Signaling events in the hypoxic induction of alcohol dehydrogenase gene in Arabidopsis

Differential leaf flooding resilience in Arabidopsis thaliana is controlled by ethylene signaling-activated and age-dependent phosphorylation of ORESARA1

The phytohormone ethylene is a major regulator of plant adaptive responses to flooding. In flooded plant tissues, ethylene quickly increases to high concentrations owing to its low solubility and diffusion rates in water. Ethylene accumulation in submerged plant tissues makes it a reliable cue for triggering flood acclimation responses, including metabolic adjustments to cope with flood-induced hypoxia. However, persistent ethylene accumulation also accelerates leaf senescence. Stress-induced senescence hampers photosynthetic capacity and stress recovery. In submerged Arabidopsis, senescence follows a strict age-dependent pattern starting with the older leaves. Although mechanisms underlying ethylene-mediated senescence have been uncovered, it is unclear how submerged plants avoid indiscriminate breakdown of leaves despite high systemic ethylene accumulation. We demonstrate that although submergence triggers leaf-age-independent activation of ethylene signaling via EIN3 in Arabidopsis, senescence is initiated only in old leaves. EIN3 stabilization also leads to overall transcript and protein accumulation of the senescence-promoting transcription factor ORESARA1 (ORE1) in both old and young leaves during submergence. However, leaf-age-dependent senescence can be explained by ORE1 protein activation via phosphorylation specifically in old leaves, independent of the previously identified age-dependent control of ORE1 via miR164. A systematic analysis of the roles of the major flooding stress cues and signaling pathways shows that only the combination of ethylene and darkness is sufficient to mimic submergence-induced senescence involving ORE1 accumulation and phosphorylation. Hypoxia, most often associated with flooding stress in plants, appears to have no role in these processes. Our results reveal a mechanism by which plants regulate the speed and pattern of senescence during environmental stresses such as flooding. Age-dependent ORE1 activity ensures that older, expendable leaves are dismantled first, thus prolonging the life of younger leaves and meristematic tissues that are vital to whole-plant survival.

Genomic analysis of the emergent aquatic plant Sparganium stoloniferum provides insights into its clonality, local adaptation and demographic history

Clonal propagation and extensive dispersal of seeds and asexual propagules are two important features of aquatic plants that help them adapt to aquatic environments. Accurate measurements of clonality and effective clonal dispersal are essential for understanding the evolution of aquatic plants. Here, we first assembled a high-quality chromosome-level genome of a widespread emergent aquatic plant Sparganium stoloniferum to provide a reference for its population genomic study. We then performed high-depth resequencing of 173 individuals from 20 populations covering different basins across its range in China. Population genomic analyses revealed three genetic lineages reflecting the northeast (NE), southwest (SW) and northwest (NW) of its geographical distribution. The NE lineage diverged in the middle Pleistocene while the SW and NW lineages diverged until about 2400 years ago. Clonal relationship analyses identified nine populations as monoclonal population. Dispersal of vegetative propagules was identified between five populations covering three basins in the NE lineage, and dispersal distance was up to 1041 km, indicating high dispersibility in emergent aquatic plant species. We also identified lineage-specific positively selected genes that are likely to be involved in adaptations to saline wetlands and high-altitude environments. Our findings accurately measure the clonality, determine the dispersal range and frequency of vegetative propagules, and detect genetic signatures of local adaptation in a widespread emergent aquatic plant species, providing new perspectives on the evolution of aquatic plants.

Genomic convergence underlying high-altitude adaptation in alpine plants

Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection. However, genomic evidence for convergent adaptation to extreme environments remains scarce. Here, we assembled reference genomes of two alpine plants, Saussurea obvallata (Asteraceae) and Rheum alexandrae (Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes, we elucidated genomic convergence underlying high-altitude adaptation in alpine plants. Our results detected convergent contractions of disease-resistance genes in alpine genomes, which might be an energy-saving strategy for surviving in hostile environments with only a few pathogens present. We identified signatures of positive selection on a set of genes involved in reproduction and respiration (e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self-incompatibility, cell wall modification, DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive "greenhouse" morphology. Our integrative data provide novel insights into convergent evolution at a high-taxonomic level, aiding in a deep understanding of genetic adaptation to complex environments.

Ethylene: A Master Regulator of Plant-Microbe Interactions under Abiotic Stresses

The plant phytohormone ethylene regulates numerous physiological processes and contributes to plant-microbe interactions. Plants induce ethylene production to ward off pathogens after recognition of conserved microbe-associated molecular patterns (MAMPs). However, plant immune responses against pathogens are essentially not different from those triggered by neutral and beneficial microbes. Recent studies indicate that ethylene is an important factor for beneficial plant-microbial association under abiotic stress such as salt and heat stress. The association of beneficial microbes with plants under abiotic stresses modulates ethylene levels which control the expression of ethylene-responsive genes (ERF), and ERFs further regulate the plant transcriptome, epi-transcriptome, Na⁺/K⁺ homeostasis and antioxidant defense mechanisms against reactive oxygen species (ROS). Understanding ethylene-dependent plant-microbe interactions is crucial for the development of new strategies aimed at enhancing plant tolerance to harsh environmental conditions. In this review, we underline the importance of ethylene in beneficial plant-microbe interaction under abiotic stresses.

Ethylene augments root hypoxia tolerance via growth cessation and reactive oxygen species amelioration

Flooded plants experience impaired gas diffusion underwater, leading to oxygen deprivation (hypoxia). The volatile plant hormone ethylene is rapidly trapped in submerged plant cells and is instrumental for enhanced hypoxia acclimation. However, the precise mechanisms underpinning ethylene-enhanced hypoxia survival remain unclear. We studied the effect of ethylene pretreatment on hypoxia survival of Arabidopsis (Arabidopsis thaliana) primary root tips. Both hypoxia itself and re-oxygenation following hypoxia are highly damaging to root tip cells, and ethylene pretreatments reduced this damage. Ethylene pretreatment alone altered the abundance of transcripts and proteins involved in hypoxia responses, root growth, translation, and reactive oxygen species (ROS) homeostasis. Through imaging and manipulating ROS abundance in planta, we demonstrated that ethylene limited excessive ROS formation during hypoxia and subsequent re-oxygenation and improved oxidative stress survival in a PHYTOGLOBIN1-dependent manner. In addition, we showed that root growth cessation via ethylene and auxin occurred rapidly and that this quiescence behavior contributed to enhanced hypoxia tolerance. Collectively, our results show that the early flooding signal ethylene modulates a variety of processes that all contribute to hypoxia survival.

