna in palm biology. micrornas are small rnas of 20-25 nucleotides in length, with important functions in the regulation of gene expression. recent genome sequencing of the palm species elaeis guineensis, elaeis oleifera and phoenix dactylifera have enabled the discovery of mirna ge ... | 2016 | 26919984 |
| bioinformatic identification and analysis of extensins in the plant kingdom. | extensins (exts) are a family of plant cell wall hydroxyproline-rich glycoproteins (hrgps) that are implicated to play important roles in plant growth, development, and defense. structurally, exts are characterized by the repeated occurrence of serine (ser) followed by three to five prolines (pro) residues, which are hydroxylated as hydroxyproline (hyp) and glycosylated. some exts have tyrosine (tyr)-x-tyr (where x can be any amino acid) motifs that are responsible for intramolecular or intermol ... | 2016 | 26918442 |
| atp binding cassette g transporters and plant male reproduction. | the function of atp binding cassette g (abcg) transporters in the regulation of plant vegetative organs development has been well characterized in various plant species. in contrast, their function in reproductive development particularly male reproductive development received considerably less attention till some abcg transporters was reported to be associated with anther and pollen wall development in arabidopsis thaliana and rice (oryza sativa) during the past decade. this mini-review summari ... | 2016 | 26906115 |
| heterologous expression of atwrky57 confers drought tolerance in oryza sativa. | drought stress is a severe environmental factor that greatly restricts plant distribution and crop production. recently, we have found that overexpressing atwrky57 enhanced drought tolerance in arabidopsis thaliana. in this study, we further reported that the arabidopsis wrky57 transcription factor was able to confer drought tolerance to transgenic rice (oryza sativa) plants. the enhanced drought tolerance of transgenic rice was resulted from the lower water loss rates, cell death, malondialdehy ... | 2016 | 26904091 |
| the arabidopsis transcriptional regulator dpb3-1 enhances heat stress tolerance without growth retardation in rice. | the enhancement of heat stress tolerance in crops is an important challenge for food security to facilitate adaptation to global warming. in arabidopsis thaliana, the transcriptional regulator dna polymerase ii subunit b3-1 (dpb3-1)/nuclear factor y subunit c10 (nf-yc10) has been reported as a positive regulator of dehydration-responsive element binding protein 2a (dreb2a), and the overexpression of dpb3-1 enhances heat stress tolerance without growth retardation. here, we show that dpb3-1 inter ... | 2016 | 26841113 |
| the della protein slr1 integrates and amplifies salicylic acid- and jasmonic acid-dependent innate immunity in rice. | gibberellins are a class of tetracyclic plant hormones that are well known to promote plant growth by inducing the degradation of a class of nuclear growth-repressing proteins, called dellas. in recent years, ga and dellas are also increasingly implicated in plant responses to pathogen attack, although our understanding of the underlying mechanisms is still limited, especially in monocotyledonous crop plants. aiming to further decipher the molecular underpinnings of ga- and della-modulated plant ... | 2016 | 26829979 |
| different sets of post-embryonic development genes are conserved or lost in two caryophyllales species (reaumuria soongorica and agriophyllum squarrosum). | reaumuria soongorica and sand rice (agriophyllum squarrosum) belong to the clade of caryophyllales and are widely distributed in the desert regions of north china. both plants have evolved many specific traits and adaptation strategies to cope with recurring environmental threats. however, the genetic basis that underpins their unique traits and adaptation remains unknown. in this study, the transcriptome data of r. soongorica and sand rice were compared with three other species with previously ... | 2016 | 26815143 |
| frequent chloroplast rna editing in early-branching flowering plants: pilot studies on angiosperm-wide coexistence of editing sites and their nuclear specificity factors. | rna editing by cytidine-to-uridine conversions is an essential step of rna maturation in plant organelles. some 30-50 sites of c-to-u rna editing exist in chloroplasts of flowering plant models like arabidopsis, rice or tobacco. we now predicted significantly more rna editing in chloroplasts of early-branching angiosperm genera like amborella, calycanthus, ceratophyllum, chloranthus, illicium, liriodendron, magnolia, nuphar and zingiber. nuclear-encoded rna-binding pentatricopeptide repeat (ppr) ... | 2016 | 26809609 |
