Expression Profile Analysis of the Low-Oxygen Response in Arabidopsis Root Cultures[W] (original) (raw)
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Expression Profile Analysis of the Low-Oxygen Response in Arabidopsis Root Cultures
THE PLANT CELL ONLINE, 2002
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.
2009
† Background and Aims Oxygen can fall to low concentrations within plant tissues, either because of environmental factors that decrease the external oxygen concentration or because the movement of oxygen through the plant tissues cannot keep pace with the rate of oxygen consumption. Recent studies document that plants can decrease their oxygen consumption in response to relatively small changes in oxygen concentrations to avoid internal anoxia. The molecular mechanisms underlying this response have not been identified yet. The aim of this study was to use transcript and metabolite profiling to investigate the genomic response of arabidopsis roots to a mild decrease in oxygen concentrations. † Methods Arabidopsis seedlings were grown on vertical agar plates at 21, 8, 4 and 1 % (v/v) external oxygen for 0 . 5, 2 and 48 h. Roots were analysed for changes in transcript levels using Affymetrix whole genome DNA microarrays, and for changes in metabolite levels using routine GC-MS based metabolite profiling. Root extension rates were monitored in parallel to investigate adaptive changes in growth. † Key Results The results show that root growth was inhibited and transcript and metabolite profiles were significantly altered in response to a moderate decrease in oxygen concentrations. Low oxygen leads to a preferential up-regulation of genes that might be important to trigger adaptive responses in the plant. A small but highly specific set of genes is induced very early in response to a moderate decrease in oxygen concentrations. Genes that were down-regulated mainly encoded proteins involved in energy-consuming processes. In line with this, root extension growth was significantly decreased which will ultimately save ATP and decrease oxygen consumption. This was accompanied by a differential regulation of metabolite levels at short-and long-term incubation at low oxygen. † Conclusions The results show that there are adaptive changes in root extension involving large-scale reprogramming of gene expression and metabolism when oxygen concentration is decreased in a very narrow range.
Reactive Oxygen Species-Driven Transcription in Arabidopsis under Oxygen Deprivation
Plant Physiology, 2012
Reactive oxygen species (ROS) play an important role as triggers of gene expression during biotic and abiotic stresses, among which is low oxygen (O2). Previous studies have shown that ROS regulation under low O2 is driven by a RHO-like GTPase that allows tight control of hydrogen peroxide (H2O2) production. H2O2 is thought to regulate the expression of heat shock proteins, in a mechanism that is common to both O2 deprivation and to heat stress. In this work, we used publicly available Arabidopsis (Arabidopsis thaliana) microarray datasets related to ROS and O2 deprivation to define transcriptome convergence pattern. Our results show that although Arabidopsis response to anoxic and hypoxic treatments share a common core of genes related to the anaerobic metabolism, they differ in terms of ROS-related gene response. We propose that H2O2 production under O2 deprivation is a trait present in a very early phase of anoxia, and that ROS are needed for the regulation of a set of genes belo...
Strategies of Gene Action in Arabidopsis during Hypoxia
Annals of Botany, 1997
Different plant species vary widely in their degree of tolerance to anaerobic stress. The precise molecular mechanisms underlying such tolerance are unknown, but both enzymes of the alcoholic fermentation pathway, pyruvate decarboxylase and alcohol dehydrogenase, are strongly induced during conditions of low oxygen. We have isolated two adh and two pdc genes in Arabidopsis thaliana (L.)Heynh. The patterns of expression of these genes have identified two sets of alcoholic fermentation pathway genes, each of which might play a different role in the adaptive response of the plant to anoxia. One set is strongly induced by low oxygen stress mainly in the roots, while the other set is expressed constitutively in both roots and leaves. Arabidopsis also has two haemoglobin genes, only one of which is induced by hypoxia. We are investigating the components of the signal transduction pathways leading to adh and pdc induction. Implications of our findings for metabolic engineering of plants to improve flooding tolerance are discussed.
2003
Transposon tagging with modi®ed maize Ds±GUS constructs was used to isolate genes induced by oxygen deprivation in Arabidopsis thaliana. Seedlings of 800 gene-trap (DsG) and 600 enhancer-trap (DsE) lines were grown on vertically positioned plates for 1 week, oxygen deprived for up to 24 h and stained for GUS activity. Oxygen deprivation induced intricate patterns of gene expression in seedlings of 65 lines. The insertion site and phenotypes of 15 lines were examined. Surprisingly, none of the insertions were into genes that encode known anaerobic polypeptides. Insertions were identi®ed within or adjacent to genes encoding proteins of regulatory, enzymatic, mitochondrial protein import and unknown function, as well as adjacent to genes encoding a putative receptor-like kinase and putative sensor-histidine kinase. Four lines had signi®cantly lower ADH activity after 24 h of oxygen deprivation and three of these showed reduced stress tolerance. Two lines with wild-type levels of ADH were low-oxygen intolerant. Paradoxically, several lines had signi®cantly higher ADH activity after 12 h of oxygen deprivation but reduced stress tolerance. Caffeine treatment, which increased ADH speci®c activity in wild-type seedlings under aerobic conditions, was suf®cient to increase GUS staining in seven of the 15 lines, providing evidence that these genes may be regulated by cytosolic calcium levels. These results demonstrate the effectiveness of the Ds±GUS tagging system in the identi®cation of genes that are regulated in response to oxygen deprivation and a calcium second messenger.
