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Arabidopsis Thaliana (arabidopsi + thaliana)
Kinds of Arabidopsis Thaliana Terms modified by Arabidopsis Thaliana Selected AbstractsThe Arabidopsis class VIII myosin ATM2 is involved in endocytosisCYTOSKELETON, Issue 6 2008Amirali Sattarzadeh Abstract Members of the class XI of the myosin superfamily comprising higher plant, actin-based molecular motors have been shown to be involved in peroxisome and Golgi vesicle trafficking comparable to yeast and animal class V myosins. The tasks of the second class of myosins of higher plants, class VIII, are unclear. In this study the class VIII myosin ATM2 from the model plant Arabidopsis thaliana was selected for the examination of cargo specificity in vivo. Fluorescent protein-fusion plasmid constructs with fragments of the ATM2 cDNA were generated and used for Agrobacterium tumefaciens -based transient transformation of Nicotiana benthamiana leaves. The resulting subcellular localization patterns were recorded by live imaging with confocal laser scanning microscopy (CLSM) in epidermal leaf cells. Expression of a nearly full-length construct displayed labeling of filaments and vesicles, a head + neck fragment led to decoration of filaments only. However, expression of fluorescent protein-tagged C-terminal tail domain constructs labeled vesicular structures of different appearance. Most importantly, coexpression of different RFP/YFP-ATM2 tail fusion proteins showed colocalization and, hence, binding to the same type of vesicular target. Further coexpression experiments of RFP/YFP-ATM2 tail fusion proteins with the endosomal marker FYVE and the endosomal tracer FM4-64 demonstrated colocalization with endosomes. Colocalization was also detected by expression of the CFP-tagged membrane receptor BRI1 as marker, which is constantly recycled via endosomes. Occasionally the ATM2 tail targeted to sites at the plasma membrane closely resembling the pattern obtained upon expression of the YFP-ATM1 C-terminal tail. ATM1 is known for its localization at the plasma membrane at sites of plasmodesmata. Cell Motil. Cytoskeleton 2008. © 2008 Wiley-Liss, Inc. [source] Primer and interviews: Gene regulation in Arabidopsis thalianaDEVELOPMENTAL DYNAMICS, Issue 9 2009Julie C. Kiefer Abstract The animal and plant kingdoms use many of the same molecular tools to build decidedly different multicellular organisms. Learning how plants approach challenges common to both kingdoms can inspire new ways of thinking in the animal biologist. This primer introduces how a weed from the mustard family, Arabidopsis thaliana, has been used to work through developmental problems. It also compares and contrasts gene regulation tools in animals and plants. Accompanying the primer is a discussion of current topics in root development with Arabidopsis researchers Philip N. Benfey, Ph.D., and Kenneth D. Birnbaum, Ph.D. Developmental Dynamics 238:2449,2458, 2009. © 2009 Wiley-Liss, Inc. [source] Life history in a model system: opening the black box with Arabidopsis thalianaECOLOGY LETTERS, Issue 7 2009C. Jessica E. Metcalf Abstract A broad research programme in Arabidopsis thaliana has provided estimates of selection on specific alleles in specific contexts, and identified geographic patterns of alleles in genes linked to timing of flowering. A closely related field has successfully captured many key axes of the evolution of timing of flowering in other monocarpic species through statistical and demographic modelling of large empirical databases. There has as yet been no synthesis between these two fields. Here we examine ways in which the two fields inform each other, and how this synergy will shape our knowledge of life-history evolution as a whole. [source] Elevated CO2 and herbivory influence trait integration in Arabidopsis thalianaECOLOGY LETTERS, Issue 9 2004M. Gabriela Bidart-Bouzat Abstract We lack information on how elevated CO2, and its interaction with other factors like herbivory, affect levels and patterns of trait integration in plants. We experimentally tested the hypothesis that elevated CO2 disrupts and restructures functional associations among plant traits, in the selfing annual, Arabidopsis thaliana. We tested for these effects both in the presence and absence of herbivory by larvae of the diamondback moth, Plutella xylostella. Elevated CO2, both alone and combined with moth herbivory, modified integrated trait responses. In addition, integration under different environments was genotype-specific. These results imply that global changes in CO2 are likely to cause divergent evolutionary outcomes among populations of plants that differ in the initial structure of their quantitative genetic variation. [source] Comparison of the Electrochemical Behavior of the High Molecular Mass Cadmium Proteins in Arabidopsis thaliana and in Vegetable Plants on Using Preparative Native Continuous Polyacrylamide Gel Electrophoresis (PNC-PAGE)ELECTROANALYSIS, Issue 1 2006Bernd Kastenholz Abstract In Arabidopsis cytosol (supernatant) and in supernatants of vegetable plants high molecular mass cadmium proteins with molecular mass 200,kDa were isolated by using preparative native continuous polyacrylamide gel electrophoresis (PNC-PAGE). Because of a different electrochemical behavior of the Cd proteins in Arabidopsis and endive supernatants on using the same PAGE method, it is concluded that the high molecular mass cadmium proteins of Arabidopsis and endive possess different isoelectric points. Consequently, different chemical structures of the Cd proteins