Plant Cell Hybrigenics The Protein Interactions Experts
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow PPT slides of all figures
Right arrow Supplemental Data
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via CrossRef
Right arrow Citing Articles via Web of Science (107)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Klok, E. J.
Right arrow Articles by Dennis, E. S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Klok, E. J.
Right arrow Articles by Dennis, E. S.
Agricola
Right arrow Articles by Klok, E. J.
Right arrow Articles by Dennis, E. S.
The Plant Cell, Vol. 14, 2481-2494, October 2002, Copyright © 2002,
American Society of Plant Biologists

Expression Profile Analysis of the Low-Oxygen Response in Arabidopsis Root Cultures

Erik Jan Klok1,a, Iain W. Wilsona, Dale Wilsonb, Scott C. Chapmanc, Rob M. Ewingd, Shauna C. Somervillee, W. James Peacocka, Rudy Dolferusa and Elizabeth S. Dennisa

a Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia
b Commonwealth Scientific and Industrial Research Organization Mathematical and Information Sciences, Macquarie University, North Ryde, New South Wales, Australia
c Commonwealth Scientific and Industrial Research Organization Plant Industry, Long Pocket Laboratories, Indooroopilly, Queensland 4068, Australia
d Incyte Genomics, Palo Alto, California 94043
e Department of Plant Biology, Carnegie Institution of Washington, Stanford, California 94305

1 To whom correspondence should be addressed. E-mail erikjan.klok{at}csiro.au; fax 61-2-6246-5000

We used DNA microarray technology to identify genes involved in the low-oxygen response of Arabidopsis root cultures. A microarray containing 3500 cDNA clones was screened with cDNA samples taken at various times (0.5, 2, 4, and 20 h) after transfer to low-oxygen conditions. A package of statistical tools identified 210 differentially expressed genes over the four time points. Principal component analysis showed the 0.5-h response to contain a substantially different set of genes from those regulated differentially at the other three time points. The differentially expressed genes included the known anaerobic proteins as well as transcription factors, signal transduction components, and genes that encode enzymes of pathways not known previously to be involved in low-oxygen metabolism. We found that the regulatory regions of genes with a similar expression profile contained similar sequence motifs, suggesting the coordinated transcriptional control of groups of genes by common sets of regulatory factors.




This article has been cited by other articles:


Home page
 Plant Physiol.Home page
V. Banti, F. Mafessoni, E. Loreti, A. Alpi, and P. Perata
The Heat-Inducible Transcription Factor HsfA2 Enhances Anoxia Tolerance in Arabidopsis
Plant Physiology, March 1, 2010; 152(3): 1471 - 1483.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
D. Moldovan, A. Spriggs, J. Yang, B. J. Pogson, E. S. Dennis, and I. W. Wilson
Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis
J. Exp. Bot., January 1, 2010; 61(1): 165 - 177.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
J. A. Christianson, D. J. Llewellyn, E. S. Dennis, and I. W. Wilson
Global Gene Expression Responses to Waterlogging in Roots and Leaves of Cotton (Gossypium hirsutum L.)
Plant Cell Physiol., January 1, 2010; 51(1): 21 - 37.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
R. Narsai, K. A. Howell, A. Carroll, A. Ivanova, A. H. Millar, and J. Whelan
Defining Core Metabolic and Transcriptomic Responses to Oxygen Availability in Rice Embryos and Young Seedlings
Plant Physiology, September 1, 2009; 151(1): 306 - 322.
[Abstract] [Full Text] [PDF]

