The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. …
Genetic transformation is often associated with different rearrangements of the plant genome at the site of insertion. Therefore the question remains weather these T-DNA insertion sites are more prone to genotoxic stresses. Here, we studied the impact of propagation through generations, the influence of gene stacking and of photo oxidative stress caused by high light intensity on the stability of the transgene and its flanking regions in the model plant Arabidopsis thaliana. Conformational Sensitive Capillary Electrophoresis (CSCE), RFLP and sequencing were deployed in this analysis in order to study the proximal 100 bp and the long range T-DNA flanking sequences. By screening seven transgenic lines no evidence for occurrence of mutation events were found, implying that the flanking regions of the studied T-DNA insertion events are relatively stable ...
Jasmonic acid and its methyl ester, methyl jasmonate (MeJA), are plant signaling molecules that affect plant growth and gene expression. Primary root growth of wild-type Arabidopsis thaliana seedlings was inhibited 50% when seedlings were grown on agar medium containing 0.1 M MeJA. An ethyl methanesulfonate mutant (jar1) with decreased sensitivity to MeJA inhibition of root elongation was isolated and characterized. Genetic data indicated the trait was recessive and controlled by a single Mendelian factor. MeJA-induced polypeptides were detected in Arabidopsis leaves by antiserum to a MeJA-inducible vegetative storage protein from soybean. The induction of these proteins by MeJA in the mutant was at least 4-fold less in jar1 compared to wild type. In contrast, seeds of jar1 plants were more sensitive than wild type to inhibition of germination by abscisic acid. These results suggest that the defect in jar1 affects a general jasmonate response pathway, which may regulate multiple genes in ...
Jasmonic acid and its methyl ester, methyl jasmonate (MeJA), are plant signaling molecules that affect plant growth and gene expression. Primary root growth of wild-type Arabidopsis thaliana seedlings was inhibited 50% when seedlings were grown on agar medium containing 0.1 M MeJA. An ethyl methanesulfonate mutant (jar1) with decreased sensitivity to MeJA inhibition of root elongation was isolated and characterized. Genetic data indicated the trait was recessive and controlled by a single Mendelian factor. MeJA-induced polypeptides were detected in Arabidopsis leaves by antiserum to a MeJA-inducible vegetative storage protein from soybean. The induction of these proteins by MeJA in the mutant was at least 4-fold less in jar1 compared to wild type. In contrast, seeds of jar1 plants were more sensitive than wild type to inhibition of germination by abscisic acid. These results suggest that the defect in jar1 affects a general jasmonate response pathway, which may regulate multiple genes in ...
Zea mays MATH-BTB protein (ZmMAB1) has been shown to have a role in regulation and proper asimetric cell divisions during the male and female gametophyte development. Its role has been demonstrated in proteasomal degradation as part of a ubiquitin E3 ligase complex. ZmMAB1 gene expression in Zea mays is precisely regulated, and the protein product is a short-lived protein. Therefore ZmMAB1 gene expression research in a homolougus system is difficult. Cullin is a structural component of many E3 ligases. It has been shown that Cul3a protein from Arabidopsis thaliana (L.) Heynh. forms complexes with MAB1 from Zea mays, so Arabidopsis thaliana has been chosen for expression regulation research of MAB1 in a heterologous system. For the cause of better understanding the role and regulation of ZmMAB1 protein, GFP florescent protein labeled ZmMAB1 protein has been inserted in the genome of A. thaliana with bacterium Agrobacterium tumefaciens. Goal of this thesis was to determine on which level of ...
calphotos.berkeley.edu. Arabidopsis thaliana (Mouse-ear cress) is a flowering plant belonging to the family Brassicaceae which contains economically important brassica and mustard species. Arabidopsis thaliana was the first plant to have its genome sequenced. Arabidopsis thaliana is not of economic value itself, but has risen to prominence because of its small size, short generation time and small genome, which make it an ideal plant to use for research. The Arabidopsis thaliana genome has a haploid chromosome number of 5, containing 135 Mb with 32,000 protein-coding genes. The reference proteome is derived from the genome sequence published in 2000 for the ecotype Columbia (http://www.nature.com/nature/journal/v408/n6814/full/408796a0.html). ...
For genetic analysis of mechanisms of leaf morphogenesis, we chose Arabidopsis thaliana (L.) Heynh. as a model for leaf development in dicotyledonous plants. Leaves of the angustifolia mutant were the same length as but narrower and thicker than wild-type leaves. The total number of cells in leaf blades of angustifolia plants was the same as in the wild type. At the cellular level in the angustifolia mutant it was found that the cells were smaller in the leaf-width direction and larger in the leaf-thickness direction than in wild type, revealing the function of the ANGUSTIFOLIA gene, which is to control leaf morphology by regulating polarity-specific cell elongation. The existence of similar genes that regulate leaf development in the length direction was, therefore, predicted. Three loci and several alleles associated with short-leaved mutants were newly isolated as rotundifolia mutants. The rotundifolia3 mutant had the same number of cells as the wild type, with reduced cell elongation in the ...
Gene expression profiling studies are usually performed on pooled samples grown under tightly controlled experimental conditions to suppress variability among individuals and increase experimental reproducibility. In addition, to mask unwanted residual effects, the samples are often subjected to relatively harsh treatments that are unrealistic in a natural context. Here, we show that expression variations among individual wild-type Arabidopsis thaliana plants grown under the same macroscopic growth conditions contain as much information on the underlying gene network structure as expression profiles of pooled plant samples under controlled experimental perturbations. We advocate the use of subtle uncontrolled variations in gene expression between individuals to uncover functional links between genes and unravel regulatory influences. As a case study, we use this approach to identify ILL6 as a new regulatory component of the jasmonate response pathway. ...
In the year 2000, the first complete nuclear genome of a plant species - Arabidopsis thaliana - was released into the wild (a.k.a to bunch of salivating scientists). Less than twenty years later, we had a total of 1135 genomes… for Arabidopsis alone! Today were talking about Arabidopsis races, and how they are a powerful tool for unravelling plant secrets.. Arabidopsis likely diverged from its closest relative about 10 million years ago, and the invasive weed has since spread through Northern Eurasia. In the literally millions of years following, the species diversified into hundreds of race-like ecotypes: populations of plants that have settled in, and then adapted to, certain geological areas. While there has been some cross-talk (i.e, cross breeding) between the ecotypes, there has also been a whole lot of time spent alone - leading to evolution of traits that can differ from one ecotype to the next. Arabidopsis ecotypes (also called accessions) can differ from each other in their size, ...
AtTome: Arabidopsis Transcriptome Functional Genomics Database. gebd Arabidopsis Genome Browser. iSect Tools, iView Tools and Gene Expression Atlas. Collection of Arabidopsis T-DNA/Ds, Full-length cDNA, Marker, EST, MPSS, SAGE, miRNA, sRNA, Arabidopsis Tiling Array and Gene Expression Data. Created and developed by Huaming Chen
AtTome: Arabidopsis Transcriptome Functional Genomics Database. gebd Arabidopsis Genome Browser. iSect Tools, iView Tools and Gene Expression Atlas. Collection of Arabidopsis T-DNA/Ds, Full-length cDNA, Marker, EST, MPSS, SAGE, miRNA, sRNA, Arabidopsis Tiling Array and Gene Expression Data. Created and developed by Huaming Chen
AtTome: Arabidopsis Transcriptome Functional Genomics Database. gebd Arabidopsis Genome Browser. iSect Tools, iView Tools and Gene Expression Atlas. Collection of Arabidopsis T-DNA/Ds, Full-length cDNA, Marker, EST, MPSS, SAGE, miRNA, sRNA, Arabidopsis Tiling Array and Gene Expression Data. Created and developed by Huaming Chen
AtTome: Arabidopsis Transcriptome Functional Genomics Database. gebd Arabidopsis Genome Browser. iSect Tools, iView Tools and Gene Expression Atlas. Collection of Arabidopsis T-DNA/Ds, Full-length cDNA, Marker, EST, MPSS, SAGE, miRNA, sRNA, Arabidopsis Tiling Array and Gene Expression Data. Created and developed by Huaming Chen
Phytohormones auxins play an important role in plant growth development and abiotic stress responses. The active auxin may be released from the amino acid conjugates by the action of auxin-amidohydrolase enzymes, which thereby participate in the auxin homeostasis. The aim of this study was to investigate the role of auxin-amidohydrolase AtILL2 from Arabidopsis thaliana in the plant response to salinity and osmotic stress. Four homozygous lines of A. thaliana ecotypes Ws of potential overexpressors for AtILL2 fusion protein with GFP and / or His tags were analyzed. The presence of transgene was verified as insertion into DNA, RNA transcript, and recombinant protein by using PCR, RT-PCR, SDS-PAGE, affinity chromatography and western-hybridization assay. In three lines, the presence of transgene in genomic DNA and RNA transcript was confirmed, although the recombinant protein was not demonstrated in any of the lines. Root growth bioassay confirmed the increased resistance of one line to the ...
