| [an overview of flowering transition in higher plants]. | in higher plant, flowering transition represents a crucial transition from the vegetative stage to the reproductive stage in life cycle. this process is controlled by both endogenous and environmental factors. in arabidopsis thaliana, four pathways, photoperiod pathway, vernalization pathway, autonomous pathway, and ga pathway were involved in flowering control. these flowering transition pathways are shown to be highly conserved in arabidopsis and other higher plants including rice (oryza sativ ... | 2007 | 17905707 |
| members of the plant nima-related kinases are involved in organ development and vascularization in poplar, arabidopsis and rice. | nima-related kinases (neks) are a family of serine/threonine kinases that have been linked to cell-cycle regulation in fungi and mammals. information regarding the function of neks in plants is very limited. we screened the three plant species that have had their genomes sequenced in an attempt to improve our understanding of their role in plants. we retrieved seven members in arabidopsis thaliana, nine in populus trichocarpa and six in oryza sativa. phylogenetic analysis showed that plant neks ... | 2007 | 17886359 |
| the ancient subclasses of arabidopsis actin depolymerizing factor genes exhibit novel and differential expression. | the actin depolymerizing factor (adf) gene family of arabidopsis thaliana encodes 11 functional protein isovariants in four ancient subclasses. we report the characterization of the tissue-specific and developmental expression of all arabidopsis adf genes and the subcellular localization of several protein isovariants. the four subclasses exhibited distinct expression patterns as examined by qrt-pcr and histochemical assays of a gus reporter gene under the control of individual adf regulatory se ... | 2007 | 17877706 |
| genome-wide analysis of the phospholipase d family in oryza sativa and functional characterization of pld beta 1 in seed germination. | phospholipase d (pld) plays a critical role in plant growth and development, as well as in hormone and stress responses. pld encoding genes constitute a large gene family that are present in higher plants. there are 12 members of the pld family in arabidopsis thaliana and several of them have been functionally characterized; however, the members of the pld family in oryza sativa remain to be fully described. through genome-wide analysis, 17 pld members found in different chromosomes have been id ... | 2007 | 17876344 |
| sulfate assimilation in basal land plants - what does genomic sequencing tell us? | sulfate assimilation is a pathway providing reduced sulfur for the synthesis of cysteine, methionine, co-enzymes such as iron-sulfur centres, thiamine, lipoic acid, or coenzyme a, and many secondary metabolites, e.g., glucosinolates or alliins. the pathway is relatively well understood in flowering plants, but very little information exists on sulfate assimilation in basal land plants. since the finding of a putative 3'-phosphoadenosine 5'-phosphosulfate reductase in physcomitrella patens, an en ... | 2007 | 17853355 |
| genome-wide analysis of sina family in plants and their phylogenetic relationships. | sina genes in plants are part of a multigene family with 5 members in arabidopsis thaliana, 10 members in populus trichocarpa, 6 members in oryza sativa, at least 6 members in zea mays and at least 1 member in physcomitrella patens. six members in maize were confirmed by rt-pcr. all sinas have one ring domain and one sina domain. these two domains are highly conserved in plants. according to the motif organization and phylogenetic tree, sina family members were divided into 2 groups. in addition ... | 2008 | 17852340 |
| helitrons on a roll: eukaryotic rolling-circle transposons. | rolling-circle eukaryotic transposons, known as helitron transposons, were first discovered in plants (arabidopsis thaliana and oryza sativa) and in the nematode caenorhabditis elegans. to date, helitrons have been identified in a diverse range of species, from protists to mammals. they represent a major class of eukaryotic transposons and are fundamentally different from classical transposons in terms of their structure and mechanism of transposition. helitrons seem to have a major role in the ... | 2007 | 17850916 |
| large-scale, lineage-specific expansion of a bric-a-brac/tramtrack/broad complex ubiquitin-ligase gene family in rice. | selective ubiquitination of proteins is directed by diverse families of ubiquitin-protein ligases (or e3s) in plants. one important type uses cullin-3 as a scaffold to assemble multisubunit e3 complexes containing one of a multitude of bric-a-brac/tramtrack/broad complex (btb) proteins that function as substrate recognition factors. we previously described the 80-member btb gene superfamily in arabidopsis thaliana. here, we describe the complete btb superfamily in rice (oryza sativa spp japonica ... | 2007 | 17720868 |
| towards the molecular basis of heterosis. | heterosis describes the superior performance of heterozygous hybrid plants over their homozygous parental inbred lines. despite the rediscovery of this phenomenon a century ago and its paramount agronomic importance, the genetic and molecular basis of heterosis remains enigmatic. recently, various pioneer studies described differences in genome organization and gene expression of hybrids and their parental inbred lines. at the genomic level, a significant loss of colinearity at many loci between ... | 2007 | 17720610 |
| transcript level regulation of the vacuolar h(+)-atpase subunit isoforms vha-a, vha-e and vha-g in arabidopsis thaliana. | the presence of isogenes encoding v-atpase subunits seems to be a characteristic for plants. twenty-eight genes encode for the 13 different subunits in arabidopsis thaliana, 23 genes each are known in tomato (solanum lycopersicum) and can be identified in rice (oryza sativa), respectively. in arabidopsis the four subunits vha-b, -e, -g and -a are encoded by three isogenes each. the transcript levels of these subunits were analysed by in silico evaluation of transcript pattern derived from the na ... | 2007 | 17710654 |
| comparative genomic analysis of the hsp70s from five diverse photosynthetic eukaryotes. | we have identified 24 members of the dnak subfamily of heat shock 70 proteins (hsp70s) in the complete genomes of 5 diverse photosynthetic eukaryotes. the hsp70s are a ubiquitous protein family that is highly conserved across all domains of life. eukaryotic hsp70s are found in a number of subcellular compartments in the cell: cytoplasm, mitochondrion (mt), chloroplast (cp), and endoplasmic reticulum (er). although the hsp70s have been the subject of intense study in model organisms, very little ... | 2007 | 17688196 |
| genome-wide analysis of aba-responsive elements abre and ce3 reveals divergent patterns in arabidopsis and rice. | in plants, complex regulatory mechanisms are at the core of physiological and developmental processes. the phytohormone abscisic acid (aba) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. the underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecu ... | 2007 | 17672917 |
| [advanced study on serk genes family]. | somatic embryogenesis receptor-like kinase (serk) genes were identified in different plant species, such as daucus carota, arabidopsis thaliana and oryza sativa. studies of these genes showed that they have conserved structures and expression patterns. these genes are not only expressed in embryogenic tissues, but also in post-embryogenic development. they function in embryogenesis and reproductive development and defences in particular, related signal transduction pathways. | 2007 | 17650484 |
