Arabidopsis thaliana
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PROVIDER: PRJNA132271 | ENA |
REPOSITORIES: ENA
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Project description:To study the genes regulated by transcription factor SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7 (SPL7) in Arabidopsis thaliana, we conducted chromatin immunoprecipitation-based sequencing (ChIP-seq) in 35S:FALG-SPL7 transgenic plant and spl7 mutant, and genome-wide sequencing-based transcript profiling of Arabidopsis thaliana wild-type plants and of spl7 mutant under MS medium and MS supplement with 5µM CuSO4. These experiments led to the identification of genes that are direct target of SPL7 and genes differentially expressed in an SPL7-dependent or Cu-dependent manner. This study provides a framework for the identification of SPL7 regulated genes towards characterization of SPL7 in copper homeostasis.
2014-04-15 | GSE45213 | GEO
Project description:The present work describes the effects on iron homeostasis when copper transport was deregulated in Arabidopsis thaliana by overexpressing copper transporters (COPTOE). A genome-wide analysis conducted on COPT1OE plants, highlighted that iron homeostasis gene expression was affected, both under copper deficiency and excess. Among the inhibited genes were those encoding the iron uptake machinery and their transcriptional regulators. Subsequently, COPTOE seedlings contained less iron and were more sensitive than controls to iron deficiency. These results emphasized the importance of appropriate spatiotemporal copper uptake for iron homeostasis under copper deficiency. The deregulation of copper-I uptake difficulted the transcriptional activation of the subgroup Ib of basic helix-loop-helix (bHLH-Ib) factors. Oppositely, copper excess inhibited the expression of the master regulator FIT but activate bHLH-Ib expression in COPTOE plants, in both cases leading to the lack of an adequate iron uptake response. As copper increased in the media, iron-III was accumulated in roots, accounting for a defective iron mobilization to the aerial parts, and this effect was exacerbated in COPTOE plants. Thus, iron-III overloading in roots inhibited local iron deficiency responses, aimed to metal uptake from soil, leading to a general lower iron content in the COPTOE seedlings. The understanding of the role of copper uptake in iron metabolism could be applied for increasing crops resistance to iron deficiency
2020-02-04 | GSE143857 | GEO
Project description:To study the genes regulated by transcription factor SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7 (SPL7) in Arabidopsis thaliana, we conducted chromatin immunoprecipitation-based sequencing (ChIP-seq) in 35S:FALG-SPL7 transgenic plant and spl7 mutant, and genome-wide sequencing-based transcript profiling of Arabidopsis thaliana wild-type plants and of spl7 mutant under MS medium and MS supplement with 5µM CuSO4. These experiments led to the identification of genes that are direct target of SPL7 and genes differentially expressed in an SPL7-dependent or Cu-dependent manner. This study provides a framework for the identification of SPL7 regulated genes towards characterization of SPL7 in copper homeostasis. ChIP-Seq: Chromatin isolation was performed with 7-day-old whole seedlings of spl7 mutant (negative control) and 35S:FALG-SPL7 transgene (sample) grown on standard MS medium under continuous white light according to Bowler et al. (2004). The resuspended chromatin pellet was sonicated at 4°C with a Diagenode Bioruptor set at high intensity for 10 min (30 s on, 30 s off intervals). The DNA was sheared to an average size of approximately 500 bp. Chromatin was immunoprecipitated with FLAG antibody (Sigma) according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol Rev.3. Reverse cross-linked DNA was purified and used for sequencing libraries construction following the manufacture’s protocol (Illumina). RNA-Seq: DNase I-treated total RNA was prepared from 7-day-old whole seedlings of wild type (Col-0) and spl7 mutant grown on standard MS medium and MS supplement with 5µM CuSO4 under continuous white light (WL). First- and second-strand cDNA were generated using SuperScript II and random hexamer primers. Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction following the manufacturer’s protocol (Illumina). Tophat was used to map the sequence reads to the Arabidopsis genome and only uniquely mapped reads were used in subsequent analyses. mRNA profiles of 7-day-old whole seedlings of wild type (Col-0) or spl7 mutant grown on standard MS medium and MS supplement with 5µM CuSO4 under continuous white light (WL) were generated by deep sequencing using illumine HiSeq2000.