We investigated the role of membrane fatty acids in basal proton leaks and uncoupling protein (UCP)-dependent proton conductance in Arabidopsis mitochondria. Using wild-type cells, cold-sensitive fad2 mutant cells, deficient in ω-6-oleate desaturase, and cold-tolerant FAD3+ transformant cells, overexpressing ω-3-linoleate desaturase, we showed that basal proton leak in the non-phosphorylating state was dependent on lipid composition. The extent of membrane proton leak was drastically reduced in the fad2 mutant, containing low amounts of polyunsaturated fatty acids. Conversely, this proton leak was higher in FAD3+ mitochondria that exhibit a higher polyunsaturated fatty acid content and high protein to lipid ratio. The dependency of membrane leaks upon membrane potential was higher in FAD3+ and lower in fad2. UCP content was higher in both the fad2 mutant and FAD3+ transgenic lines compared with wild-type cells and so was the UCP activity, assayed by the reduction of phosphorylation yield ...
Author Summary During growth and development, all plants and animals must replicate their DNA. This process is regulated to ensure that all sequences are completely and accurately replicated and is limited to S phase of the cell cycle. In the cell, DNA is packaged with histone proteins into chromatin, and both DNA and histones are subject to epigenetic modifications that affect chromatin state. Euchromatin and heterochromatin are chromatin states marked by epigenetic modifications specifying open and closed conformations, respectively. Using the model plant Arabidopsis thaliana, we show that the time at which a DNA sequence replicates is influenced by the epigenetic modifications to the surrounding chromatin. DNA replication occurs in two phases, with euchromatin replicating in early and mid S phase and heterochromatin replicating late. DNA replication time has been linked to gene expression in other organisms, and this is also true in Arabidopsis because more genes are active in euchromatin when
It has been more than 50 years since Arabidopsis (Arabidopsis thaliana) was first introduced as a model organism to understand basic processes in plant biology. A well-organized scientific community has used this small reference plant species to make numerous fundamental plant biology discoveries (Provart et al., 2016). Due to an extremely well-annotated genome and advances in high-throughput sequencing, our understanding of this organism and other plant species has become even more intricate and complex. Computational resources, including CyVerse,3 Araport,4 The Arabidopsis Information Resource (TAIR),5 and BAR,6 have further facilitated novel findings with just the click of a mouse. As we move toward understanding biological systems, Arabidopsis researchers will need to use more quantitative and computational approaches to extract novel biological findings from these data. Here, we discuss guidelines, skill sets, and core competencies that should be considered when developing curricula or ...
Brassinosteroids (BRs) are endogenous plant hormones and are essential for normal plant growth and development. MicroRNAs (miRNAs) of Arabidopsis thaliana are involved in mediating cell proliferation in leaves, stress tolerance, and root development. The specifics of BR mechanisms involving miRNAs are unknown. Using customized miRNA array analysis, we identified miRNAs from A. thaliana ecotype Columbia (Col-0) regulated by 24-epibrassinolide (EBR, a highly active BR). We found that miR395a was significantly up-regulated by EBR treatment and validated its expression under these conditions. miR395a was over expressed in leaf veins and root tissues in EBR-treated miR395a promoter::GUS plants. We integrated bioinformatics methods and publicly available DNA microarray data to predict potential targets of miR395a. GUN5-a multifunctional protein involved in plant metabolic functions such as chlorophyll synthesis and the abscisic acid (ABA) pathway-was identified as a possible target. ABI4 and ABI5, both genes
The composition of the individual eukaryotes genome and its variation within a species remain poorly defined. Even for a sequenced genome such as that of the model plant Arabidopsis thaliana accession Col-0, the large arrays of heterochromatic repeats are incompletely sequenced, with gaps of uncertain size persisting in them. Using geographically separate populations of A. thaliana, we assayed variation in the heterochromatic repeat arrays using two independent methods and identified significant polymorphism among them, with variation by as much as a factor of two in the centromeric 180 bp repeat, in the 45S rDNA arrays and in the Athila retroelements. In the accession with highest genome size as measured by flow cytometry, Loh-0, we found more than a two-fold increase in 5S RNA gene copies relative to Col-0; results from fluorescence in situ hybridization with 5S probes were consistent with the existence of size polymorphism between Loh-0 and Col-0 at the 5S loci. Comparative genomic hybridization
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Regulation of gene expression is crucial for organism growth, and it is one of the challenges in systems biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size and the inclusion of mutants. We then analyze two sets of genes, whose activity is likely to be relevant to lateral root initiation in Arabidopsis, and assess causality of their regulatory interactions by integrating sequence analysis with the intersection of the results of the best performing methods on time series and mutants. The methods applied capture known interactions ...
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Read "Activities of antioxidant enzymes of Arabidopsis thaliana plants during cold hardening to hypothermia, Russian Journal of Plant Physiology" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
The ability of the AtERFs to regulate transcription in plant cells was tested by using transient assays (Figure 5). A luciferase (LUC)-encoding reporter gene, 4×HLS, which contains four copies of the GCC box sequence from the Arabidopsis HOOKLESS1 (HLS1) promoter (Lehman et al., 1996) fused to LUC, and an effector plasmid consisting of each AtERF under the control of the cauliflower mosaic virus (CaMV) 35S promoter (Figure 5A) were delivered to Arabidopsis leaves by particle bombardment. LUC activity increased at least 12-fold when the reporter plasmid was coexpressed with AtERF1, AtERF2, or AtERF5 effector plasmids (Figure 5B). No such increase in LUC activity by the AtERFs was detected when a LUC reporter plasmid containing a mutated GCC box (ATCCTCC) was used (data not shown). These data indicate that AtERF1, AtERF2, and AtERF5 are able to function as GCC box sequence-specific transactivators in Arabidopsis leaves.. Some genes containing the GCC box in their promoter region are known to be ...