| osvil1 controls flowering time in rice by suppressing oslf under short days and by inducing ghd7 under long days. | osvil1 is associated with a prc2-like complex through its fibronectin type iii domain to activate flowering by suppressing oslf under sd and delay flowering by inducing ghd7 under ld. polycomb repressive complex 2 (prc2) inhibits the expression of target genes by modifying histone proteins. although several genes that epigenetically regulate flowering time have been identified in arabidopsis thaliana and rice (oryza sativa), the molecular mechanism by which prc2 affects flowering time has not be ... | 2016 | 26795142 |
| h3k36ac is an evolutionary conserved plant histone modification that marks active genes. | in eukaryotic cells, histones are subject to a large number of posttranslational modifications whose sequential or combinatorial action affects chromatin structure and genome function. we identified acetylation at lys-36 in histone h3 (h3k36ac) as a new chromatin modification in plants. the h3k36ac modification is evolutionary conserved in seed plants, including the gymnosperm norway spruce (picea abies) and the angiosperms rice (oryza sativa), tobacco (nicotiana tabacum), and arabidopsis (arabi ... | 2016 | 26764380 |
| bottlenecks in carotenoid biosynthesis and accumulation in rice endosperm are influenced by the precursor-product balance. | the profile of secondary metabolites in plants reflects the balance of biosynthesis, degradation and storage, including the availability of precursors and products that affect the metabolic equilibrium. we investigated the impact of the precursor-product balance on the carotenoid pathway in the endosperm of intact rice plants because this tissue does not normally accumulate carotenoids, allowing us to control each component of the pathway. we generated transgenic plants expressing the maize phyt ... | 2016 | 25857664 |
| temporal dynamics, population characterization and mycotoxins accumulation of fusarium graminearum in eastern china. | trichothecene genotype composition, mycotoxin production, genetic diversity, and population structure were analyzed, using 185 fusarium strains collected from wheat (triticum aestivum l.) throughout the jiangsu province during 1976, 1983, 1998, 2006, and 2014. the results showed that 3-acetyldeoxynivalenol (3adon) was consistently the predominant type in this region over 40 years, and the nivalenol (niv) type has emerged since 1998. long-term rotation of wheat and rice (oryza sativa l.), rather ... | 2016 | 27853184 |
| crystal structure of os79 (os04g0206600) from oryza sativa: a udp-glucosyltransferase involved in the detoxification of deoxynivalenol. | fusarium head blight is a plant disease with significant agricultural and health impact which affects cereal crops such as wheat, barley, and maize and is characterized by reduced grain yield and the accumulation of trichothecene mycotoxins such as deoxynivalenol (don). studies have identified trichothecene production as a virulence factor in fusarium graminearum and have linked don resistance to the ability to form don-3-o-glucoside in wheat. here, the structures of a deoxynivalenol:udp-glucosy ... | 2016 | 27715009 |
| molecular progress on the mapping and cloning of functional genes for blast disease in rice (oryza sativa l.): current status and future considerations. | rice blast disease, which is caused by the fungal pathogen magnaporthe oryzae, is a recurring problem in all rice-growing regions of the world. the use of resistance (r) genes in rice improvement breeding programmes has been considered to be one of the best options for crop protection and blast management. alternatively, quantitative resistance conferred by quantitative trait loci (qtls) is also a valuable resource for the improvement of rice disease resistance. in the past, intensive efforts ha ... | 2016 | 25394538 |
| evolution of compatibility range in the rice-magnaporthe oryzae system: an uneven distribution of r genes between rice subspecies. | efficient strategies for limiting the impact of pathogens on crops require a good understanding of the factors underlying the evolution of compatibility range for the pathogens and host plants, i.e., the set of host genotypes that a particular pathogen genotype can infect and the set of pathogen genotypes that can infect a particular host genotype. until now, little is known about the evolutionary and ecological factors driving compatibility ranges in systems implicating crop plants. we studied ... | 2016 | 26667186 |
| serotonin attenuates biotic stress and leads to lesion browning caused by a hypersensitive response to magnaporthe oryzae penetration in rice. | the hypersensitive response (hr) of plants is one of the earliest responses to prevent pathogen invasion. a brown dot lesion on a leaf is visual evidence of the hr against the blast fungus magnaporthe oryzae in rice, but tracking the browning process has been difficult. in this study, we induced the hr in rice cultivars harboring the blast resistance gene pit by inoculation of an incompatible m. oryzae strain, which generated a unique resistance lesion with a brown ring (halo) around the brown f ... | 2016 | 26603141 |