with molecular mass 200,kDa are present in Arabidopsis thaliana and in endive. During the electrophoretic separation of vegetable metalloproteins by using the Model 491 Prep Cell from BioRad, electroanalytical processes like electrode reactions may play an important role. [source] Proteomics in globe artichoke: Protein extraction and sample complexity reduction by PEG fractionationELECTROPHORESIS, Issue 9 2009Alberto Acquadro Abstract Here, we report the first leaf proteome analysis for globe artichoke. Three protein extraction protocols were tested and a reproducible Mg/NP-40-based method was established. Ribulose-1,5-biphosphate carboxylase-oxygenase (RuBisCO) is a highly abundant leaf protein, and its presence masks co-localizing, less abundant proteins. To remove RuBisCO from the sample, and thereby improve spot resolution, a PEG fractionation approach was elaborated. 2-DE profiles of various PEG fractions showed that the fractionation procedure was successful in excluding most of the RuBisCO, allowing for the detection of many low-abundance proteins. Western blot analysis was able to confirm the reduction in RuBisCO content achieved by PEG fractionation. In all, 841 distinct protein spots were detected, and 40 of these, selected from the RuBisCO region of the 2-DE profile, were successfully identified by MS. A number of homologues of these proteins also co-localize with RuBisCO in Arabidopsis thaliana. [source] The exopolysaccharide of Rhizobium sp.ENVIRONMENTAL MICROBIOLOGY, Issue 8 2008Brassica napus roots but contributes to root colonization, YAS34 is not necessary for biofilm formation on Arabidopsis thaliana Summary Microbial exopolysaccharides (EPSs) play key roles in plant,microbe interactions, such as biofilm formation on plant roots and legume nodulation by rhizobia. Here, we focused on the function of an EPS produced by Rhizobium sp. YAS34 in the colonization and biofilm formation on non-legume plant roots (Arabidopsis thaliana and Brassica napus). Using random transposon mutagenesis, we isolated an EPS-deficient mutant of strain YAS34 impaired in a glycosyltransferase gene (gta). Wild type and mutant strains were tagged with a plasmid-born GFP and, for the first time, the EPS produced by the wild-type strain was seen in the rhizosphere using selective carbohydrate probing with a fluorescent lectin and confocal laser-scanning microscopy. We show for the fist time that Rhizobium forms biofilms on roots of non-legumes, independently of the EPS synthesis. When produced by strain YAS34 wild type, EPS is targeted at specific parts of the plant root system. Nutrient fluctuations, root exudates and bacterial growth phase can account for such a production pattern. The EPS synthesis in Rhizobium sp. YAS34 is not essential for biofilm formation on roots, but is critical to colonization of the basal part of the root system and increasing the stability of root-adhering soil. Thus, in Rhizobium sp. YAS34 and non-legume interactions, microbial EPS is implicated in root,soil interface, root colonization, but not in biofilm formation. [source] Erratum: Developmental phytotoxicity of metal oxide nanoparticles to Arabidopsis thalianaENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 6 2010Chang Woo Lee No abstract is available for this article. [source] Developing transgenic arabidopsis plants to be metal-specific bioindicatorsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 1 2003Beth A. Krizek Abstract Deoxyribonucleic acid (DNA) microarrays provide a means to assess genome-wide expression patterns after exposure of an organism to different xenobiotics. Potential uses for this technology include identification of unknown toxicants, assessment of toxicity of new compounds, and characterization of the cellular mechanisms of toxicant action. Here we describe another use of DNA microarrays in toxicant-specific gene discovery. Combining results from two DNA microarray experiments, we have identified genes from the model plant Arabidopsis thaliana that are induced in response to one but not other heavy metals. The promoters of these genes should be useful in developing metal-specific transgenic biomonitors. To test this idea, we have fused the promoter of one of the newly identified Ni-inducible genes (AHB1) to the ,-glucuronidase (GUS) reporter gene. Arabidopsis plants containing the AHB1::GUS transgene show reporter gene activity when they are grown on media containing Ni but not when grown on media containing Cd, Cu, Zn, or without added metals. Thus, this approach has resulted in the creation of a transgenic strain of Arabidopsis that can report on the presence and concentration of Ni in plant growth media. Such transgenic models can serve as cheap and efficient biomonitors of bioavailable heavy metal contamination in soils and sediments. [source] LIKELIHOOD-BASED INFERENCE IN ISOLATION-BY-DISTANCE MODELS USING THE SPATIAL DISTRIBUTION OF LOW-FREQUENCY ALLELESEVOLUTION, Issue 11 2009John Novembre Estimating dispersal distances from population genetic data provides an important alternative to logistically taxing methods for directly observing dispersal. Although methods for estimating dispersal rates between a modest number of discrete demes are well developed, methods of inference applicable to "isolation-by-distance" models are much less established. Here, we present a method for estimating ,,2, the product of population density (,) and the variance of the dispersal displacement distribution (,2). The method is based on the assumption that low-frequency alleles are identical by descent. Hence, the extent of geographic clustering of such alleles, relative to their frequency in the population, provides information about ,,2. We show that a novel likelihood-based method can infer this composite parameter with a modest bias in a lattice model of isolation-by-distance. For calculating the likelihood, we use an importance sampling approach to average over the unobserved intraallelic genealogies, where the intraallelic genealogies are modeled as a pure birth process. The approach also leads to a likelihood-ratio test of isotropy of dispersal, that is, whether dispersal distances on two axes are different. We test the performance of our methods using simulations of new mutations in a lattice model and illustrate its use with a dataset from Arabidopsis thaliana. [source] PLASTICITY TO LIGHT CUES AND RESOURCES IN ARABIDOPSIS THALIANA: TESTING FOR ADAPTIVE VALUE AND COSTSEVOLUTION, Issue 6 2000Lisa A. Dorn Abstract Plants shaded by neighbors or overhead foliage experience both a reduction in the ratio of red to far red light (R:FR), a specific cue perceived by phytochrome, and reduced photosynthetically active radiation (PAR), an essential resource. We tested the adaptive value of plasticity to crowding and to the cue and resource components of foliage shade in the annual plant Arabidopsis thaliana by exposing 36 inbred families from four natural populations to four experimental treatments: (1) high density, full sun; (2) low density, full sun; (3) low density, neutral shade; and (4) low density, low R:FR-simulated foliage shade. Genotypic selection analysis within each treatment revealed strong environmental differences in selection on plastic life-history traits. We used specific contrasts to measure plasticity to density and foliage shade, to partition responses to foliage shade into phytochrome-mediated responses to the R:FR cue and responses to PAR, and to test whether plasticity was adaptive (i.e., in the same direction as selection in each environment). Contrary to expectation, we found no evidence for adaptive plasticity to density. However, we observed both adaptive and maladaptive responses to foliage shade. In general, phytochrome-mediated plasticity to the R:FR cue of foliage shade was adaptive and counteracted maladaptive growth responses to reduced PAR. These results support the prediction that active developmental responses to environmental cues are more likely to be adaptive than are passive resource-mediated responses. Multiple regression analysis detected a few costs of adaptive plasticity and adaptive homeostasis, but such costs were infrequent and their expression depended on the environment. Thus, costs of plasticity may occasionally constrain the evolution of adaptive responses to foliage shade in Arabidopsis, but this constraint may differ among environments and is far from ubiquitous. [source] The allene oxide cyclase family of Arabidopsis thaliana , localization and cyclizationFEBS JOURNAL, Issue 10 2008Florian Schaller Jasmonates are derived from oxygenated fatty acids (oxylipins) via the octadecanoid pathway and are characterized by a pentacyclic ring structure. They have regulatory functions as signaling molecules in plant development and adaptation to environmental stress. Recently, we solved the structure of allene oxide cyclase 2 (AOC2) of Arabidopsis thaliana, which is, together with the other three AOCs, a key enzyme in the biosynthesis of jasmonates, in that it releases the first cyclic and biologically active metabolite , 12-oxo-phytodienoic acid (OPDA). On the basis of models for the bound substrate, 12,13(S)-epoxy-9(Z),11,15(Z)-octadecatrienoic acid, and the product, OPDA, we proposed that a conserved Glu promotes the reaction by anchimeric assistance. According to this hypothesis, the transition state with a pentadienyl carbocation and an oxyanion is stabilized by a strongly bound water molecule and favorable ,,, interactions with aromatic residues in the cavity. Stereoselectivity results from steric restrictions to the necessary substrate isomerizations imposed by the protein environment. Here, site-directed mutagenesis was used to explore and verify the proposed reaction mechanism. In a comparative analysis of the AOC family from A. thaliana involving enzymatic characterization, in vitro import, and transient expression of AOC,enhanced green fluorescent protein fusion proteins for analysis of subcellular targeting, we demonstrate that all four AOC isoenzymes may contribute to jasmonate biosynthesis, as they are all located in chloroplasts and, in concert with the allene oxide synthase, they are all able to convert 13(S)-hydroperoxy-9(Z),11(E),15(Z)-octadecatrienoic acid into enantiomerically pure cis(+)-OPDA. [source] Characterization and expression analysis of the aspartic protease gene family of Cynara cardunculus L.FEBS JOURNAL, Issue 10 2007Catarina Pimentel Cardosin A and cardosin B are two aspartic proteases mainly found in the pistils of cardoon Cynara cardunculus L., whose flowers are traditionally used in several Mediterranean countries in the manufacture of ewe's cheese. We have been characterizing cardosins at the biochemical, structural and molecular levels. In this study, we show that the cardoon aspartic proteases are encoded by a multigene family. The genes for cardosin A and cardosin B, as well as those for two new cardoon aspartic proteases, designated cardosin C and cardosin D, were characterized, and their expression in C. cardunculus L. was analyzed by RT-PCR. Together with cardosins, a partial clone of the cyprosin B gene was isolated, revealing that cardosin and cyprosin genes coexist in the genome of the same plant. As a first approach to understanding what dictates the flower-specific pattern of cardosin genes, the respective gene 5, regulatory sequences were fused with the reporter ,-glucuronidase and introduced into Arabidopsis thaliana. A subsequent deletion analysis of the promoter region of the cardosin A gene allowed the identification of a region of approximately 500 bp essential for gene expression in transgenic flowers. Additionally, the relevance of the leader intron of the cardosin A and B genes for gene expression was evaluated. Our data showed that the leader intron is essential for cardosin B gene expression in A. thaliana. In silico analysis revealed the presence of potential regulatory motifs that lay within the aforementioned regions and therefore might be important in the regulation of cardosin expression. [source] The thioredoxin-independent isoform of chloroplastic glyceraldehyde-3-phosphate dehydrogenase is selectively regulated by glutathionylationFEBS JOURNAL, Issue 1 2007Mirko Zaffagnini In animal cells, many proteins have been shown to undergo glutathionylation under conditions of oxidative stress. By contrast, very little is known about this post-translational modification in plants. In the present work, we showed, using mass spectrometry, that the recombinant chloroplast A4 -glyceraldehyde-3-phosphate dehydrogenase (A4 -GAPDH) from Arabidopsis thaliana is glutathionylated with either oxidized glutathione or reduced glutathione and H2O2. The formation of a mixed disulfide between glutathione and A4 -GAPDH resulted in the inhibition of enzyme activity. A4 -GAPDH was also inhibited by oxidants such as H2O2. However, the effect of glutathionylation was reversed by reductants, whereas oxidation resulted in irreversible enzyme inactivation. On the other hand, the major isoform of photosynthetic GAPDH of higher plants (i.e. the AnBn -GAPDH isozyme in either A2B2 or A8B8 conformation) was sensitive to oxidants but did not seem to undergo glutathionylation significantly. GAPDH catalysis is based on Cys149 forming a covalent intermediate with the substrate 1,3-bisphosphoglycerate. In the presence of 1,3-bisphosphoglycerate, A4 -GAPDH was fully protected from either oxidation or glutathionylation. Site-directed mutagenesis of Cys153, the only cysteine located in close proximity to the GAPDH active-site Cys149, did not affect enzyme inhibition by glutathionylation or oxidation. Catalytic Cys149 is thus suggested to be the target of both glutathionylation and thiol oxidation. Glutathionylation could be an important mechanism of regulation and protection of chloroplast A4 -GAPDH from irreversible oxidation under stress. [source] Hydroperoxide reduction by thioredoxin-specific glutathione peroxidase isoenzymes of Arabidopsis thalianaFEBS JOURNAL, Issue 24 2006Aqib Iqbal Arabidopsis thaliana contains eight glutathione peroxidase (GPX) homologs (AtGPX1,8). Four mature GPX isoenzymes with different subcellular distributions, AtGPX1, -2, -5 and -6, were overexpressed in Escherichia coli and characterized. Interestingly, these recombinant proteins were able to reduce H2O2, cumene hydroperoxide, phosphatidylcholine and linoleic acid hydroperoxides using thioredoxin but not glutathione or NADPH as an electron donor. The reduction activities of the recombinant proteins with H2O2 were 2,7 times higher than those with cumene hydroperoxide. Km values for thioredoxin and H2O2 were 2.2,4.0 and 14.0,25.4 µm, respectively. These finding suggest that GPX isoenzymes may function to detoxify H2O2 and organic hydroperoxides using thioredoxin in vivo and may also be involved in regulation of the cellular redox homeostasis by maintaining the thiol/disulfide or NADPH/NADP balance. [source] Isoprenoid biosynthesis in plants , 2C -methyl- d -erythritol-4-phosphate synthase (IspC protein) of Arabidopsis thalianaFEBS JOURNAL, Issue 19 2006Felix Rohdich The ispC gene of Arabidopsis thaliana was expressed in pseudomature form without the putative plastid-targeting sequence in a recombinant Escherichia coli strain. The recombinant protein was purified by affinity chromatography and was shown to catalyze the formation of 2C -methyl- d -erythritol 4-phosphate from 1-deoxy- d -xylulose 5-phosphate at a rate of 5.6 µmol·min,1·mg,1 (kcat 4.4 s,1). The Michaelis constants for 1-deoxy- d -xylulose 5-phosphate and the cosubstrate NADPH are 132 and 30 µm, respectively. The enzyme has an absolute requirement for divalent metal ions, preferably Mn2+ and Mg2+, and is inhibited by fosmidomycin with a Ki of 85 nm. The pH optimum is 8.0. NADH can substitute for NADPH, albeit at a low rate (14% as compared to NADPH). The enzyme catalyzes the reverse reaction at a rate of 2.1 µmol·min -1·mg -1. [source] The crystal structure of a plant 2C -methyl- D -erythritol 4-phosphate cytidylyltransferase exhibits a distinct quaternary structure compared to bacterial homologues and a possible role in feedback regulation for cytidine monophosphateFEBS JOURNAL, Issue 5 2006Mads Gabrielsen The homodimeric 2C -methyl- d -erythritol 4-phosphate cytidylyltransferase contributes to the nonmevalonate pathway of isoprenoid biosynthesis. The crystal structure of the catalytic domain of the recombinant enzyme derived from the plant Arabidopsis thaliana has been solved by molecular replacement and refined to 2.0 Å resolution. The structure contains cytidine monophosphate bound in the active site, a ligand that has been acquired from the bacterial expression system, and this observation suggests a mechanism for feedback regulation of enzyme activity. Comparisons with bacterial enzyme structures, in particular the enzyme from Escherichia coli, indicate that whilst individual subunits overlay well, the arrangement of subunits in each functional dimer is different. That distinct quaternary structures are available, in conjunction with the observation that the protein structure contains localized areas of disorder, suggests that conformational flexibility may contribute to the function of this enzyme. [source] Functional dissection of two Arabidopsis PsbO proteinsFEBS JOURNAL, Issue 9 2005PsbO PsbO protein is an extrinsic subunit of photosystem II (PSII) and has been proposed to play a central role in stabilization of the catalytic manganese cluster. Arabidopsis thaliana has two psbO genes that express two PsbO proteins; PsbO1 and PsbO2. We reported previously that a mutant plant that lacked PsbO1 (psbo1) showed considerable growth retardation despite the presence of PsbO2 [Murakami, R., Ifuku, K., Takabayashi, A., Shikanai, T., Endo, T., and Sato, F. (2002) FEBS Lett523, 138,142]. In the present study, we characterized the functional differences between PsbO1 and PsbO2. We found that PsbO1 is the major isoform in the wild-type, and the amount of PsbO2 in psbo1 was significantly less than the total amount of PsbO in the wild-type. The amount of PsbO as well as the efficiency of PSII in psbo1 increased as the plants grew; howeVER, it neVER reached the total PsbO level observed in the wild-type, suggesting that the poor activity of PSII in psbo1 was caused by a shortage of PsbO. In addition, an in vitro reconstitution experiment using recombinant PsbOs and urea-washed PSII particles showed that oxygen evolution was better recoVERed by PsbO1 than by PsbO2. Further analysis using chimeric and mutated PsbOs suggested that the amino acid changes Val186,Ser, Leu246,Ile, and Val204,Ile could explain the functional difference between the two PsbOs. Therefore we concluded that both the lower expression level and the inferior functionality of PsbO2 are responsible for the phenotype observed in psbo1. [source] Studies into factors contributing to substrate specificity of membrane-bound 3-ketoacyl-CoA synthasesFEBS JOURNAL, Issue 19 2002Brenda J. Blacklock We are interested in constructing a model for the substrate-binding site of fatty acid elongase-1 3-ketoacyl CoA synthase (FAE1 KCS), the enzyme responsible for production of very long chain fatty acids of plant seed oils. Arabidopsis thaliana and Brassica napus FAE1 KCS enzymes are highly homologous but the seed oil content of these plants suggests that their substrate specificities differ with respect to acyl chain length. We used in vivo and in vitro assays of Saccharomyces cerevisiae -expressed FAE1 KCSs to demonstrate that the B. napus FAE1 KCS enzyme favors longer chain acyl substrates than the A. thaliana enzyme. Domains/residues responsible for substrate specificity were investigated by determining catalytic activity and substrate specificity of chimeric enzymes of A. thaliana and B. napus FAE1 KCS. The N-terminal region, excluding the transmembrane domain, was shown to be involved in substrate specificity. One chimeric enzyme that included A. thaliana sequence from the N terminus to residue 114 and B. napus sequence from residue 115 to the C terminus had substrate specificity similar to that of A. thaliana FAE1 KCS. However, a K92R substitution in this chimeric enzyme changed the specificity to that of the B. napus enzyme without loss of catalytic activity. Thus, this study was successful in identifying a domain involved in determining substrate specificity in FAE1 KCS and in engineering an enzyme with novel activity. [source] Highly efficient targeting and accumulation of a Fab fragment within the secretory pathway and apoplast of Arabidopsis thalianaFEBS JOURNAL, Issue 15 2001Koen Peeters To further improve antibody production in plants, constructs were designed to minimize transgene silencing and to retain a Fab fragment within the secretory pathway of transgenic Arabidopsis thaliana plants. The levels of antibody accumulation suggest that placing the sequences that encode Fd and light chain under the control of nonidentical 3, regions reduces susceptibility to post-transcriptional gene silencing compared with when the individual polypeptide-encoding sequences are placed under the control of identical 3, regions. High levels of accumulation (up to 6% of total soluble protein) were found for both secreted and intracellularly targeted antibody fragments. Immunofluorescence microscopic analysis showed that Fab fragments devoid of any additional C-terminal sequence were efficiently secreted, whereas retention of Fab fragments within the endomembrane system of the secretory pathway was achieved by C-terminal fusion of the DIKDEL sequence to the antibody light chain. Furthermore, analysis by immunoprecipitation and ELISA showed that intracellular retention of antibody fragments did not affect antigen-binding activity, and more than 80% of the isolated antibody fragments were found to bind antigen. Taken together, our results provide improvements to the technology of recombinant antibody production in transgenic plants. [source] Cloning of the guanylate kinase homologues AGK-1 and AGK-2 from Arabidopsis thaliana and characterization of AGK-1FEBS JOURNAL, Issue 2 2000Vinod Kumar Guanylate kinase is an essential enzyme for nucleotide metabolism, phosphorylating GMP to GDP or dGMP to dGDP. The low molecular mass cytosolic forms of guanylate kinase are implicated