Strawberry FaSnRK1α Regulates Anaerobic Respiratory Metabolism under Waterlogging

Sucrose nonfermenting-1-related protein kinase 1 (SnRK1) is a central integrator of plant stress and energy starvation signalling pathways. We found that the FaSnRK1α-overexpression (OE) roots had a higher respiratory rate and tolerance to waterlogging than the FaSnRK1α-RNAi roots, suggesting that FaSnRK1α plays a positive role in the regulation of anaerobic respiration under waterlogging. FaSnRK1α upregulated the activity of anaerobic respiration-related enzymes including hexokinase (HK), phosphofructokinase (PFK), pyruvate kinase (PK), pyruvate decarboxylase (PDC), alcohol dehydrogenase (ADH) and lactate dehydrogenase (LDH). FaSnRK1α also enhanced the ability to quench reactive oxygen species (ROS) by increasing antioxidant enzyme activities. We sequenced the transcriptomes of the roots of both wild-type (WT) and FaSnRK1α-RNAi plants, and the differentially expressed genes (DEGs) were clearly enriched in the defence response, response to biotic stimuli, and cellular carbohydrate metabolic process. In addition, 42 genes involved in glycolysis and 30 genes involved in pyruvate metabolism were significantly regulated in FaSnRK1α-RNAi roots. We analysed the transcript levels of two anoxia-related genes and three ERFVIIs, and the results showed that FaADH1, FaPDC1, FaHRE2 and FaRAP2.12 were upregulated in response to FaSnRK1α, indicating that FaSnRK1α may be involved in the ethylene signalling pathway to improve waterlogging tolerance. In conclusion, FaSnRK1α increases the expression of ERFVIIs and further activates anoxia response genes, thereby enhancing anaerobic respiration metabolism in response to low-oxygen conditions during waterlogging.

Physiology of Plant Responses to Water Stress and Related Genes: A Review

Drought and waterlogging seriously affect the growth of plants and are considered severe constraints on agricultural and forestry productivity; their frequency and degree have increased over time due to global climate change. The morphology, photosynthetic activity, antioxidant enzyme system and hormone levels of plants could change in response to water stress. The mechanisms of these changes are introduced in this review, along with research on key transcription factors and genes. Both drought and waterlogging stress similarly impact leaf morphology (such as wilting and crimping) and inhibit photosynthesis. The former affects the absorption and transportation mechanisms of plants, and the lack of water and nutrients inhibits the formation of chlorophyll, which leads to reduced photosynthetic capacity. Constitutive overexpression of 9-cis-epoxydioxygenase (NCED) and acetaldehyde dehydrogenase (ALDH), key enzymes in abscisic acid (ABA) biosynthesis, increases drought resistance. The latter forces leaf stomata to close in response to chemical signals, which are produced by the roots and transferred aboveground, affecting the absorption capacity of CO2, and reducing photosynthetic substrates. The root system produces adventitious roots and forms aerenchymal to adapt the stresses. Ethylene (ETH) is the main response hormone of plants to waterlogging stress, and is a member of the ERFVII subfamily, which includes response factors involved in hypoxia-induced gene expression, and responds to energy expenditure through anaerobic respiration. There are two potential adaptation mechanisms of plants (“static” or “escape”) through ETH-mediated gibberellin (GA) dynamic equilibrium to waterlogging stress in the present studies. Plant signal transduction pathways, after receiving stress stimulus signals as well as the regulatory mechanism of the subsequent synthesis of pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) enzymes to produce ethanol under a hypoxic environment caused by waterlogging, should be considered. This review provides a theoretical basis for plants to improve water stress tolerance and water-resistant breeding.

The role of alanine synthesis and nitrate-induced nitric oxide production during hypoxia stress in Cucurbita pepo nectaries

Floral nectar is a sugary solution produced by nectaries to attract and reward pollinators. Nectar metabolites, such as sugars, are synthesized within the nectary during secretion from both pre-stored and direct phloem-derived precursors. In addition to sugars, nectars contain nitrogenous compounds such as amino acids; however, little is known about the role(s) of nitrogen (N) compounds in nectary function. In this study, we investigated N metabolism in Cucurbita pepo (squash) floral nectaries in order to understand how various N-containing compounds are produced and determine the role of N metabolism in nectar secretion. The expression and activity of key enzymes involved in primary N assimilation, including nitrate reductase (NR) and alanine aminotransferase (AlaAT), were induced during secretion in C. pepo nectaries. Alanine (Ala) accumulated to about 35% of total amino acids in nectaries and nectar during peak secretion; however, alteration of vascular nitrate supply had no impact on Ala accumulation during secretion, suggesting that nectar(y) amino acids are produced by precursors other than nitrate. In addition, nitric oxide (NO) is produced from nitrate and nitrite, at least partially by NR, in nectaries and nectar. Hypoxia-related processes are induced in nectaries during secretion, including lactic acid and ethanolic fermentation. Finally, treatments that alter nitrate supply affect levels of hypoxic metabolites, nectar volume and nectar sugar composition. The induction of N metabolism in C. pepo nectaries thus plays an important role in the synthesis and secretion of nectar sugar.

The role of ethylene in metabolic acclimations to low oxygen

Submerged plants ultimately suffer from shortage in cellular oxygen availability (hypoxia) as a result of impaired gas diffusion underwater. The gaseous plant hormone ethylene is rapidly entrapped in submerged plant tissues and is an established regulator of morphological and anatomical flood-adaptive responses. Multiple recent discoveries suggest that ethylene also plays a crucial role in hypoxia anticipation and metabolic acclimation during plant submergence. Ethylene was shown to accelerate and enhance the hypoxic response through enhanced stability of specific transcription factors (group VII ethylene response factors). Moreover, we suggest that ethylene could play an important role in the induction of autophagy and promote reactive oxygen species amelioration, thereby contributing to enhanced survival during flooding, hypoxia, and reoxygenation stress.