| genomic distribution of simple sequence repeats in brassica rapa. | simple sequence repeats (ssrs) represent short tandem duplications found within all eukaryotic organisms. to examine the distribution of ssrs in the genome of brassica rapa ssp. pekinensis, ssrs from different genomic regions representing 17.7 mb of genomic sequence were surveyed. ssrs appear more abundant in non-coding regions (86.6%) than in coding regions (13.4%). comparison of ssr densities in different genomic regions demonstrated that ssr density was greatest within the 5'-flanking regions ... | 2007 | 17646709 |
| novel exon combinations generated by alternative splicing of gene fragments mobilized by a cacta transposon in glycine max. | the recent discoveries of transposable elements carrying host gene fragments such as the pack-mules (mutator-like transposable elements) of maize (zea mays), rice (oryza sativa) and arabidopsis thaliana, the helitrons of maize and the tgm-express of soybeans, revealed a widespread genetic mechanism with the potential to rearrange genomes and create novel chimeric genes affecting genomic and proteomic diversity. not much is known with regard to the mechanisms of gene fragment capture by those tra ... | 2007 | 17629935 |
| actin binding protein 29 from lilium pollen plays an important role in dynamic actin remodeling. | villin/gelsolin/fragmin superfamily proteins have been shown to function in tip-growing plant cells. however, genes encoding gelsolin/fragmin do not exist in the arabidopsis thaliana and rice (oryza sativa) databases, and it is possible that these proteins are encoded by villin mrna splicing variants. we cloned a 1006-bp full-length cdna from lilium longiflorum that encodes a 263-amino acid predicted protein sharing 100% identity with the n terminus of 135-abp (lilium villin) except for six c-te ... | 2007 | 17586658 |
| small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants. | multicellular organisms produce small cysteine-rich antimicrobial peptides as an innate defense against pathogens. while defensins, a well-known class of such peptides, are common among eukaryotes, there are other classes restricted to the plant kingdom. these include thionins, lipid transfer proteins and snakins. in earlier work, we identified several divergent classes of small putatively secreted cysteine-rich peptides (crps) in legumes [graham et al. (2004)plant physiol. 135, 1179-97]. here, ... | 2007 | 17565583 |
| genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice. | in angiosperms, the stigma provides initial nutrients and guidance cues for pollen grain germination and tube growth. however, little is known about the genes that regulate these processes in rice (oryza sativa). here, we generate rice stigma-specific or -preferential gene expression profiles through comparing genome-wide expression patterns of hand-dissected, unpollinated stigma at anthesis with seven tissues, including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds 5 d ... | 2007 | 17556504 |
| phylogenetic and expression analysis of znf-an1 genes in plants. | in plants, znf-an1 genes are part of a multigene family with 13 members in arabidopsis thaliana, 19 members in populus trichocarpa, 17 members in oryza sativa, at least 11 members in zea mays, and 2 members in chlamydomonas reinhardtii. all znf-an1 genes contain the znf-an1 domain. according to the phylogenetic analysis of the znf-an1 domain, we divided plant znf-an1 genes into two types. the coding sequences of most type i members do not possess any introns, while most type ii members do posses ... | 2007 | 17524611 |
| the rice (e)-beta-caryophyllene synthase (ostps3) accounts for the major inducible volatile sesquiterpenes. | terpenoids serve as both constitutive and inducible defense chemicals in many plant species, and volatile terpenes participate in plant a indirect defense by attracting natural enemies of the herbivores. the rice (oryza sativa l.) genome contains about 50 genes encoding putative terpene synthases (tpss). here we report that two of the rice sesquiterpene synthase genes, ostps3 and ostps13, encode (e)-beta-caryophyllene synthase and (e,e)-farnesol synthase, respectively. in vitro, the recombinant ... | 2007 | 17524436 |
| progesterone: its occurrence in plants and involvement in plant growth. | progesterone is a mammalian gonadal hormone. in the current study, we identified and quantified progesterone in a range of higher plants by using gc-ms and examined its effects on the vegetative growth of plants. the growth of arabidopsis (arabidopsis thaliana) seedlings was promoted by progesterone at low concentrations but suppressed at higher concentrations under both light and dark growth conditions. the growth of the gibberellin-deficient mutant lh of pea (pisum sativum) was also promoted b ... | 2007 | 17512025 |
| comparative cross-species alternative splicing in plants. | alternative splicing (as) can add significantly to genome complexity. plants are thought to exhibit less as than animals. an algorithm, based on expressed sequence tag (est) pairs gapped alignment, was developed that takes advantage of the relatively small intron and exon size in plants and directly compares pairs of ests to search for as. est pairs gapped alignment was first evaluated in arabidopsis (arabidopsis thaliana), rice (oryza sativa), and tomato (solanum lycopersicum) for which annotat ... | 2007 | 17496110 |
| gc-ei-tof-ms analysis of in vivo carbon-partitioning into soluble metabolite pools of higher plants by monitoring isotope dilution after 13co2 labelling. | the established gc-ei-tof-ms method for the profiling of soluble polar metabolites from plant tissue was employed for the kinetic metabolic phenotyping of higher plants. approximately 100 typical gc-ei-ms mass fragments of trimethylsilylated and methoxyaminated metabolite derivatives were structurally interpreted for mass isotopomer analysis, thus enabling the kinetic study of identified metabolites as well as the so-called functional group monitoring of yet non-identified metabolites. the monit ... | 2015 | 17475294 |
| chitinases in oryza sativa ssp. japonica and arabidopsis thaliana. | chitinases (ec3.2.1.14), found in a wide range of organisms, catalyze the hydrolysis of chitin and play a major role in defense mechanisms against fungal pathogens. the alignment and typical domains were analyzed using basic local alignment search tool (blast) and simple modular architecture research tool (smart), respectively. on the basis of the annotations of rice (oryza sativa l.) and arabidopsis genomic sequences and using the bio-software signalp3.0, tmhmm2.0, targetp1.1, and big-pi predic ... | 2007 | 17469786 |
| pea late bloomer1 is a gigantea ortholog with roles in photoperiodic flowering, deetiolation, and transcriptional regulation of circadian clock gene homologs. | genes controlling the transition to flowering have been studied in several species, including arabidopsis (arabidopsis thaliana) and rice (oryza sativa), but have not yet received much attention in legumes. here, we describe a new allelic series of late-flowering, photoperiod-insensitive mutants in the pea (pisum sativum) late bloomer1 (late1) gene and show that late1 is an ortholog of arabidopsis gigantea. mutants display defects in phytochrome b-dependent deetiolation under red light and in th ... | 2007 | 17468223 |