Identification of late O 3 -responsive genes in Arabidopsis thaliana by cDNA microarray analysis
Physiologia Plantarum, 2006
To better understand the response of a plant to O 3 stress, an integrated microarray analysis was performed on Arabidopsis plants exposed during 2 days to purified air or 150 nl l ÿ1 O 3 , 8 h dayÿ1. Agilent Arabidopsis 2 Oligo Microarrays were used of which the reliability was confirmed by quantitative real-time PCR of nine randomly selected genes. We confirmed the O 3 responsiveness of heat shock proteins (HSPs), glutathione-S-tranferases and genes involved in cell wall stiffening and microbial defence. Whereas, a previous study revealed that during an early stage of the O 3 stress response, gene expression was strongly dependent on jasmonic acid and ethylene, we report that at a later stage (48 h) synthesis of jasmonic acid and ethylene was downregulated. In addition, we observed the simultaneous induction of salicylic acid synthesis and genes involved in programmed cell death and senescence. Also typically, the later stage of the response to O 3 appeared to be the induction of the complete pathway leading to the biosynthesis of anthocyanin diglucosides and the induction of thioredoxin-based redox control. Surprisingly absent in the list of induced genes were genes involved in ASC-dependent antioxidation, few of which were found to be induced after 12 h of O 3 exposure in another study. We discuss these and other particular results of the microarray analysis and provide a map depicting significantly affected genes and their pathways highlighting their interrelationships and subcellular localization.
Plant Physiology, 2003
We manipulated the enzyme activity levels of the alcohol fermentation pathway, pyruvate decarboxylase (PDC), and alcohol dehydrogenase (ADH) in Arabidopsis using sense and antisense overexpression of the corresponding genes (PDC1, PDC2, and ADH1). Transgenic plants were analyzed for levels of fermentation and evaluated for changes in hypoxic survival. Overexpression of either Arabidopsis PDC1 or PDC2 resulted in improved plant survival.
Faculty of 1000 evaluation for Regulation of the Arabidopsis transcriptome by oxidative stress
F1000 - Post-publication peer review of the biomedical literature, 2001
Oxidative stress, resulting from an imbalance in the accumulation and removal of reactive oxygen species such as hydrogen peroxide (H 2 O 2), is a challenge faced by all aerobic organisms. In plants, exposure to various abiotic and biotic stresses results in accumulation of H 2 O 2 and oxidative stress. Increasing evidence indicates that H 2 O 2 functions as a stress signal in plants, mediating adaptive responses to various stresses. To analyze cellular responses to H 2 O 2 , we have undertaken a large-scale analysis of the Arabidopsis transcriptome during oxidative stress. Using cDNA microarray technology, we identified 175 non-redundant expressed sequence tags that are regulated by H 2 O 2. Of these, 113 are induced and 62 are repressed by H 2 O 2. A substantial proportion of these expressed sequence tags have predicted functions in cell rescue and defense processes. RNA-blot analyses of selected genes were used to verify the microarray data and extend them to demonstrate that other stresses such as wilting, UV irradiation, and elicitor challenge also induce the expression of many of these genes, both independently of, and, in some cases, via H 2 O 2 .
Scientific Reports, 2020
Due to climate change, economically important crop plants will encounter flooding periods causing hypoxic stress more frequently. This may lead to reduced yields and endanger food security. As roots are the first organ to be affected by hypoxia, the ability to sense and respond to hypoxic stress is crucial. At the molecular level, therefore, fine-tuning the regulation of gene expression in the root is essential for hypoxia tolerance. Using an RNA-Seq approach, we investigated transcriptome modulation in tomato roots of the cultivar ‘Moneymaker’, in response to short- (6 h) and long-term (48 h) hypoxia. Hypoxia duration appeared to have a significant impact on gene expression such that the roots of five weeks old tomato plants showed a distinct time-dependent transcriptome response. We observed expression changes in 267 and 1421 genes under short- and long-term hypoxia, respectively. Among these, 243 genes experienced changed expression at both time points. We identified tomato genes...
The Plant Journal, 2010
Plants often experience challenging hypoxic conditions imposed by soil waterlogging or complete flooding. In rice, Sub1A, a flooding-induced ethylene responsive factor (ERF) plays a crucial role in submergence tolerance. In this study, we examined two Arabidopsis Hypoxia Responsive ERF genes (HRE1 and HRE2), belonging to the same ERF group as Sub1A. Transgenic Arabidopsis plants, which over-expressed HRE1, showed an improved tolerance of anoxia, whereas a double-knockout mutant hre1hre2 was more susceptible than the wild type. HRE1 over-expressing plants showed an increased activity in the fermentative enzymes pyruvate decarboxylase and alcohol dehydrogenase together with increased ethanol production under hypoxia, but not in normoxia. Whole-genome microarray analyses suggested that an over-expression of HRE1, but not HRE2, increased the induction of most anaerobic genes under hypoxia. Real-time quantitative (q)PCR analyses confirmed a positive effect of HRE1 over-expression on several anaerobic genes, whereas the double-knockout mutant hre1hre2 showed a decreased expression in the same genes after 4 h of hypoxia. Single-knockout mutants did not show significant differences from the wild type. We found that the regulation of HRE1 and HRE2 by low oxygen relies on different mechanisms, since HRE1 requires protein synthesis to be induced while HRE2 does not. HRE2 is likely to be regulated post-transcriptionally by mRNA stabilization. We propose that HRE1 and HRE2 play a partially redundant role in low oxygen signalling in Arabidopsis thaliana, thus improving the tolerance of the plant to the stress by enhancing anaerobic gene expression and ethanolic fermentation.