Home page
 Mol PlantHome page
D. M. Bond, E. S. Dennis, B. J. Pogson, and E. J. Finnegan
Histone Acetylation, VERNALIZATION INSENSITIVE 3, FLOWERING LOCUS C, and the Vernalization Response
Mol Plant, July 1, 2009; 2(4): 724 - 737.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
J. A. Christianson, I. W. Wilson, D. J. Llewellyn, and E. S. Dennis
The Low-Oxygen-Induced NAC Domain Transcription Factor ANAC102 Affects Viability of Arabidopsis Seeds following Low-Oxygen Treatment
Plant Physiology, April 1, 2009; 149(4): 1724 - 1738.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
C. Cosio and C. Dunand
Specific functions of individual class III peroxidase genes
J. Exp. Bot., February 1, 2009; 60(2): 391 - 408.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
J. T. van Dongen, A. Frohlich, S. J. Ramirez-Aguilar, N. Schauer, A. R. Fernie, A. Erban, J. Kopka, J. Clark, A. Langer, and P. Geigenberger
Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of arabidopsis plants
Ann. Bot., January 1, 2009; 103(2): 269 - 280.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
L. Magneschi and P. Perata
Rice germination and seedling growth in the absence of oxygen
Ann. Bot., January 1, 2009; 103(2): 181 - 196.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
J. Kreuzwieser, J. Hauberg, K. A. Howell, A. Carroll, H. Rennenberg, A. H. Millar, and J. Whelan
Differential Response of Gray Poplar Leaves and Roots Underpins Stress Adaptation during Hypoxia
Plant Physiology, January 1, 2009; 149(1): 461 - 473.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
Z. Zhang, L. Wei, X. Zou, Y. Tao, Z. Liu, and Y. Zheng
Submergence-responsive MicroRNAs are Potentially Involved in the Regulation of Morphological and Metabolic Adaptations in Maize Root Cells
Ann. Bot., October 1, 2008; 102(4): 509 - 519.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
T. Hewezi, M. Leger, and L. Gentzbittel
A Comprehensive Analysis of the Combined Effects of High Light and High Temperature Stresses on Gene Expression in Sunflower
Ann. Bot., July 1, 2008; 102(1): 127 - 140.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
W. L. Allan, J. P. Simpson, S. M. Clark, and B. J. Shelp
{gamma}-Hydroxybutyrate accumulation in Arabidopsis and tobacco plants is a general response to abiotic stress: putative regulation by redox balance and glyoxylate reductase isoforms
J. Exp. Bot., June 1, 2008; 59(9): 2555 - 2564.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
P. Muhlenbock, M. Plaszczyca, M. Plaszczyca, E. Mellerowicz, and S. Karpinski
Lysigenous Aerenchyma Formation in Arabidopsis Is Controlled by LESION SIMULATING DISEASE1
PLANT CELL, November 1, 2007; 19(11): 3819 - 3830.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
Y. Manabe, N. Tinker, A. Colville, and B. Miki
CSR1, the Sole Target of Imidazolinone Herbicide in Arabidopsis thaliana
Plant Cell Physiol., September 1, 2007; 48(9): 1340 - 1358.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
F. Mus, A. Dubini, M. Seibert, M. C. Posewitz, and A. R. Grossman
Anaerobic Acclimation in Chlamydomonas reinhardtii: ANOXIC GENE EXPRESSION, HYDROGENASE INDUCTION, AND METABOLIC PATHWAYS
J. Biol. Chem., August 31, 2007; 282(35): 25475 - 25486.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
W.-G. Choi and D. M. Roberts
Arabidopsis NIP2;1, a Major Intrinsic Protein Transporter of Lactic Acid Induced by Anoxic Stress
J. Biol. Chem., August 17, 2007; 282(33): 24209 - 24218.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
F. Alferez, G. Y. Zhong, and J. K. Burns
A citrus abscission agent induces anoxia- and senescence-related gene expression in Arabidopsis
J. Exp. Bot., July 1, 2007; 58(10): 2451 - 2462.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
F. Qiu, Y. Zheng, Z. Zhang, and S. Xu
Mapping of QTL Associated with Waterlogging Tolerance during the Seedling Stage in Maize
Ann. Bot., June 1, 2007; 99(6): 1067 - 1081.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
K. Pasentsis, V. Falara, I. Pateraki, D. Gerasopoulos, and A. K. Kanellis
Identification and expression profiling of low oxygen regulated genes from Citrus flavedo tissues using RT-PCR differential display