| compact genes are highly expressed in the moss physcomitrella patens. | compact genes contain short and few introns, and they are highly expressed in different animal genomes. recently, it has been shown that in oryza sativa and arabidopsis thaliana, highly expressed genes tend to be least compact, containing long and many introns. it has been suggested that selection on genome organization may have acted differently in plants compared with animals. gene expression can be estimated as the number of hits when comparing a gene sequence with publicly available expresse ... | 2007 | 17465932 |
| barren inflorescence2 encodes a co-ortholog of the pinoid serine/threonine kinase and is required for organogenesis during inflorescence and vegetative development in maize. | organogenesis in plants is controlled by meristems. axillary meristems, which give rise to branches and flowers, play a critical role in plant architecture and reproduction. maize (zea mays) and rice (oryza sativa) have additional types of axillary meristems in the inflorescence compared to arabidopsis (arabidopsis thaliana) and thus provide an excellent model system to study axillary meristem initiation. previously, we characterized the barren inflorescence2 (bif2) mutant in maize and showed th ... | 2007 | 17449648 |
| cgkb: an annotation knowledge base for cowpea (vigna unguiculata l.) methylation filtered genomic genespace sequences. | cowpea [vigna unguiculata (l.) walp.] is one of the most important food and forage legumes in the semi-arid tropics because of its ability to tolerate drought and grow on poor soils. it is cultivated mostly by poor farmers in developing countries, with 80% of production taking place in the dry savannah of tropical west and central africa. cowpea is largely an underexploited crop with relatively little genomic information available for use in applied plant breeding. the goal of the cowpea genomic ... | 2007 | 17445272 |
| genome-wide analysis of the auxin response factors (arf) gene family in rice (oryza sativa). | auxin response factors (arfs) are transcription factors that bind with specificity to tgtctc-containing auxin response elements (auxres) found in promoters of primary/early auxin response genes and mediate responses to the plant hormone auxin. the arf genes are represented by a large multigene family in plants. a comprehensive genome-wide analysis was carried out in this study to find all arfs in arabidopsis (arabidopsis thaliana) and rice (oryza sativa subsp. japonica), 23 and 25 arf genes, nam ... | 2007 | 17408882 |
| transcript profiling of the anoxic rice coleoptile. | rice (oryza sativa) seeds can germinate in the complete absence of oxygen. under anoxia, the rice coleoptile elongates, reaching a length greater than that of the aerobic one. in this article, we compared and investigated the transcriptome of rice coleoptiles grown under aerobic and anaerobic conditions. the results allow drawing a detailed picture of the modulation of the transcripts involved in anaerobic carbohydrate metabolism, suggesting up-regulation of the steps required to produce and met ... | 2007 | 17369434 |
| a novel bioinformatics approach identifies candidate genes for the synthesis and feruloylation of arabinoxylan. | arabinoxylans (axs) are major components of graminaceous plant cell walls, including those in the grain and straw of economically important cereals. despite some recent advances in identifying the genes encoding biosynthetic enzymes for a number of other plant cell wall polysaccharides, the genes encoding enzymes of the final stages of ax synthesis have not been identified. we have therefore adopted a novel bioinformatics approach based on estimation of differential expression of orthologous gen ... | 2007 | 17351055 |
| a wuschel-like homeobox gene represses a yabby gene expression required for rice leaf development. | yabby and wuschel-like homeobox (wox) genes have been shown to play important roles in lateral organ formation and meristem function. here, we report the characterization of functional relationship between rice (oryza sativa) yab3 and wox3 in rice leaf development. rice yab3 is closely related to maize (zea mays) zmyab14 and arabidopsis (arabidopsis thaliana) filamentous flower (fil), whereas rice wox3 is highly conserved with maize narrow sheath1 (ns1) and ns2 and arabidopsis pressed flower (pr ... | 2007 | 17351053 |
| genebins: a database for classifying gene expression data, with application to plant genome arrays. | to interpret microarray experiments, several ontological analysis tools have been developed. however, current tools are limited to specific organisms. | 2007 | 17349060 |
| an unusual posttranscriptional processing in two betaine aldehyde dehydrogenase loci of cereal crops directed by short, direct repeats in response to stress conditions. | various abilities to synthesize and accumulate glycine betaine (gb) are crucial for angiosperms to develop salt and drought tolerances. in higher plants, gb is synthesized by a two-step oxidation of choline via an intermediate form of betaine aldehyde, and catalyzed by choline monooxygenase and betaine aldehyde dehydrogenase (badh). in this study, numerous truncated and/or recombinant transcripts of two badh homologs resulting from an unusual posttranscriptional processing were detected in rice ... | 2007 | 17337526 |
| characterization of two brassinosteroid c-6 oxidase genes in pea. | c-6 oxidation genes play a key role in the regulation of biologically active brassinosteroid (br) levels in the plant. they control br activation, which involves the c-6 oxidation of 6-deoxocastasterone (6-deoxocs) to castasterone (cs) and in some cases the further conversion of cs to brassinolide (bl). c-6 oxidation is controlled by the cyp85a family of cytochrome p450s, and to date, two cyp85as have been isolated in tomato (solanum lycopersicum), two in arabidopsis (arabidopsis thaliana), one ... | 2007 | 17322341 |
| plntfdb: an integrative plant transcription factor database. | transcription factors (tfs) are key regulatory proteins that enhance or repress the transcriptional rate of their target genes by binding to specific promoter regions (i.e. cis-acting elements) upon activation or de-activation of upstream signaling cascades. tfs thus constitute master control elements of dynamic transcriptional networks. tfs have fundamental roles in almost all biological processes (development, growth and response to environmental factors) and it is assumed that they play immen ... | 2007 | 17286856 |
| plant atp-binding cassette transporters. | the atp-binding cassette (abc) protein superfamily is one of the largest known, with over 120 members in both arabidopsis thaliana and rice (oryza sativa). most, but not all, abc proteins are modularly organized membrane proteins ("abc transporters") that mediate mgatp-energized transmembrane transport and/or regulate other transporters. the range of processes in which members of the various subclasses of plant abc transporters have been implicated encompasses polar auxin transport, lipid catabo ... | 2007 | 17263663 |
| oscsld1, a cellulose synthase-like d1 gene, is required for root hair morphogenesis in rice. | root hairs are long tubular outgrowths that form on the surface of specialized epidermal cells. they are required for nutrient and water uptake and interact with the soil microflora. here we show that the oryza sativa cellulose synthase-like d1 (oscsld1) gene is required for root hair development, as rice (oryza sativa) mutants that lack oscsld1 function develop abnormal root hairs. in these mutants, while hair development is initiated normally, the hairs elongate less than the wild-type hairs a ... | 2007 | 17259288 |