Our knowledge of natural genetic variation is increasing at an extremely rapid pace, affording an opportunity to come to a much richer understanding of how effects of specific genes are dependent on the genetic background. To achieve a systematic understanding of such GxG interactions, it is desirable to develop genome editing tools that can be rapidly deployed across many different genetic varieties. We present an efficient CRISPR/Cas9 toolbox of super module (SM) vectors. These vectors are based on a previously described fluorescence protein marker expressed in seeds allowing identification of transgene-free mutants. We have used this vector series to delete genomic regions ranging from 1.7 to 13 kb in different natural accessions of the wild plant Arabidopsis thaliana. Based on results from 53 pairs of sgRNAs targeting individual nucleotide binding site leucine-rich repeat (NLR) genes, we provide a comprehensive overview of obtaining heritable deletions. The SM series of CRISPR/Cas9 vectors enables
Size limits on molecular movement among female gametes. Cellular decisions can be influenced by information communicated from neighboring cells. Communication can occur via signaling or through the direct transfer of molecules. Movement of RNAs and proteins has frequently been observed among symplastically connected plant cells. In flowering plants, the female gametes, the egg cell and central cell, are closely apposed within the female gametophyte. Here we investigated the ability of fluorescently labeled dyes and small RNAs to move from the Arabidopsis thaliana central cell to the egg apparatus following microinjection. These results define a size limit of at least 20 kDa for symplastic movement between the two gametes, somewhat larger than that previously observed in Torenia fournieri. Our results indicate that symplastic connectivity in Arabidopsis thaliana changes after fertilization and suggest that prior to fertilization mechanisms are in place to facilitate small RNA movement from the central
Environmental stresses, including ammonium (NH4 +) nourishment, can damage key mitochondrial components through the production of surplus reactive oxygen species (ROS) in the mitochondrial electron transport chain. However, alternative electron pathways are significant for efficient reductant dissipation in mitochondria during ammonium nutrition. The aim of this study was to define the role of external NADPH-dehydrogenase (NDB1) during oxidative metabolism of NH4 +-fed plants. Most plant species grown with NH4 + as the sole nitrogen source experience a condition known as "ammonium toxicity syndrome". Surprisingly, transgenic Arabidopsis thaliana plants suppressing NDB1 were more resistant to NH4 + treatment. The NDB1 knock-down line was characterized by milder oxidative stress symptoms in plant tissues when supplied with NH4 +. Mitochondrial ROS accumulation, in particular, was attenuated in the NDB1 knock-down plants during NH4 + treatment. Enhanced antioxidant defense, primarily concerning the ...
Author: Engelhorn, J.; Genre: Thesis; Published in Print: 2011; Title: Identification of developmental functions for Arabidopsis thaliana genes by a reverse genetics approach based on analysis of H3K27me3 distribution
LOCUS ATU53502 11862 bp DNA PLN 05-MAY-1996 DEFINITION Arabidopsis thaliana chromosome I cosmid g17311 DNA. ACCESSION U53502 KEYWORDS . SOURCE thale cress strain=Columbia. ORGANISM Arabidopsis thaliana Eukaryotae; mitochondrial eukaryotes; Viridiplantae; Charophyta/Embryophyta group; Embryophyta; Magnoliophyta; Magnoliopsida; Capparales; Brassicaceae; Arabidopsis. REFERENCE 1 (bases 1 to 11862) AUTHORS Goodman,H.M. and Gallant,P. TITLE Sequence of cosmid g17311 from Arabidopsis thaliana chromosome I JOURNAL Unpublished REFERENCE 2 (bases 1 to 11862) AUTHORS Goodman,H.M. and Gallant,P. TITLE Direct Submission JOURNAL Submitted (03-APR-1996) John Morris, Molecular Biology, Massachusetts General Hospital / Harvard Medical School, 50 Blossom St., Boston, MA 02114, USA FEATURES Location/Qualifiers source 1..11862 /organism="Arabidopsis thaliana" /strain="Columbia" /chromosome="I" /map="1; between m132 and mi157 at 159 cM" misc_feature 1..7505 /note="sequence overlap with cosmid g8261" misc_feature ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Guazatine is a potent inhibitor of polyamine oxidase (PAO) activity. In agriculture, guazatine is used as non-systemic contact fungicide efficient in the protection of cereals and citrus fruits against disease. The composition of guazatine is complex, mainly constituted by a mixture of synthetic guanidated polyamines (polyaminoguanidines). Here, we have studied the effects from exposure to guazatine in the weed Arabidopsis thaliana. We report that micromolar concentrations of guazatine are sufficient to inhibit growth of Arabidopsis seedlings and induce chlorosis, whereas germination is barely affected. We observed the occurrence of quantitative variation in the response to guazatine between 107 randomly chosen Arabidopsis accessions. This enabled us to undertake genome-wide association (GWA) mapping that identified a locus on chromosome one associated with guazatine tolerance. CHLOROPHYLLASE 1 (CLH1) within this locus was studied as candidate gene, together with its paralog (CLH2). The analysis ...
Volatile allyl isothiocyanate (AITC) derives from the biodegradation of the glucosinolate sinigrin and has been associated with growth inhibition in several plants, including the model plant Arabidopsis thaliana. However, the underlying cellular mechanisms of this feature remain scarcely investigated in plants. In this study, we present evidence of an AITC-induced inhibition of actin-dependent intracellular transport in A. thaliana. A transgenic line of A. thaliana expressing yellow fluorescent protein (YFP)-tagged actin filaments was used to show attenuation of actin filament movement by AITC. This appeared gradually in a time- and dose-dependent manner and resulted in actin filaments appearing close to static. Further, we employed four transgenic lines with YFP-fusion proteins labeling the Golgi apparatus, endoplasmic reticulum (ER), vacuoles and peroxisomes to demonstrate an AITC-induced inhibition of actin-dependent intracellular transport of or, in these structures, consistent with the decline in
Plant defense responses are constitutively activated in the Arabidopsis thaliana ssi2 mutant plant. In addition, the ssi2 mutant allele confers a dwarf phenotype. The SSI2 gene encodes a stearoyl-ACP-desaturase, which converts stearic acid (18:0) to oleic acid (18:1), suggesting a role for lipids in plant defense. Microarray analysis identified several genes which encode putative acyl hydrolases/lipases that are expressed at elevated levels in the leaves of ssi2, in comparison to the wild type plant. One gene in particular, At5g14180, was expressed at 60-fold greater level in ssi2 than in the wild type plant. To study the involvement of At5g14180 in plant defense and lipid metabolism, two transgenic lines containing T-DNA insertions within the At5g14180 gene were identified. These two T-DNA insertional alleles of the At5g14180 gene attenuate the ssi2-conferred heightened resistance to a virulent strain of Pseudomonas syringae pv. maculicola in the ssi2 At5g14180 double mutant plant. Furthermore, ...
www.alaskawildflowers.us. The Brassicaceae Arabidopsis lyrata subsp. lyrata is a close relative of the model organism Arabidopsis thaliana, from which is diverged around 10 million years ago. A. lyrata is an outcrossing diploid and, unlike the (generally) self-fertilising A. thaliana, has stable and spatially restricted populations or subspecies. This means that comparisons between the genomes of the closely related species could reveal the genetic basis of the invasive spread of A. thaliana and would also provide valuable data on the evolution of the A. thaliana genome.. The genome of A. lyrata subsp. lyrata is around 50% larger than A. thaliana (207 Mb and 125 Mb respectively) and is predicted to contain more protein coding genes (32,670 genes compared to 27,025 genes in A. thaliana). Analysis of their genomes suggest that reduction in genome size is the result of large-scale rearrangements and hundreds of thousands of small deletions found throughout the genome. ...
The in vivo activity of the alternative pathway (V-alt) has been studied using the oxygen isotope fractionation method in leaves of Arabidopsis thaliana modified for the expression of the AtAOX1a gene by anti-sense (AS-12) or overexpression (XX-2). Under non-stressful conditions, V-alt was similar in all plant lines regardless of its different alternative pathway capacities (V-alt). Total leaf respiration (V-t) and V-alt were directly related to growth light conditions while electron partitioning between the cytochrome pathway (CP) and alternative pathway (AP) was unchanged by light levels. Interestingly, the AP functioned at full capacity in anti-sense plants under both growth light conditions. The role of the AP in response to a high light stress induced by short-term high light treatment (HLT) was also studied. In wild type and XX-2, both CP and AP rates increased proportionally after HLT while in AS-12, where the AP was unable to increase its rate, the CP accommodated all the increase in ...
Iron is an essential element for plant survival. However, in excess, it is deleterious to the organism. In the present thesis we describe a functional genomic approach and a mutant screen directed towards increasing our understanding of iron homeostasis in the Strategy I model plant Arabidopsis thaliana. For the functional genomic approach, Affymetrix ATH-1 microarrays were hybridized with RNA extracted from iron-deficient and sufficient Arabidopsis plants. The resulting datasets were analyzed, and ten genes were chosen for further studies. Eight of them did not appear to be related to iron regulation. The other two belong to a small sub-family of four genes. All four were up-regulated in shoots and roots of iron-deficient plants. We hypothesize that all four provide redundancy to each other. Finally, we show the screening of mutant plants with potential disruptions in iron-homeostasis system. One mutation was mapped to locus At2g34740 which encodes AtATase2 (EC 2.4.2.14). The mutation disrupted ...
