Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of arabidopsis plants

Abstract

Background and AimsOxygen 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.MethodsArabidopsis 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 ResultsThe 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.ConclusionsThe 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.

Waterproofing Crops: Effective Flooding Survival Strategies

“…Evaluation of metabolic gymnastics in response to oxygen deprivation and flooding has been accomplished often in concert with the evaluation of transcriptomes and translatomes (Branco-Price et al, 2008;Kreuzwieser et al, 2009;van Dongen et al, 2009;Narsai et al, 2011;Barding et al, 2012). In a comparative study of rice and wheat, changes in metabolites were considered along with alterations in the proteome (ShingakiWells et al, 2011).…”

The Heat-Inducible Transcription Factor HsfA2 Enhances Anoxia Tolerance in Arabidopsis

“…Little is known, however, about the mechanisms of anoxia tolerance in other plant species. Even flood-intolerant species such as Arabidopsis (Arabidopsis thaliana) trigger many genes generally associated with flooding tolerance (Klok et al, 2002;Branco-Price et al, 2005Loreti et al, 2005;van Dongen et al, 2009), suggesting that the regulation of flooding tolerance and the differences between species are far more complex than previously thought.…”

Defining Core Metabolic and Transcriptomic Responses to Oxygen Availability in Rice Embryos and Young Seedlings

“…Despite differences in tolerance to anaerobic conditions, plant size, and life cycle, the use of transcriptomic approaches to study the response to anaerobic conditions in Arabidopsis (Arabidopsis thaliana; Liu et al, 2005;Loreti et al, 2005;Van Dongen et al, 2009), rice (Oryza sativa; Lasanthi- Kudahettige et al, 2007;Magneschi and Perata, 2009), and poplar (Populus 3 canescens; Kreuzwieser et al, 2009) reveals similar changes in primary carbon metabolism. However, more global analysis of these studies also reveals that the number of genes that displayed significant changes in abundance varied greatly between species; in Arabidopsis, only 1,266 transcripts were altered in abundance in response to anoxia (Klok et al, 2002;Liu et al, 2005), 3,134 probe sets were observed to change sig-nificantly in rice coleoptiles under the conditions analyzed (Lasanthi-Kudahettige et al, 2007), while as many as 5,000 transcripts were altered in roots of poplar (Kreuzwieser et al, 2009).…”