| daylength measurements by rice plants in photoperiodic short-day flowering. | plants set seed at appropriate seasons. one major mechanism responsible for this adaptation involves photoperiodic flowering. most plants are classified as either long-day plants, which flower under a longer photoperiod, or short-day plants, which flower under a shorter photoperiod. a third group, day-neutral plants, is not responsive to changes in photoperiod. during the past decade, molecular analysis has revealed at the molecular level how the long-day plant arabidopsis thaliana measures dayl ... | 2007 | 17241908 |
| plant gene and alternatively spliced variant annotator. a plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species. | the completion of the rice (oryza sativa) genome draft has brought unprecedented opportunities for genomic studies of the world's most important food crop. previous rice gene annotations have relied mainly on ab initio methods, which usually yield a high rate of false-positive predictions and give only limited information regarding alternative splicing in rice genes. comparative approaches based on expressed sequence tags (ests) can compensate for the drawbacks of ab initio methods because they ... | 2007 | 17220363 |
| molecular characterization the yabby gene family in oryza sativa and expression analysis of osyabby1. | members of the yabby gene family have a general role that promotes abaxial cell fate in a model eudicot, arabidopsis thaliana. to understand the function of yabby genes in monocots, we have isolated all yabby genes in oryza sativa (rice), and revealed the spatial and temporal expression pattern of one of these genes, osyabby1. in rice, eight yabby genes constitute a small gene family and are classified into four groups according to sequence similarity, exon-intron structure, and organ-specific e ... | 2007 | 17216490 |
| curated genome annotation of oryza sativa ssp. japonica and comparative genome analysis with arabidopsis thaliana. | we present here the annotation of the complete genome of rice oryza sativa l. ssp. japonica cultivar nipponbare. all functional annotations for proteins and non-protein-coding rna (nprna) candidates were manually curated. functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible nprnas (including 58 antisense transcripts) were found. almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experi ... | 2007 | 17210932 |
| birth and death of genes promoted by transposable elements in oryza sativa. | despite a wide distribution of transposable elements (tes) in the genomes of higher eukaryotes, much of their evolutionary significance remains unclear. recent studies have indicated that tes are involved with biological processes such as gene regulation and the generation of new exons in mammals. in addition, the completion of the genome sequencings in arabidopsis thaliana and oryza sativa has permitted scientist to describe a genome-wide overview in plants. in this study, we examined the posit ... | 2007 | 17210233 |
| the plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. | formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. this facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. a major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. the same terms are sometim ... | 2007 | 17142475 |
| plantqtl-ge: a database system for identifying candidate genes in rice and arabidopsis by gene expression and qtl information. | we have designed and implemented a web-based database system, called plantqtl-ge, to facilitate quantitatine traits locus (qtl) based candidate gene identification and gene function analysis. we collected a large number of genes, gene expression information in microarray data and expressed sequence tags (ests) and genetic markers from multiple sources of oryza sativa and arabidopsis thaliana. the system integrates these diverse data sources and has a uniform web interface for easy access. it sup ... | 2007 | 17142239 |
| comparative overviews of clock-associated genes of arabidopsis thaliana and oryza sativa. | in higher plants, circadian rhythms are highly relevant to a wide range of biological processes. to such circadian rhythms, the clock (oscillator) is central, and recent intensive studies on the model higher plant arabidopsis thaliana have begun to shed light on the molecular mechanisms underlying the functions of the central clock. such representative clock-associated genes of a. thaliana are the homologous cca1 and lhy genes, and five prr genes that belong to a small family of pseudo-response ... | 2007 | 17132630 |
| combining expression and comparative evolutionary analysis. the cobra gene family. | plant cell shape is achieved through a combination of oriented cell division and cell expansion and is defined by the cell wall. one of the genes identified to influence cell expansion in the arabidopsis (arabidopsis thaliana) root is the cobra (cob) gene that belongs to a multigene family. three members of the atcob gene family have been shown to play a role in specific types of cell expansion or cell wall biosynthesis. functional orthologs of one of these genes have been identified in maize (z ... | 2007 | 17098858 |
| patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of o. sativa and a. thaliana. | numerous previous studies have elucidated 2 surprising patterns of spliceosomal intron evolution in diverse eukaryotes over the past roughly 100 myr. first, rates of recent intron gain in a wide variety of eukaryotic lineages have been surprisingly low, far too low to explain modern intron densities. second, intron losses have outnumbered intron gains over a variety of lineages. for several reasons, land plants might be expected to have comparatively high rates of intron gain and thus to represe ... | 2007 | 17065597 |
| conservation and diversification of meristem maintenance mechanism in oryza sativa: function of the floral organ number2 gene. | to elucidate the genetic mechanism that regulates meristem maintenance in monocots, here we have examined the function of the gene floral organ number2 (fon2) in oryza sativa (rice). mutations in fon2 cause enlargement of the floral meristem, resulting in an increase in the number of floral organs, although the vegetative and inflorescence meristems are largely normal. molecular cloning reveals that fon2 encodes a small secreted protein, containing a cle domain, that is closely related to clavat ... | 2006 | 17056620 |
| prediction of trans-antisense transcripts in arabidopsis thaliana. | natural antisense transcripts (nats) are coding or non-coding rnas with sequence complementarity to other transcripts (sense transcripts). these rnas could potentially regulate the expression of their sense partner(s) at either the transcriptional or post-transcriptional level. experimental and computational methods have demonstrated the widespread occurrence of nats in eukaryotes. however, most previous studies only focused on cis-nats with little attention being paid to nats that originate in ... | 2006 | 17040561 |