TY - CHAP. T1 - Ds Transposon Mutant Lines for Saturation Mutagenesis of the Arabidopsis genome. AU - Kuromori, Takashi. AU - Hirayama, Takashi. PY - 2010/3/30. Y1 - 2010/3/30. N2 - Analysis of genetic mutations is one of the most effective techniques for investigating gene function.We now have methods that allow for mass production of mutant lines and cells created by gene disruption or silencing in model organisms, and great progress is being made in the use of those tools for comprehensive phenotypic analysis. In plants, insertion mutations can be produced using T-DNA or transposons, making it possible to monitor the effects of a defect in a single gene. Through bulk storage of mutations in the form of seeds, which is not an option in animal models, it is now feasible to use insertion mutations to analyze every gene in a model plant genome, especially Arabidopsis. This makes Arabidopsis useful not only as a model organism for plant research, but also as the only multicellular organism in ...
       The system developed in this work, XcisClique, consists of a comprehensive infrastructure for annotated genome and gene expression data for Arabidopsis thaliana. XcisClique models cis-regulatory elements as regular expressions and detects maximal bicliques of genes and motifs, called itemsets. An itemset consists of a set of genes (called a geneset) and a set of motifs (called a motifset) such that every motif in the motifset occurs in the promoter of every gene in the geneset. XcisClique differs from existing tools of the same kind in that, it offers a common platform for the integration of sequence and gene expression data. Itemsets identified by XcisClique are not only evaluated for statistical over-representation in sequence data, but are also examined with respect to the expression patterns of the corresponding geneset. Thus, the results produced are biologically directed. XcisClique is also the only tool of its kind for Arabidopsis thaliana, and can also be used for ...
The Arabidopsis Information Portal (AIP), a resource expected to provide access to all community data and combine outputs into a single user-friendly interface, has emerged from community discussions over the last 23 months. These discussions began during two closely linked workshops in early 2010 that established the International Arabidopsis Informatics Consortium (IAIC). The design of the AIP will provide core functionality while remaining flexible to encourage multiple contributors and constant innovation. An IAIC-hosted Design Workshop in December 2011 proposed a structure for the AIP to provide a framework for the minimal components of a functional community portal while retaining flexibility to rapidly extend the resource to other species. We now invite broader participation in the AIP development process so that the resource can be implemented in a timely manner.. ...
These are [I]Arabidopsis thaliana[/I] plants used in this study. On the left is a plant under normal growth conditions, while on the right is a plant treated with doxycycline, which has significantly stunted its growth but is protected against aging as evidenced by its fresher appearance.
When primary Arabidopsis roots grow down a tilted agar plate, they do not elongate following the gravitational vector along a straight line, but instead they slant noticeably to the right-hand. This process is seen mostly in the ecotypes Wassilewskji
Is there anyone out there who can spare an aliquot of an Arabidopsis cDNA expression library that could be used for cloning genes by functional complementation of E. coli mutants? I am searching for (i) a whole plant cDNA library and (ii) a root-specific cDNA library. The libraries would be used to look for genes involved in nutrient assimilation. I would be most grateful for any help. Best wishes John L Wray Plant Sciences Laboratory School of Biology Research Division of Environmental & Evolutionary Biology University of St Andrwes St Andrews Fife KY16 9TA United Kingdom ...
Author: Duan, G. Y. et al.; Genre: Journal Article; Published online: 2013-12-24; Open Access; Keywords: Arabidopsis thaliana|br/| ; Title: Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana
We have characterized an Arabidopsis homeobox gene coding for a putative DNA binding protein that represents an early marker for vascular development. The full-length cDNA encodes a protein of 833 amino acids that we have designated Athb-8; it contains the conserved DNA binding domain that characterizes the HD-Zip family of transcription factors. RNA analysis showed that the Athb-8 gene is expressed during the vegetative and the reproductive phases of plant growth. A higher steady-state level of the Athb-8 mRNA was found in flowering stem and root. In situ mRNA analysis of Arabidopsis plants demonstrated that Athb-8 expression is restricted to the procambial cells of embryo and developing organs. Moreover, Athb-8-GUS expression was found in single parenchyma cells which are differentiating into tracheary elements in wounded tobacco transgenic plants. Finally, we showed that the auxin, indole-3-acetic acid, which is involved in vascular development and differentiation, modulates the expression of ...
Floral dip is a transformation method that results in the insertion of T-DNA into the genome of unfertilized ovary cells. This thesis describes the transformation of Arabidopsis thaliana plants with T-DNA from pH7WG2,0 TROL-HA-FLAG plasmid vector. TROL is a transmembrane protein that regulates electron transport flow on the thylakoid membranes of chloroplasts. Addition of protein tags HA and FLAG to the TROL protein allows easier immunodetection analysis and enables further studies of the plant TROL protein function. In order to show the success of plant transformation with the TROL-HA-FLAG protein gene, the plants were subjected to multiple analyses such as seed selection method on growth plates with an added antibiotic, plant DNA PCR analysis and immunodetection analysis of plant leaf proteins. Due to the immunodetection analysis, I managed to confirm the localization of TROL-HA-FLAG protein in chloroplast thylakoid membranes of transformed plants. Further research could better show if ...
To better understand the genetic mechanisms underlying plant leaf development, we have performed a large-scale screening for Arabidopsis thaliana mutants to identify those displaying abnormally shaped or sized leaves. One of the stronger mutant phenotypes found was that of the ultracurvata1 (ucu1) mutants, whose vegetative and cauline leaves are spirally rolled downwards and show a reduced expansion along the longitudinal axis, in contrast to wild type leaves, which are flattened organs. We have identified one recessive and two semidominant ucu1 alleles, the most extreme of which cause severe dwarfism and a constitutive photomorphogenic response. Following a map-based strategy, we have cloned the UCU1 gene, which was found to encode an intracellular kinase closely related to SHAGGY, one of the components of the Wingless/Wnt animal signalling pathway. The responses of ucu1 mutants to exogenous plant hormones and the genetic analyses of double mutants involving ucu1 alleles indicate that UCU1 is a key
Pro dehydrogenase (PDH) catalyzes the first and rate-limiting step in the Pro catabolic pathway. In Arabidopsis, this enzyme is encoded by At-PDH. To investigate the role of Pro catabolism in plants, we generated transgenic Arabidopsis plants with altered levels of PDH by sense (PDH-S plants) and antisense (PDH-AS plants) strategies. Free Pro levels were reduced by up to 50% in PDH-S plants under ...
