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Arabidopsis Genome (arabidopsi + genome)
Selected AbstractsPlant genomes do a balancing actMOLECULAR ECOLOGY, Issue 13 2009MATTHEW E. HUDSON Balancing selection is one mechanism that may explain why diversity is maintained in wild populations. However, relatively few examples of genes showing evidence of balancing selection have been identified, particularly in plants. In this issue, Reininga et al. (2009) present three Arabidopsis loci that show strong evidence of balancing selection. The loci, discovered using a genome-scanning approach, encode proteins with diverse predicted functions: starch synthesis and control of gene expression. These three genes were identified by scanning only a small fraction of the Arabidopsis genome, suggesting that balancing selection may be more prevalent than previously known. [source] Characterization of Arabidopsis genes involved in biosynthesis of polyamines in abiotic stress responses and developmental stagesPLANT CELL & ENVIRONMENT, Issue 11 2003K. URANO ABSTRACT To characterize the genes for enzymes involved in the biosynthesis of polyamines (PAs), their expression profiles were investigated and the levels of PAs in Arabidopsis thaliana quantified. In the Arabidopsis genome, eight genes involved in PAs biosynthesis were identified and the expression profiles of these genes were analysed, not only under abiotic stress to determine whether they were stress-inducible, constitutive, or stress-repressible, but also in various organs to show their tissue specificity. AtADC2 and AtSPMS mRNAs, encoding arginine decarboxylase and spermine synthase, clearly increased in response to NaCl and dehydration and abscisic acid treatments. Stress-inducible accumulation of AtADC2 mRNA correlated with putrescine (Put) accumulation under NaCl and dehydration treatments. In a cold condition, AtSAMDC2 mRNA increased significantly. AtADC2 and AtSAMDC2 mRNA were expressed in sexual organs such as flowers, buds and immature siliques. PAs also accumulated in sexual organs. These results suggest that the transcripts of eight genes involved in PA biosynthesis show different profiles of expression not only in response to environmental stress but also during plant development. [source] The Arabidopsis ClpB/Hsp100 family of proteins: chaperones for stress and chloroplast developmentTHE PLANT JOURNAL, Issue 1 2007Ung Lee Summary The Casein lytic proteinase/heat shock protein 100 (Clp/Hsp100) proteins are chaperones that act to remodel/disassemble protein complexes and/or aggregates using the energy of ATP. In plants, one of the best-studied proteins from this family is cytosolic ClpB1 (At1g74310), better known in Arabidopsis as AtHsp101, which is a heat shock protein required for acclimation to high temperatures. Three other ClpB homologues have been identified in the Arabidopsis genome (ClpB2, ClpB3 and ClpB4; At4g14670, At5g15450 and At2g25140). To define further the roles of these chaperones in plants we investigated their intracellular localization, evolutionary relationships, patterns of expression and the phenotypes of corresponding T-DNA insertion mutants. We first found that ClpB2 was misannotated; there is no functional ClpB/Hsp100 gene at this locus. By fusing the putative transit peptides of ClpB3 and ClpB4 with GFP, we showed that these proteins are targeted to the chloroplast and mitochondrion, respectively, and we therefore designated them as ClpB-p and ClpB-m. Phylogenetic analysis supports two major lineages of ClpB proteins in plants, an ,eukaryotic', cytosol/nuclear-localized group containing AtHsp101, and an organelle-localized lineage, containing both ClpB-p and ClpB-m. Although AtHsp101, ClpB-p and ClpB-m transcripts all accumulate dramatically at high temperatures, the T-DNA insertion mutants of ClpB-p and ClpB-m show no evidence of seedling heat stress phenotypes similar to those observed in AtHsp101 mutants. Strikingly, ClpB-p knockouts were seedling lethals, failing to accumulate chlorophyll or properly develop chloroplasts. Thus, in plants, the function of ClpB/Hsp100 proteins is not restricted to heat stress, but a specific member of the family provides housekeeping functions that are essential to chloroplast development. [source] The stability of the Arabidopsis transcriptome in transgenic plants expressing the marker genes nptII and uidATHE PLANT JOURNAL, Issue 6 2005Souad El