J. Exp. Bot., June 1, 2007; 58(8): 2203 - 2216.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
R. Lasanthi-Kudahettige, L. Magneschi, E. Loreti, S. Gonzali, F. Licausi, G. Novi, O. Beretta, F. Vitulli, A. Alpi, and P. Perata
Transcript Profiling of the Anoxic Rice Coleoptile
Plant Physiology, May 1, 2007; 144(1): 218 - 231.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
L. A. Kempema, X. Cui, F. M. Holzer, and L. L. Walling
Arabidopsis Transcriptome Changes in Response to Phloem-Feeding Silverleaf Whitefly Nymphs. Similarities and Distinctions in Responses to Aphids
Plant Physiology, February 1, 2007; 143(2): 849 - 865.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
L. Onate-Sanchez, J. P. Anderson, J. Young, and K. B. Singh
AtERF14, a Member of the ERF Family of Transcription Factors, Plays a Nonredundant Role in Plant Defense
Plant Physiology, January 1, 2007; 143(1): 400 - 409.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
R. Deeken, J. C. Engelmann, M. Efetova, T. Czirjak, T. Muller, W. M. Kaiser, O. Tietz, M. Krischke, M. J. Mueller, K. Palme, et al.
An Integrated View of Gene Expression and Solute Profiles of Arabidopsis Tumors: A Genome-Wide Approach
PLANT CELL, December 1, 2006; 18(12): 3617 - 3634.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
R. W. King, T. Moritz, L. T. Evans, J. Martin, C. H. Andersen, C. Blundell, I. Kardailsky, and P. M. Chandler
Regulation of Flowering in the Long-Day Grass Lolium temulentum by Gibberellins and the FLOWERING LOCUS T Gene
Plant Physiology, June 1, 2006; 141(2): 498 - 507.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
Y. Wu, A. C. Machado, R. G. White, D. J. Llewellyn, and E. S. Dennis
Expression Profiling Identifies Genes Expressed Early During Lint Fibre Initiation in Cotton
Plant Cell Physiol., January 1, 2006; 47(1): 107 - 127.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
M. H. Dixon, S. A. Hill, M. B. Jackson, R. G. Ratcliffe, and L. J. Sweetlove
Physiological and Metabolic Adaptations of Potamogeton pectinatus L. Tubers Support Rapid Elongation of Stem Tissue in the Absence of Oxygen
Plant Cell Physiol., January 1, 2006; 47(1): 128 - 140.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
N. Nicot, J.-F. Hausman, L. Hoffmann, and D. Evers
Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress
J. Exp. Bot., November 1, 2005; 56(421): 2907 - 2914.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
S. AGARWAL and A. GROVER
Isolation and Transcription Profiling of Low-O2 Stress-Associated cDNA Clones from the Flooding-stress-tolerant FR13A Rice Genotype
Ann. Bot., October 1, 2005; 96(5): 831 - 844.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
B. MOHANTY, S. P. T. KRISHNAN, S. SWARUP, and V. B. BAJIC
Detection and Preliminary Analysis of Motifs in Promoters of Anaerobically Induced Genes of Different Plant Species
Ann. Bot., September 1, 2005; 96(4): 669 - 681.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
A. U. IGAMBERDIEV, K. BARON, N. MANAC'H-LITTLE, M. STOIMENOVA, and R. D. HILL
The Haemoglobin/Nitric Oxide Cycle: Involvement in Flooding Stress and Effects on Hormone Signalling
Ann. Bot., September 1, 2005; 96(4): 557 - 564.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
S. GONZALI, E. LORETI, G. NOVI, A. POGGI, A. ALPI, and P. PERATA
The Use of Microarrays to Study the Anaerobic Response in Arabidopsis
Ann. Bot., September 1, 2005; 96(4): 661 - 668.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
J. BAILEY-SERRES and R. CHANG
Sensing and Signalling in Response to Oxygen Deprivation in Plants and Other Organisms
Ann. Bot., September 1, 2005; 96(4): 507 - 518.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
C. BRANCO-PRICE, R. KAWAGUCHI, R. B. FERREIRA, and J. BAILEY-SERRES
Genome-wide Analysis of Transcript Abundance and Translation in Arabidopsis Seedlings Subjected to Oxygen Deprivation
Ann. Bot., September 1, 2005; 96(4): 647 - 660.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
I. W. Wilson, G. C. Kennedy, J. W. Peacock, and E. S. Dennis
Microarray Analysis Reveals Vegetative Molecular Phenotypes of Arabidopsis Flowering-time Mutants
Plant Cell Physiol., August 1, 2005; 46(8): 1190 - 1201.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
