Ethylene Differentially Modulates Hypoxia Responses and Tolerance across Solanum Species

The increasing occurrence of floods hinders agricultural crop production and threatens global food security. The majority of vegetable crops are highly sensitive to flooding and it is unclear how these plants use flooding signals to acclimate to impending oxygen deprivation (hypoxia). Previous research has shown that the early flooding signal ethylene augments hypoxia responses and improves survival in Arabidopsis. To unravel how cultivated and wild Solanum species integrate ethylene signaling to control subsequent hypoxia acclimation, we studied the transcript levels of a selection of marker genes, whose upregulation is indicative of ethylene-mediated hypoxia acclimation in Arabidopsis. Our results suggest that ethylene-mediated hypoxia acclimation is conserved in both shoots and roots of the wild Solanum species bittersweet (Solanum dulcamara) and a waterlogging-tolerant potato (Solanum tuberosum) cultivar. However, ethylene did not enhance the transcriptional hypoxia response in roots of a waterlogging-sensitive potato cultivar, suggesting that waterlogging tolerance in potato could depend on ethylene-controlled hypoxia responses in the roots. Finally, we show that ethylene rarely enhances hypoxia-adaptive genes and does not improve hypoxia survival in tomato (Solanum lycopersicum). We conclude that analyzing genes indicative of ethylene-mediated hypoxia acclimation is a promising approach to identifying key signaling cascades that confer flooding tolerance in crops.

Two Rumex species from contrasting hydrological niches regulate flooding tolerance through distinct mechanisms

Global climate change has increased flooding events, which affect both natural vegetation dynamics and crop productivity. The flooded environment is lethal for most plant species because it restricts gas exchange and induces an energy and carbon crisis. Flooding survival strategies have been studied in Oryza sativa, a cultivated monocot. However, our understanding of plant adaptation to natural flood-prone environments remains scant, even though wild plants represent a valuable resource of tolerance mechanisms that could be used to generate stress-tolerant crops. Here we identify mechanisms that mediate the distinct flooding survival strategies of two related wild dicot species: Rumex palustris and Rumex acetosa. Whole transcriptome sequencing and metabolite profiling reveal flooding-induced metabolic reprogramming specific to R. acetosa. By contrast, R. palustris uses the early flooding signal ethylene to increase survival by regulating shade avoidance and photomorphogenesis genes to outgrow submergence and by priming submerged plants for future low oxygen stress. These results provide molecular resolution of flooding survival strategies of two species occupying distinct hydrological niches. Learning how these contrasting flood adaptive strategies evolved in nature will be instrumental for the development of stress-tolerant crop varieties that deliver enhanced yields in a changing climate.

Root transcript profiling of two Rorippa species reveals gene clusters associated with extreme submergence tolerance

Complete submergence represses photosynthesis and aerobic respiration, causing rapid mortality in most terrestrial plants. However, some plants have evolved traits allowing them to survive prolonged flooding, such as species of the genus Rorippa, close relatives of Arabidopsis (Arabidopsis thaliana). We studied plant survival, changes in carbohydrate and metabolite concentrations, and transcriptome responses to submergence of two species, Rorippa sylvestris and Rorippa amphibia. We exploited the close relationship between Rorippa species and the model species Arabidopsis by using Arabidopsis GeneChip microarrays for whole-genome transcript profiling of roots of young plants exposed to a 24-h submergence treatment or air. A probe mask was used based on hybridization of genomic DNA of both species to the arrays, so that weak probe signals due to Rorippa species/Arabidopsis mismatches were removed. Furthermore, we compared Rorippa species microarray results with those obtained for roots of submerged Arabidopsis plants. Both Rorippa species could tolerate deep submergence, with R. sylvestris surviving much longer than R. amphibia. Submergence resulted in the induction of genes involved in glycolysis and fermentation and the repression of many energy-consuming pathways, similar to the low-oxygen and submergence response of Arabidopsis and rice (Oryza sativa). The qualitative responses of both Rorippa species to submergence appeared roughly similar but differed quantitatively. Notably, glycolysis and fermentation genes and a gene encoding sucrose synthase were more strongly induced in the less tolerant R. amphibia than in R. sylvestris. A comparison with Arabidopsis microarray studies on submerged roots revealed some interesting differences and potential tolerance-related genes in Rorippa species.

