First published online February 25, 2005; 10.1104/pp.104.055475
Plant Physiology 137:1115-1129 (2005)
© 2005 American Society of Plant Biologists
ENVIRONMENTAL STRESS AND ADAPTATION
Global Transcription Profiling Reveals Comprehensive Insights into Hypoxic Response in Arabidopsis1,[w]
Fenglong Liu,
Tara VanToai,
Linda P. Moy,
Geoffrey Bock,
Lara D. Linford and
John Quackenbush*
The Institute for Genomic Research, Rockville, Maryland 20850 (F.L., L.P.M., G.B., L.D.L., J.Q.); Soil Drainage Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Columbus, Ohio 43210 (T.V.); Department of Biochemistry, George Washington University, Washington, District of Columbia 20037 (J.Q.); Department of Chemical Engineering, University of Maryland, College Park, Maryland 20742 (J.Q.); and Department of Biostatistics, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland 21205 (J.Q.)
Plants have evolved adaptation mechanisms to sense oxygen deficiency in their environments and make coordinated physiological and structural adjustments to enhance their hypoxic tolerance. To gain insight into how plants respond to low-oxygen stress, gene expression profiling using whole-genome DNA amplicon microarrays was carried out at seven time points over 24 h, in wild-type and transgenic PSAG12:ipt Arabidopsis (Arabidopsis thaliana) plants under normoxic and hypoxic conditions. Transcript levels of genes involved in glycolysis and fermentation pathways, ethylene synthesis and perception, calcium signaling, nitrogen utilization, trehalose metabolism, and alkaloid synthesis were significantly altered in response to oxygen limitation. Analysis based on gene ontology assignments suggested a significant down-regulation of genes whose functions are associated with cell walls, nucleosome structures, water channels, and ion transporters and a significant up-regulation of genes involved in transcriptional regulation, protein kinase activity, and auxin responses under conditions of oxygen shortage. Promoter analysis on a cluster of up-regulated genes revealed a significant overrepresentation of the AtMYB2-binding motif (GT motif), a sugar response element-like motif, and a G-box-related sequence, and also identified several putative anaerobic response elements. Finally, quantitative real-time polymerase chain reactions using 29 selected genes independently verified the microarray results. This study represents one of the most comprehensive analyses conducted to date investigating hypoxia-responsive transcriptional networks in plants.
1 This work was supported by grants from the National Science Foundation.
[w] The online version of this article contains Web-only data.
Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.104.055475.
* Corresponding author; e-mail johnq{at}tigr.org; fax 301–838–0208.
Received October 21, 2004;
returned for revision December 20, 2004;
accepted December 30, 2004.
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