| rate and polarity of gene fusion and fission in oryza sativa and arabidopsis thaliana. | eukaryotic gene fusion and fission events are mechanistically more complicated than in prokaryotes, and their quantitative contributions to genome evolution are still poorly understood. we have identified all differentially composite or split genes in 2 fully sequenced plant genomes, oryza sativa and arabidopsis thaliana. out of 10,172 orthologous gene pairs, 60 (0.6% of the total) revealed a verified fusion or fission event in either lineage after the divergence of o. sativa and a. thaliana. po ... | 2007 | 17035354 |
| plant methionine sulfoxide reductase a and b multigenic families. | methionine oxidation to methionine sulfoxide (metso), which results in modification of activity and conformation for many proteins, is reversed by an enzyme present in most organisms and termed as methionine sulfoxide reductase (msr). on the basis of substrate stereospecificity, two types of msr, a and b, that do not share any sequence similarity, have been identified. in the present review, we first compare the multigenic msr families in the three plant species for which the genome is fully seq ... | 2006 | 17031545 |
| the floral organ number4 gene encoding a putative ortholog of arabidopsis clavata3 regulates apical meristem size in rice. | to understand the molecular mechanism regulating meristem development in the monocot rice (oryza sativa), we describe here the isolation and characterization of three floral organ number4 (fon4) alleles and the cloning of the fon4 gene. the fon4 mutants showed abnormal enlargement of the embryonic and vegetative shoot apical meristems (sams) and the inflorescence and floral meristems. likely due to enlarged sams, fon4 mutants produced thick culms (stems) and increased numbers of both primary rac ... | 2006 | 17012407 |
| the reactive oxygen species network pathways:an essential prerequisite for perception of pathogen attack and the acquired disease resistance in plants. | availability of complete arabidopsis (arabidopsis thaliana) and rice (oryza sativa) genome sequences, together with molecular recourses of functional genomics and proteomics have revolutionized our understanding of reactive oxygen species (ros) signalling network mediating disease resistance in plants. so far, ros have been associated with aging, cellular and molecular alteration in animal and plant cells. recently,concluding evidences suggest that ros network is essential to induce disease resi ... | 2006 | 17006022 |
| the arabidopsis unannotated secreted peptide database, a resource for plant peptidomics. | in the era of genomics, if a gene is not annotated, it is not investigated. due to their small size, genes encoding peptides are often missed in genome annotations. secreted peptides are important regulators of plant growth, development, and physiology. identification of additional peptide signals by sequence homology searches has had limited success due to sequence heterogeneity. a bioinformatics approach was taken to find unannotated arabidopsis (arabidopsis thaliana) peptides. arabidopsis chr ... | 2006 | 16998087 |
| plant proteome analysis: a 2004-2006 update. | since the appearance of the review entitled "plant proteome analysis" in proteomics in february 2004 (cánovas, f. m., dumas-gaudot, e., recorbert, g., jorrín, j. et al., proteomics 2004, 4, 285-298), about 200 original articles focusing on plant proteomics have been published. although this represents less than 1% of the global proteomics output during this period, it nevertheless reflects an increase in activity over the period 1999-2004. these papers concern the proteome of at least 35 plant s ... | 2006 | 16991197 |
| divergence of the dof gene families in poplar, arabidopsis, and rice suggests multiple modes of gene evolution after duplication. | it is widely accepted that gene duplication is a primary source of genetic novelty. however, the evolutionary fate of duplicated genes remains largely unresolved. the classical ohno's duplication-retention-non/neofunctionalization theory, and the recently proposed alternatives such as subfunctionalization or duplication-degeneration-complementation, and subneofunctionalization, each can explain one or more aspects of gene fate after duplication. duplicated genes are also affected by epigenetic c ... | 2006 | 16980566 |
| identification of a new family of plant proteins loosely related to glutaredoxins with four cxxc motives. | the annotation of the recently released populus trichocarpa genome, has allowed us to characterize extensively the multigenic families of the redoxin proteins. proteins with two cysteines separated by two amino acids (cxxc motif) are often involved in redox reactions by promoting the formation, reduction or isomerization of disulfide bonds or by binding prosthetic groups or metals. we report here the presence of a new protein family in higher plants, constituted of 19 members in populus trichoca ... | 2006 | 16915354 |
| the endo-beta-mannanase gene families in arabidopsis, rice, and poplar. | mannans are widespread hemicellulosic polysaccharides in plant cell walls. hydrolysis of the internal beta-1,4-d: -mannopyranosyl linkage in the backbone of mannans is catalyzed by endo-beta-mannanase. plant endo-beta-mannanase has been well studied for its function in seed germination. its involvement in other plant biological processes, however, remains poorly characterized or elusive. the completed genome sequences of arabidopsis (arabidopsis thaliana), rice (oryza sativa), and poplar (populu ... | 2007 | 16897088 |
| genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and arabidopsis. | the basic/helix-loop-helix (bhlh) transcription factors and their homologs form a large family in plant and animal genomes. they are known to play important roles in the specification of tissue types in animals. on the other hand, few plant bhlh proteins have been studied functionally. recent completion of whole genome sequences of model plants arabidopsis (arabidopsis thaliana) and rice (oryza sativa) allows genome-wide analysis and comparison of the bhlh family in flowering plants. we have ide ... | 2006 | 16896230 |
| cross genome comparisons of serine proteases in arabidopsis and rice. | serine proteases are one of the largest groups of proteolytic enzymes found across all kingdoms of life and are associated with several essential physiological pathways. the availability of arabidopsis thaliana and rice (oryza sativa) genome sequences has permitted the identification and comparison of the repertoire of serine protease-like proteins in the two plant species. | 2006 | 16895613 |
| whole-genome analysis of oryza sativa reveals similar architecture of two-component signaling machinery with arabidopsis. | the two-component system (tcs), which works on the principle of histidine-aspartate phosphorelay signaling, is known to play an important role in diverse physiological processes in lower organisms and has recently emerged as an important signaling system in plants. employing the tools of bioinformatics, we have characterized tcs signaling candidate genes in the genome of oryza sativa l. subsp. japonica. we present a complete overview of tcs gene families in o. sativa, including gene structures, ... | 2006 | 16891544 |
| rna interference-based gene silencing as an efficient tool for functional genomics in hexaploid bread wheat. | insertional mutagenesis and gene silencing are efficient tools for the determination of gene function. in contrast to gain- or loss-of-function approaches, rna interference (rnai)-induced gene silencing can possibly silence multigene families and homoeologous genes in polyploids. this is of great importance for functional studies in hexaploid wheat (triticum aestivum), where most of the genes are present in at least three homoeologous copies and conventional insertional mutagenesis is not effect ... | 2006 | 16861570 |