Flooding: the survival strategies of plants

Floodplains and wetlands are highly suitable for plant ecological studies, whether for agricultural interests, nature conservation or basic science. Traditional work has entailed a descriptive approach at the community or individual plant level. Nowadays these studies are evolving into physiological research on relationships between flooding stress and vegetation zonation. Current experiments aim to unravel the adaptive mechanisms whereby terrestrial plants cope with the peculiar conditions of the floodplain, from the whole plant down to the cell.

Photoreceptors CRYTOCHROME2 and phytochrome B control chromatin compaction in Arabidopsis

Development and acclimation processes to the environment are associated with large-scale changes in chromatin compaction in Arabidopsis (Arabidopsis thaliana). Here, we studied the effects of light signals on chromatin organization. A decrease in light intensity induces a large-scale reduction in chromatin compaction. This low light response is reversible and shows strong natural genetic variation. Moreover, the degree of chromatin compaction is affected by light quality signals relevant for natural canopy shade. The photoreceptor CRYPTOCHROME2 appears a general positive regulator of low light-induced chromatin decompaction. Phytochrome B also controls light-induced chromatin organization, but its effect appears to be dependent on the genetic background. We present a model in which chromatin compaction is regulated by the light environment via CRYPTOCHROME2 protein abundance, which is controlled by phytochrome B action.

Light quality-mediated petiole elongation in Arabidopsis during shade avoidance involves cell wall modification by xyloglucan endotransglucosylase/hydrolases

Some plants can avoid shaded conditions via rapid shoot elongation, thus growing into better lit areas in a canopy. Cell wall-modifying mechanisms promoting this elongation response, therefore, are important regulatory points during shade avoidance. Two major cell wall-modifying protein families are expansins and xyloglucan endotransglucosylase/hydrolases (XTHs). The role of these proteins during shade avoidance was studied in Arabidopsis (Arabidopsis thaliana). In response to two shade cues, low red to far-red light (implying neighbor proximity) and green shade (mimicking dense canopy conditions), Arabidopsis showed classic shade avoidance features: petiole elongation and leaf hyponasty. Measurement of the apoplastic proton flux in green shade-treated petioles revealed a rapid efflux of protons into the apoplast within minutes, unlike white light controls. This apoplastic acidification probably provides the acidic pH required for the optimal activity of cell wall-modifying proteins like expansins and XTHs. Acid-induced extension, expansin susceptibility, and extractable expansin activity were similar in petioles from white light- and shade-treated plants. XTH activity, however, was high in petioles exposed to shade treatments. Five XTH genes (XTH9, -15, -16, -17, and -19) were positively regulated by low red to far-red light conditions, while the latter four and XTH22 showed a significant up-regulation also in response to green shade. Consistently, knockout mutants for two of these XTH genes also had reduced or absent shade avoidance responses to these light signals. These results point toward the cell wall as a vital regulatory point during shade avoidance.

Hormone- and light-mediated regulation of heat-induced differential petiole growth in Arabidopsis

Plants react quickly and profoundly to changes in their environment. A sudden increase in temperature, for example, induces differential petiole growth-driven upward leaf movement (hyponastic growth) in Arabidopsis (Arabidopsis thaliana). We show that accessions that face the strongest fluctuations in diurnal temperature in their natural habitat are least sensitive for heat-induced hyponastic growth. This indicates that heat-induced hyponastic growth is a trait subject to natural selection. The response is induced with kinetics remarkably similar to ethylene- and low light-induced hyponasty in several accessions. Using pharmacological assays, transcript analysis, and mutant analyses, we demonstrate that ethylene and the photoreceptor protein phytochrome B are negative regulators of heat-induced hyponastic growth and that low light, phytochrome A, auxin, polar auxin transport, and abscisic acid are positive regulators of heat-induced hyponastic growth. Furthermore, auxin, auxin polar transport, phytochrome A, phytochrome B, and cryptochromes are required for a fast induction of heat-induced hyponastic growth.