Genome sequences can be conceptualized as arrangements of motifs or words. The frequencies and positional distributions of these words within particular non-coding genomic segments provide important insights into how the words function in processes such as mRNA stability and regulation of gene expression. Using an enumerative word discovery approach, we investigated the frequencies and positional distributions of all 65,536 different 8-letter words in the genome of Arabidopsis thaliana. Focusing on promoter regions, introns, and 3 and 5 untranslated regions (3UTRs and 5UTRs), we compared word frequencies in these segments to genome-wide frequencies. The statistically interesting words in each segment were clustered with similar words to generate motif logos. We investigated whether words were clustered at particular locations or were distributed randomly within each genomic segment, and we classified the words using gene expression information from public repositories. Finally, we investigated
Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing.: Massively parallel sequencing of DNA by pyrosequencing technology offers much hi
The central problem of genetics is gene interaction since genes in the course of individual organism development interact with other genes, thats why their effects may change. Studies for the last 100 years managed to discover that the entire diversity of inter-gene interactions is presented in four major forms: complementarity, epistasis, polymery, and modifying effect of genes. However, gene interaction mechanism which is reflected on the segregation nature of variously crossed hybrids has not been sufficiently studied. Exclusive of molecular genetics, biochemistry and physiology, a genetic analysis of inheritance of characteristics in gene interaction taken by itself cannot reveal nature of this interaction. Lately, molecular-genetic and physiological studies on A. thaliana mutants have enabled to isolate and sequence a wide range of genes controlling certain links of the signalling chain. At the same time, effect of the plant development regulation signalling system on interaction of these genes in
p,In plants, tasiRNAs form a class of endogenous secondary siRNAs produced through the action of RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) upon microRNA-mediated cleavage of non-coding TAS RNAs. In Arabidopsis thaliana, TAS1, TAS2 and TAS4 tasiRNA production proceeds via a single cleavage event mediated by 22nt-long or/and asymmetric miRNAs in an ARGONAUTE-1 (AGO1)-dependent manner. By contrast, tasiRNA production from TAS3 seems to follow the so-called two-hit process, where dual targeting of TAS3, specifically mediated by the 21nt-long, symmetric miR390, initiates AGO7-dependent tasiRNA production. Interestingly, features for TAS3 tasiRNA production differ in other plant species and we show here that such features also enable TAS3 tasiRNA biogenesis in Arabidopsis, and that a single miR390 targeting event is, in fact, sufficient for this process, suggesting that the one-hit model underpins all the necessary rudiments of secondary siRNA biogenesis from plant TAS transcripts. Further results ...
Sex-biased genes are genes with a preferential or specific expression in one sex and tend to show an accelerated rate of evolution in animals. Various hypotheses-which are not mutually exclusive-have been put forth to explain observed patterns of rapid evolution. One possible explanation is positive selection, but this has been shown only in few animal species and mostly for male-specific genes. Here, we present a large-scale study that investigates evolutionary patterns of sex-biased genes in the predominantly self-fertilizing plant Arabidopsis thaliana. Unlike most animal species, A. thaliana does not possess sex chromosomes, its flowers develop both male and female sexual organs, and it is characterized by low outcrossing rates. Using cell-specific gene expression data, we identified genes whose expression is enriched in comparison with all other tissues in the male and female gametes (sperm, egg, and central cell), as well as in synergids, pollen, and pollen tubes, which also play an ...
Brief periods of heat stress of even a few days can have a detrimental effect on yield production worldwide causing devastating economical and sociological impacts. Here we report on the identification of a new heat-response regulon in plants controlled by the multiprotein bridging factor 1c (MBF1c) protein of Arabidopsis thaliana. Members of the highly conserved MBF1 protein family function as non DNA-binding transcriptional co-activators involved in regulating metabolic and development pathways in different organisms from yeast to humans. Nonetheless, our studies suggest that MBF1c from Arabidopsis functions as a transcriptional regulator which binds DNA and controls the expression of 36 different transcripts during heat stress, including the important transcriptional regulator DRE-binding protein 2A (DREB2A), two heat shock transcription factors (HSFs), and several zinc finger proteins. We further identify CTAGA as a putative response element for MBF1c, demonstrate that the DNA-binding domain ...
Nitric oxide (NO) and ethylene are signalling molecules that are synthesized in response to oxygen depletion. Non-symbiotic plant haemoglobins (Hbs) have been demonstrated to act in roots under oxygen depletion to scavenge NO. Using Arabidopsis thaliana plants, the online emission of NO or ethylene was directly quantified under normoxia, hypoxia (0.1-1.0% O2), or full anoxia. The production of both gases was increased with reduced expression of either of the Hb genes GLB1 or GLB2, whereas NO emission decreased in plants overexpressing these genes. NO emission in plants with reduced Hb gene expression represented a major loss of nitrogen equivalent to 0.2mM nitrate per 24h under hypoxic conditions. Hb gene expression was greatly enhanced in flooded roots, suggesting induction by reduced oxygen diffusion. The function could be to limit loss of nitrogen under NO emission. NO reacts with thiols to form S-nitrosylated compounds, and it is demonstrated that hypoxia substantially increased the content ...
We use five general approaches to create genetically diverse plants:. (1) Directed Transformation. Directed transformation of plants based on known gene sequence. We have hundreds of transgenic potato, tomato, tobacco, and Arabidopsis plant lines on hand and the transformation of rice and Lotus is established and routinely applied.. (2) Creation of Mutant Collections. Generation of large Arabidopsis mutant collections using T-DNA random insertion/activation lines or ethyl methanesulfonate (EMS) mutagenesis. We currently have about 67,000 T-DNA-tagged lines and large stocks of EMS mutagenised Arabidopsis seed. These collections are used for forward screening.. (3) RILs and NILs. Generation of recombinant inbred lines and near isogenic lines. We have recombinant inbred lines (RILs) and near isogenic inbred lines (NILs) from about 350 homogenised naturally-occurring Arabidopsis accessions (ecotypes) and are currently generating four RIL and one NIL population(s). Tomato introgression lines are also ...
general regulatory factor 10 (GRF10); FUNCTIONS IN: protein phosphorylated amino acid binding, ATP binding; INVOLVED IN: brassinosteroid mediated signaling pathway; LOCATED IN: mitochondrion, chloroplast stroma, plasma membrane, cytoplasm; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 17 growth stages; CONTAINS InterPro DOMAIN/s: 14-3-3 protein (InterPro:IPR000308); BEST Arabidopsis thaliana protein match is: general regulatory factor 11 (TAIR:AT1G34760.1); Has 2707 Blast hits to 2699 proteins in 383 species: Archae - 0; Bacteria - 0; Metazoa - 1258; Fungi - 330; Plants - 762; Viruses - 0; Other Eukaryotes - 357 (source: NCBI BLink ...
Arabidopsis AT5G10810.1 protein: implicated in pyrimidine biosynthesis, regulation of transcription from Pol II promoter, and the cell cycle; GenBank U67398
Analyses of functional genetic diversity in natural populations may provide important new insights into gene function and are necessary to understand the evolutionary processes maintaining diversity itself. The importance of including diversity within and between local populations in such studies is often ignored although many of the processes affecting genetic diversity act on this scale. Here we examine the molecular diversity in RPW8 (Recognition of Powdery Mildew), a gene conferring broad-spectrum resistance to powdery mildews in Arabidopsis thaliana stock-center accessions. Our eight UK study populations of the weedy A. thaliana were from locations judged to be subject to a minimum of anthropogenic disturbance and potentially long established. The majority of populations comprised considerable variation both in disease phenotype and RPW8 genotype. Although resistant individuals shared a major RPW8 genotype, no single allele was uniquely associated with resistance. It is concluded that RPW8 ...
The trehalose-6-phosphate synthase AtTPS I is involved in regulating sugar metabolism and partitioning in connection with plant morphogenesis and development in an as yet unknown fashion. AtTPS I expressed in yeast supports the synthesis of trehalose as well as an essential regulatory function in glucose consumption. The gene is essential for embryo development in Arabidopsis and its overproduction leads to sugar insensitivity as well as increased drought tolerance. Here we report on AtTPS I protein containing complexes in Arabidopsis and in yeast. AtTPS I co-migrated in FPLC separated extracts with 600-800 kDa protein complexes containing the cell cycle kinase CDKA; I and tubulin. In two hybrid experiments, the N-terminal domain of AtTPS I interacted with CDKA; I and the CDKA; I interacting kinesin KCA 1. In vitro precipitation tests using CDKA; I affinity beads showed that AtTPS 1 co-precipitated with KCA 1 and tubulin. This protein complex was predominantly observed in inflorescence tissue. ...