2014-04-15 | E-GEOD-45213 | biostudies-arrayexpress
Project description:Copper and iron are essential micronutrients for most living organisms because they participate as cofactors in biological processes including respiration, photosynthesis and oxidative stress protection. In many eukaryotic organisms, including yeast and mammals, copper and iron homeostases are highly interconnected; however such interdependence is not well established in higher plants. Here we propose that COPT2, a high-affinity copper transport protein, functions under copper and iron deficiencies in Arabidopsis thaliana. COPT2 is a plasma membrane protein that functions in copper acquisition and distribution. Characterization of the COPT2 expression pattern indicates a synergic response to copper and iron limitation in roots. We have characterized a knockout of COPT2, copt2-1, that leads to increased resistance to simultaneous copper and iron deficiencies, measured as reduced leaf chlorosis and improved maintenance of the photosynthetic apparatus. We propose that COPT2 expression could play a dual role under Fe deficiency. First, COPT2 participates in the attenuation of copper deficiency responses driven by iron limitation maybe aimed to minimize further iron consume. On the other hand, global expression analyses of copt2-1 mutants versus wild type Arabidopsis plants indicate that low phosphate responses are increased in copt2-1 plants. In this sense, COPT2 function under Fe deficiency counteracts low phosphate responses. These results open up new biotechnological approaches to fight iron deficiency in crops. Four biological replicates of Arabidopsis seedlings were generated for 2 genotypes, Col-0 and copt2-1 mutant; and 3 growth condictions; first one an iron(Fe) and copper(Cu) sufficient medium (+Fe + Cu), second one an Fe deficient and Cu sufficient medium (-Fe+Cu) and third one an Fe and Cu deficient medium (-Fe-Cu). For each growth one comparasion was made, copt2-1 mutant versus Col-0; in each comparasion four biological replicates were made, two replicas were labeled with Cy5 for the mutant sample and Cy3 for the Col-0 sample, while the other two replicas were reversed-labeled.
2013-06-05 | E-GEOD-42642 | biostudies-arrayexpress
Project description:Copper and iron are essential micronutrients for most living organisms because they participate as cofactors in biological processes including respiration, photosynthesis and oxidative stress protection. In many eukaryotic organisms, including yeast and mammals, copper and iron homeostases are highly interconnected; however such interdependence is not well established in higher plants. Here we propose that COPT2, a high-affinity copper transport protein, functions under copper and iron deficiencies in Arabidopsis thaliana. COPT2 is a plasma membrane protein that functions in copper acquisition and distribution. Characterization of the COPT2 expression pattern indicates a synergic response to copper and iron limitation in roots. We have characterized a knockout of COPT2, copt2-1, that leads to increased resistance to simultaneous copper and iron deficiencies, measured as reduced leaf chlorosis and improved maintenance of the photosynthetic apparatus. We propose that COPT2 expression could play a dual role under Fe deficiency. First, COPT2 participates in the attenuation of copper deficiency responses driven by iron limitation maybe aimed to minimize further iron consume. On the other hand, global expression analyses of copt2-1 mutants versus wild type Arabidopsis plants indicate that low phosphate responses are increased in copt2-1 plants. In this sense, COPT2 function under Fe deficiency counteracts low phosphate responses. These results open up new biotechnological approaches to fight iron deficiency in crops.
2013-06-05 | GSE42642 | GEO
Project description:Iron (Fe) and copper (Cu) are essential metal micronutrients that are necessary for many redox reactions. The uptake of these metals is tightly regulated in plants. Some redox processes can alternatively use Fe-containing proteins or Cu-containing proteins, depending on nutritional status. Copper deficiency can rescue a Cucumis melo Fe uptake deficient mutant, and Fe deficiency can result in increased accumulation of Cu. However, the system responsible for Fe-deficiency-regulated Cu-uptake is unknown. To understand the genes and gene networks associated with Fe-deficiency regulated Cu uptake and Fe-Cu cross-talk, we conducted transcriptomic profiling of roots and rosettes of spl7 (a Cu uptake deficient mutant in arabidopsis) and Col-0 (WT) grown under Fe, Cu and simultaneous Fe and Cu deficiency conditions.
2018-03-01 | GSE104916 | GEO
Project description:Higher plants have developed sophisticated mechanisms to efficiently acquire and use micronutrients such as copper and iron. In the present work, we studied effects produced by the presence of a wide copper range in growth media and altered copper transport on iron homeostasis in Oryza sativa plants. The global analysis of gene expression in the rice seedlings grown under copper deficiency versus excess in the medium showed an increased expression of the genes involved in iron homeostasis. Different iron-related genes are expressed under either copper deficiency and excess, such as those that encode ferredoxin and transcriptional regulator IRON-RELATED TRANSCRIPTION FACTOR 2 (OsIRO2), respectively. As expected, the expression of OsCOPT1, which encodes a high affinity copper transport protein, was up-regulated under copper deficiency, and the expression of OsIRO2 targets were increased under copper excess. Arabidopsis COPT1 overexpression (C1OE) in rice causes root shortening under copper excess, modifies the expression of the putative Fe-sensing factor HEMERYTHRIN MOTIF-CONTAINING REALLY INTERESTING NEW GENE- AND ZINC-FINGER (OsHRZ1) and enhances the expression of OsIRO2 and its targets, which suggests a role of copper in iron signaling. Our studies conducted under simultaneous copper and iron deficiencies indicate that C1OE plants are more sensitive than the wild-type controls to root growth inhibition. The C1OE rice plants grown on soil contained higher endogenous iron concentration in grains than the wild-type plants (both brown and white grains). The results obtained herein showed the interaction between homeostatic networks of iron and copper, and suggest that strategies to obtain crops with optimized nutrient concentrations in edible parts should take into account this interaction.
2017-06-20 | GSE89109 | GEO
Project description:Purpose: plants exposed to multiple simultaneous adverse growth conditions trigger molecular responses that differ from the sum of those to individual stressors. Copper and iron are fundamental elements required for proper photosynthesis, energy production, DNA metabolism and hormone sensing, among all. Therefore, copper and iron deprivation limits plant yield. In natural environments, simultaneous deficiency to copper and iron can occur. As part of a multiple high-throughput study to identify combinatorial responses to both copper and iron deficiency, proteomic profiling of Arabidopsis thaliana rosette leaves exposed to copper and/or iron deficiencies have been conducted.
2020-06-22 | PXD013598 | Pride
Project description:Purpose: plants exposed to multiple simultaneous adverse growth conditions trigger molecular responses that differ from the sum of those to individual stressors. Copper and iron are fundamental elements required for proper photosynthesis, energy production, DNA metabolism and hormone sensing, among all. Therefore, copper and iron deprivation limits plant yield. In natural environments, simultaneous deficiency to copper and iron can occur. As part of a multiple high-throughput study to identify combinatorial responses to both copper and iron deficiency, RNA-Seq profiling of Arabidopsis thaliana rosette leaves exposed to copper and/or iron deficiencies have been conducted. Methods: RNA-Seq libraries were prepared from total RNA of whole rosettes of 20-d-old plants treated for control conditions, copper deficiency, iron deficiency or simultaneous deficiency to both copper and iron for 10 d and sequenced using Illumina protocols. 2 independent plants were RNA-Seq-sequenced per treatment. Adaptor sequences were removed with Trimmomatic and the resulting reads mapped to the Arabidopsis genome (Araport11) with Tophat 2.1.1. Read counts and differential expression analysis were conducted with Cufflinks/Cuffdiff. Results: for RNA-Seq analysis a Tophat/Cuffdiff pipeline was designed. Each sample provided app. 9 million reads. After applying a cut-off of absolute log2(FC) ≥ 1 to controls and a FDR ≤ 0.05, copper deficiency led to 83 differentially expressed genes, followed by 1708 during iron deficiency, while the combinatorial treatment altered 2056 transcripts. Comparison of differential expressed genes among treatments indicated that double deficiency led to app. 45% rewiring of all detected transcriptional changes. Conclusions: our data support that combinatorial copper and iron deficiency treatments in plants triggers transcriptional responses that differ from those to single deficiencies.
2020-06-11 | GSE125894 | GEO
Project description:Iron and copper are important environmental nutrients for plant growth. However, the molecular mechanisms of both iron and copper signaling that integrate the two pathways remain poorly understood. The Arabidopsis thaliana high affinity copper transporter COPT5, is a tonoplast localized permease involved in copper remobilization. Here, a global expression microarray analysis of the copt5 mutant points out the induction of iron deficiency responses, including NATURAL RESISTANCE-ASSOCIATED MACROPHAGE PROTEIN 4 (NRAMP4), a tonoplast-localized iron transporter. The copper requirement in iron perception and uptake from the media becomes more evident in the double nramp3nramp4 mutant, unable to remobilize iron from vacuoles, that is highly sensitive to copper deficiency. Furthermore, COPT5 expression is altered under iron deficiency and the copt5 mutant is sensitive to iron deficiency and is unable to perceive iron in the media under copper deficiency. Noteworthy, iron deficiency post-transcriptionally restraints the copper-dependent superoxide dismutase protein levels and the subsequent activity. As a consequence of its increased iron deficiency responses, the copt5 mutant present lower levels of both copper- and iron-dependent superoxide dismutase activities. Moreover, the copt5 mutant mobilizes faster its iron storage pools and presents higher levels of iron in cotyledons and seeds. These results underline the importance of internal metal pools in the understanding of copper and iron deficiency responses and their crosstalk that are critical for governing proper plant development in response to combined metal scarcities in soils.
2017-05-30 | GSE91044 | GEO