Ouakfaoui Summary The ATH1 Arabidopsis GeneChip from Affymetrix was used to search for transcriptome changes in Arabidopsis associated with the strong expression of transgenes regulated by constitutive promoters. The insertion and expression of the commonly used marker genes, uidA and nptII, did not induce changes to the expression patterns of the approximately 24 000 genes that were screened under optimal growth conditions and under physiological stress imposed by low temperatures. Approximately 8000 genes (35% of the Arabidopsis genome) underwent changes in gene expression in both wild-type and transgenic plants under abiotic stresses such as salt, dehydration, cold, and heat. This study provides detailed information on the extent of non-targeted or pleiotropic effects of transgenes on plants and shows that the transgenic and non-transgenic plants were equivalent in their global patterns of transcription. This information may help to extend our understanding and interpretation of the principle of substantial equivalence which is used as a first step in the biosafety evaluation of transgenic crops. [source] Large-scale screening of Arabidopsis circadian clock mutants by a high-throughput real-time bioluminescence monitoring systemTHE PLANT JOURNAL, Issue 1 2004Kiyoshi Onai Summary Using a high-throughput real-time bioluminescence monitoring system, we screened large numbers of Arabidopsis thaliana mutants for extensively altered circadian rhythms. We constructed reporter genes by fusing a promoter of an Arabidopsis flowering-time gene , either GIGANTEA (GI) or FLOWERING LOCUS T (FT) , to a modified firefly luciferase gene (LUC+), and we transferred the fusion gene (PGI::LUC+ or PFT::LUC+) into the Arabidopsis genome. After mutagenesis with ethyl methanesulfonate, 50 000 M2 seedlings carrying the PGI::LUC+ and 50 000 carrying PFT::LUC+ were screened their bioluminescence rhythms. We isolated six arrhythmic (AR) mutants and 29 other mutants that showed more than 3 h difference in the period length or phase of rhythms compared with the wild-type strains. The shortest period length was 16 h, the longest 27 h. Five of the six AR mutants carrying PGI::LUC+ showed arrhythmia in bioluminescence rhythms in both constant light and constant dark. These five AR mutants also showed arrhythmia in leaf movement rhythms in constant light. Genetic analysis revealed that each of the five AR mutants carried a recessive mutation in a nuclear gene and the mutations belonged to three complementation groups, and at least one of which was mapped on a novel locus. Our results suggest that the three loci identified here may contain central clock or clock-related genes, at least one of which may be a novel. [source] A collection of 11 800 single-copy Ds transposon insertion lines in ArabidopsisTHE PLANT JOURNAL, Issue 6 2004Takashi Kuromori Summary More than 10 000 transposon-tagged lines were constructed by using the Activator (Ac)/Dissociation (Ds) system in order to collect insertional mutants as a useful resource for functional genomics of Arabidopsis. The flanking sequences of the Ds element in the 11 800 independent lines were determined by high-throughput analysis using a semi-automated method. The sequence data allowed us to map the unique insertion site on the Arabidopsis genome in each line. The Ds element of 7566 lines is inserted in or close to coding regions, potentially affecting the function of 5031 of 25 000 Arabidopsis genes. Half of the lines have Ds insertions on chromosome 1 (Chr. 1), in which donor lines have a donor site. In the other half, the Ds insertions are distributed throughout the other four chromosomes. The intrachromosomal distribution of Ds insertions varies with the donor lines. We found that there are hot spots for Ds transposition near the ends of every chromosome, and we found some statistical preference for Ds insertion targets at the nucleotide level. On the basis of systematic analysis of the Ds insertion sites in the 11 800 lines, we propose the use of Ds -tagged lines with a single insertion in annotated genes for systematic analysis of phenotypes (phenome analysis) in functional genomics. We have opened a searchable database of the insertion-site sequences and mutated genes (http://rarge.gsc.riken.go.jp/) and are depositing these lines in the RIKEN BioResource Center as available resources (http://www.brc.riken.go.jp/Eng/). [source] | ||||||||||