Arabidopsis thaliana was transformed with constructs composed of the aquaporin AthH2 promoter and the coding sequence of beta-glucuronidase (GUS) as reporter gene. The transgenic plants obtained were treated with different light qualities or phytohormones and the activity of the AthH2 promoter was determined in situ using a specific GUS assay. With blue light (400-550 nm) and white light, significant activation of the promoter was observed. The same was true for the application of gibberellic acid (GA) and abscisic acid (ABA). In contrast, red light and indole-3-acetic acid (IAA) had only minor effects on the promoter activity. The significance of sequence elements with relation to GA or ABA was confirmed by deletion analyses of the AthH2 promoter. Likewise, a promoter segment with importance for hydathoid specific expression was identified.. ...
Under natural conditions, plants have to cope with a multitude of stresses, two of those are light-stress and herbivory. Plants have evolved several mechanisms to avoid the damage done by strong and fluctuating light and one important photoprotection mechanism is the qE-type of non-photochemical quenching (NPQ) where the PsbS protein is involved. We have compared. Arabidopsis thaliana wild type and two "photoprotection genotypes", npq4 and oePsbS that, respectively, lack and overexpress PsbS. In dual-choice feeding experiments on field-grown plants with a specialist (Plutella xylostella) and a generalist (Spodoptera littoralis) insect herbivore, both herbivores preferred the plants with higher expression of PsbS. Also both herbivores survived equally well on the different genotypes but for oviposition, female adults of Plutella xylostella preferred plants with lower expression of PsbS. No difference in the amount and composition of the ten most prominent glucosinolates - the most important ...
Zhang, P.-J., Broekgaarden, C., Zheng, S.-J., Snoeren, T. A. L., van Loon, J. J. A., Gols, R. and Dicke, M. (2013), Jasmonate and ethylene signaling mediate whitefly-induced interference with indirect plant defense in Arabidopsis thaliana. New Phytologist, 197: 1291-1299. doi: 10.1111/nph.12106 ...
Functional genomics tools provide researchers with the ability to apply high-throughput techniques to determine the function and interaction of a diverse range of genes. Mutagenised plant populations are one such resource that facilitate gene characterisation. They allow complex physiological responses to be correlated with the expression of single genes in planta, through either reverse genetics where target genes are mutagenised to assay the affect, or through forward genetics where populations of mutant lines are screened to identify those whose phenotype diverges from wild type for a particular trait. One limitation of these types of populations is the prevalence of gene redundancy within plant genomes, which can mask the affect of individual genes. Activation or enhancer populations, which not only provide knock-out but also dominant activation mutations, can facilitate the study of such genes. We have developed a population of almost 50,000 activation tagged A. thaliana lines that have been
The Arabidopsis genome contains approximately 200 genes that encode proteins with similarity to the nucleotide binding site and other domains characteristic of plant resistance proteins. Through a reiterative process of sequence analysis and reannotation, we identified 149 NBS-LRR-encoding genes in the Arabidopsis (ecotype Columbia) genomic sequence. Fifty-six of these genes were corrected from earlier annotations. At least 12 are predicted to be pseudogenes. As described previously, two distinct groups of sequences were identified: those that encoded an N-terminal domain with Toll/Interleukin-1 Receptor homology (TIR-NBS-LRR, or TNL), and those that encoded an N-terminal coiled-coil motif (CC-NBS-LRR, or CNL). The encoded proteins are distinct from the 58 predicted adapter proteins in the previously described TIR-X, TIR-NBS, and CC-NBS groups. Classification based on protein domains, intron positions, sequence conservation, and genome distribution defined four subgroups of CNL proteins, eight ...
The disproportionately large number of mutations recovered in the HOTHEAD complementation group suggest that this locus may represent an unusually large gene (or at least a very large target for the mutagen EMS). One corroborating piece of evidence comes from our analysis of recombination frequencies between different hth alleles. Based on estimates derived from these recombination data the HTH locus may span as much as 1.6 cM. This is dramatically larger than similar recombination estimates for other Arabidopsis genes (0.07 cM for GA1; Koornneefet al. 1983; 0.01 cM for CSR1; Mouradet al. 1994). A number of possibilities may explain this discrepancy. First, it is possible that the apparent recombinants actually represent reversion of one of the two mutations (presumably hth-8, since hth-10 was present in both crosses). While we have not attempted to measure this directly, we consider this an unlikely explanation since it would indicate a spontaneous reversion rate of 1.6 × 10−2. Second, it is ...
In Arabidopsis roots, the transcription factor MYB72 plays a dual role in the onset of rhizobacteria-induced systemic resistance (ISR) and plant survival under conditions of limited iron availability. Previously, it was shown that MYB72 coordinates the expression of a gene module that promotes synthesis and excretion of iron-mobilizing phenolic compounds in the rhizosphere, a process that is involved in both iron acquisition and ISR signaling. Here, we show that volatile organic compounds (VOCs) from ISR-inducing Pseudomonas bacteria are important elicitors of MYB72. In response to VOC treatment, MYB72 is co-expressed with the iron uptake-related genes FERRIC REDUCTION OXIDASE2 (FRO2) and IRON-REGULATED TRANSPORTER1 (IRT1) in a manner that is dependent on FER-LIKE IRON DEFICIENCY TRANSCRIPTION FACTOR (FIT), indicating that MYB72 is an intrinsic part of the plants iron-acquisition response that is typically activated upon iron starvation. However, VOC-induced MYB72 expression is activated ...
Omics is a science that comprehensively embraces the four disciplines of genomics, transcriptomics, proteomics and metabolomics (Fig. 2), and has developed rapidly in the past decade triggered by improvements in genome decoding techniques and processing speed. These improvements have led to some remarkable milestones in genomic research, including sequencing of the complete genomes of the flowering plant Arabidopsis thaliana, rice and soy-bean.. Similarly, the DNA microarray technique used in transcriptome analysis, the analysis of RNA transcribed from DNA, has also improved dramatically over the past decade. In this technique, hundreds of thousands of single-stranded DNA fragments are fixed in holes or spots on a glass substrate, and fluorescently labeled RNA are dropped onto the substrate surface. RNA complementary to a DNA fragment will become bound to the DNA, which causes the combined compound to emit fluorescent light. From the fluorescence intensity of each spot, researchers can ...
The twisted dwarf1 (twd1) mutant from Arabidopsis thaliana was identified in a screen for plant architecture mutants. The TWD1 gene encodes a 42 kDa FK506-binding protein (AtFKBP42) that possesses similarity to multidomain PPIases such as mammalian FKBP51 and FKBP52, which are known to be components …
TY - JOUR. T1 - AMAP. T2 - A pipeline for whole-genome mutation detection in Arabidopsis thaliana. AU - Ishii, Kotaro. AU - Kazama, Yusuke. AU - Hirano, Tomonari. AU - Hamada, Michiaki. AU - Ono, Yukiteru. AU - Yamada, Mieko. AU - Abe, Tomoko. PY - 2016. Y1 - 2016. N2 - Detection of mutations at the whole-genome level is now possible by the use of high-throughput sequencing. However, determining mutations is a time-consum-ing process due to the number of false positives provided by mutation-detecting programs. AMAP (automated mutation analysis pipeline) was developed to overcome this issue. AMAP integrates a set of well-validated programs for mapping (BWA), removal of potential PCR duplicates (Picard), realignment (GATK) and detection of mutations (SAMtools, GATK, Pindel, BreakDancer and CNVnator). Thus, all types of mutations such as base substitution, deletion, insertion, translocation and chromosomal rearrangement can be detected by AMAP. In addition, AMAP automatically distinguishes false ...
Thermomorphogenesis is defined as the suite of morphological changes that together are likely to contribute to adaptive growth acclimation to usually elevated ambient temperature [ 1, 2 ]. While many details of warmth-induced signal transduction are still elusive, parallels to light signaling recently became obvious (reviewed in [ 3 ]). It involves photoreceptors that can also sense changes in ambient temperature [ 3-5 ] and act, for example, by repressing protein activity of the central integrator of temperature information PHYTOCHROME-INTERACTING FACTOR 4 (PIF4 [ 6 ]). In addition, PIF4 transcript accumulation is tightly controlled by the evening complex member EARLY FLOWERING 3 [ 7, 8 ]. According to the current understanding, PIF4 activates growth-promoting genes directly but also via inducing auxin biosynthesis and signaling, resulting in cell elongation. Based on a mutagenesis screen in the model plant Arabidopsis thaliana for mutants with defects in temperature-induced hypocotyl ...
