Comparative analysis between plant species of transcriptional and metabolic responses to hypoxia

Abstract

Summary• The variation in tolerance to low oxygen is likely explained by divergent sets of molecular and metabolic responses between species.• We analysed the versatility of the response to low oxygen of primary metabolism by comparing nine previously published metabolome profiling studies. Data were juxtaposed with expression profiles of genes encoding enzymes involved in the metabolic pathways of rice, Arabidopsis and poplar. Furthermore, full transcript profiles were compared to determine commonalities in the expression of orthologous genes and genes that serve similar functions.• Activation of fermentation and the accumulation of alanine plus succinate were observed in all species, but transcriptional regulation of these metabolic pathways varied. Global analysis of orthologue expression revealed that most differentially expressed genes either had no orthologues or were not affected in the other species. Expression analysis of nearly all gene clusters with common functions varied significantly between species.• The resemblance of the metabolic response to hypoxia indicates that this occurs independent of the level of tolerance. However, regulation of these processes at transcriptional level varied between species. An important role is suggested for signalling and post-transcriptional regulation to be involved in the mechanisms that lead to tolerance to hypoxia.

Oxygen Sensing via the Ethylene Response Transcription Factor RAP2.12 Affects Plant Metabolism and Performance under Both Normoxia and Hypoxia

“…This was accompanied by a strong increase in the levels of many amino acids, such as Val, Ala, Ser, Thr, Met, Leu, Ile, Asp, Lys, Cyt, Pro, Orn, Glu, Gln, GABA, Arg, Phe, and Trp (Fig. 5, B and C), a response that has also been found to be a characteristic of hypoxic conditions in the past Narsai et al, 2011;António et al, 2016). Interestingly, there was also an increase in important metabolites deriving from amino acids, Figure 4.…”

“…5C). These changes in TCA cycle intermediates have been found to be a characteristic response to hypoxic conditions in previous studies (Geigenberger et al, 2000;van Dongen et al, 2009;Narsai et al, 2011;António et al, 2016), indicating an inhibition of succinate dehydrogenase (SDH; also known as complex II of the mitochondrial electron transport chain), bifurcation of the TCA cycle, and inhibition of respiration (Rocha et al, 2010;António et al, 2016.). This was accompanied by a strong increase in the levels of many amino acids, such as Val, Ala, Ser, Thr, Met, Leu, Ile, Asp, Lys, Cyt, Pro, Orn, Glu, Gln, GABA, Arg, Phe, and Trp (Fig.…”

Waterproofing Crops: Effective Flooding Survival Strategies

“…These meta-analyses demonstrate common themes of low-oxygen response in monocots and eudicots. The primary response includes the upregulation of genes and metabolites associated with enhanced glycolytic and fermentative pathways as well as the accumulation of Ala, g-aminobutyric acid, and succinate Narsai et al, 2011). Although anaerobic metabolism typically decreases ATP yield per mole of Glc from 34 to 36 to as few as 2, there is strong evidence that some plants enhance metabolism in a manner that boosts the net yield of ATP generated under anaerobiosis.…”

“…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).…”

Regulation of poly(A) RNA retention in the nucleus as a survival strategy of plants during hypoxia

“…Therefore, many plants have developed an alternative response to low-oxygen conditions: the production of alanine from pyruvate by alanine aminotransferase (AlaAT). 5,6 This process includes the generation of 2-oxoglutarate as a co-product that can be further metabolized to succinate via the TCA cycle, thereby providing additional ATP per molecule of sucrose metabolized. 7 Plants are able to respond quickly to reduced levels of oxygen in the environment.…”