T. Hisamatsu, R. W. King, C. A. Helliwell, and M. Koshioka
The Involvement of Gibberellin 20-Oxidase Genes in Phytochrome-Regulated Petiole Elongation of Arabidopsis
Plant Physiology, June 1, 2005; 138(2): 1106 - 1116.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
E. Loreti, A. Poggi, G. Novi, A. Alpi, and P. Perata
A Genome-Wide Analysis of the Effects of Sucrose on Gene Expression in Arabidopsis Seedlings under Anoxia
Plant Physiology, March 1, 2005; 137(3): 1130 - 1138.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
F. Liu, T. VanToai, L. P. Moy, G. Bock, L. D. Linford, and J. Quackenbush
Global Transcription Profiling Reveals Comprehensive Insights into Hypoxic Response in Arabidopsis
Plant Physiology, March 1, 2005; 137(3): 1115 - 1129.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
A. U. Igamberdiev and R. D. Hill
Nitrate, NO and haemoglobin in plant adaptation to hypoxia: an alternative to classic fermentation pathways
J. Exp. Bot., December 1, 2004; 55(408): 2473 - 2482.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
C. Tesniere, M. Pradal, A. El-Kereamy, L. Torregrosa, P. Chatelet, J.-P. Roustan, and C. Chervin
Involvement of ethylene signalling in a non-climacteric fruit: new elements regarding the regulation of ADH expression in grapevine
J. Exp. Bot., October 1, 2004; 55(406): 2235 - 2240.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
J. P. HAMMOND, M. R. BROADLEY, and P. J. WHITE
Genetic Responses to Phosphorus Deficiency
Ann. Bot., September 1, 2004; 94(3): 323 - 332.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
C. Gachon, A. Mingam, and B. Charrier
Real-time PCR: what relevance to plant studies?
J. Exp. Bot., July 1, 2004; 55(402): 1445 - 1454.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
H. Rolletschek, W. Weschke, H. Weber, U. Wobus, and L. Borisjuk
Energy state and its control on seed development: starch accumulation is associated with high ATP and steep oxygen gradients within barley grains
J. Exp. Bot., June 1, 2004; 55(401): 1351 - 1359.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
L. Rizhsky, S. Davletova, H. Liang, and R. Mittler
The Zinc Finger Protein Zat12 Is Required for Cytosolic Ascorbate Peroxidase 1 Expression during Oxidative Stress in Arabidopsis
J. Biol. Chem., March 19, 2004; 279(12): 11736 - 11743.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
S. Baud, M.-N. Vaultier, and C. Rochat
Structure and expression profile of the sucrose synthase multigene family in Arabidopsis
J. Exp. Bot., February 1, 2004; 55(396): 397 - 409.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
A.-L. Paul, A. C. Schuerger, M. P. Popp, J. T. Richards, M. S. Manak, and R. J. Ferl
Hypobaric Biology: Arabidopsis Gene Expression at Low Atmospheric Pressure
Plant Physiology, January 1, 2004; 134(1): 215 - 223.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
K. L. Bologa, A. R. Fernie, A. Leisse, M. Ehlers Loureiro, and P. Geigenberger
A Bypass of Sucrose Synthase Leads to Low Internal Oxygen and Impaired Metabolic Performance in Growing Potato Tubers
Plant Physiology, August 1, 2003; 132(4): 2058 - 2072.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
J. P. Hammond, M. J. Bennett, H. C. Bowen, M. R. Broadley, D. C. Eastwood, S. T. May, C. Rahn, R. Swarup, K. E. Woolaway, and P. J. White
Changes in Gene Expression in Arabidopsis Shoots during Phosphate Starvation and the Potential for Developing Smart Plants
Plant Physiology, June 1, 2003; 132(2): 578 - 596.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
J. T. van Dongen, U. Schurr, M. Pfister, and P. Geigenberger
Phloem Metabolism and Function Have to Cope with Low Internal Oxygen
Plant Physiology, April 1, 2003; 131(4): 1529 - 1543.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
P. W. Hunt, E. J. Klok, B. Trevaskis, R. A. Watts, M. H. Ellis, W. J. Peacock, and E. S. Dennis
Increased level of hemoglobin 1 enhances survival of hypoxic stress and promotes early growth in Arabidopsis thaliana
PNAS, December 24, 2002; 99(26): 17197 - 17202.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
ASPB Publications THE PLANT CELL PLANT PHYSIOLOGY
Copyright © 2002 by the American Society of Plant Biologists