| genome-wide comparative analyses of domain organisation of repertoires of protein kinases of arabidopsis thaliana and oryza sativa. | a comparative analysis on protein kinases encoded in the completely sequenced genomes of two plant species, namely arabidopsis thaliana and oryza sativa spp japonica cv. nipponbare is reported in the current study. we have analysed 836 and 1386 kinases identified from a. thaliana and the o. sativa genomes respectively. their classification into known subfamilies reveals selective expansions of the plant receptor kinase subfamily comprising of ser/thr receptor kinases. the presence of calcium dep ... | 2006 | 16843620 |
| isolation and characterization of a new na+/h+ antiporter gene osnha1 from rice (oryza sativa l.). | the full-length cdna (3612 bp) of osnha1 was cloned by rt-pcr approach from rice (oryza sativa l.), which encodes a putative plasma membrane na+/h+ antiporter. its deduced protein, osnha1, has 11 transmembrane domains and a significant similarity to a plasma membrane na+/h+ antiporter atnha1 from arabidopsis thaliana. phylogenetic analysis showed that the osnha1 clusters with the plasma membrane na+/h+ antiporters from various organisms. the semi-quantitative rt-pcr assay revealed that the expre ... | 2006 | 16753814 |
| genome-wide analysis of plant glutaredoxin systems. | the recent release of the first tree genome (populus trichocarpa) has allowed a comparison to be made of the multigenic glutaredoxin (grx) and glutathione reductase (gr) families of this tree with those of other sequenced organisms and especially of the two other fully sequenced plant species, arabidopsis thaliana and oryza sativa. grxs are small proteins involved in disulphide bridge or protein-glutathione adduct reduction, and they are maintained in a reduced form using glutathione and an nadp ... | 2006 | 16720602 |
| the atl gene family from arabidopsis thaliana and oryza sativa comprises a large number of putative ubiquitin ligases of the ring-h2 type. | ubiquitin ligases play an important regulatory role in the control of protein degradation processes via the ubiquitin/26s proteasome pathway in eukaryotes. these enzymes participate in substrate specification and mediate the transfer of ubiquitin to target proteins. a large number of ubiquitin ligases are predicted in the eukaryotes whose genomes have been sequenced; in arabidopsis thaliana more than 1300 genes are thought to encode ubiquitin ligases. at least three classes of ubiquitin ligases ... | 2006 | 16557337 |
| rice hydroperoxide lyases with unique expression patterns generate distinct aldehyde signatures in arabidopsis. | hydroperoxide lyase (hpl) genes encode enzymes that catalyze the cleavage of fatty acid hydroperoxides into aldehydes and oxoacids. there are three hpls in rice (oryza sativa), designated oshpl1 through oshpl3. to explore the possibility of differential functional activities among these genes, we have examined their expression patterns and biochemical properties of their encoded products. transcript analysis indicates that these genes have distinct patterns and levels of expression. oshpl1 is ub ... | 2006 | 16531481 |
| plastid cues posttranscriptionally regulate the accumulation of key enzymes of the methylerythritol phosphate pathway in arabidopsis. | plastid isoprenoids (including hormones and photosynthetic pigments) are essential for plant growth and development, but relatively little is known of how the production of their metabolic precursors via the recently elucidated methylerythritol phosphate (mep) pathway is regulated. we have identified an arabidopsis (arabidopsis thaliana) mutant that survives an otherwise lethal block of the mep pathway with fosmidomycin (fsm). in rif10 (resistant to inhibition with fsm 10) plants, the accumulati ... | 2006 | 16531478 |
| survey of conserved alternative splicing events of mrnas encoding sr proteins in land plants. | the serine/arginine-rich (sr) protein family plays an important role in constitutive and alternative splicing (as). these proteins regulate as in a tissue-specific and stress-responsive manner. pre-mrnas encoding sr proteins are often alternatively spliced, and these as events may be important for the regulation of as events of other pre-mrnas. in this study, we analyzed as events of sr proteins in arabidopsis thaliana and oryza sativa (rice). we found three sets of as events conserved between a ... | 2006 | 16520337 |
| the genomic view of genes responsive to the antagonistic phytohormones, abscisic acid, and gibberellin. | we now have the various genomics tools for monocot (oryza sativa) and a dicot (arabidopsis thaliana) plant. plant is not only a very important agricultural resource but also a model organism for biological research. it is important that the interaction between aba and ga is investigated for controlling the transition from embryogenesis to germination in seeds using genomics tools. these studies have investigated the relationship between dormancy and germination using genomics tools. genomics too ... | 2005 | 16492467 |
| the gh3 family in plants: genome wide analysis in rice and evolutionary history based on est analysis. | the gh3 gene family in arabidopsis, implicated in hormonal homeostasis through the conjugation of indolacetic and jasmonic acids to amino acids, is involved in a broad range of plant growth and development processes. in this work, the analysis of the gh3 family in the genome of oryza sativa identified 13 hypothetical orfs. est analysis and rt-pcr assays demonstrated that 12 of them were active genes. an extensive est analysis of the gh3 family performed on 26 plant species was used to estimate t ... | 2006 | 16488558 |
| genome histories clarify evolution of the expansin superfamily: new insights from the poplar genome and pine ests. | expansins comprise a superfamily of plant cell wall-loosening proteins that has been divided into four distinct families, expa, expb, exla and exlb. in a recent analysis of arabidopsis thaliana and oryza sativa expansins, we proposed a further subdivision of the families into 17 clades, representing independent lineages in the last common ancestor of monocots and eudicots. this division was based on both traditional sequence-based phylogenetic trees and on position-based trees, in which genomic ... | 2006 | 16411016 |
| orthologid: automation of genome-scale ortholog identification within a parsimony framework. | the determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. until now, most researchers use pairwise distance comparisons algorithms, such as blast, cog, rbh, rsd and inparanoid, to determine gene orthology. in contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and ... | 2006 | 16410324 |
| the role of osbri1 and its homologous genes, osbrl1 and osbrl3, in rice. | since first identifying two alleles of a rice (oryza sativa) brassinosteroid (br)-insensitive mutant, d61, that were also defective in an orthologous gene in arabidopsis (arabidopsis thaliana) brassinosteroid insensitive1 (bri1), we have isolated eight additional alleles, including null mutations, of the rice bri1 gene osbri1. the most severe mutant, d61-4, exhibited severe dwarfism and twisted leaves, although pattern formation and differentiation were normal. this severe shoot phenotype was ca ... | 2006 | 16407447 |
| genome-wide analysis of the erf gene family in arabidopsis and rice. | genes in the erf family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants. in this study, a comprehensive computational analysis identified 122 and 139 erf family genes in arabidopsis (arabidopsis thaliana) and rice (oryza sativa l. subsp. japonica), respectively. a complete overview of this gene family in arabidopsis is presented, including the gene structures, phylogeny, chromosome locations, and conserved motifs. ... | 2006 | 16407444 |
| ramosa2 encodes a lateral organ boundary domain protein that determines the fate of stem cells in branch meristems of maize. | genetic control of grass inflorescence architecture is critical given that cereal seeds provide most of the world's food. seeds are borne on axillary branches, which arise from groups of stem cells in axils of leaves and whose branching patterns dictate most of the variation in plant form. normal maize (zea mays) ears are unbranched, and tassels have long branches only at their base. the ramosa2 (ra2) mutant of maize has increased branching with short branches replaced by long, indeterminate one ... | 2006 | 16399802 |
| genome-wide comparative analysis of the iqd gene families in arabidopsis thaliana and oryza sativa. | calcium signaling plays a prominent role in plants for coordinating a wide range of developmental processes and responses to environmental cues. stimulus-specific generation of intracellular calcium transients, decoding of calcium signatures, and transformation of the signal into cellular responses are integral modules of the transduction process. several hundred proteins with functions in calcium signaling circuits have been identified, and the number of downstream targets of calcium sensors is ... | 2005 | 16368012 |
| structure and architecture of the maize genome. | maize (zea mays or corn) plays many varied and important roles in society. it is not only an important experimental model plant, but also a major livestock feed crop and a significant source of industrial products such as sweeteners and ethanol. in this study we report the systematic analysis of contiguous sequences of the maize genome. we selected 100 random regions averaging 144 kb in size, representing about 0.6% of the genome, and generated a high-quality dataset for sequence analysis. this ... | 2005 | 16339807 |
| study of cis-cinnamic acid in arabidopsis thaliana. | trans-cinnamic acid (ca) can be isomerized to cis-ca in arabidopsis thaliana extract under sunlight. piperonylic acid treatment of arabidopsis under ultraviolet (uv) light increased the level of cis-ca in these treated tissues. similarly, cis-ca was also detected from oryza sativa seedlings grown under sunlight. these results suggest that cis-ca may occur in planta. application of cis-ca to seedlings of both wild type arabidopsis and auxin-insensitive mutants, aux1 and axr2, resulted in nearly i ... | 2016 | 16310363 |
| evolutionary expansion, gene structure, and expression of the rice wall-associated kinase gene family. | the wall-associated kinase (wak) gene family, one of the receptor-like kinase (rlk) gene families in plants, plays important roles in cell expansion, pathogen resistance, and heavy-metal stress tolerance in arabidopsis (arabidopsis thaliana). through a reiterative database search and manual reannotation, we identified 125 oswak gene family members from rice (oryza sativa) japonica cv nipponbare; 37 (approximately 30%) oswaks were corrected/reannotated from earlier automated annotations. of the 1 ... | 2005 | 16286450 |
| the role of mass spectrometry in plant systems biology. | large-scale analyses of proteins and metabolites are intimately bound to advancements in ms technologies. the aim of these non-targeted "omic" technologies is to extend our understanding beyond the analysis of only parts of the system. here, metabolomics and proteomics emerged in parallel with the development of novel mass analyzers and hyphenated techniques such as gas chromatography coupled to time-of-flight mass spectrometry (gc-tof-ms) and multidimensional liquid chromatography coupled to ma ... | 2008 | 16284938 |
| conservation and divergence of light-regulated genome expression patterns during seedling development in rice and arabidopsis. | genome-wide 70-mer oligonucleotide microarrays of rice (oryza sativa) and arabidopsis thaliana were used to profile genome expression changes during light-regulated seedling development. we estimate that the expression of approximately 20% of the genome in both rice and arabidopsis seedlings is regulated by white light. qualitatively similar expression profiles from seedlings grown under different light qualities were observed in both species; however, a quantitatively weaker effect on genome ex ... | 2005 | 16284311 |
| computational detection of micrornas targeting transcription factor genes in arabidopsis thaliana. | micrornas, an abundant class of tiny non-coding rnas, have emerged as negative regulators for translational repression or cleavage of target mrnas by the manner of complementary base paring in plants and animals. recent studies have demonstrated that many known micrornas have a remarkable propensity to target genes involved in development, particularly those of transcription factor genes. therefore, an overall detection of arabidopsis thaliana micrornas targeting transcription factor genes will ... | 2005 | 16221572 |
| comparative plant genomics resources at plantgdb. | plantgdb (http://www.plantgdb.org/) is a database of plant molecular sequences. expressed sequence tag (est) sequences are assembled into contigs that represent tentative unique genes. est contigs are functionally annotated with information derived from known protein sequences that are highly similar to the putative translation products. tentative gene ontology terms are assigned to match those of the similar sequences identified. genome survey sequences are assembled similarly. the resulting ge ... | 2005 | 16219921 |
| the dark side of green fluorescent protein. | here, severe interference of chlorophyll with green fluorescent protein (gfp) fluorescence is described for medicago (medicago truncatula), rice (oryza sativa) and arabidopsis (arabidopsis thaliana). this interference disrupts the proportional relationship between gfp content and fluorescence that is intrinsic to its use as a quantitative reporter. the involvement of chlorophyll in the loss of gfp fluorescence with leaf age was shown in vivo, by the removal of chlorophyll through etiolation or b ... | 2005 | 16219071 |
| transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots. | it is not known how representative the arabidopsis thaliana complement of transcription factors (tfs) is of other plants. the availability of rice (oryza sativa) genome sequences makes possible a comparative analysis of tfs between monocots and eudicots, the two major monophyletic groups of angiosperms. here, we identified 1611 tf genes that belong to 37 gene families in rice, comparable to the 1510 in arabidopsis. several gene subfamilies, but no families, were found to be lineage-specific. phy ... | 2005 | 16217612 |
| genomic research in eucalyptus. | eucalyptus l'hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. with the sequencing of the genomes of arabidopsis thaliana and oryza sativa and the recent completion of the first tree genome sequence, populus trichocarpa, attention has turned to the current status of genomic research in eucalyptus. for sev ... | 2005 | 16175457 |