| emergence of wheat blast in bangladesh was caused by a south american lineage of magnaporthe oryzae. | in february 2016, a new fungal disease was spotted in wheat fields across eight districts in bangladesh. the epidemic spread to an estimated 15,000 hectares, about 16 % of the cultivated wheat area in bangladesh, with yield losses reaching up to 100 %. within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from bangladeshi fields. | 2016 | 27716181 |
| a new recessive gene conferring resistance against rice blast. | rice blast (causative pathogen magnaporthe oryzae) represents a major biotic constraint over rice production. while numerous genes for resistance have been found in both japonica and indica germplasm, as yet the diversity harbored by aus germplasm has not been widely exploited. | 2016 | 27637926 |
| population structure analysis and association mapping of blast resistance in indica rice (oryza sativa l.) landraces. | rice blast caused by magnaporthe oryzae is one of the most devastating rice diseases worldwide. to understand the genetic diversity of indica landrace accessions and identify simple sequence repeat (ssr) markers that are associated with blast resistance, a population of 276 indica landraces from across the world was constructed. this population was then used to evaluate the blast-resistance phenotype through artificial inoculation under controlled conditions in 2012 and 2013. the genetic diversi ... | 2016 | 27525942 |
| defence responses in rice plants in prior and simultaneous applications of cladosporium sp. during leaf blast suppression. | an alternative method to control rice blast (magnaporthe oryzae) is to include biological agent in the disease management strategy. the objective of this study was to assess the leaf blast-suppressing effects of rice phylloplane fungi. one cladosporium sp. phylloplane fungus was shown to possess biocontrolling traits based on its morphological characteristics and an analysis of its 18s ribosomal dna. experiments aimed at determining the optimal time to apply the bioagent and the mechanisms invol ... | 2016 | 27515526 |
| host specialization of the blast fungus magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements. | magnaporthe oryzae (anamorph pyricularia oryzae) is the causal agent of blast disease of poaceae crops and their wild relatives. to understand the genetic mechanisms that drive host specialization of m. oryzae, we carried out whole genome resequencing of four m. oryzae isolates from rice (oryza sativa), one from foxtail millet (setaria italica), three from wild foxtail millet s. viridis, and one isolate each from finger millet (eleusine coracana), wheat (triticum aestivum) and oat (avena sativa) ... | 2016 | 27194050 |
| cuticular defects in oryza sativa atp-binding cassette transporter g31 mutant plants cause dwarfism, elevated defense responses and pathogen resistance. | the cuticle covers the surface of the polysaccharide cell wall of leaf epidermal cells and forms an essential diffusion barrier between plant and environment. homologs of the atp-binding cassette (abc) transporter atabcg32/hvabcg31 clade are necessary for the formation of a functional cuticle in both monocots and dicots. here we characterize the osabcg31 knockout mutant and hairpin rna interference (rnai)-down-regulated osabcg31 plant lines having reduced plant growth and a permeable cuticle. th ... | 2016 | 27121976 |
| development of disease-resistant rice by pathogen-responsive expression of wrky45. | wrky45 is an important transcription factor in the salicylic acid signalling pathway in rice that mediates chemical-induced resistance against multiple pathogens. its constitutive overexpression confers extremely strong resistance against magnaporthe oryzae and xanthomonas oryzae pv. oryzae to rice, but has adverse effects on agronomic traits. here, a new strategy to confer rice with strong disease resistance without any negative effects on agronomic traits was established by expressing wrky45 u ... | 2016 | 26448265 |
| the broadly effective recessive resistance gene xa5 of rice is a virulence effector-dependent quantitative trait for bacterial blight. | mutations in disease susceptibility (s) genes, here referred to as recessive resistance genes, have promise for providing broad durable resistance in crop species. however, few recessive disease resistance genes have been characterized. here, we show that the broadly effective resistance gene xa5,for resistance to bacterial blight of rice (oryza sativa), is dependent on the effector genes present in the pathogen. specifically, the effectiveness of xa5 in preventing disease by strains of xanthomo ... | 2016 | 26991395 |
