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Characterization of differentially expressed genes to Cu stress in Brassica nigra by Arabidopsis genome arrays

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Abstract

Phytoremediation is an efficient and promising cleanup technology to extract or inactivate heavy metals and several organic and inorganic pollutants from soil and water. In this study, different Brassica nigra L. ecotypes, including Diyarbakır, collected from mining areas were exposed to different concentrations of copper and harvested after 72 h of Cu stress for the assessment of phytoremediation capacity. The Diyarbakır ecotype was called as “metallophyte” because of surviving at 500 μM Cu. To better understand Cu stress mechanism, ArabidopsisATH1 genome array was used to compare the gene expression in root and shoot tissues of B. nigra under 25 μM Cu. The response to Cu was much stronger in roots (88 genes showing increased or decreased mRNA levels) than in leaf tissues (24 responding genes). These genes were classified into the metal transport and accumulation-related genes, signal transduction and metabolism-related genes, and transport facilitation genes. Glutathione pathway-related genes (γ-ECS, PC, etc.) mRNAs were identified as differentially expressed in root and shoot tissues. QRT-PCR validation experiments showed that γ-ECS and PC expression was upregulated in the shoot and leaf tissues of the 100 μM Cu-subjected B. nigra-tolerant ecotype. This is the first study showing global expression profiles in response to Cu stress in B. nigra by Arabidopsis genome array. This work presented herein provides a well-illustrated insight into the global gene expression to Cu stress response in plants, and identified genes from microarray data will serve as molecular tools for the phytoremediation applications in the future.

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Acknowledgements

This project was supported by The Scientific and Technological Council of Turkey (TUBITAK-1040211) and the COST Action 859 “Phytotechnologies to promote sustainable land use and improve food safety”.

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Authors and Affiliations

  1. The Scientific and Technological Research Council of Turkey (TUBITAK); Marmara Research Center; Genetic Engineering and Biotechnology Institute; Plant Molecular Biology and Genetics Laboratory, 21, 41470, Gebze, Kocaeli, Turkey

    Birsen Cevher-Keskin, Yasemin Yıldızhan & Bayram Yüksel

  2. Faculty of Science, Department of Botany, Istanbul University, Istanbul, Turkey

    Eda Dalyan

  3. Faculty of Science and Arts, Department of Molecular Biology and Genetics, Uşak University, 1 Eylül Campus, Uşak, Turkey

    Abdul Razaque Memon

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  1. Birsen Cevher-Keskin
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  2. Yasemin Yıldızhan
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Correspondence to Birsen Cevher-Keskin.

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Responsible editor: Yi-ping Chen

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Suppl. Data 1

The effect of 500 μM Cu concentration in leaf tissue of non-tolerant Brassica nigra cv. CGN06619. Leaf necrosis was observed althought Cu content remained stable. (PNG 462 kb)

High resolution image (TIF 668 kb)

Suppl. Data 2

Pearson’s Correlation analysis was performed after the normalization of the signals from root and leaf tissues of 25 μM Cu treated B. nigra 6619. (PNG 392 kb)

High resolution image (TIF 34 kb)

Suppl. Data 3

Expression levels of significantly up (-) and down (+) regulated Cu –stress responsive transcripts in B.nigra 6619 ecotype roots exposed to 72 h 25 μM Cu stress compared to control conditions (Hoagland Solution-no copper) obtained with Affymetrix GeneChip Arabidopsis Genome Array (ATH1-121501 GeneChip) and three biological replicates. (DOCX 23 kb)

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Cevher-Keskin, B., Yıldızhan, Y., Yüksel, B. et al. Characterization of differentially expressed genes to Cu stress in Brassica nigra by Arabidopsis genome arrays. Environ Sci Pollut Res 26, 299–311 (2019). https://doi.org/10.1007/s11356-018-3577-7

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