Betsuyaku, Shigeyuki (2005) Molecular dissection of Arabidopsis RAR1 and SGT1 functions in plant immunity. PhD thesis, Universität zu Köln.. Budhiraja, Ruchika (2005) Post-translational modification of proteins by SUMO in Arabidopsis thaliana. PhD thesis, Universität zu Köln.. Consonni, Chiara (2005) The function of MLO, a negative regulator of defence, is conserved in monocot and dicot plants. PhD thesis, Universität zu Köln.. Dittgen, Jan (2005) Genetische Analyse der Nichtwirtsresistenz gegenüber biotrophen Mehltaupilzen in Arabidopsis thaliana. PhD thesis, Universität zu Köln.. Ihnatowicz, Anna (2005) Functional Analysis of the D- and E- subunits of photosystem I in Arabidopsis thaliana. PhD thesis, Universität zu Köln.. Lauri, Andrea (2005) Molecular analysis of petal development by X-ChIP and two-hybrid technology. PhD thesis, Universität zu Köln.. Mauch, Stefan (2005) Molekulare Mechanismen der MLA-vermittelten Resistenz. PhD thesis, Universität zu Köln.. Mukhtar, Muhammad ...
TY - JOUR. T1 - Infrared laser-mediated local gene induction in medaka, zebrafish and Arabidopsis thaliana. AU - Deguchi, Tomonori. AU - Itoh, Mariko. AU - Urawa, Hiroko. AU - Matsumoto, Tomohiro. AU - Nakayama, Sohei. AU - Kawasaki, Takashi. AU - Kitano, Takeshi. AU - Oda, Shoji. AU - Mitani, Hiroshi. AU - Takahashi, Taku. AU - Todo, Takeshi. AU - Sato, Junichi. AU - Okada, Kiyotaka. AU - Hatta, Kohei. AU - Yuba, Shunsuke. AU - Kamei, Yasuhiro. PY - 2009/12. Y1 - 2009/12. N2 - Heat shock promoters are powerful tools for the precise control of exogenous gene induction in living organisms. In addition to the temporal control of gene expression, the analysis of gene function can also require spatial restriction. Recently, we reported a new method for in vivo, single-cell gene induction using an infrared laser-evoked gene operator (IR-LEGO) system in living nematodes (Caenorhabditis elegans). It was demonstrated that infrared (IR) irradiation could induce gene expression in single cells without ...
Cyclic nucleotide binding proteins in the Arabidopsis thaliana and Oryza sativa genomes.: This paper provides a molecular framework for the discussion of cyclic
The ASRP website organizes information about Arabidopsis thaliana small RNAs. This site is funded by NSF grant MCB-1231726. All small RNAs have either been isolated by the ASRP or published by other labs ...
Domain architectures containing the following SCOP superfamilies 53623,_gap_,53244 in Arabidopsis thaliana 10. Domain architectures illustrate each occurrence of 53623,_gap_,53244.
Domain architecture and assignment details (superfamily, family, region, evalue) for AT1G10870.1 from Arabidopsis thaliana 10. Plus protein sequence and external database links.
AP2 (APETALA2) and EREBPs (ethylene-responsive element binding proteins) are the prototypic members of a family of transcription factors unique to plants, whose distinguishing characteristic is that they contain the so-called AP2 DNA-binding domain. AP2/ REBP genes form a large multigene family, and they play a variety of roles throughout the plant life cycle: from being key regulators of several developmental processes, like floral organ identity determination or control of leaf epidermal cell identity, to forming part of the mechanisms used by plants to respond to various types of biotic and environmental stress. The molecular and biochemical characteristics of the AP2/EREBP transcription factors and their diverse functions are reviewed here, and this multigene family is analyzed within the context of the Arabidopsis thaliana genome sequence project. ...
PAN Czytelnia Czasopism, In silico prediction and characterization of three-dimensional structure of Actin-1 of Arabidopsis thaliana - BioTechnologia
Mono- and Stereopictres of 5.0 Angstrom coordination sphere of Iron atom in PDB 1qo4: Arabidopsis Thaliana Peroxidase A2 At Room Temperature
Principal Investigator:NAITO Satoshi, Project Period (FY):1995 - 1996, Research Category:Grant-in-Aid for Scientific Research (B), Section:一般, Research Field:植物生理
The Genetics Society of America (GSA), founded in 1931, is the professional membership organization for scientific researchers and educators in the field of genetics. Our members work to advance knowledge in the basic mechanisms of inheritance, from the molecular to the population level.. Online ISSN: 1943-2631. ...
FtsH (filamentation-temperature-sensitive protein H) proteases are a family of membrane-bound enzymes present in eubacteria, animals, and plants. Besides the 12 genes encoding proteolytically active members of the FtsH family in the genome of Arabidopsis, there are five genes coding for members that are assumed to be proteolytically inactive due to mutations in the protease domain; these are termed FtsHi (i for inactive). Despite their lack of proteolytic activity, these FtsHi members seem to be important for chloroplast and plant development as four out of five homozygous knockout-mutants of FtsHis are embryo-lethal. Here, we analysed the Darwinian fitness of weak homozygous (ftshi1,3,4) and heterozygous (ftshi/FTSHi2,4,5) mutants. We compared the growth and development of these mutants to their respective wild-type Arabidopsis plants under controlled laboratory conditions and in the field, and we also evaluated the photosynthetic efficiency by pulse-amplitude modulation fluorescence. ...
Next-day shipping cDNA ORF clones derived from AT1G63290 Aldolase-type TIM barrel family protein available at GenScript, starting from $99.00.
Molecular Plant-Microbe Interactions 22:840-848...Yongqing Li, Britney O. Pennington, and Jian Hua...© 2009 The American Phytopathological Society...The Arabidopsis thaliana genome contains more than 200 rapidly evolved resistance (R)-like genes coding for nucleotide binding leucine-rich repeat (NB-LRR) and their related proteins. A dozen of them are shown to play key roles in plant responses to biotic attacks, and they need to be repressed in...
Welcome to the online resource for supplemental information for the Mockler labs genome-wide mapping of alternative splicing in Arabidopsis thaliana. Alternative splicing can enhance transcriptome plasticity and proteome diversity. In plants, alternative splicing can be manifested at different developmental stages, and is frequently associated with specific tissue types or environmental conditions such as abiotic stress. We mapped the Arabidopsis transcriptome at single-base resolution using the Illumina platform for ultrahigh-throughput RNA sequencing (RNA-seq). Deep transcriptome sequencing confirmed a majority of annotated introns and identified thousands of novel alternatively spliced mRNA isoforms. Our analysis suggests that at least ∼42% of intron-containing genes in Arabidopsis are alternatively spliced; this is significantly higher than previous estimates based on cDNA/expressed sequence tag sequencing. Random validation confirmed that novel splice isoforms empirically predicted by ...
The proportion of non-tandem duplicated loci detected by DNA hybridization and the segregation of RFLPs using 90 independent randomly isolated cDNA probes was estimated by segregation analysis to be 17%. The 14 cDNA probes showing duplicate loci in progeny derived from a cross between Arabidopsis-thaliana ecotypes Columbia x Landsberg erecta detected an average of 3.6 loci per probe (ranging from 2 to 6). The 50 loci detected with these 14 probes were arranged on a genetic map of 587 cM and assigned to the five A. Thaliana chromosomes. An additional duplicated locus was detected in progeny from a cross between Landsberg erecta x Niederzenz. The majority of duplicated loci were on different chromosomes, and when linkage between duplicate locus pairs was detected, these loci were always separated by at least 15 cM. When partial nucleotide sequence data were compared with GENBANK databases, the identities of 2 cDNA clones which recognized duplicate unlinked sequences in the A. Thaliana genome were
Unlike animals, plants develop continuously in response to their environment. This developmental plasticity comes about because plant organs are constantly produced from a pool of undifferentiated stem cells at the tip of the shoot. Plants need to accomplish at least three things to convert undifferentiated cells in this pool into lateral organs such as leaves and petals. Firstly the pool of stem cells needs to be able to maintain itself, so that the rate of generation of new stem cells is equal to the rate of differentiation of the old cells. Secondly the position of the newly formed organ needs to be defined and its boundaries established. Finally the newly developing organ needs to adopt a specific tissue and cell identity - the cells need to know whether they are to become hairs or stomata, petals or ovules. We are interested in how a limited set of genes is able to direct these processes.. Although we mainly use the model plant Arabidopsis thaliana, we use a range of other species to make ...