primarily in the regulation of the supply of guanine nucleotides to cell signalling pathways. The high molecular mass and membrane-associated forms of guanylate kinase homologues, notably found in neuronal tissues, are assigned roles in cell junction organization and transmembrane regulation. Here, we describe the first plant guanylate kinase-encoding genes, AGK1 and AGK2, from Arabidopsis thaliana. The nucleotide sequences of their genomic and cDNA clones predict proteins that carry N-terminal and C-terminal extensions of the guanylate kinase-like domain. The amino acid sequences of this domain share 46,52% identity with guanylate kinases from yeast, Escherichia coli, human, mouse and Caenorhabditis elegans. Arabidopsis guanylate kinases (AGKs) exhibit a high degree of conservation of active site residues and sequence motifs in common with other nucleoside monophosphate kinases, which suggests overall structural similarity of the plant proteins. Although bacterially expressed AGK-1 is enzymatically much less active than yeast guanylate kinase, its kinase domain is shown to complement yeast GUK1 recessive lethal mutations. AGKs are expressed ubiquitously in plant tissues with highest transcriptional activity detected in roots. The identification of AGKs provides new perspectives for understanding the role of guanylate kinases in plant cell signalling pathways. [source] EMBRYO YELLOW gene, encoding a subunit of the conserved oligomeric Golgi complex, is required for appropriate cell expansion and meristem organization in Arabidopsis thalianaGENES TO CELLS, Issue 6 2008Takaaki Ishikawa We identified an embryo yellow (eye) mutation in Arabidopsis that leads to the abnormal coloration and morphology of embryos. The eye mutant formed bushy plants, with aberrant organization of the shoot apical meristem (SAM) and unexpanded leaves with irregular phyllotaxy. The epidermal cells of the eye mutant were much smaller than that of the wild-type. Thus, EYE is required for expansion of cells and organs, and for formation of the organized SAM. Hydrophobic layers of epidermal cells were also disrupted, suggesting that EYE might be involved in the generation of the extra-cellular matrix. The mutated gene encoded a protein that is homologous to Cog7, a subunit of the conserved oligomeric Golgi (COG) complex, which is required for the normal morphology and function of the Golgi appratus. The eye mutation caused mislocalization of a Golgi protein. In addition, the size of the Golgi apparatus was also altered. Thus, EYE might be involved in transport or retention of Golgi-localized proteins and in maintenance of Golgi morphology. We propose that some Golgi-localized proteins, distributions of which are controlled by EYE, play important roles in expansion of cells and organs, and in formation of the properly organized SAM in plants. [source] Vacuolar membrane dynamics revealed by GFP-AtVam3 fusion proteinGENES TO CELLS, Issue 7 2002Tomohiro Uemura Background: The plant vacuole is a multifunctional organelle that has various physiological functions. The vacuole dynamically changes its function and shape, dependent on developmental and physiological conditions. Our current understanding of the dynamic processes of vacuolar morphogenesis has suffered from the lack of a marker for observing these processes in living cells. Results: We have developed transgenic Arabidopsis thaliana expressing a vacuolar syntaxin-related molecule (AtVam3/SYP22) fused with green fluorescent protein (GFP). Observations using confocal laser scanning microscopy demonstrated that the plant vacuole contained a dynamic membrane system that underwent a complex architectural remodelling. Three-dimensional reconstitution and time-lapse analysis of GFP-fluorescence images revealed that cylindrical and sheet-like structures were present in the vacuolar lumen and were moving dynamically. The movement, but not the structure itself, was abolished by cytochalasin D, an inhibitor of actin polymerization. This moving structure, which sometimes penetrated through the vacuolar lumen, possessed a dynamic membrane architecture similar to the previously recognized ,transvacuolar strand.' Conclusion: We propose two possible models for the formation of the vacuolar lumenal structure. Membrane structures including protruding tubules and reticular networks have recently been recognized in many other organelles, and may be actively involved in intra- and/or inter-organelle signalling. [source] Polyploidy-Associated Genomic Instability in Arabidopsis thalianaGENESIS: THE JOURNAL OF GENETICS AND DEVELOPMENT, Issue 4 2010Yixing Wang Formation of polyploid organisms by fertilization of unreduced gametes in meiotic mutants is believed to be a common phenomenon in species evolution. However, not well understood is how species in nature generally exist as haploid and diploid organisms in a long evolutionary time while polyploidization must have repeatedly occurred via meiotic mutations. Here, we show that the ploidy increased for two consecutive generations due to unreduced but viable gametes in the Arabidopsis cyclin a1;2-2 (also named tardy asynchronousmeiosis-2) mutant, but the resultant octaploid plants produced progeny of either the same or reduced ploidy via genomic reductions during meiosis and pollen mitosis. Ploidy reductions through sexual reproduction were also observed in independently generated artificial octaploid and hexaploid Arabidopsis plants. These results demonstrate that octaploid is likely the maximal ploidy produced through sexual reproduction in Arabidopsis. The polyploidy-associated genomic instability may be a general phenomenon that constrains ploidy levels in species evolution. [source] An ecologist's guide to ecogenomicsJOURNAL OF ECOLOGY, Issue 1 2007N. J. OUBORG Summary 1Currently, plant ecologists are increasingly adopting approaches and techniques from molecular biology. The new field of ecogenomics aims at understanding the mechanistic basis for adaptation and phenotypic variation by using genomic techniques to investigate the mechanistic and evolutionary basis of species interactions, and focuses on identifying the genes affected by evolution. 