Molecular characterization of the submergence response of the Arabidopsis thaliana ecotype Columbia

Authors

  • Seung Cho Lee,

    1. Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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  • Angelika Mustroph,

    1. Department of Plant Physiology, University of Bayreuth, Universitaetsstrasse 30, 95440 Bayreuth, Germany
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  • Rashmi Sasidharan,

    1. Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
    2. Centre for Biosystems Genomics, 6708 PB Wageningen, the Netherlands
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  • Divya Vashisht,

    1. Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
    2. Centre for Biosystems Genomics, 6708 PB Wageningen, the Netherlands
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  • Ole Pedersen,

    1. Freshwater Biological Laboratory, Department of Biology, University of Copenhagen, Helsingørsgade 51, DK-3400 Hillerød, Denmark
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  • Teruko Oosumi,

    1. Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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  • Laurentius A.C.J. Voesenek,

    1. Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
    2. Centre for Biosystems Genomics, 6708 PB Wageningen, the Netherlands
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  • Julia Bailey-Serres

    1. Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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Author for correspondence:
Julia Bailey-Serres
Tel: +1 951 827 3738
Email: serres@ucr.edu

Summary

  • A detailed description of the molecular response of Arabidopsis thaliana to submergence can aid the identification of genes that are critical to flooding survival.
  • Rosette-stage plants were fully submerged in complete darkness and shoot and root tissue was harvested separately after the O2 partial pressure of the petiole and root had stabilized at c. 6 and 0.1 kPa, respectively. As controls, plants were untreated or exposed to darkness. Following quantitative profiling of cellular mRNAs with the Affymetrix ATH1 platform, changes in the transcriptome in response to submergence, early darkness, and O2-deprivation were evaluated by fuzzy k-means clustering. This identified genes co-regulated at the conditional, developmental or organ-specific level. Mutants for 10 differentially expressed HYPOXIA-RESPONSIVE UNKNOWN PROTEIN (HUP) genes were screened for altered submergence tolerance.
  • The analysis identified 34 genes that were ubiquitously co-regulated by submergence and O2 deprivation. The biological functions of these include signaling, transcription, and anaerobic energy metabolism. HUPs comprised 40% of the co-regulated transcripts and mutants of seven of these genes were significantly altered in submergence tolerance.
  • The results define transcriptomic adjustments in response to submergence in the dark and demonstrate that the manipulation of HUPs can alter submergence tolerance.

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