| comparative nutritional compositions and proteomics analysis of transgenic xa21 rice seeds compared to conventional rice. | transgenic rice expressing the xa21 gene have enhanced resistant to most devastating bacterial blight diseases caused by xanthomonas oryzae pv. oryzae (xoo). however, identification of unintended modifications, owing to the genetic modification, is an important aspect of transgenic crop safety assessment. in this study, the nutritional compositions of seeds from transgenic rice plants expressing the xa21 gene were compared against non-transgenic rice seeds. in addition, to detect any changes in ... | 2016 | 26948618 |
| a chloroplast-localized protein lesion and lamina bending affects defence and growth responses in rice. | understanding how plants allocate their resources to growth or defence is of long-term importance to the development of new and improved varieties of different crops. using molecular genetics, plant physiology, hormone analysis and next-generation sequencing (ngs)-based transcript profiling, we have isolated and characterized the rice (oryza sativa) lesion and lamina bending (llb) gene that encodes a chloroplast-targeted putative leucine carboxyl methyltransferase. loss of llb function results i ... | 2016 | 26864209 |
| comparative study of the physicochemical, compositional and functional properties of eight flours obtained from different plant materials found in colombia. | the physicochemical, compositional and functional properties of flour from green plantains (musa acuminata) of the large green plantain variety, oyster mushrooms (pleorotus ostreatus), pineapple peel (ananas comosus) of the 'apple pineapple' variety, yellow peas (pisum sativum), chickpeas (cicer arietinum), whole grain rice (oryza sativa), whole grain corn (zea mays) and whole grain white quinoa (chenopodium quinoa) were evaluated by using one-way analysis of variance, pearson correlations and p ... | 2016 | 27091150 |
| genetic architecture of flowering phenology in cereals and opportunities for crop improvement. | cereal crop species including bread wheat (triticum aestivum l.), barley (hordeum vulgare l.), rice (oryza sativa l.), and maize (zea mays l.) provide the bulk of human nutrition and agricultural products for industrial use. these four cereals are central to meet future demands of food supply for an increasing world population under a changing climate. a prerequisite for cereal crop production is the transition from vegetative to reproductive and grain-filling phases starting with flower initiat ... | 2016 | 28066466 |
| the control of flowering time by environmental factors. | the timing of flowering is determined by endogenous genetic components as well as various environmental factors, such as day length, temperature, and stress. the genetic elements and molecular mechanisms that rule this process have been examined in the long-day-flowering plant arabidopsis thaliana and short-day-flowering rice (oryza sativa). however, reviews of research on the role of those factors are limited. here, we focused on how flowering time is influenced by nutrients, ambient temperatur ... | 2016 | 27995671 |
| a reduction of sucrose phosphate synthase (sps) activity affects sucrose/starch ratio in leaves but does not inhibit normal plant growth in rice. | sucrose phosphate synthase (sps) has been shown to mediate sucrose/starch ratio in plant leaves through studies of 'starch leaf' species that mainly accumulate starch in their leaves. however, the contribution of sps to sucrose/starch ratio in rice leaves, which mainly accumulate sucrose (i.e., 'sugar leaf'), has not been confirmed due to inconsistencies in the results of previous studies. in this study, we analyzed mutant lines with reduced sps activity, which were generated using tos17 inserti ... | 2016 | 27968995 |
| comparative genomic analysis of the grf genes in chinese pear (pyrus bretschneideri rehd), poplar (populous), grape (vitis vinifera), arabidopsis and rice (oryza sativa). | growth-regulating factors (grfs) are plant-specific transcription factors that have important functions in regulating plant growth and development. previous studies on grf family members focused either on a single or a small set of genes. here, a comparative genomic analysis of the grf gene family was performed in poplar (a model tree species), arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots), rice (a model plant for monocots) and chinese pea ... | 2016 | 27933074 |
| novoplasty: de novo assembly of organelle genomes from whole genome data. | the evolution in next-generation sequencing (ngs) technology has led to the development of many different assembly algorithms, but few of them focus on assembling the organelle genomes. these genomes are used in phylogenetic studies, food identification and are the most deposited eukaryotic genomes in genbank. producing organelle genome assembly from whole genome sequencing (wgs) data would be the most accurate and least laborious approach, but a tool specifically designed for this task is lacki ... | 2016 | 27924028 |
| genome-wide characterisation and expression profile of the grapevine atl ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members. | the arabidopsis tóxicos en levadura (atl) protein family is a class of e3 ubiquitin ligases with a characteristic ring-h2 zn-finger structure that mediates diverse physiological processes and stress responses in plants. we carried out a genome-wide survey of grapevine (vitis vinifera l.) atl genes and retrieved 96 sequences containing the canonical atl ring-h2 domain. we analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. clustering ... | 2016 | 27910910 |
| rice cyo1, an ortholog of arabidopsis thaliana cotyledon chloroplast biogenesis factor atcyo1, is expressed in leaves and involved in photosynthetic performance. | in the dicotyledonous plant arabidopsis thaliana, the cotyledon chloroplast biogenesis factor atcyo1 is crucial for the biogenesis of cotyledon chloroplasts. arabidopsis mutants lacking atcyo1 have pale cotyledons but develop normal mature leaves. in the monocotyledonous plant oryza sativa, the gene oscyo1 has high sequence identity to atcyo1, but its function is unknown. we examined the role of oscyo1 in o. sativa. we first confirmed that transformation with oscyo1 could recover the phenotype o ... | 2016 | 27835768 |
| nj cluster analysis of the snrk2, pyr/pyl/rcar, and abf genes in tibetan hulless barley. | the abscisic acid (aba) signaling pathway is known as one of the most important signaling pathways in plants and is mediated by multiple regulators. the genes snrk2, pyr/pyl/rcar, and abf are relevant to both aba-dependent and -independent signaling pathways. to elucidate the profile of these genes from tibetan hulless barley (hordeum vulgare l. var. nudum hook. f.), we collected available sequences from rna-seq data, together with ncbi data from five other model plant species (arabidopsis thali ... | 2016 | 27819745 |
| turning rice meiosis into mitosis. | introduction of clonal reproduction through seeds (apomixis) in crops has the potential to revolutionize agriculture by allowing self-propagation of any elite variety, in particular f1 hybrids. in the sexual model plant arabidopsis thaliana synthetic clonal reproduction through seeds can be artificially implemented by (i) combining three mutations to turn meiosis into mitosis (mime) and (ii) crossing the obtained clonal gametes with a line expressing modified cenh3 and whose genome is eliminated ... | 2016 | 27767093 |
| a flow cytometric method for estimating s-phase duration in plants. | the duration of the dna synthesis stage (s phase) of the cell cycle is fundamental in our understanding of cell cycle kinetics, cell proliferation, and dna replication timing programs. most s-phase duration estimates that exist for plants are based on indirect measurements. we present a method for directly estimating s-phase duration by pulse-labeling root tips or actively dividing suspension cells with the halogenated thymidine analog 5-ethynl-2'-deoxyuridine (edu) and analyzing the time course ... | 2016 | 27697785 |
| ossgl, a novel duf1645 domain-containing protein, confers enhanced drought tolerance in transgenic rice and arabidopsis. | drought is a major environmental factor that limits plant growth and crop productivity. genetic engineering is an effective approach to improve drought tolerance in various crops, including rice (oryza sativa). functional characterization of relevant genes is a prerequisite when identifying candidates for such improvements. we investigated ossgl (oryza sativa stress tolerance and grain length), a novel duf1645 domain-containing protein from rice. ossgl was up-regulated by multiple stresses and l ... | 2016 | 28083013 |
| rolling-circle amplification of centromeric helitrons in plant genomes. | the unusual eukaryotic helitron transposons can readily capture host sequences and are, thus, evolutionarily important. they are presumed to amplify by rolling-circle replication (rcr) because some elements encode predicted proteins homologous to rcr prokaryotic transposases. in support of this replication mechanism, it was recently shown that transposition of a bat helitron generates covalently closed circular intermediates. another strong prediction is that rcr should generate tandem helitron ... | 2016 | 27553634 |
| quantification of hydrogen peroxide in plant tissues using amplex red. | reactive oxygen species (ros) are by-products of photosynthesis and respiration in plant tissues. abiotic and biotic stressors also induce the production and temporary accumulation of ros in plants, including hydrogen peroxide (h2o2), whereby they can act as secondary messengers/chemical mediators in plant defense signaling and lead to programmed cell death. h2o2 acts as a hub for critical information flow in plants. despite such key roles in fundamental cellular processes, reliable determinatio ... | 2016 | 27476009 |
| identification and expression analysis of oslpr family revealed the potential roles of oslpr3 and 5 in maintaining phosphate homeostasis in rice. | phosphorus (p), an essential macronutrient, is often limiting in soils and affects plant growth and development. in arabidopsis thaliana, low phosphate root1 (lpr1) and its close paralog lpr2 encode multicopper oxidases (mcos). they regulate meristem responses of root system to phosphate (pi) deficiency. however, the roles of lpr gene family in rice (oryza sativa) in maintaining pi homeostasis have not been elucidated as yet. | 2016 | 27716044 |
| heterogeneous evolution of ty3-gypsy retroelements among bamboo species. | ty3-gypsy long-terminal repeat retroelements are ubiquitously found in many plant genomes. this study reports the occurrence of heterogeneous ty3-gypsy retroelements in four representative bamboo species: phyllostachys heterocycla (carr.) mitford cv. pubescens, p. heterocycla (carr.) mitford cv. heterocycla, dendrocalamopsis oldhami, and pleioblastus fortunei. using degenerate oligonucleotide primers corresponding to the conserved domains of reverse transcriptase (rt) genes of ty3-gypsy retroele ... | 2016 | 27706589 |
| an easy method for plant polysome profiling. | translation of mrna to protein is a fundamental and highly regulated biological process. polysome profiling is considered as a gold standard for the analysis of translational regulation. the method described here is an easy and economical way for fractionating polysomes from various plant tissues. a sucrose gradient is made without the need for a gradient maker by sequentially freezing each layer. cytosolic extracts are then prepared in a buffer containing cycloheximide and chloramphenicol to im ... | 2016 | 27684295 |
| global analysis of truncated rna ends reveals new insights into ribosome stalling in plants. | high-throughput approaches for profiling the 5' ends of rna degradation intermediates on a genome-wide scale are frequently applied to analyze and validate cleavage sites guided by micrornas (mirnas). however, the complexity of the rna degradome other than mirna targets is currently largely uncharacterized, and this limits the application of rna degradome studies. we conducted a global analysis of 5'-truncated mrna ends that mapped to coding sequences (cdss) of arabidopsis thaliana, rice (oryza ... | 2016 | 27742800 |
| carotenogenesis is regulated by 5'utr-mediated translation of phytoene synthase splice variants. | phytoene synthase (psy) catalyzes the highly regulated, frequently rate-limiting synthesis of the first biosynthetically formed carotene. while psy constitutes a small gene family in most plant taxa, the brassicaceae, including arabidopsis (arabidopsis thaliana), predominantly possess a single psy gene. this monogenic situation is compensated by the differential expression of two alternative splice variants (asv), which differ in length and in the exon/intron retention of their 5'utrs. asv1 cont ... | 2016 | 27729470 |
| a rice ca2+ binding protein is required for tapetum function and pollen formation. | in flowering plants, successful male reproduction requires the sophisticated interaction between somatic anther wall layers and reproductive cells. timely degradation of the innermost tissue of the anther wall layer, the tapetal layer, is critical for pollen development. ca(2+) is a well-known stimulus for plant development, but whether it plays a role in affecting male reproduction remains elusive. here we report a role of defective in exine formation 1 (osdex1) in rice (oryza sativa), a ca(2+) ... | 2016 | 27663411 |
| modd mediates deactivation and degradation of osbzip46 to negatively regulate aba signaling and drought resistance in rice. | plants have evolved complicated protective mechanisms to survive adverse conditions. previously, we reported that the transcription factor osbzip46 regulates abscisic acid (aba) signaling-mediated drought tolerance in rice (oryza sativa) by modulating stress-related genes. an intrinsic d domain represses osbzip46 activity, but the detailed mechanism for the repression of osbzip46 activation remains unknown. here, we report an osbzip46-interacting protein, modd (mediator of osbzip46 deactivation ... | 2016 | 27468891 |
| vacuolar spx-mfs transporters are essential for phosphate adaptation in plants. | to survive in most soils in which inorganic phosphate (pi) levels are limited and constantly changing, plants universally use the vacuoles as cellular pi "sink" and "source" to maintain pi homeostasis. however, the transporters that mediate pi sequestration into the vacuoles remain unknown. recently, we and other 2 groups independently identified the members of sps-msf family as the candidates for tonoplast pi transporters in arabidopsis thaliana and oryza sativa. we and liu et al. demonstrated ... | 2016 | 27467463 |
| corrigendum: overexpression of rice glutaredoxin osgrx_c7 and osgrx_c2.1 reduces intracellular arsenic accumulation and increases tolerance in arabidopsis thaliana. | [this corrects the article on p. 740 in vol. 7, pmid: 27313586.]. | 2016 | 27462345 |