2While the entire toolbox of genomics is only available for model species such as Arabidopsis thaliana, we describe the options open to ecologists interested in pursuing an ecogenomics research program on ecologically relevant traits or phenomena in non-model species, for which part of the genomic toolbox may be currently unavailable. In these non-model species, a viable ecogenomics research program is possible with relatively modest effort. 3Four challenges to further development of ecogenomics are described and discussed: (i) the ecogenomic study of non-model species; (ii) reconciliation of experimental languages of ecology and evolutionary biology with molecular biology; (iii) development of specific ecogenomic data analysis tool; and (iv) adoption of a multidisciplinary cooperative research culture. 4An important task for ecologists is to provide the necessary ecological input (the ,eco' part) to ecogenomics. [source] Differential genetic influences on competitive effect and response in Arabidopsis thalianaJOURNAL OF ECOLOGY, Issue 5 2005JAMES F. CAHILL JR Summary 1Competition plays an important role in structuring populations and communities, but our understanding of the genetic basis of competitive ability is poor. This is further complicated by the fact that plants can express both competitive effect (target plant influence upon neighbour growth) and competitive response (target plant growth as a function of a neighbour) abilities, with these ecological characteristics potentially being independent. 2Using the model plant species Arabidopsis thaliana, we investigated patterns of intraspecific variation in competitive effect and response abilities and their relationships to other plant traits and resource supply rates. 3Both competitive effect and response were measured for 11 genotypes, including the Columbia ecotype and 10 derived mutant genotypes. Plants were grown alone, with intragenotypic competition, and with intergenotypic competition in a replicated blocked design with high nutrient and low nutrient soil nutrient treatments. We quantified competitive effect and response on absolute and per-gram bases. 4Competitive effect and response varied among genotypes, with the relative competitive abilities of genotypes consistent across fertilization treatments. Overall, high rates of fertilization increased competitive effect and competitive response abilities of all genotypes. Both competitive effect and response were correlated with neighbour biomass, though genotype-specific traits also influenced competitive response. 5At the genotype level, there was no correlation between competitive effect and response in either fertilization treatment. Overall patterns in competitive response appeared consistent among inter- and intragenotypic competition treatments, indicating that a target genotype's response to competition was not driven by the genetic identity of the competitor. 6These findings indicate that within A. thaliana, there is the potential for differential selection on competitive effect and response abilities, and that such selection may influence different sets of plant traits. The concept of a single competitive ability for a given plant is not supported by these data, and we suggest continued recognition of these dual competitive abilities is essential to understanding the potential role of competition in influencing intra- and interspecific processes. [source] Behavioural responses of the seven-spot ladybird Coccinella septempunctata to plant headspace chemicals collected from four crop Brassicas and Arabidopsis thaliana, infested with Myzus persicaeAGRICULTURAL AND FOREST ENTOMOLOGY, Issue 4 2008R. D. Girling Abstract 1,Insects using olfactory stimuli to forage for prey/hosts are proposed to encounter a ,reliability,detectability problem', where the usability of a stimulus depends on its reliability as an indicator of herbivore presence and its detectability. 2,We investigated this theory using the responses of female seven-spot ladybirds Coccinella septempunctata (Coleoptera: Coccinellidae) to plant headspace chemicals collected from the peach-potato aphid Myzus persicae and four commercially available Brassica cultivars; Brassica rapa L. cultivar ,turnip purple top', Brassica juncea L. cultivar ,red giant mustard', Brassica napus L. cultivar ,Apex', Brassica napus L. cultivar ,Courage' and Arabidopsis thaliana. For each cultivar/species, responses to plants that were undamaged, previously infested by M. persicae and infested with M. persicae, were investigated using dual-choice Petri dish bioassays and circular arenas. 