New insights into the role of lipids in plant hypoxia responses

In plants, hypoxia (low-oxygen stress) is induced by soil waterlogging or submergence and this major abiotic stress has detrimental effects on plant growth, development, distribution, and productivity. To survive low-oxygen stress, plants have evolved a set of morphological, physiological, and biochemical adaptations. These adaptations integrate metabolic acclimation and signaling networks allowing plants to endure or escape from low-oxygen environments by altering their metabolism and growth. Lipids are ubiquitously involved in regulating plant responses to hypoxia and post-hypoxic reoxygenation. In particular, the polyunsaturation of long-chain acyl-CoAs regulates hypoxia sensing in plants by modulating acyl-CoA-binding protein-Group VII ethylene response factor dynamics. Moreover, unsaturated very-long-chain ceramide species protect plants from hypoxia-induced cellular damage by regulating the kinase activity of CONSTITUTIVE TRIPLE RESPONSE1 in the ethylene signaling pathway. Finally, the oxylipin jasmonate specifically regulates plant responses to reoxygenation stress by transcriptionally modulating antioxidant biosynthesis. Here we provide an overview of the roles of lipid remodeling and signaling in plant responses to hypoxia/reoxygenation and their effects on the downstream events affecting plant survival. In addition, we highlight the key remaining challenges in this important field.

Submergence deactivates wound-induced plant defence against herbivores

Flooding is a common and critical disaster in agriculture, because it causes defects in plant growth and even crop loss. An increase in herbivore populations is often observed after floods, which leads to additional damage to the plants. Although molecular mechanisms underlying the plant responses to flooding have been identified, how plant defence systems are affected by flooding remains poorly understood. Herein, we show that submergence deactivates wound-induced defence against herbivore attack in Arabidopsis thaliana. Submergence rapidly suppressed the wound-induced expression of jasmonic acid (JA) biosynthesis genes, resulting in reduced JA accumulation. While plants exposed to hypoxia in argon gas exhibited similar reduced wound responses, the inhibitory effects were initiated after short-term submergence without signs for lack of oxygen. Instead, expression of ethylene-responsive genes was increased after short-term submergence. Blocking ethylene signalling by ein2-1 mutation partially restored suppressed expression of several wound-responsive genes by submergence. In addition, submergence rapidly removed active markers of histone modifications at a gene locus involved in JA biosynthesis. Our findings suggest that submergence inactivates defence systems of plants, which would explain the proliferation of herbivores after flooding.

Hyo-Jun Lee et al. show that submergence in Arabidopsis deactivates wound-induced defence against herbivore attack by suppressing the expression of jasmonic acid biosynthesis genes and increasing expression of ethylene-responsive genes. These results shed light on how flooding may impact plant defence systems.

The Anaerobic Product Ethanol Promotes Autophagy-Dependent Submergence Tolerance in Arabidopsis

In response to hypoxia under submergence, plants switch from aerobic respiration to anaerobic fermentation, which leads to the accumulation of the end product, ethanol. We previously reported that Arabidopsis thaliana autophagy-deficient mutants show increased sensitivity to ethanol treatment, indicating that ethanol is likely involved in regulating the autophagy-mediated hypoxia response. Here, using a transcriptomic analysis, we identified 3909 genes in Arabidopsis seedlings that were differentially expressed in response to ethanol treatment, including 2487 upregulated and 1422 downregulated genes. Ethanol treatment significantly upregulated genes involved in autophagy and the detoxification of reactive oxygen species. Using transgenic lines expressing AUTOPHAGY-RELATED PROTEIN 8e fused to green fluorescent protein (GFP-ATG8e), we confirmed that exogenous ethanol treatment promotes autophagosome formation in vivo. Phenotypic analysis showed that deletions in the alcohol dehydrogenase gene in adh1 mutants result in attenuated submergence tolerance, decreased accumulation of ATG proteins, and diminished submergence-induced autophagosome formation. Compared to the submergence-tolerant Arabidopsis accession Columbia (Col-0), the submergence-intolerant accession Landsberg erecta (Ler) displayed hypersensitivity to ethanol treatment; we linked these phenotypes to differences in the functions of ADH1 and the autophagy machinery between these accessions. Thus, ethanol promotes autophagy-mediated submergence tolerance in Arabidopsis.

Maintenance of photosynthetic capacity in flooded tomato plants with reduced ethylene sensitivity

Ethylene is considered one of the most important plant hormones orchestrating plant responses to flooding stress. However, ethylene may induce deleterious effects on plants, especially when produced at high rates in response to stress. In this paper, we explored the effect of attenuated ethylene sensitivity in the Never ripe (Nr) mutant on leaf photosynthetic capacity of flooded tomato plants. We found out that reduced ethylene perception in Nr plants was associated with a more efficient photochemical and non-photochemical radiative energy dissipation capability in response to flooding. The data correlated with the retention of chlorophyll and carotenoids content in flooded Nr leaves. Moreover, leaf area and specific leaf area were higher in Nr, indicating that ethylene would exert a negative role in leaf growth and expansion under flooded conditions. Although stomatal conductance was hampered in flooded Nr plants, carboxylation activity was not affected by flooding in the mutant, suggesting that ethylene is responsible for inducing non-stomatal limitations to photosynthetic CO₂ uptake. Upregulation of several cysteine protease genes and high protease activity led to Rubisco protein loss in response to ethylene under flooding. Reduction of Rubisco content would, at least in part, account for the reduction of its carboxylation efficiency in response to ethylene in flooded plants. Therefore, besides its role as a trigger of many adaptive responses, perception of ethylene entails limitations in light and dark photosynthetic reactions by speeding up the senescence process that leads to a progressive disassembly of the photosynthetic machinery in leaves of flooded tomato plants.

Sub1 Rice: Engineering Rice for Climate Change

By the year 2100, the number of people on Earth is expected to increase by ∼50%, placing increasing demands on food production in a time when a changing climate is predicted to compromise crop yields. Feeding this future world requires scientifically informed innovations in agriculture. Here, we describe how a rice gene conferring tolerance to prolonged submergence has helped farmers in South and Southeast Asia mitigate rice crop failure during floods. We discuss how planting of this new variety benefited socially disadvantaged groups. This example indicates that investment in agricultural improvement can protect farmers from risks associated with a changing climate.