Submergence induces expansin gene expression in flooding-tolerant Rumex palustris and not in flooding-intolerant R. acetosa

Ethylene-enhanced leaf elongation upon submergence is part of the survival mechanism of Rumex palustris Sm. plants that grow in frequently flooded areas. Other Rumex species, like R. acetosa L., do not possess this ability and can therefore only survive in habitats that are not frequently inundated. Expansins are proteins that induce extension of isolated cell walls, and therefore might play a role in the stimulation of petiole elongation, also in Rumex. We report here on the identification of several gene sequences encoding for alpha-expansins in R. palustris and R. acetosa plants. The pattern of transcript accumulation of one of these genes, Rp-EXP1, could be correlated with the pattern of leaf elongation in R. palustris after submergence or ethylene treatment. Induction of expansin gene activity was not found in R. acetosa upon these treatments, indicating that ethylene induces the expression of expansin genes in leaves of species that exhibit flooding-induced shoot elongation.

1-aminocyclopropane-1-carboxylate oxidase activity limits ethylene biosynthesis in Rumex palustris during submergence

Submergence strongly stimulates petiole elongation in Rumex palustris, and ethylene accumulation initiates and maintains this response in submerged tissues. cDNAs from R. palustris corresponding to a 1-aminocyclopropane-1-carboxylate (ACC) oxidase gene (RP-ACO1) were isolated from elongating petioles and used to study the expression of the corresponding gene. An increase in RP-ACO1 messenger was observed in the petioles and lamina of elongating leaves 2 h after the start of submergence. ACC oxidase enzyme activity was measured in homogenates of R. palustris shoots, and a relevant increase was observed within 12 h under water with a maximum after 24 h. We have shown previously that the ethylene production rate of submerged shoots does not increase significantly during the first 24 h of submergence (L.A.C.J. Voesenek, M. Banga, R. H. Thier, C.M. Mudde, F.M. Harren, G.W.M. Barendse, C.W.P.M. Blom [1993] Plant Physiol 103: 783-791), suggesting that under these conditions ACC oxidase activity is inhibited in vivo. We found evidence that this inhibition is caused by a reduction of oxygen levels. We hypothesize that an increased ACC oxidase enzyme concentration counterbalances the reduced enzyme activity caused by low oxygen concentration during submergence, thus sustaining ethylene production under these conditions. Therefore, ethylene biosynthesis seems to be limited at the level of ACC oxidase activity rather than by ACC synthase in R. palustris during submergence.

A homolog of the Arabidopsis thaliana ERS gene is actively regulated in Rumex palustris upon flooding

A cDNA homologous to the ethylene-response sensors (ERS/ETR1) from Arabidopsis thaliana was isolated from a Rumex palustris cDNA library. This cDNA, RP-ERS1, was 2421 bp long and shared 66% nucleotide homology with ETR1 and ERS in their coding regions. The transcript level of RP-ERS1 was actively regulated during the leafelongation response of R. palustris upon flooding. RP-ERS1 transcript levels increased after submergence, and also after exposure to high concentrations of ethylene and carbon dioxide and low concentrations of oxygen. These results suggest that R. palustris plants may respond to flooding stress by increasing the number of their ethylene receptors.

Ethylene production and petiole growth in rumex plants induced by soil waterlogging: the application of a continuous flow system and a laser driven intracavity photoacoustic detection system

Petiole growth of Rumex acetosa L., Rumex crispus L., and Rumex palustris Sm. in response to soil waterlogging was studied in relation to production of the gaseous plant hormone ethylene. Ethylene production was monitored in a flow-through system and a recently developed laser driven photoacoustic detection system, which allowed ethylene measurements as low as 6 picoliters per liter. R. acetosa showed a two-fold increase in ethylene production correlated with a slight enhancement of the growth of the petiole that developed during the waterlogging treatment. Both R. crispus and R. palustris showed a strong petiole elongation of existing as well as newly formed petioles, which was correlated with a 20-fold increase in ethylene production after approximately 7 days. Increased rates of ethylene production in R. palustris were related to a strong increase in 1-aminocyclopropane-1-carboxylic acid (ACC) concentration and a slight, but detectable, increase in ethylene forming enzyme activity. In R. acetosa on the other hand, only a very small increase in ACC concentration was observed. Changes in ethylene production in Rumex are strongly correlated with variation in ACC content and ethylene forming enzyme activity. The interaction between ethylene production/internal concentration and ethylene sensitivity of the three Rumex species is discussed in relation to their field location in a flooding gradient and their differential resistance toward waterlogging and submergence.