| plant photoreceptors: phylogenetic overview. | plants possess photoreceptors to perceive light which controls most aspects of their lives. three photoreceptor families are well characterized: cryptochromes (crys), phototropins (phots), and phytochromes (phys). two putative families have been identified more recently: zeitlupes (ztls) and uv-b photoreceptors (uli). using arabidopsis thaliana and oryza sativa photoreceptor sequences as references, we have searched for photoreceptor encoding genes in the major phyla of plant kingdom. for each p ... | 2005 | 16170454 |
| wheat cultivar-specific proteins in grain revealed by 2-de and their application to cultivar identification of flour. | wheat flour proteins were studied to identify the cultivar-specific proteins and use them to identify cultivars in flours. proteins extracted from flours of japanese wheat (cultivars hokushin, horoshirikomugi, kitanokaori and kachikei 33) and canadian wheat (canada western red spring wheat no. 1; 1cw) were analyzed by 2-de with ief gels over three ph ranges: ph 4-7, ph 5-8, and ph 6-11. this system enabled detection of more than 1600 protein spots. we recognized that among 50 protein spots showi ... | 2005 | 16152659 |
| the wp mutation of glycine max carries a gene-fragment-rich transposon of the cacta superfamily. | we used soybean (glycine max) cdna microarrays to identify candidate genes for a stable mutation at the wp locus in soybean, which changed a purple-flowered phenotype to pink, and found that flavanone 3-hydroxylase cdnas were overexpressed in purple flower buds relative to the pink. restriction fragment length polymorphism analysis and rna gel blots of purple and pink flower isolines, as well as the presence of a 5.7-kb transposon insertion in the wp mutant allele, have unequivocally shown that ... | 2005 | 16141454 |
| light-regulated overexpression of an arabidopsis phytochrome a gene in rice alters plant architecture and increases grain yield. | the phytochromes are a family of red/far-red light absorbing photoreceptors that control plant developmental and metabolic processes in response to changes in the light environment. we report here the overexpression of arabidopsis thaliana phytochrome a (phya) gene in a commercially important indica rice variety (oryza sativa l. pusa basmati-1). the expression of the transgene was driven by the light-regulated and tissue-specific rice rbcs promoter. several independent homozygous sixth generatio ... | 2006 | 16136335 |
| genome-wide identification of potential plant e2f target genes. | entry into the s phase of the cell cycle is controlled by e2f transcription factors that induce the transcription of genes required for cell cycle progression and dna replication. although the e2f pathway is highly conserved in higher eukaryotes, only a few e2f target genes have been experimentally validated in plants. we have combined microarray analysis and bioinformatics tools to identify plant e2f-responsive genes. promoter regions of genes that were induced at the transcriptional level in a ... | 2005 | 16126853 |
| green sperm. identification of male gamete promoters in arabidopsis. | previously, in an effort to better understand the male contribution to fertilization, we completed a maize (zea mays) sperm expressed sequence tag project. here, we used this resource to identify promoters that would direct gene expression in sperm cells. we used reverse transcription-polymerase chain reaction to identify probable sperm-specific transcripts in maize and then identified their best sequence matches in the arabidopsis (arabidopsis thaliana) genome. we tested five different arabidop ... | 2005 | 16055690 |
| [isolation, characterization and expression analysis of male sterility gene homology sequence in wheat]. | one 134 bp fragment was amplified in anthers of male sterile and fertile wheat using one pair of degenerated primer designed based on the conserved domain of ms2 gene in arabidopsis thaliana and oryza sativa, and one 1604 bp male sterility gene homology sequence was extended by in silico cloning based on the 134 bp fragment. the amino acids encoded by the male sterility gene homology sequence include a 200 amino acid conserved domain of male sterility, and this sequence expressed only in wheat m ... | 2005 | 16018182 |
| systematic spatial analysis of gene expression during wheat caryopsis development. | the cereal caryopsis is a complex tissue in which maternal and endosperm tissues follow distinct but coordinated developmental programs. because of the hexaploid genome in wheat (triticum aestivum), the identification of genes involved in key developmental processes by genetic approaches has been difficult. to bypass this limitation, we surveyed 888 genes that are expressed during caryopsis development using a novel high-throughput mrna in situ hybridization method. this survey revealed novel di ... | 2005 | 16006577 |
| mustang is a novel family of domesticated transposase genes found in diverse angiosperms. | while transposons have traditionally been viewed as genomic parasites or "junk dna," the discovery of transposon-derived host genes has fueled an ongoing debate over the evolutionary role of transposons. in particular, while mobility-related open reading frames have been known to acquire host functions, the contribution of these types of events to the evolution of genes is not well understood. here we report that genome-wide searches for mutator transposase-derived host genes in arabidopsis thal ... | 2005 | 15987878 |
| mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes. | transfers of organelle dna to the nucleus established several thousand functional genes in eukaryotic chromosomes over evolutionary time. recent transfers have also contributed nonfunctional plastid (pt)- and mitochondrion (mt)-derived dna (termed nupts and numts, respectively) to plant nuclear genomes. the two largest transferred organelle genome copies are 131-kb nuptdna in rice (oryza sativa) and 262-kb numtdna in arabidopsis (arabidopsis thaliana). these transferred copies were compared in d ... | 2005 | 15951485 |
| effects of free proline accumulation in petunias under drought stress. | petunias (petunia hybrida cv. 'mitchell') accumulate free proline (pro) under drought-stress conditions. it is therefore believed that pro acts as an osmoprotectant in plants subjected to drought conditions. petunia plants were transformed by delta(1)-pyrroline-5-carboxylate synthetase genes (atp5cs from arabidopsis thaliana l. or osp5cs from oryza sativa l.). the transgenic plants accumulated pro and their drought tolerance was tested. the pro content amounted to 0.57-1.01% of the total amino a ... | 2005 | 15928013 |
| mutations in the arabidopsis phosphoinositide phosphatase gene sac9 lead to overaccumulation of ptdins(4,5)p2 and constitutive expression of the stress-response pathway. | phosphoinositides (pis) are signaling molecules that regulate cellular events including vesicle targeting and interactions between membrane and cytoskeleton. phosphatidylinositol (ptdins)(4,5)p(2) is one of the best characterized pis; studies in which ptdins(4,5)p(2) localization or concentration is altered lead to defects in the actin cytoskeleton and exocytosis. ptdins(4,5)p(2) and its derivative ins(1,4,5)p(3) accumulate in salt, cold, and osmotically stressed plants. ptdins(4,5)p(2) signalin ... | 2005 | 15923324 |