Ethylene signaling involves in seeds germination upon submergence and antioxidant response elicited confers submergence tolerance to rice seedlings

BACKGROUND

Flooding has negative impact on agriculture. The plant hormone ethylene is involved in plant growth and stress responses, which are important role in tolerance and adaptation regulatory mechanisms during submergence stress. Ethylene signaling crosstalk with gibberellin signaling enhances tolerance in lowland rice (Flood Resistant 13A) through a quiescence strategy or in deepwater rice through an escape strategy when rice is submerged. Information regarding ethylene-mediated priming in submergence stress tolerance in rice is scant. Here, we used 1-aminocyclopropane-1-carboxylic acid, an ethylene precursor, to evaluate the response in submerged rice seedlings.

RESULTS

The germination rate and mean germination times of rice seeds was higher in seedlings under submergence only when ethylene signaling was inhibited by supplemented with silver nitrate (AgNO₃). Reduced leaf chlorophyll contents and induced senescence-associated genes in rice seedlings under submergence were relieved by pretreatment with an ethylene precursor. The ethylene-mediated priming by pretreatment with an ethylene precursor enhanced the survival rate and hydrogen peroxide (H₂O₂) and superoxide (O₂^-) anion accumulation and affected antioxidant response in rice seedlings.

CONCLUSIONS

Pretreatment with an ethylene precursor leads to reactive oxygen species generation, which in turn triggered the antioxidant response system, thus improving the tolerance of rice seedlings to complete submergence stress. Thus, H₂O₂ signaling may contribute to ethylene-mediated priming to submergence stress tolerance in rice seedlings.

Novel Insights Into the Early Stages of Ratoon Stunting Disease of Sugarcane Inferred from Transcript and Protein Analysis

Despite of the importance of ratoon stunting disease, little is known on the responses of sugarcane to its causal agent, the vascular bacterial endophyte Leifsonia xyli subsp. xyli. The transcriptome and proteome of young plants of a susceptible cultivar with no symptoms of stunting but with relative low and high bacterial titers were compared at 30 and 60 days after inoculation. Increased bacterial titers were associated with alterations in the expression of 267 cDNAs and in the abundance of 150 proteins involved in plant growth, hormone metabolism, signal transduction and defense responses. Some alterations are predicted to benefit the pathogen, such as the up-regulation of genes involved in the synthesis of methionine. Also, genes and proteins of the cell division cycle were all down-regulated in plants with higher titers at both times. It is hypothesized that the negative effects on cell division related to increased bacterial titers is cumulative over time and its modulation by other host and environmental factors results in the stunting symptom.

Arabidopsis thaliana alcohol dehydrogenase is differently affected by several redox modifications

In plant cells, many stresses, including low oxygen availability, result in a higher production of reactive oxygen species (ROS) and reactive nitrogen species (RNS). These molecules can lead to redox-dependent post-translational modification of proteins Cys residues. Here, we studied the effect of different redox modifications on alcohol dehydrogenase (ADH) from Arabidopsis thaliana. ADH catalyzes the last step of the ethanol fermentation pathway used by plants to cope with energy deficiency during hypoxic stress. Arabidopsis suspension cell cultures showed decreased ADH activity upon exposure to H2O2, but not to the thiol oxidizing agent diamide. We purified recombinant ADH and observed a significant decrease in the enzyme activity by treatments with H2O2 and diethylamine NONOate (DEA/NO). Treatments leading to the formation of a disulfide bond between ADH and glutathione (protein S-glutathionylation) had no negative effect on the enzyme activity. LC-MS/MS analysis showed that Cys47 and Cys243 could make a stable disulfide bond with glutathione, suggesting redox sensitivity of these residues. Mutation of ADH Cys47 to Ser caused an almost complete loss of the enzyme activity while the Cys243 to Ser mutant had increased specific activity. Incubation of ADH with NAD+ or NADH prevented inhibition of the enzyme by H2O2 or DEA/NO. These results suggest that binding of ADH with its cofactors may limit availability of Cys residues to redox modifications. Our study demonstrates that ADH from A. thaliana is subject to different redox modifications. Implications of ADH sensitivity to ROS and RNS during hypoxic stress conditions are discussed.

Hypoxia enhances lignification and affects the anatomical structure in hydroponic cultivation of carrot taproot

Hypoxia enhances lignification of carrot root. Hypoxia stress was thought to be one of the major abiotic stresses that inhibiting the growth and development of higher plants. The genes encoding the plant alcohol dehydrogenase (ADH-P) were induced when suffering hypoxia. To investigate the impact of hypoxia on the carrot root growth, carrot plants were cultivated in the hydroponics with or without aeration. Morphological characteristics, anatomical structure, lignin content, and the expression profiles of DcADH-P genes and lignin biosynthesis-related genes were measured. Six DcADH-P genes were identified from the carrot genome. The expression profiles of only three (DcADH-P1, DcADH-P2, and DcADH-P3) genes could be detected and the other three (DcADH-P4, DcADH-P5, and DcADH-P6) could not be detected when carrot cultivated in the solution without aeration. In addition, carrot roots had more lignin content, aerenchyma and less fresh weight when cultivated in the solution without aeration. These results suggested that hypoxia could enhance the lignification and affect anatomical structure of the carrot root. However, the expression levels of the genes related to lignin biosynthesis were down-regulated under the hypoxia. The enhancement of lignification may be the consequence of the structure changes in the carrot root. Our work was potentially helpful for studying the effect of hypoxia on carrot growth and may provide useful information for carrot hydroponics.

Signal Dynamics and Interactions during Flooding Stress

Flooding is detrimental for nearly all higher plants, including crops. The compound stress elicited by slow gas exchange and low light levels under water is responsible for both a carbon and an energy crisis ultimately leading to plant death. The endogenous concentrations of four gaseous compounds, oxygen, carbon dioxide, ethylene, and nitric oxide, change during the submergence of plant organs in water. These gases play a pivotal role in signal transduction cascades, leading to adaptive processes such as metabolic adjustments and anatomical features. Of these gases, ethylene is seen as the most consistent, pervasive, and reliable signal of early flooding stress, most likely in tight interaction with the other gases. The production of reactive oxygen species (ROS) in plant cells during flooding and directly after subsidence, during which the plant is confronted with high light and oxygen levels, is characteristic for this abiotic stress. Low, well-controlled levels of ROS are essential for adaptive signaling pathways, in interaction with the other gaseous flooding signals. On the other hand, excessive uncontrolled bursts of ROS can be highly damaging for plants. Therefore, a fine-tuned balance is important, with a major role for ROS production and scavenging. Our understanding of the temporal dynamics of the four gases and ROS is basal, whereas it is likely that they form a signature readout of prevailing flooding conditions and subsequent adaptive responses.

Molecular and physiological characterization of AtHIGD1 in Arabidopsis

Flooding is a principal stress that limits plant productivity. The sensing of low oxygen levels (hypoxia) plays a critical role in the signaling pathway that functions in plants in flooded environments. In this study, to investigate hypoxia response mechanisms in Arabidopsis, we identified three hypoxia-related genes and subjected one of these genes, Arabidopsis thaliana HYPOXIA-INDUCED GENE DOMAIN 1 (AtHIGD1), to molecular characterization including gene expression analysis and intracellular localization of the encoded protein. AtHIGD1 was expressed in various organs but was preferentially expressed in developing siliques. Confocal microscopy of transgenic plants harboring eGFP-tagged AtHIGD1 indicated that AtHIGD1 is localized to mitochondria. Importantly, plants overexpressing AtHIGD1 exhibited increased resistance to hypoxia compared to wild type. Our results represent the first report of a biological function for an HIGD protein in plants and indicate that AtHIGD1 is a mitochondrial protein that plays an active role in mitigating the effects of hypoxia on plants.

Ethylene-Regulated Glutamate Dehydrogenase Fine-Tunes Metabolism during Anoxia-Reoxygenation

Ethylene is an essential hormone in plants that is involved in low-oxygen and reoxygenation responses. As a key transcription factor in ethylene signaling, ETHYLENE INSENSITIVE3 (EIN3) activates targets that trigger various responses. However, most of these targets are still poorly characterized. Through analyses of our microarray data and the published Arabidopsis (Arabidopsis thaliana) EIN3 chromatin immunoprecipitation sequencing data set, we inferred the putative targets of EIN3 during anoxia-reoxygenation. Among them, GDH2, which encodes one subunit of glutamate dehydrogenase (GDH), was chosen for further studies for its role in tricarboxylic acid cycle replenishment. We demonstrated that both GDH1 and GDH2 are induced during anoxia and reoxygenation and that this induction is mediated via ethylene signaling. In addition, the results of enzymatic assays showed that the level of GDH during anoxia-reoxygenation decreased in the ethylene-insensitive mutants ein2-5 and ein3eil1 Global metabolite analysis indicated that the deamination activity of GDH might regenerate 2-oxoglutarate, which is a cosubstrate that facilitates the breakdown of alanine by alanine aminotransferase when reoxygenation occurs. Moreover, ineffective tricarboxylic acid cycle replenishment, disturbed carbohydrate metabolism, reduced phytosterol biosynthesis, and delayed energy regeneration were found in gdh1gdh2 and ethylene mutants during reoxygenation. Taken together, these data illustrate the essential role of EIN3-regulated GDH activity in metabolic adjustment during anoxia-reoxygenation.

Arabidopsis CML38, a Calcium Sensor That Localizes to Ribonucleoprotein Complexes under Hypoxia Stress

During waterlogging and the associated oxygen deprivation stress, plants respond by the induction of adaptive programs, including the redirected expression of gene networks toward the synthesis of core hypoxia-response proteins. Among these core response proteins in Arabidopsis (Arabidopsis thaliana) is the calcium sensor CML38, a protein related to regulator of gene silencing calmodulin-like proteins (rgsCaMs). CML38 transcripts are up-regulated more than 300-fold in roots within 6 h of hypoxia treatment. Transfer DNA insertional mutants of CML38 show an enhanced sensitivity to hypoxia stress, with lowered survival and more severe inhibition of root and shoot growth. By using yellow fluorescent protein (YFP) translational fusions, CML38 protein was found to be localized to cytosolic granule structures similar in morphology to hypoxia-induced stress granules. Immunoprecipitation of CML38 from the roots of hypoxia-challenged transgenic plants harboring CML38pro::CML38:YFP followed by liquid chromatography-tandem mass spectrometry analysis revealed the presence of protein targets associated with messenger RNA ribonucleoprotein (mRNP) complexes including stress granules, which are known to accumulate as messenger RNA storage and triage centers during hypoxia. This finding is further supported by the colocalization of CML38 with the mRNP stress granule marker RNA Binding Protein 47 (RBP47) upon cotransfection of Nicotiana benthamiana leaves. Ruthenium Red treatment results in the loss of CML38 signal in cytosolic granules, suggesting that calcium is necessary for stress granule association. These results confirm that CML38 is a core hypoxia response calcium sensor protein and suggest that it serves as a potential calcium signaling target within stress granules and other mRNPs that accumulate during flooding stress responses.

The Alcohol Dehydrogenase Gene Family in Melon (Cucumis melo L.): Bioinformatic Analysis and Expression Patterns

Alcohol dehydrogenases (ADH), encoded by multigene family in plants, play a critical role in plant growth, development, adaptation, fruit ripening and aroma production. Thirteen ADH genes were identified in melon genome, including 12 ADHs and one formaldehyde dehydrogenease (FDH), designated CmADH1-12 and CmFDH1, in which CmADH1 and CmADH2 have been isolated in Cantaloupe. ADH genes shared a lower identity with each other at the protein level and had different intron-exon structure at nucleotide level. No typical signal peptides were found in all CmADHs, and CmADH proteins might locate in the cytoplasm. The phylogenetic tree revealed that 13 ADH genes were divided into three groups respectively, namely long-, medium-, and short-chain ADH subfamily, and CmADH1,3-11, which belongs to the medium-chain ADH subfamily, fell into six medium-chain ADH subgroups. CmADH12 may belong to the long-chain ADH subfamily, while CmFDH1 may be a Class III ADH and serve as an ancestral ADH in melon. Expression profiling revealed that CmADH1, CmADH2, CmADH10 and CmFDH1 were moderately or strongly expressed in different vegetative tissues and fruit at medium and late developmental stages, while CmADH8 and CmADH12 were highly expressed in fruit after 20 days. CmADH3 showed preferential expression in young tissues. CmADH4 only had slight expression in root. Promoter analysis revealed several motifs of CmADH genes involved in the gene expression modulated by various hormones, and the response pattern of CmADH genes to ABA, IAA and ethylene were different. These CmADHs were divided into ethylene-sensitive and -insensitive groups, and the functions of CmADHs were discussed.

Ethylene plays an essential role in the recovery of Arabidopsis during post-anaerobiosis reoxygenation

Ethylene is known to play an essential role in mediating hypoxic responses in plants. Here, we show that in addition to regulating hypoxic responses, ethylene also regulates cellular responses in the reoxygenation stage after anoxic treatment in Arabidopsis. We found that expression of several ethylene biosynthetic genes and ethylene-responsive factors, including ERF1 and ERF2, was induced during reoxygenation. Compared with the wild type, two ethylene-insensitive mutants (ein2-5 and ein3eil1) were more sensitive to reoxygenation and displayed damaged phenotypes during reoxygenation. To characterize the role of ethylene, we applied microarray analysis to Col-0, ein2-5 and ein3eil1 under reoxygenation conditions. Our results showed that gene transcripts involved in reactive oxygen species (ROS) detoxification, dehydration response and metabolic processes were regulated during reoxygenation. Moreover, ethylene signalling may participate in regulating these responses and maintaining the homeostasis of different phytohormones. Our work presents evidence that ethylene has distinct functions in recovery after anoxia and provides insight into the reoxygenation signalling network.

The symbiosis with the arbuscular mycorrhizal fungus Rhizophagus irregularis drives root water transport in flooded tomato plants

It is known that the presence of arbuscular mycorrhizal fungi within the plant roots enhances the tolerance of the host plant to different environmental stresses, although the positive effect of the fungi in plants under waterlogged conditions has not been well studied. Tolerance of plants to flooding can be achieved through different molecular, physiological and anatomical adaptations, which will affect their water uptake capacity and therefore their root hydraulic properties. Here, we investigated the root hydraulic properties under non-flooded and flooded conditions in non-mycorrhizal tomato plants and plants inoculated with the arbuscular mycorrhizal fungus Rhizophagus irregularis. Only flooded mycorrhizal plants increased their root hydraulic conductivity, and this effect was correlated with a higher expression of the plant aquaporin SlPIP1;7 and the fungal aquaporin GintAQP1. There was also a higher abundance of the PIP2 protein phoshorylated at Ser280 in mycorrhizal flooded plants. The role of plant hormones (ethylene, ABA and IAA) in root hydraulic properties was also taken into consideration, and it was concluded that, in mycorrhizal flooded plants, ethylene has a secondary role regulating root hydraulic conductivity whereas IAA may be the key hormone that allows the enhancement of root hydraulic conductivity in mycorrhizal plants under low oxygen conditions.

Hypoxia and bicarbonate could limit the expression of iron acquisition genes in Strategy I plants by affecting ethylene synthesis and signaling in different ways

In a previous work, it was shown that bicarbonate (one of the most important factors causing Fe chlorosis in Strategy I plants) can limit the expression of several genes involved in Fe acquisition. Hypoxia is considered another important factor causing Fe chlorosis, mainly on calcareous soils. However, to date it is not known whether hypoxia aggravates Fe chlorosis by affecting bicarbonate concentration or by specific negative effects on Fe acquisition. Results found in this work show that hypoxia, generated by eliminating the aeration of the nutrient solution, can limit the expression of several Fe acquisition genes in Fe-deficient Arabidopsis, cucumber and pea plants, like the genes for ferric reductases AtFRO2, PsFRO1 and CsFRO1; iron transporters AtIRT1, PsRIT1 and CsIRT1; H(+) -ATPase CsHA1; and transcription factors AtFIT, AtbHLH38, and AtbHLH39. Interestingly, the limitation of the expression of Fe-acquisition genes by hypoxia did not occur in the Arabidopsis ethylene constitutive mutant ctr1, which suggests that the negative effect of hypoxia is related to ethylene, an hormone involved in the upregulation of Fe acquisition genes. As for hypoxia, results obtained by applying bicarbonate to the nutrient solution suggests that ethylene is also involved in its negative effect, since ACC (1-aminocyclopropane-1-carboxylic acid; ethylene precursor) partially reversed the negative effect of bicarbonate on the expression of Fe acquisition genes. Taken together, the results obtained show that hypoxia and bicarbonate could induce Fe chlorosis by limiting the expression of Fe acquisition genes, probably because each factor negatively affects different steps of ethylene synthesis and/or signaling.

Ethylene and reactive oxygen species are involved in root aerenchyma formation and adaptation of wheat seedlings to oxygen-deficient conditions

Exposing plants to hypoxic conditions greatly improves their anoxic stress tolerance by enhancing the activities of glycolysis and fermentation in roots. Ethylene may also be involved in these adaptive responses because its synthesis is increased in roots under hypoxic conditions. Here it is reported that pre-treatment of wheat seedlings with an ethylene precursor, 1-aminocyclopropanecarboxylic acid (ACC), enhanced accumulation of ethylene in the roots of wheat seedlings, and enhanced their tolerance of oxygen-deficient conditions through increasing the expression of genes encoding ethanol fermentation enzymes, alcohol dehydrogenase and pyruvate decarboxylase, in the roots. Lysigenous aerenchyma formation in root was induced by ACC pre-treatment and was further induced by growth under oxygen-deficient conditions. ACC pre-treatment increased the expression of three genes encoding respiratory burst oxidase homologue (a plant homologue of gp91(phox) in NADPH oxidase), which has a role in the generation of reactive oxygen species (ROS), in roots of seedlings. Co-treatment with ACC and an NADPH oxidase inhibitor, diphenyleneiodonium, partly suppressed the ACC-induced responses. These results suggest that ethylene and ROS are involved in adaptation of wheat seedlings to oxygen-deficient conditions through controlling lysigenous aerenchyma formation and the expression of genes encoding ethanol fermentation enzymes.

Nep1-like protein from Moniliophthora perniciosa induces a rapid proteome and metabolome reprogramming in cells of Nicotiana benthamiana

NEP1 (necrosis- and ethylene-inducing peptide 1)-like proteins (NLPs) have been identified in a variety of taxonomically unrelated plant pathogens and share a common characteristic of inducing responses of plant defense and cell death in dicotyledonous plants. Even though some aspects of NLP action have been well characterized, nothing is known about the global range of modifications in proteome and metabolome of NLP-treated plant cells. Here, using both proteomic and metabolomic approaches we were able to identify the global molecular and biochemical changes in cells of Nicotiana benthamiana elicited by short-term treatment with MpNEP2, a NLP of Moniliophthora perniciosa, the basidiomycete responsible for the witches' broom disease on cocoa (Theobroma cacao L.). Approximately 100 protein spots were collected from 2-DE gels in each proteome, with one-third showing more than twofold differences in the expression values. Fifty-three such proteins were identified by mass spectrometry (MS)/MS and mapped into specific metabolic pathways and cellular processes. Most MpNEP2 upregulated proteins are involved in nucleotide-binding function and oxidoreductase activity, whereas the downregulated proteins are mostly involved in glycolysis, response to stress and protein folding. Thirty metabolites were detected by gas spectrometry (GC)/MS and semi-quantified, of which eleven showed significant differences between the treatments, including proline, alanine, myo-inositol, ethylene, threonine and hydroxylamine. The global changes described affect the reduction-oxidation reactions, ATP biosynthesis and key signaling molecules as calcium and hydrogen peroxide. These findings will help creating a broader understanding of NLP-mediated cell death signaling in plants.

Isolation of an alcohol dehydrogenase cDNA from and characterization of its expression in chrysanthemum under waterlogging

A PCR strategy was used to isolate a full-length CgADH (alcohol dehydrogenase) cDNA from chrysanthemum. The gene putatively encodes a 378 residue polypeptides, which shares 95% homology with tomato alcohol dehydrogenase class III. Endogenous ethylene generated in waterlogged Chrysanthemum zawadskii was enhanced by exogenous ethylene but decreased by 1-methylcyclopropene (1-MCP), an inhibitor of ethylene action. In waterlogged roots, the transcription of the gene encoding alcohol dehydrogenase (ADH, EC 1.1.1.1) increased rapidly but transiently, peaking at 7.5 fold the non-waterlogged level after 2h of stress. Waterlogging elevated ADH activity after a prolonged episode of stress. The exogenous supply of 40μLL(-1) ethylene suppressed the production of ethanol, while that of 4μLL(-1) 1-MCP enhanced it. Ethylene appeared to suppress an acceleration of both CgADH expression and fermentation, and alleviates ethanolic fermentation probably through by as a signal to acceleration of waterlogging-induced aerenchyma formation. This supports the previously observed phenomenon that the expression level of ADH gene is regulated by the local level of physiologically active ethylene. The relevance of the CgADH gene in relation to chrysanthemum waterlogging was discussed as well.

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.

Susceptibility to plant disease: more than a failure of host immunity

Susceptibility to infectious diseases caused by pathogens affects most plants in their natural habitat and leads to yield losses in agriculture. However, plants are not helpless because their immune system can deal with the vast majority of attackers. Nevertheless, adapted pathogens are able to circumvent or avert host immunity making plants susceptible to these uninvited guests. In addition to the failure of the plant immune system, there are other host processes that contribute to plant disease susceptibility. In this review, we discuss recent studies that show the active role played by the host in supporting disease, focusing mainly on biotrophic stages of infection. Plants attract pathogens, enable their entry and accommodation, and facilitate nutrient provision.

Molecular elements of low-oxygen signaling in plants

Oxygen and its limitation are emerging as a crucial factor in plant fitness, growth and development. Recent studies revealed the mechanisms by which oxygen is perceived by plant cells. This sensory system partly relies on an oxygen-mediated branch of the N-end rule pathway for protein degradation acting on a specific clade of ethylene responsive transcription factors (ERF-VII). A complementary regulative step is provided by aerobic sequestration of an ERF-VII protein at the plasma membrane and its timely release when hypoxia occurs. Complete absence of oxygen triggers the transient accumulation of reactive hydrogen peroxide and induces an additional set of reactive oxygen species-related genes involved in both signaling and attenuation of oxidative stress. Moreover, temporary hypoxic environments that are built up as consequence of dense cell packing have been demonstrated to trigger cell-fate determination in maize anthers. Similarly, limited oxygen delivery in bulky fruit or tuber tissues growing in aerobic conditions were shown to stimulate anaerobic-like responses. These advances in low-oxygen signaling and its effect on cell development highlight the importance of taking hypoxia into account in agronomical practices as well as in breeding programs.

Ethylene--and oxygen signalling--drive plant survival during flooding

Flooding is a widely occurring environmental stress both for natural and cultivated plant species. The primary problems associated with flooding arise due to restricted gas diffusion underwater. This hampers gas exchange needed for the critical processes of photosynthesis and respiration. Plant acclimation to flooding includes the adaptation of a suite of traits that helps alleviate or avoid these stressful conditions and improves or restores exchange of O2 and CO2 . The manifestation of these traits is, however, reliant on the timely perception of signals that convey the underwater status. Flooding-associated reduced gas diffusion imposes a drastic change in the internal gas composition within submerged plant organs. One of the earliest changes is an increase in the levels of the gaseous plant hormone ethylene. Depending on the species, organ, flooding conditions and time of the day, plants will also subsequently experience a reduction in oxygen levels. This review provides a comprehensive overview on the roles of ethylene and oxygen as critical signals of flooding stress. It includes a discussion of the dynamics of these gases in plants when underwater, their interaction, current knowledge of their perception mechanisms and the resulting downstream changes that mediate important acclimative processes that allow endurance and survival under flooded conditions.

Patterns of cis-element enrichment reveal potential regulatory modules involved in the transcriptional regulation of anoxia response of japonica rice

Unlike other cereal species, rice is able to germinate and elongate under anoxia. The regulatory mechanism that configures the transcriptome of rice during anaerobic germination is yet to be established. In this study, the major regulatory modules among anoxia-responsive genes in rice identified from published microarray data were predicted by ab initio analysis of cis-regulatory information content. Statistically overrepresented sequence motifs were detected from bona fide promoter sequences [-1000 to +200], revealing various patterns of cis-element enrichment that are highly correlated with bZIP, ERF and MYB types of transcription factors. As implied by the cis-element enrichment patterns, combinatorial mechanisms configure the overall changes in gene expression during anoxic germination and coleoptile elongation. High enrichment of cis-elements associated with ARF, bZIP, ERF, MYB and WRKY (SUSIBA2) transcription factors was also detected among the glycolytic and fermentative associated genes that were upregulated during anoxia. The patterns established from the global analysis of cis-element distribution for upregulated and downregulated genes and their associations with potential cognate regulatory transcription factors indicate the significant roles of ethylene and abscisic acid mediated signaling during coleoptile elongation under anoxia. In addition, the regulation of genes encoding enzymes in the glycolytic and fermentative metabolism could be associated with abscisic acid and auxin in rice coleoptiles to maintain sugar and ATP levels for longer survival.