3,There was no evidence that ladybirds responded to headspace chemicals from aphids alone. Ladybirds significantly preferred headspace chemicals from B. napus cv. Apex that were undamaged compared with those from plants infested with aphids. For the other four species/cultivars, there was a consistent trend of the predators being recorded more often in the half of the Petri dish containing plant headspace chemicals from previously damaged and infested plants compared with those from undamaged ones. Furthermore, the mean distance ladybirds walked to reach aphid-infested A. thaliana was significantly shorter than to reach undamaged plants. These results suggest that aphid-induced plant chemicals could act as an arrestment or possibly an attractant stimulus to C. septempunctata. However, it is also possible that C. septempunctata could have been responding to aphid products, such as honeydew, transferred to the previously damaged and infested plants. 4,The results provide evidence to support the ,reliability,detectability' theory and suggest that the effectiveness of C. septempunctata as a natural enemy of aphids may be strongly affected by which species and cultivar of Brassica are being grown. [source] Current Opinions on the Functions of Tocopherol Based on the Genetic Manipulation of Tocopherol Biosynthesis in PlantsJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 9 2008Yin Li Abstract As a member of an important group of lipid soluble antioxidants, tocopherols play a paramount role in the daily diet of humans and animals. Recently, genes required for tocochromanol biosynthesis pathway have been identified and cloned with the help of genomics-based approaches and molecular manipulation in the model organisms: Arabidopsis thaliana and Synechocystis sp. PCC 6803. At the basis of these foundations, genetic manipulation of tocochromanol biosynthesis pathway can give rise to strategies that enhance the level of tocochromanol content or convert the constitution of tocochromanol. In addition, genetic manipulations of the tocochromanol biosynthesis pathway provide help for the study of the function of tocopherol in plant systems. The present article summarizes recent advances and pays special attention to the functions of tocopherol in plants. The roles of tocopherol in the network of reactive oxygen species, antioxidants and phytohormones to maintain redox homeostasis and the functions of tocopherol as a signal molecule in chloroplast-to-nucleus signaling to regulate carbohydrate metabolism are also discussed. [source] Expression of a High Mobility Group Protein Isolated from Cucumis sativus Affects the Germination of Arabidopsis thaliana under Abiotic Stress ConditionsJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 5 2008Ji Young Jang Abstract Although high mobility group B (HMGB) proteins have been identified from a variety of plant species, their importance and functional roles in plant responses to changing environmental conditions are largely unknown. Here, we investigated the functional roles of a CsHMGB isolated from cucumber (Cucumis sativus L.) in plant responses to environmental stimuli. Under normal growth conditions or when subjected to cold stress, no differences in plant growth were found between the wild-type and transgenic Arabidopsis thaliana overexpressing CsHMGB. By contrast, the transgenic Arabidopsis plants displayed retarded germination compared with the wild-type plants when grown under high salt or dehydration stress conditions. Germination of the transgenic plants was delayed by the addition of abscisic acid (ABA), implying that CsHMGB affects germination through an ABA-dependent way. The expression of CsHMGB had affected only the germination stage, and CsHMGB did not affect the seedling growth of the transgenic plants under the stress conditions. The transcript levels of several germination-responsive genes were modulated by the expression of CsHMGB in Arabidopsis. Taken together, these results suggest that ectopic expression of a CsHMGB in Arabidopsis modulates the expression of several germination-responsive genes, and thereby affects the germination of Arabidopsis plants under different stress conditions. [source] A Microarray Based Genomic Hybridization Method for Identification of New Genes in Plants: Case Analyses of Arabidopsis and OryzaJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 6 2007Chuanzhu Fan Abstract To systematically estimate the gene duplication events in closely related species, we have to use comparative genomic approaches, either through genomic sequence comparison or comparative genomic hybridization (CGH). Given the scarcity of complete genomic sequences of plant species, in the present study we adopted an array based CGH to investigate gene duplications in the genus Arabidopsis. Fragment genomic DNA from four species, namely Arabidopsis thaliana, A. lyrata subsp. lyrata, A. lyrata subsp. petraea, and A. halleri, was hybridized to Affymetrix (Santa Clara, CA, USA) tiling arrays that are designed from the genomic sequences of A. thaliana. Pairwise comparisons of signal intensity were made to infer the potential duplicated candidates along each phylo-genetic branch. Ninety-four potential candidates of gene duplication along the genus were identified. Among them, the majority (69 of 94) were A. thaliana lineage specific. This result indicates that the array based CGH approach may be used to identify candidates of duplication in other plant genera containing closely related species, such as Oryza, particularly for the AA genome species. We compared the degree of gene duplication through retrotransposon between O. sativa and A. thaliana and found a strikingly higher number of chimera retroposed genes in rice. The higher rate of gene duplication through retroposition and other mechanisms may indicate that the grass species is able to adapt to more diverse environments. [source] | ||||||||||||||||||||||||||||