Author Summary The production and turnover of messenger RNAs (mRNAs) are conserved processes in eukaryotes, from single-cell organisms to plants and mammals. To some degree, this is also true for modulators of these processes, such as the Paf1 and SKI complexes. One particular protein, SKI8, has been described to have a role in the SKI complex, which influences mRNA stability, both in yeast and in mammals. Moreover, in yeast SKI8 has an additional role in meiotic recombination, whereas in humans it influences mRNA production through association with the Paf1 complex. This functional divergence is commonly thought to arise from differences in protein sequence between the yeast and mammalian SKI8 homologs. Here we show that the conserved SKI8 homolog of the model plant Arabidopsis acts in the SKI complex as well as the Paf1 complex, similar to human. However, using an Arabidopsis ski8 mutant as a tool, we show that yeast SKI8 can fulfill all roles of Arabidopsis SKI8 if introduced into Arabidopsis cells.
Frugoli, J. A. et al "Catalase Is Encoded by a Multigene Family in Arabidopsis thaliana (L.) Heynh." Plant Physiology 112.1 (1996): 327-336. Web. 19 Feb. 2018. ...
MAP kinase 4; The ANPs-MKK6-MPK4 module is involved in the regulation of plant cytokinesis during meiosis and mitosis. Essential to promote the progression of cytokinesis and for cellularization (formation of the cell plate) during male-specific meiotic. Involved in cortical microtubules organization and stabilization by regulating the phosphorylation state of microtubule-associated proteins such as MAP65-1. Involved in root hair development process. Negative regulator of systemic acquired resistance (SAR) and salicylic acid- (SA) mediated defense response. Required for jasmonic acid- [...] (376 aa ...
The original set of 420 RILs were derived from a cross between Bay-0 (accession N954) and Shahdara (accession N929); two accessions obtained from the NASC European Arabidopsis Stock Centre. Bay-0 and Shahdara were chosen because of their well characterized genetic, geographical, and ecological differences. Lines were propagated by single seed descent through the sixth generation (F6) without selection. One plant per line was then used for genotyping (420 RILs x 38 markers) and selfed to obtain F7 seeds. F8 seed stock generated by bulk multiplication of F7 plants are available for analysis for 411 of these RILs. Data sets in WebQTL include up to 415 BXS accessions and the two parental stock.. How to obtain these lines: The entire extant set of 411 lines was donated to the NASC and ABRC in 2002 and is available (Stock number N57920 and CS57920) for £450 / US $720 (academic fee). A core set of 18 lines are also available from the NASC and and ABRC (stock numbers N57922 and CS57922) for £25 / US ...
The Pecinka lab is hosted by the Department of Plant Breeding and Genetics at the Max Planck Institute for Plant Breeding Research in Cologne, Germany. Our goal is to understand molecular and evolutionary mechanisms shaping plant genomes and epigenomes. We analyze how DNA sequence variation is generated by various mutagenic factors and how these forces are counteracted by the genome repair and maintenance mechanisms. To this end we use the model plant Arabidopsis thaliana and several other Brassicaceae and analyze them by forward and reverse genetics, molecular, biochemical, cytogenetic and bioinformatic methods. read more... ...
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The goal of the Pecinka lab is to understand molecular mechanisms shaping plant genomes. To this end we use the model plant Arabidopsis thaliana and several other Brassicaceae and analyze them by using forward and reverse genetics, molecular, biochemical, cytogenetic and bioinformatic methods. Pecinka lab is hosted by the Department of Plant Breeding and Genetics at the Max Planck Institute for Plant Breeding Research in Cologne, Germany. Our wiki site was developed under OpenWetWare, an open access effort to promote sharing of information among biologists. read more... ...
Tbingen-based developmental geneticists research organ development in the plant embryo. In the beginning is the fertilized egg cell. Following numerous cell divisions, it then develops into a complex organism with different organs and tissues. The largely unexplained process whereby the cells simply "know" the organs into which they should later develop is an astonishing phenomenon. Scientists from the Center for Plant Molecular Biology (ZMBP) of the University of Tbingen and the University of Wageningen, in cooperation with colleagues from the Max Planck Institute for Developmental Biology, have investigated how this process is controlled. Based on their studies of the thale cress, Arabidopsis thaliana, they have succeeded in demonstrating how the plant forms its first roots: the root founder cell in the tiny group of cells contained in the seed is activated by a combination of a plant hormone and a transcription factor. These insights could contribute to the breeding of plants with a ...
STYLISH 1; Transcription activator that binds DNA on 5-ACTCTAC-3 and promotes auxin homeostasis-regulating gene expression (e.g. YUC genes), as well as genes affecting stamen development, cell expansion and timing of flowering. Synergistically with other SHI- related proteins, regulates gynoecium, stamen and leaf development in a dose-dependent manner, controlling apical-basal patterning. Promotes style and stigma formation, and influences vascular development during gynoecium development. May also have a role in the formation and/or maintenance of the shoot apical meristem (SAM) (370 aa ...
AtPP2CG1 (Arabidopsis thaliana protein phosphatase 2C G Group 1) was predicted as an abiotic stress candidate gene by bioinformatic analysis in our previous study. The gene encodes a putative protein phosphatase 2C that belongs to Group G of PP2C. There is no report of Group G genes involved in abiotic stress so far. Real-time RT-PCR analysis showed that AtPP2CG1 expression was induced by salt, dr ...
Abiotic environmental stress, such as salinity and drought, is a major limitation in agricultural productivity. Plants have evolved organelle-to-nucleus signaling pathways that modify nuclear gene transcription in order to sustain or restore function in stressed organelles. In Arabidopsis thaliana, such signaling triggered by mitochondrial dysfunction is termed mitochondrial retrograde regulation (MRR) and enables plant cells to tolerate abiotic stresses such as salinity. Using transcriptomics and transgenic plants, Vanderauwera et al. showed that the transcription factor WRKY15 reduced salt tolerance in A. thaliana by inducing the unfolded protein response (UPR) in the endoplasmic reticulum (ER) in response to salt stress. Transgenic plants that overexpressed WRKY15 (WRKY15OE) showed an increase in dose-dependent sensitivity to increasing NaCl concentrations compared with wild-type plants, exhibiting stunted growth, cellular degeneration, and decreased chlorophyll production. Transcriptomics in ...
Cell production sustains growth; additionally, we suggest that cell production can regulate organ growth rate. The regulation of organ growth rate has traditionally been viewed from two distinct perspectives. The first is a purely spatial perspective, in which the position of the zone of rapid elongation and its size are considered to be specified by positional controls acting on the process of expansion. This view has been applied explicitly to morphogenesis (Cooke and Lu, 1992; Kaplan, 1992) and is commonly implicit in physiological studies that characterize spatial profiles of expansion (Sharp et al., 1988). The second perspective is cellular. Recognizing that the extent of the zone of rapid elongation is determined by the trajectory of the cells that move through it, the cellular view holds that the trajectory of the cells is specified when the cell is formed, just prior to its leaving the meristem. A model based on cells acting independently and even stochastically has been used to predict ...
Unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT4G21500.1); Has 30201 Blast hits to 17322 protei /.../780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink ...