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Comparison of transcriptomic responses to individual and combinatorial copper and iron deficiencies in Arabidopsis thaliana rosettes.

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE125894 | GEO | 2020/06/11

REPOSITORIES: GEO

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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.