| testing the recent theories for the origin of the hermaphrodite flower by comparison of the transcriptomes of gymnosperms and angiosperms. | different theories for the origin of the angiosperm hermaphrodite flower make different predictions concerning the overlap between the genes expressed in the male and female cones of gymnosperms and the genes expressed in the hermaphrodite flower of angiosperms. the mostly male (mm) theory predicts that, of genes expressed primarily in male versus female gymnosperm cones, an excess of male orthologs will be expressed in flowers, excluding ovules, while out of male (oom) and out of female (oof) t ... | 2010 | 20682074 |
| biochemical changes associated with in vivo rbcl fragmentation by reactive oxygen species under chilling-light conditions. | during physiological stress, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) degradation is accelerated, which is considered to be one of the key factors responsible for photosynthetic decline. a recent study has shown that the large subunit (rbcl) of rubisco is directly fragmented by hydroxyl radicals in cucumis sativus leaves under chilling-light conditions. in the present study, we investigated biochemical aspects associated with this in vivo rbcl fragmentation by reactive oxygen sp ... | 2010 | 20653886 |
| diversification and specialization of plant rbr ubiquitin ligases. | rbr ubiquitin ligases are components of the ubiquitin-proteasome system present in all eukaryotes. they are characterized by having the rbr (ring - ibr - ring) supradomain. in this study, the patterns of emergence of rbr genes in plants are described. | 2010 | 20644651 |
| analysis of bac clones containing homologous sequences on the end of the xq arm and on chromosome 7 in the dioecious plant silene latifolia. | silene latifolia is a model dioecious plant with morphologically distinguishable xy sex chromosomes. the end of the xq arm is quite different from that of the yp arm, although both are located at opposite ends of their respective chromosomes relative to a pseudo-autosomal region. the xq arm does not seem to originate from the same autosome as the yp arm. bacterial artificial chromosome clone #15b12 has an insert containing a 130-kb stretch in which a 313-bp satellite dna is repeated 420 times. p ... | 2010 | 20616862 |
| early evolution of bhlh proteins in plants. | basic-helix-loop-helix (bhlh) proteins are a large family of eukaryotic transcription factors. in plants, they have been shown to be key regulators of a diverse array of developmental and metabolic pathways. we have recently shown that the diversity of bhlh proteins in angiosperms is ancient. most of the bhlh subfamilies present in seed plants such as arabidopsis thaliana and oryza sativa are also present in early diverging groups of land plants, including mosses and lycophytes. in contrast, the ... | 2010 | 20523129 |
| knockout of a bacterial-type atp-binding cassette transporter gene, atstar1, results in increased aluminum sensitivity in arabidopsis. | atp-binding cassette (abc) transporters represent a large family in plants, but the functions of most of these transporters are unknown. here we report a gene, atstar1, only encoding an atp-binding domain of a bacterial-type abc transporter in arabidopsis (arabidopsis thaliana). atstar1 is an ortholog of rice (oryza sativa) osstar1, which has been implicated in aluminum (al) tolerance. knockout of atstar1 resulted in increased sensitivity to al and earlier flowering. unlike osstar1, atstar1 was ... | 2010 | 20498340 |
| identification and application of a rice senescence-associated promoter. | sag39 is a rice (oryza sativa) gene that encodes a cysteine protease. sag39 shares 55% homology with the arabidopsis (arabidopsis thaliana) senescence-associated protein sag12. the promoter for sag39 (p(sag39)) was isolated, and sag39 expression was determined to be relatively low in mature leaves, while not expressed in the endosperm. sag39 mrna levels increased as senescence progressed, with maximum accumulation of transcripts at late senescence stages. gel retardation assays indicated that tw ... | 2010 | 20439547 |
| comparative genomics of flowering time pathways using brachypodium distachyon as a model for the temperate grasses. | brachypodium distachyon (brachypodium) is a model for the temperate grasses which include important cereals such as barley, wheat and oats. comparison of the brachypodium genome (accession bd21) with those of the model dicot arabidopsis thaliana and the tropical cereal rice (oryza sativa) provides an opportunity to compare and contrast genetic pathways controlling important traits. we analysed the homologies of genes controlling the induction of flowering using pathways curated in arabidopsis re ... | 2010 | 20419097 |
| ap2/erebp transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signalling. | to optimize acclimation responses to environmental growth conditions, plants integrate and weigh a diversity of input signals. signal integration within the signalling networks occurs at different sites including the level of transcription factor activation. accumulating evidence assigns a major and diversified role in environmental signal integration to the family of apetala 2/ethylene response element binding protein (ap2/erebp) transcription factors. presently, the plant transcription factor ... | 2010 | 20411284 |
| cop: a database for characterizing co-expressed gene modules with biological information in plants. | using a large dataset (10 022 assays) obtained from public plant microarray databases, we developed the cop database for associating co-expressed gene modules with biological information such as gene ontology terms and, if available, metabolic pathway names. the confeito algorithm developed previously in our laboratory, which is suitable to calculate the interconnectivity between genes in co-expressed gene network, was applied to extract co-expressed gene modules. the database includes the gene ... | 2010 | 20305269 |
| a conserved mechanism of bract suppression in the grass family. | suppression of inflorescence leaf, or bract, growth has evolved multiple times in diverse angiosperm lineages, including the poaceae and brassicaceae. studies of arabidopsis thaliana mutants have revealed several genes involved in bract suppression, but it is not known if these genes play a similar role in other plants with suppressed bracts. we identified maize (zea mays) tassel sheath (tsh) mutants, characterized by the loss of bract suppression, that comprise five loci (tsh1-tsh5). we used ma ... | 2010 | 20305121 |
| tc-motifs at the tata-box expected position in plant genes: a novel class of motifs involved in the transcription regulation. | the tata-box and tata-variants are regulatory elements involved in the formation of a transcription initiation complex. both have been conserved throughout evolution in a restricted region close to the transcription start site (tss). however, less than half of the genes in model organisms studied so far have been found to contain either one of these elements. indeed different core-promoter elements are involved in the recruitment of the tata-box-binding protein. here we assessed the possibility ... | 2010 | 20222994 |
| identification of shared single copy nuclear genes in arabidopsis, populus, vitis and oryza and their phylogenetic utility across various taxonomic levels. | although the overwhelming majority of genes found in angiosperms are members of gene families, and both gene- and genome-duplication are pervasive forces in plant genomes, some genes are sufficiently distinct from all other genes in a genome that they can be operationally defined as 'single copy'. using the gene clustering algorithm mcl-tribe, we have identified a set of 959 single copy genes that are shared single copy genes in the genomes of arabidopsis thaliana, populus trichocarpa, vitis vin ... | 2010 | 20181251 |
| codon usage biases of transposable elements and host nuclear genes in arabidopsis thaliana and oryza sativa. | transposable elements (tes) are mobile genetic entities ubiquitously distributed in nearly all genomes. high frequency of codons ending in a/t in tes has been previously observed in some species. in this study, the biases in nucleotide composition and codon usage of te transposases and host nuclear genes were investigated in the at-rich genome of arabidopsis thaliana and the gc-rich genome of oryza sativa. codons ending in a/t are more frequently used by tes compared with their host nuclear gene ... | 2009 | 20172490 |
| the central element protein zep1 of the synaptonemal complex regulates the number of crossovers during meiosis in rice. | zep1, a transverse filament (tf) protein, is the rice (oryza sativa) homolog of arabidopsis thaliana zyp1. in the tos17-insertional zep1 mutants, homologous chromosomes align along the entire length of the chromosome, but the synaptonemal complex is not assembled in early prophase i. crossovers are well formed, and 12 bivalents could be detected from diakinesis to metaphase i, which leads to equal chromosomal segregation in anaphase i. moreover, the number of crossovers has a tendency to be incr ... | 2010 | 20154151 |
| metabolome and photochemical analysis of rice plants overexpressing arabidopsis nad kinase gene. | the chloroplastic nad kinase (nadk2) is reported to stimulate carbon and nitrogen assimilation in arabidopsis (arabidopsis thaliana), which is vulnerable to high light. since rice (oryza sativa) is a monocotyledonous plant that can adapt to high light, we studied the effects of nadk2 expression in rice by developing transgenic rice plants that constitutively expressed the arabidopsis chloroplastic nadk gene (nk2 lines). nk2 lines showed enhanced activity of nadk and accumulation of the nadp(h) p ... | 2010 | 20154096 |
| microrna-mediated signaling involved in plant root development. | microrna (mirna), recently recognized as a critical post-transcriptional modulator of gene expression, is involved in numerous biological processes in both animals and plants. although eudicots and monocots, such as the model plants arabidopsis (arabidopsis thaliana) and rice (oryza sativa), possess distinct root systems, several homologous mirna families are reported to be involved in root growth control in both plants. consistent with recent notion that numerous signaling pathways are implicat ... | 2010 | 20138828 |
| quantitative analysis of plant polyamines including thermospermine during growth and salinity stress. | arabidopsis thaliana was thought to contain two spermine synthase genes, acaulis 5 (acl5) and spms. recent investigations, however, revealed that the acl5 gene encodes thermospermine synthase. in this study, we have established a simple method to separate two isomers of tetraamine, spermine and thermospermine, in extracts from plant tissues of less than 500 mg. polyamines (pas) extracted from plant tissues were benzoylated, and the derivatives were completely resolved by high-performance liquid ... | 2010 | 20137962 |
| over-expression of osa-mir396c decreases salt and alkali stress tolerance. | salt and alkali stress are two of the main environmental factors limiting rice production. thus, understanding the mechanisms of salinity and alkali stress tolerance is necessary to modify rice to increase its resistance to salinity and alkaline stress. micrornas (mirnas) are approximately 21-nucleotide rnas that are ubiquitous regulators of gene expression in eukaryotic organisms. in plants, mirnas constitute one of five classes of small rnas that function primarily as negative regulators for g ... | 2010 | 20135324 |
| genome-wide analysis of ethylene-responsive element binding factor-associated amphiphilic repression motif-containing transcriptional regulators in arabidopsis. | the ethylene-responsive element binding factor-associated amphiphilic repression (ear) motif is a transcriptional regulatory motif identified in members of the ethylene-responsive element binding factor, c2h2, and auxin/indole-3-acetic acid families of transcriptional regulators. sequence comparison of the core ear motif sites from these proteins revealed two distinct conservation patterns: lxlxl and dlnxxp. proteins containing these motifs play key roles in diverse biological functions by negat ... | 2010 | 20097792 |
| characterization of the rice pho1 gene family reveals a key role for ospho1;2 in phosphate homeostasis and the evolution of a distinct clade in dicotyledons. | phosphate homeostasis was studied in a monocotyledonous model plant through the characterization of the pho1 gene family in rice (oryza sativa). bioinformatics and phylogenetic analysis showed that the rice genome has three pho1 homologs, which cluster with the arabidopsis (arabidopsis thaliana) atpho1 and atpho1;h1, the only two genes known to be involved in root-to-shoot transfer of phosphate. in contrast to the arabidopsis pho1 gene family, all three rice pho1 genes have a cis-natural antisen ... | 2010 | 20081045 |
| the wus homeobox-containing (wox) protein family. | the wox genes form a plant-specific subclade of the eukaryotic homeobox transcription factor superfamily, which is characterized by the presence of a conserved dna-binding homeodomain. the analysis of wox gene expression and function shows that wox family members fulfill specialized functions in key developmental processes in plants, such as embryonic patterning, stem-cell maintenance and organ formation. these functions can be related to either promotion of cell division activity and/or prevent ... | 2009 | 20067590 |
| mef9, an e-subclass pentatricopeptide repeat protein, is required for an rna editing event in the nad7 transcript in mitochondria of arabidopsis. | rna editing in plants alters specific nucleotides from c to u in mrnas in plastids and in mitochondria. i here characterize the nuclear gene mitochondrial editing factor9 (mef9) that is required for rna editing of the site nad7-200 in the nad7 mitochondrial mrna in arabidopsis (arabidopsis thaliana). the mef9 protein belongs to the e subfamily of pentatricopeptide repeat proteins and unlike the three previously identified mitochondrial editing factors mef1 and mef11 in arabidopsis and ogr1 in ri ... | 2010 | 20018598 |
| dynamic landscapes of four histone modifications during deetiolation in arabidopsis. | although landscapes of several histone marks are now available for arabidopsis thaliana and oryza sativa, such profiles remain static and do not provide information about dynamic changes of plant epigenomes in response to developmental or environmental cues. here, we analyzed the effects of light on four histone modifications (acetylation and trimethylation of lysines 9 and 27 on histone h3: h3k9ac, h3k9me3, h3k27ac, and h3k27me3, respectively). our genome-wide profiling of h3k9ac and h3k27ac re ... | 2009 | 20008096 |
| origin and diversification of basic-helix-loop-helix proteins in plants. | basic helix-loop-helix (bhlh) proteins are a class of transcription factors found throughout eukaryotic organisms. classification of the complete sets of bhlh proteins in the sequenced genomes of arabidopsis thaliana and oryza sativa (rice) has defined the diversity of these proteins among flowering plants. however, the evolutionary relationships of different plant bhlh groups and the diversity of bhlh proteins in more ancestral groups of plants are currently unknown. in this study, we use whole ... | 2010 | 19942615 |
| evidence for a role of hexokinases as conserved glucose sensors in both monocot and dicot plant species. | the role of the hexokinases (hxks) as glucose (glc) sensors has been mainly demonstrated for arabidopsis (arabidopsis thaliana) hxk1 (athxk1) but has yet to be shown in other plant species. in our recent publication, we reported that two rice (oryza sativa) hxks, oshxk5 and oshxk6, also function as glc sensors. these two enzymes harbor both mitochondrial targeting peptides (mtps) and nuclear localization signals (nlss), and we confirmed their dual-targeting ability to nuclei and mitochondria usi ... | 2009 | 19938377 |
| genetic resources for maize cell wall biology. | grass species represent a major source of food, feed, and fiber crops and potential feedstocks for biofuel production. most of the biomass is contributed by cell walls that are distinct in composition from all other flowering plants. identifying cell wall-related genes and their functions underpins a fundamental understanding of growth and development in these species. toward this goal, we are building a knowledge base of the maize (zea mays) genes involved in cell wall biology, their expression ... | 2009 | 19926802 |
| duplication of the class i cytosolic small heat shock protein gene and potential functional divergence revealed by sequence variations flanking the {alpha}-crystallin domain in the genus rhododendron (ericaceae). | positive selection in the -crystallin domain (acd) of the chloroplast small heat shock protein (cpshsp) gene was found in a previous study and was suggested to be related to the ecological adaptation of rhododendron species in the subgenus hymenanthes. consequently, it was of interest to examine whether gene duplication and subsequent divergence have occurred in other shsp genes, for example class i cytosolic shsp genes (ct1shsps) in rhododendron in taiwan, where many endemic species have evolve ... | 2010 | 19887471 |
| isolation and phylogenetic footprinting analysis of the 5'-regulatory region of the floral homeotic gene orcpi from orchis italica (orchidaceae). | the nucleotide sequences of regulatory elements from homologous genes can be strongly divergent. phylogenetic footprinting, a comparative analysis of noncoding regions, can detect putative transcription factor binding sites (tfbss) shared among the regulatory regions of 2 or more homologous genes. these conserved motifs have the potential to serve the same regulatory function in distantly related taxa. we isolated the 5'-noncoding region of the orcpi gene, a mads-box transcription factor involve ... | 2009 | 19861638 |
| seed storage protein gene promoters contain conserved dna motifs in brassicaceae, fabaceae and poaceae. | accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate dna sequences bound by several interacting factors. enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. this provides a basis for the computational identification of cis-regulato ... | 2009 | 19843335 |
| functional analyses of lonely guy cytokinin-activating enzymes reveal the importance of the direct activation pathway in arabidopsis. | cytokinins play crucial roles in diverse aspects of plant growth and development. spatiotemporal distribution of bioactive cytokinins is finely regulated by metabolic enzymes. lonely guy (log) was previously identified as a cytokinin-activating enzyme that works in the direct activation pathway in rice (oryza sativa) shoot meristems. in this work, nine arabidopsis thaliana log genes (at log1 to log9) were predicted as homologs of rice log. seven at logs, which are localized in the cytosol and nu ... | 2009 | 19837870 |
| indel-associated mutation rate varies with mating system in flowering plants. | a recently proposed mutational mechanism, indel-associated mutation (idam), posits that heterozygous insertions/deletions (indels) increase the point mutation rate at nearby nucleotides due to errors during meiosis. this mechanism could have especially dynamic consequences for the evolution of plant genomes, because the high degree of variation in the rate of self-fertilization among plant species causes differences in the heterozygosity of alleles, including indel alleles, segregating in plant ... | 2010 | 19825943 |
| construction of a rice glycosyltransferase phylogenomic database and identification of rice-diverged glycosyltransferases. | glycosyltransferases (gts; ec 2.4.x.y) constitute a large group of enzymes that form glycosidic bonds through transfer of sugars from activated donor molecules to acceptor molecules. gts are critical to the biosynthesis of plant cell walls, among other diverse functions. based on the carbohydrate-active enzymes (cazy) database and sequence similarity searches, we have identified 609 potential gt genes (loci) corresponding to 769 transcripts (gene models) in rice (oryza sativa), the reference mon ... | 2008 | 19825588 |
| pmrd: plant microrna database. | micrornas (mirna) are approximately 21 nucleotide-long non-coding small rnas, which function as post-transcriptional regulators in eukaryotes. mirnas play essential roles in regulating plant growth and development. in recent years, research into the mechanism and consequences of mirna action has made great progress. with whole genome sequence available in such plants as arabidopsis thaliana, oryza sativa, populus trichocarpa, glycine max, etc., it is desirable to develop a plant mirna database t ... | 2010 | 19808935 |
| biochemical insights on degradation of arabidopsis della proteins gained from a cell-free assay system. | the phytohormone gibberellic acid (ga) regulates diverse aspects of plant growth and development. ga responses are triggered by the degradation of della proteins, which function as repressors in ga signaling pathways. recent studies in arabidopsis thaliana and rice (oryza sativa) have implied that the degradation of della proteins occurred via the ubiquitin-proteasome system. here, we developed an arabidopsis cell-free system to recapitulate della protein degradation in vitro. using this cell-fr ... | 2009 | 19717618 |
| role of osphr2 on phosphorus homeostasis and root hairs development in rice (oryza sativa l.). | atphr1 plays a central role in pi-starvation signaling in arabidopsis (arabidopsis thaliana). two phr genes were isolated from rice and designated as osphr1 and osphr2 based on amino acid sequence homology to atphr1. transgenic plants with overexpression and repression of osphr1 and osphr2, respectively, were used for investigation of roles of the genes in pi-signaling pathway and pi homeostasis under pi-sufficient and deficient conditions. the results showed that both of the genes are involved ... | 2008 | 19704822 |
| unraveling the evolution of cytokinin signaling. | the conquest of the land by plants required dramatic morphological and metabolic adaptations. complex developmental programs under tight regulation evolved during this process. key regulators of plant development are phytohormones, such as cytokinins. cytokinins are adenine derivatives that affect various processes in plants. the cytokinin signal transduction system, which is mediated via a multistep variant of the bacterial two-component signaling system, is well characterized in the model plan ... | 2009 | 19675156 |
| interactions between auxin and strigolactone in shoot branching control. | in arabidopsis (arabidopsis thaliana), the carotenoid cleavage dioxygenases more axillary growth3 (max3) and max4 act together with max1 to produce a strigolactone signaling molecule required for the inhibition of axillary bud outgrowth. we show that both max3 and max4 transcripts are positively auxin regulated in a manner similar to the orthologous genes from pea (pisum sativum) and rice (oryza sativa), supporting evolutionary conservation of this regulation in plants. this regulation is import ... | 2009 | 19641034 |
| evolutionary and expression signatures of pseudogenes in arabidopsis and rice. | pseudogenes (psi) are nonfunctional genomic sequences resembling functional genes. knowledge of psis can improve genome annotation and our understanding of genome evolution. however, there has been relatively little systemic study of psis in plants. in this study, we characterized the evolution and expression patterns of psis in arabidopsis (arabidopsis thaliana) and rice (oryza sativa). in contrast to animal psis, many plant psis experienced much stronger purifying selection. in addition, plant ... | 2009 | 19641029 |
| ricearraynet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice. | microarray data can be used to derive understanding of the relationships between the genes involved in various biological systems of an organism, given the availability of databases of gene expression measurements from the complete spectrum of experimental conditions and materials. however, there have been no reports, to date, of such a database being constructed for rice (oryza sativa). here, we describe the construction of such a database, called ricearraynet (ran; http://www.ggbio.com/arrayne ... | 2009 | 19605550 |
| full-size abc transporters from the abcg subfamily in medicago truncatula. | full-size atp-binding cassette (abc) transporters belonging to the abcg subfamily are unique for plants and fungi. there is growing evidence that certain of these proteins play a role in plant defense or signaling systems. as yet, a complete set of full-size abcg protein genes has been inventoried and classified in only two plants: arabidopsis thaliana and oryza sativa. recently, a domain-based clustering analysis has predicted the presence of at least 12 genes encoding such proteins in the lotu ... | 2009 | 19589068 |
| the spatial expression patterns of drooping leaf orthologs suggest a conserved function in grasses. | the drooping leaf (dl) gene regulates carpel specification in the flower and midrib formation in the leaf in oryza sativa (rice). loss-of-function mutations in the dl locus cause homeotic transformation of carpels into stamens and lack of midrib, resulting in the drooping leaf phenotype. dl is a member of the yabby gene family and is closely related to the crabs claw (crc) gene in arabidopsis thaliana. the function of arabidopsis crc, however, differs from that of rice dl: it is responsible for ... | 2009 | 19556707 |
| expansion mechanisms and functional annotations of hypothetical genes in the rice genome. | in each completely sequenced genome, 30% to 50% of genes are annotated as uncharacterized hypothetical genes. in the rice (oryza sativa) genome, 10,918 hypothetical genes were annotated in the latest version (release 6) of the michigan state university rice genome annotation. we have implemented an integrative approach to analyze their duplication/expansion and function. the analyses show that tandem/segmental duplication and transposition/retrotransposition have significantly contributed to the ... | 2009 | 19535473 |
| posmed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants. | molecular breeding of crops is an efficient way to upgrade plant functions useful to mankind. a key step is forward genetics or positional cloning to identify the genes that confer useful functions. in order to accelerate the whole research process, we have developed an integrated database system powered by an intelligent data-retrieval engine termed posmed-plus (positional medline for plant upgrading science), allowing us to prioritize highly promising candidate genes in a given chromosomal int ... | 2009 | 19528193 |
| refining the definition of plant mitochondrial presequences through analysis of sorting signals, n-terminal modifications, and cleavage motifs. | mitochondrial protein import is a complex multistep process from synthesis of proteins in the cytosol, recognition by receptors on the organelle surface, to translocation across one or both mitochondrial membranes and assembly after removal of the targeting signal, referred to as a presequence. in plants, import has to further discriminate between mitochondria and chloroplasts. in this study, we determined the precise cleavage sites in the presequences for arabidopsis (arabidopsis thaliana) and ... | 2009 | 19474214 |
| trifldb: a database of clustered full-length coding sequences from triticeae with applications to comparative grass genomics. | the triticeae full-length cds database (trifldb) contains available information regarding full-length coding sequences (cdss) of the triticeae crops wheat (triticum aestivum) and barley (hordeum vulgare) and includes functional annotations and comparative genomics features. trifldb provides a search interface using keywords for gene function and related gene ontology terms and a similarity search for dna and deduced translated amino acid sequences to access annotations of triticeae full-length c ... | 2009 | 19448038 |
| expression level of aberrant panicle organization1 determines rice inflorescence form through control of cell proliferation in the meristem. | two types of branches, rachis branches (i.e. nonfloral) and spikelets (i.e. floral), are produced during rice (oryza sativa) inflorescence development. we previously reported that the aberrant panicle organization1 (apo1) gene, encoding an f-box-containing protein orthologous to arabidopsis (arabidopsis thaliana) unusual floral organs, suppresses precocious conversion of rachis branch meristems to spikelets to ensure generation of certain number of spikelets. here, we identified four dominant mu ... | 2009 | 19386809 |
| comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome. | alternative splicing (as) is a widespread phenomenon in higher eukaryotes but the extent to which it leads to functional protein isoforms and to proteome expansion at large is still a matter of debate. in contrast to animal species, for which as has been studied extensively at the protein and functional level, protein-centered studies of as in plant species are scarce. here we investigate the functional impact of as in dicot and monocot plant species using a comparative approach. | 2009 | 19358722 |
| in silico analysis of promoter regions from cold-induced genes in rice (oryza sativa l.) and arabidopsis thaliana reveals the importance of combinatorial control. | cold acclimation involves a number of different cellular processes that together increase the freezing tolerance of an organism. the dreb1/cbfs are transcription factors (tfs) that are prominent in the regulation of cold responses in arabidopsis thaliana, rice and many other crops. we investigated if the expression of dreb1/cbfs and co-expressed genes relies on combinatorial control by several tfs. our results support this notion and indicate that methods for studying the regulation of complex c ... | 2009 | 19321735 |
| genomic expression profiling of mature soybean (glycine max) pollen. | pollen, the male partner in the reproduction of flowering plants, comprises either two or three cells at maturity. the current knowledge of the pollen transcriptome is limited to the model plant systems arabidopsis thaliana and oryza sativa which have tri-cellular pollen grains at maturity. comparative studies on pollen of other genera, particularly crop plants, are needed to understand the pollen gene networks that are subject to functional and evolutionary conservation. in this study, we used ... | 2009 | 19265555 |
| meta-analysis of small rna-sequencing errors reveals ubiquitous post-transcriptional rna modifications. | recent advances in dna-sequencing technology have made it possible to obtain large datasets of small rna sequences. here we demonstrate that not all non-perfectly matched small rna sequences are simple technological sequencing errors, but many hold valuable biological information. analysis of three small rna datasets originating from oryza sativa and arabidopsis thaliana small rna-sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous no ... | 2009 | 19255090 |
| the pentatricopeptide repeat (ppr) gene family, a tremendous resource for plant phylogenetic studies. | * despite the paramount importance of nuclear gene data in plant phylogenetics, the search for candidate loci is believed to be challenging and time-consuming. here we report that the pentatricopeptide repeat (ppr) gene family, containing hundreds of members in plant genomes, holds tremendous potential as nuclear gene markers. * we compiled a list of 127 ppr loci that are all intronless and have a single orthologue in both rice (oryza sativa) and arabidopsis thaliana. the uncorrected p-distances ... | 2009 | 19192190 |
| highly diversified molecular evolution of downstream transcription start sites in rice and arabidopsis. | alternative usage of transcription start sites (tsss) is one of the key mechanisms to generate gene variation in eukaryotes. here, we show diversified molecular evolution of tsss in remotely related flowering plants, rice (oryza sativa) and arabidopsis (arabidopsis thaliana), by comprehensive analyses of large collections of full-length cdnas and genome sequences. we determined 45,917 representative tsss within 23,445 loci of rice and 35,313 tsss within 16,964 loci of arabidopsis, about two tsss ... | 2009 | 19118127 |
| evaluating the microtubule cytoskeleton and its interacting proteins in monocots by mining the rice genome. | microtubules (mts) are assembled by heterodimers of alpha- and beta-tubulins, which provide tracks for directional transport and frameworks for the spindle apparatus and the phragmoplast. mt nucleation and dynamics are regulated by components such as the gamma-tubulin complex which are conserved among eukaryotes, and other components which are unique to plants. following remarkable progress made in the model plant arabidopsis thaliana toward revealing key components regulating mt activities, the ... | 2009 | 19106179 |
| the uniprotkb/swiss-prot knowledgebase and its plant proteome annotation program. | the uniprot knowledgebase, uniprotkb, is the main product of the uniprot consortium. it consists of two sections, uniprotkb/swiss-prot, the manually curated section, and uniprotkb/trembl, the computer translation of the embl/genbank/ddbj nucleotide sequence database. taken together, these two sections cover all the proteins characterized or inferred from all publicly available nucleotide sequences. the plant proteome annotation program (ppap) of uniprotkb/swiss-prot focuses on the manual annotat ... | 2009 | 19084081 |
| genome-wide and expression analysis of protein phosphatase 2c in rice and arabidopsis. | the protein phosphatase 2cs (pp2cs) from various organisms have been implicated to act as negative modulators of protein kinase pathways involved in diverse environmental stress responses and developmental processes. a genome-wide overview of the pp2c gene family in plants is not yet available. | 2008 | 19021904 |
| experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity. | mitochondria in rice (oryza sativa) are vital in expanding our understanding of the cellular response to reoxygenation of tissues after anaerobiosis, the crossroads of carbon and nitrogen metabolism, and the role of respiratory energy generation in cytoplasmic male sterility. we have combined density gradient and surface charge purification techniques with proteomics to provide an in-depth proteome of rice shoot mitochondria covering both soluble and integral membrane proteins. quantitative comp ... | 2009 | 19010998 |
| integrating genes and phenotype: a wheat-arabidopsis-rice glycosyltransferase database for candidate gene analyses. | glycosyltransferases (gts) constitute a very large multi-gene superfamily, containing several thousand members identified in sequenced organisms especially in plants. gts are key enzymes involved in various biological processes such as cell wall formation, storage polysaccharides biosynthesis, and glycosylation of various metabolites. gts have been identified in rice (oryza sativa) and arabidopsis thaliana, but their precise function has been demonstrated biochemically for only a few. in this wo ... | 2009 | 19005709 |
| involvement of osspx1 in phosphate homeostasis in rice. | arabidopsis thaliana spx (syg/pho81/xpr1) domain genes have recently been shown to be involved in the phosphate (pi) signaling pathway. we show here that a rice (oryza sativa) spx gene, osspx1, is specifically induced by pi starvation in roots. suppression of osspx1 by rna interference resulted in severe signs of toxicity caused by the over-accumulation of pi, similar to that found in osphr2 (phosphate starvation response transcription factor 2) overexpressors and pho2 (phosphate-responsive muta ... | 2009 | 19000161 |
| rice blast fungus (magnaporthe oryzae) infects arabidopsis via a mechanism distinct from that required for the infection of rice. | magnaporthe oryzae is a hemibiotrophic fungal pathogen that causes rice (oryza sativa) blast. although m. oryzae as a whole infects a wide variety of monocotyledonous hosts, no dicotyledonous plant has been reported as a host. we found that two rice pathogenic strains of m. oryzae, kj201 and 70-15, interacted differentially with 16 ecotypes of arabidopsis (arabidopsis thaliana). strain kj201 infected all ecotypes with varying degrees of virulence, whereas strain 70-15 caused no symptoms in certa ... | 2009 | 18987215 |
| hormonal control of grass inflorescence development. | grass inflorescences produce the grain that feeds the world. compared to eudicots such as arabidopsis (arabidopsis thaliana), grasses have a complex inflorescence morphology that can be explained by differences in the activity of axillary meristems. advances in genomics, such as the completion of the rice (oryza sativa) and sorghum (sorghum bicolor) genomes and the recent release of a draft sequence of the maize (zea mays) genome, have greatly facilitated research in grasses. here, we review rec ... | 2008 | 18986827 |
| did rna editing in plant organellar genomes originate under natural selection or through genetic drift? | the c<-->u substitution types of rna editing have been observed frequently in organellar genomes of land plants. although various attempts have been made to explain why such a seemingly inefficient genetic mechanism would have evolved, no satisfactory explanation exists in our view. in this study, we examined editing patterns in chloroplast genomes of the hornwort anthoceros formosae and the fern adiantum capillus-veneris and in mitochondrial genomes of the angiosperms arabidopsis thaliana, beta ... | 2008 | 18939975 |
| analysis of the pumpkin phloem proteome provides insights into angiosperm sieve tube function. | increasing evidence suggests that proteins present in the angiosperm sieve tube system play an important role in the long distance signaling system of plants. to identify the nature of these putatively non-cell-autonomous proteins, we adopted a large scale proteomics approach to analyze pumpkin phloem exudates. phloem proteins were fractionated by fast protein liquid chromatography using both anion and cation exchange columns and then either in-solution or in-gel digested following further separ ... | 2009 | 18936055 |
| [construction and analysis of root cdna library in glycyrrhiza uralensis]. | to screen and isolate secondary metabolite biosynthesis-related gene for establishing the foundation of functional gene research, we construct a cdna library of glycyrrhiza uralensis. | 2008 | 18837336 |
| isolation and characterization of conserved non-coding sequences among rice (oryza sativa l.) paralogous regions. | segmental duplication is particularly frequent within plant genomes and the ability of the original single-copy gene to gain a new function for the change of regulatory elements is one of the prominent consequences of duplication. thus, it is important to study the pattern of conserved non-coding sequence (cns) between paralogous genes. we report the result of a survey of cnss among paralogous regions in rice (oryza sativa l.), as well as the comparison of cns dataset between rice and arabidopsi ... | 2009 | 18825415 |
| ehd2, a rice ortholog of the maize indeterminate1 gene, promotes flowering by up-regulating ehd1. | recent research into the flowering of rice (oryza sativa) has revealed both unique and conserved genetic pathways in the photoperiodic control of flowering compared with those in arabidopsis (arabidopsis thaliana). we discovered an early heading date2 (ehd2) mutant that shows extremely late flowering under both short- and long-day conditions in line with a background deficient in heading date1 (hd1), a rice constans ortholog that belongs to the conserved pathway. this phenotype in the ehd2 mutan ... | 2008 | 18790997 |
| the atg autophagic conjugation system in maize: atg transcripts and abundance of the atg8-lipid adduct are regulated by development and nutrient availability. | plants employ sophisticated mechanisms to recycle intracellular constituents needed for growth, development, and survival under nutrient-limiting conditions. autophagy is one important route in which cytoplasm and organelles are sequestered in bulk into vesicles and subsequently delivered to the vacuole for breakdown by resident hydrolases. the formation and trafficking of autophagic vesicles are directed in part by associated conjugation cascades that couple the autophagy-related8 (atg8) and at ... | 2009 | 18790996 |
| the f-box gene family is expanded in herbaceous annual plants relative to woody perennial plants. | f-box proteins are generally responsible for substrate recognition in the skp1-cullin-f-box complexes that are involved in protein degradation via the ubiquitin-26s proteasome pathway. in plants, f-box genes influence a variety of biological processes, such as leaf senescence, branching, self-incompatibility, and responses to biotic and abiotic stresses. the number of f-box genes in populus (populus trichocarpa; approximately 320) is less than half that found in arabidopsis (arabidopsis thaliana ... | 2008 | 18775973 |
| putative cytochrome p450 genes in rice genome (oryza sativa l. ssp. indica) and their est evidence. | we discovered 528 putative cytochrome p450s (p450s) in oryza sativa l. ssp. indica using arabidopsis thaliana p450s as database. those putative rice p450s are thought to belong to 40 families classified in arabidopsis thaliana. we compared distributions of arabidopsis thaliana and oryza sativa p450s and found the two species have similar distribution patterns. however, family distributions of two species also have some differences. for example, in rice, the gene number in families of cyp71, cyp7 ... | 2002 | 18759039 |
| presence of a latent mitochondrial targeting signal in gene on mitochondrial genome. | organelles, such as mitochondria and chloroplasts, are derived from endosymbionts. gene transfer events from organelles to the nucleus have occurred over evolutionary time. in the case that a transferred gene in the nucleus needs to go back to the original organelle, it must obtain targeting information for sorting its protein to that organelle. here, we reveal that the genes for the ribosomal proteins l2 and s4 in the arabidopsis thaliana mitochondrial (mt) genome contain information for protei ... | 2008 | 18573842 |
| developmental role and auxin responsiveness of class iii homeodomain leucine zipper gene family members in rice. | members of the class iii homeodomain leucine zipper (class iii hd-zip) gene family are central regulators of crucial aspects of plant development. to better understand the roles of five class iii hd-zip genes in rice (oryza sativa) development, we investigated their expression patterns, ectopic expression phenotypes, and auxin responsiveness. four genes, oshb1 to oshb4, were expressed in a localized domain of the shoot apical meristem (sam), the adaxial cells of leaf primordia, the leaf margins, ... | 2008 | 18567825 |
| the common function of a novel subfamily of b-box zinc finger proteins with reference to circadian-associated events in arabidopsis thaliana. | over 1,600 genes encoding putative transcription factors have been identified in the arabidopsis genome sequence, however, their physiological functions are not yet fully understood. in this study, a small subfamily of double b-box zinc finger (dbb, double b-box) genes, encoding eight putative transcription factors, were characterized with reference to the circadian rhythm and the early photomorphogenic regulation of hypocotyl elongation in response to light signals. among these, it was found th ... | 2008 | 18540109 |
| comparative analysis of divergent and convergent gene pairs and their expression patterns in rice, arabidopsis, and populus. | comparative analysis of the organization and expression patterns of divergent and convergent gene pairs in multiple plant genomes can identify patterns that are shared by more than one species or are unique to a particular species. here, we study the coexpression and interspecies conservation of divergent and convergent gene pairs in three plant species: rice (oryza sativa), arabidopsis (arabidopsis thaliana), and black cottonwood (populus trichocarpa). strongly correlated expression levels betw ... | 2008 | 18515639 |
| substitution of the gene for chloroplast rps16 was assisted by generation of a dual targeting signal. | organelle (mitochondria and chloroplasts in plants) genomes lost a large number of genes after endosymbiosis occurred. even after this major gene loss, organelle genomes still lose their own genes, even those that are essential, via gene transfer to the nucleus and gene substitution of either different organelle origin or de novo genes. gene transfer and substitution events are important processes in the evolution of the eukaryotic cell. gene loss is an ongoing process in the mitochondria and ch ... | 2008 | 18453549 |
| phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants. | gene ortholog identification is now a major objective for mining the increasing amount of sequence data generated by complete or partial genome sequencing projects. comparative and functional genomics urgently need a method for ortholog detection to reduce gene function inference and to aid in the identification of conserved or divergent genetic pathways between several species. as gene functions change during evolution, reconstructing the evolutionary history of genes should be a more accurate ... | 2008 | 18426584 |
| genome-wide analysis of heat shock transcription factor families in rice and arabidopsis. | the heat shock transcription factors (hsfs) are the major heat shock factors regulating the heat stress response. they participate in regulating the expression of heat shock proteins (hsps), which are critical in the protection against stress damage and many other important biological processes. study of the hsf gene family is important for understanding the mechanism by which plants respond to stress. the completed genome sequences of rice (oryza sativa) and arabidopsis (arabidopsis thaliana) c ... | 2008 | 18407058 |
| dual coding of sirnas and mirnas by plant transposable elements. | we recently proposed a specific model whereby mirnas encoded from short nonautonomous dna-type tes known as mites evolved from corresponding ancestral full-length (autonomous) elements that originally encoded short interfering (sirnas). our mirna-origins model predicts that evolutionary intermediates may exist as tes that encode both sirnas and mirnas, and we analyzed arabidopsis thaliana and oryza sativa (rice) genomic sequence and expression data to test this prediction. we found a number of e ... | 2008 | 18367716 |
| identification and verification of microrna in wheat (triticum aestivum). | micrornas (mirnas) are small, endogenous rnas that regulate gene expression in both plants and animals. a large number of mirnas has been identified from various animals and model plant species such as arabidopsis thaliana and rice (oryza sativa); however, characteristics of wheat (triticum aestivum) mirnas are poorly understood. here, computational identification of mirnas from wheat est sequences was preformed by using the in-house program genomicsvm, a prediction model for mirnas. this study ... | 2008 | 18357413 |
| on the expansion of the pentatricopeptide repeat gene family in plants. | pentatricopeptide repeat (ppr) proteins form a huge family in plants (450 members in arabidopsis and 477 in rice) defined by tandem repetitions of characteristic sequence motifs. some of these proteins have been shown to play a role in posttranscriptional processes within organelles, and they are thought to be sequence-specific rna-binding proteins. the origins of this family are obscure as they are lacking from almost all prokaryotes, and the spectacular expansion of the family in land plants i ... | 2008 | 18343892 |
| brachypodium genomics. | brachypodium distachyon (l.) beauv. is a temperate wild grass species; its morphological and genomic characteristics make it a model system when compared to many other grass species. it has a small genome, short growth cycle, self-fertility, many diploid accessions, and simple growth requirements. in addition, it is phylogenetically close to economically important crops, like wheat and barley, and several potential biofuel grasses. it exhibits agricultural traits similar to those of these target ... | 2008 | 18309367 |
| a maize constans-like gene, conz1, exhibits distinct diurnal expression patterns in varied photoperiods. | maize (zea mays ssp. mays l.) was domesticated from teosinte (z. mays l. ssp. parviglumis iltis & doebley), a plant requiring short day photoperiods to flower. while photoperiod sensitive landraces of maize exist, post-domestication breeding included efforts to grow maize in a broad range of latitudes. thus, modern maize is often characterized as day-neutral because time to flower is relatively unaffected by photoperiod. we report the first identification of maize constans of zea mays1 (conz1), ... | 2008 | 18301915 |
| genome-wide analysis of the rice and arabidopsis non-specific lipid transfer protein (nsltp) gene families and identification of wheat nsltp genes by est data mining. | plant non-specific lipid transfer proteins (nsltps) are encoded by multigene families and possess physiological functions that remain unclear. our objective was to characterize the complete nsltp gene family in rice and arabidopsis and to perform wheat est database mining for nsltp gene discovery. | 2008 | 18291034 |
| characterization of paralogous protein families in rice. | high gene numbers in plant genomes reflect polyploidy and major gene duplication events. oryza sativa, cultivated rice, is a diploid monocotyledonous species with a ~390 mb genome that has undergone segmental duplication of a substantial portion of its genome. this, coupled with other genetic events such as tandem duplications, has resulted in a substantial number of its genes, and resulting proteins, occurring in paralogous families. | 2008 | 18284697 |
| the rice mybleu transcription factor increases tolerance to oxygen deprivation in arabidopsis plants. | mybleu is a natural incomplete transcription factor of rice (oryza sativa), consisting of a partial myb repeat followed by a short leucine zipper. we previously showed its localization to the apical region of rice roots and coleoptiles. specifically, in coleoptiles, mybleu is expressed under both aerobic and anaerobic conditions, whereas in roots, it is expressed only under aerobic conditions. mybleu is able to dimerize with canonical leucine zippers and to activate transcription selectively. to ... | 2007 | 18251929 |
| plant metabolomics reveals conserved and divergent metabolic responses to salinity. | new metabolic profiling technologies provide data on a wider range of metabolites than traditional targeted approaches. metabolomic technologies currently facilitate acquisition of multivariate metabolic data using diverse, mostly hyphenated, chromatographic detection systems, such as gc-ms or liquid chromatography coupled to mass spectrometry, fourier-transformed infrared spectroscopy or nmr-based methods. analysis of the resulting data can be performed through a combination of non-supervised a ... | 2008 | 18251862 |
| transposable elements in coffea (gentianales: rubiacea) transcripts and their role in the origin of protein diversity in flowering plants. | transposable elements are major components of plant genomes and they influence their evolution, acting as recombination hot spots, acquiring specific cell functions or becoming part of protein-coding regions. the latter is the subject of the present analysis. this study is a report on the annotation of transposable elements (tes) in expressed sequences of coffea arabica, coffea canephora and coffea racemosa, showing the occurrence of 383 ests and 142 unigenes with te fragments in these three cof ... | 2008 | 18231813 |
| modulating rice stress tolerance by transcription factors. | plants are non-mobile organisms and have to adapt to environmental stresses mostly by modulating their growth and development in addition to physiological and biochemical changes. transcription factors (tfs) regulate genome expression in response to environmental and physiological signals, and some of them switch on plant adaptive developmental and physiological pathways. one tf is encoded by a single gene but regulates the expression of several other genes leading to the activation of complex a ... | 2008 | 21412363 |
| planttribes: a gene and gene family resource for comparative genomics in plants. | the planttribes database (http://fgp.huck.psu.edu/tribe.html) is a plant gene family database based on the inferred proteomes of five sequenced plant species: arabidopsis thaliana, carica papaya, medicago truncatula, oryza sativa and populus trichocarpa. we used the graph-based clustering algorithm mcl [van dongen (technical report ins-r0010 2000) and enright et al. (nucleic acids res. 2002; 30: 1575-1584)] to classify all of these species' protein-coding genes into putative gene families, calle ... | 2008 | 18073194 |
| intragenomic matching reveals a huge potential for mirna-mediated regulation in plants. | micrornas (mirnas) are important post-transcriptional regulators, but the extent of this regulation is uncertain, both with regard to the number of mirna genes and their targets. using an algorithm based on intragenomic matching of potential mirnas and their targets coupled with support vector machine classification of mirna precursors, we explore the potential for regulation by mirnas in three plant genomes: arabidopsis thaliana, populus trichocarpa, and oryza sativa. we find that the intrageno ... | 2007 | 18052543 |
| three type-b response regulators, arr1, arr10 and arr12, play essential but redundant roles in cytokinin signal transduction throughout the life cycle of arabidopsis thaliana. | arabidopsis thaliana has 11 members belonging to the typical type-b arr (authentic response regulator) family. among them, seven highly homologous members appear also to be conserved in rice (oryza sativa), but others are not. it was suggested that these seven arrs are commonly implicated as dna-binding transcription factors in the phosphorelay-mediated cytokinin signal transduction network in higher plants. to gain an insight into the functions of the cytokinin-associated type-b arrs, we previo ... | 2008 | 18037673 |
| gain-of-function phenotypes of chemically synthetic clavata3/esr-related (cle) peptides in arabidopsis thaliana and oryza sativa. | using 26 chemically synthetic clavata3/esr (cle) peptides, which correspond to the predicted products of the 31 arabidopsis cle genes, we investigated the cle peptide function in arabidopsis and rice. treatment with some cle peptides inhibited root elongation in rice as well as in arabidopsis. it also reduced the size of the shoot apical meristem in arabidopsis but not in rice. database searches revealed 47 putative cle genes in the rice genome and multiple cle domains in some cle genes, indicat ... | 2007 | 17991631 |
| greenphyldb: a database for plant comparative genomics. | greenphyldb (http://greenphyl.cirad.fr) is a comprehensive platform designed to facilitate comparative functional genomics in oryza sativa and arabidopsis thaliana genomes. the main functions of greenphyldb are to assign o. sativa and a. thaliana sequences to gene families using a semi-automatic clustering procedure and to create 'orthologous' groups using a phylogenomic approach. to date, greenphyldb comprises the most complete list of plant gene families, which have been manually curated (6421 ... | 2008 | 17986457 |
| gramene: a growing plant comparative genomics resource. | gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. gramene is an open-source project. all data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. gramene's core data types include genome assembly and annotations, other dna/mrna sequences, genetic and physical maps/marke ... | 2008 | 17984077 |
| a circadian rhythm set by dusk determines the expression of ft homologs and the short-day photoperiodic flowering response in pharbitis. | seasonal control of flowering through responsiveness to daylength shows extreme variation. different species flower in response to long days or short days (sds), and this difference evolved several times. the molecular mechanisms conferring these responses have been compared in detail only in arabidopsis thaliana and rice (oryza sativa) and suggest that a conserved pathway confers daylength responses through regulation of flowering locus t (ft) transcription by constans (co). we studied pharbiti ... | 2007 | 17965272 |
| osmads51 is a short-day flowering promoter that functions upstream of ehd1, osmads14, and hd3a. | although flowering regulatory mechanisms have been extensively studied in arabidopsis (arabidopsis thaliana), those in other species have not been well elucidated. here, we investigated the role of osmads51, a type i mads-box gene in the short-day (sd) promotion pathway in rice (oryza sativa). in sds osmads51 null mutants flowered 2 weeks later than normal, whereas in long days loss of osmads51 had little effect on flowering. transcript levels of three flowering regulators-ehd1, osmads14, and hd ... | 2007 | 17951465 |
| genomic organization and evolutionary conservation of plant d-type cyclins. | plants contain more genes encoding core cell cycle regulators than other organisms but it is unclear whether these represent distinct functions. d-type cyclins (cycd) play key roles in the g1-to-s-phase transition, and arabidopsis (arabidopsis thaliana) contains 10 cycd genes in seven defined subgroups, six of which are conserved in rice (oryza sativa). here, we identify 22 cycd genes in the poplar (populus trichocarpa) genome and confirm that these six cycd subgroups are conserved across higher ... | 2007 | 17951462 |
| tandem duplications of a degenerated gtp-binding domain at the origin of gtpase receptors toc159 and thylakoidal srp. | the evolutionary origin of some nuclear encoded proteins that translocate proteins across the chloroplast envelope remains unknown. therefore, sequences of gtpase proteins constituting the arabidopsis thaliana translocon at the outer membrane of chloroplast (attoc) complexes were analyzed by means of hca. in particular, attoc159 and related proteins (attoc132, attoc120, and attoc90) do not have proven homologues of prokaryotic or eukaryotic ancestry. we established that the three domains commonl ... | 2007 | 17950698 |
| maize brittle stalk2 encodes a cobra-like protein expressed in early organ development but required for tissue flexibility at maturity. | the maize (zea mays) brittle stalk2 (bk2) is a recessive mutant, the aerial parts of which are easily broken. the bk2 phenotype is developmentally regulated and appears 4 weeks after planting, at about the fifth-leaf stage. before this time, mutants are indistinguishable from wild-type siblings. afterward, all organs of the bk2 mutants turn brittle, even the preexisting ones, and they remain brittle throughout the life of the plant. leaf tension assays and bend tests of the internodes show that ... | 2007 | 17932309 |
| optimising the analysis of transcript data using high density oligonucleotide arrays and genomic dna-based probe selection. | affymetrix genechip arrays are widely used for transcriptomic studies in a diverse range of species. each gene is represented on a genechip array by a probe-set, consisting of up to 16 probe-pairs. signal intensities across probe-pairs within a probe-set vary in part due to different physical hybridisation characteristics of individual probes with their target labelled transcripts. we have previously developed a technique to study the transcriptomes of heterologous species based on hybridising g ... | 2007 | 17908303 |
| oryza sativa dicer-like4 reveals a key role for small interfering rna silencing in plant development. | micrornas and small interfering rnas (sirnas) are two classes of small regulatory rnas derived from different types of precursors and processed by distinct dicer or dicer-like (dcl) proteins. during evolution, four arabidopsis thaliana dcls and six rice (oryza sativa) dcls (os dcls) appear to have acquired specialized functions. the arabidopsis dcls are well characterized, but those in rice remain largely unstudied. here, we show that both knockdown and loss of function of rice dcl4, the homolog ... | 2007 | 17905898 |