Novel Prunus rootstock somaclonal variants with divergent ability to tolerate waterlogging

Plants require access to free water for nutrient uptake, but excess water surrounding the roots can be injurious or even lethal because it blocks the transfer of free oxygen between the soil and the atmosphere. Genetic improvement efforts in this study were focused on the increased tolerance in roots to waterlogging. Among a pool of clones generated in vitro from leaf explants of rootstock Mr.S.2/5 of Prunus cerasifera L., the S.4 clone was flood tolerant whereas the S.1 clone was sensitive. The S.4 clone formed adventitious roots on exposure to flooding. Moreover, the chlorophyll content and mitochondrial activity in the leaf and root, soluble sugar content, alcohol dehydrogenase activity and ethylene content were different between the clones. The sorbitol transporter gene (SOT1) was up-regulated during hypoxia, the alcohol dehydrogenase genes (ADH1 and ADH3) were up-regulated in the leaves and down-regulated in the roots of the S.4 clone during hypoxia, and the 1-aminocyclopropane-1-oxidase gene (ACO1) was up-regulated in the leaves and roots of the S.4 clone during hypoxia and down-regulated in the wild-type roots. In addition, in the S.4 root, hypoxia induced significant down-regulation of a glycosyltransferase-like gene (GTL), which has a yet-undefined role. Although the relevant variation in the S.4 genome has yet to be determined, genetic alteration clearly conferred a flooding-tolerant phenotype. The isolation of novel somaclonals with the same genomic background but with divergent tolerance to flooding may offer new insights in the elucidation of the genetic machinery of resistance to flooding and aid in the selection of new Prunus rootstocks to be used in various adverse environments.

Differential responses in sympatric tree species exposed to waterlogging

Climate change is projected to have a significant ecological impact on natural ecosystems, most notably through direct and indirect modifications of local precipitation regimes. In addition, anthropic activities such as the removal of vegetation, soil proofing due to building, the absence of storm drains and crop over-irrigation will all increase the occurrence of flooding. As a result, forest species, and more specifically trees, will increasingly be exposed to soil waterlogging. It is now well established that such flooding events can lead to changes in forest distribution and composition. For such reasons, it is becoming increasingly important to study forest ecosystems and more particularly the adaptive potential of tree species to better understand the ecological plasticity of forest communities to environmental modifications.

Redox biology of tuberculosis pathogenesis

Mycobacterium tuberculosis (Mtb) is one of the most successful human pathogens. Mtb is persistently exposed to numerous oxidoreductive stresses during its pathogenic cycle of infection and transmission. The distinctive ability of Mtb, not only to survive the redox stress manifested by the host but also to use it for synchronizing the metabolic pathways and expression of virulence factors, is central to its success as a pathogen. This review describes the paradigmatic redox and hypoxia sensors employed by Mtb to continuously monitor variations in the intracellular redox state and the surrounding microenvironment. Two component proteins, namely, DosS and DosT, are employed by Mtb to sense changes in oxygen, nitric oxide, and carbon monoxide levels, while WhiB3 and anti-sigma factor RsrA are used to monitor changes in intracellular redox state. Using these and other unidentified redox sensors, Mtb orchestrates its metabolic pathways to survive in nutrient-deficient, acidic, oxidative, nitrosative, and hypoxic environments inside granulomas or infectious lesions. A number of these metabolic pathways are unique to mycobacteria and thus represent potential drug targets. In addition, Mtb employs versatile machinery of the mycothiol and thioredoxin systems to ensure a reductive intracellular environment for optimal functioning of its proteins even upon exposure to oxidative stress. Mtb also utilizes a battery of protective enzymes, such as superoxide dismutase (SOD), catalase (KatG), alkyl hydroperoxidase (AhpC), and peroxiredoxins, to neutralize the redox stress generated by the host immune system. This chapter reviews the current understanding of mechanisms employed by Mtb to sense and neutralize redox stress and their importance in TB pathogenesis and drug development.

The hypoxia responsive transcription factor genes ERF71/HRE2 and ERF73/HRE1 of Arabidopsis are differentially regulated by ethylene

The AR2/ERF transcription factor genes ERF71/HRE2 and ERF73/HRE1 were induced at hypoxic conditions in Arabidopsis thaliana roots. ERF73/HRE1 but not its related gene ERF71/HRE2 was furthermore regulated by ethylene. Treatment with 1 ppm ethylene promoted ERF73/HRE1 expression fivefold. This induction did not occur in the presence of the ethylene receptor inhibitor 1-methylcyclopropene. ERF73/HRE1 expression positively regulated alcohol dehydrogenase (ADH) activity, which was analyzed as a marker enzyme for metabolic adaptation to hypoxic stress. The knock out lines erf73/hre1-1 and erf73/hre1-2 showed lowered ADH activity; the overexpressing lines ERF73/HRE1-ox1 and ERF73/HRE1-ox5 displayed elevated ADH activity. Treatment of wild-type Arabidopsis with 5% O₂ and 1 ppm ethylene resulted in higher induction of ADH activity than that observed with 5% O₂ or 1 ppm ethylene alone. ERF73/HRE1-ox1 and ERF73/HRE1-ox5 plants that were exposed to 5% O₂ did not show enhanced ADH activity after treatment with ethylene, indicating that the ethylene response with respect to ADH activity was saturated in the ERF73/HRE1ox lines. In contrast, erf73/hre1-1 and erf73/hre1-2 lines displayed ethylene-dependent ADH activity pointing to redundant factor(s) that can mediate ethylene regulation of ADH activity in the Arabidopsis root. Our data show that ethylene regulates metabolic adaptation to low oxygen stress in the Arabidopsis root through ERF73/ HRE1.

The AP2/ERF transcription factor AtERF73/HRE1 modulates ethylene responses during hypoxia in Arabidopsis

A number of APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) genes have been shown to function in abiotic and biotic stress responses, and these genes are often induced by multiple stresses. We report here the characterization of an AP2/ERF gene in Arabidopsis (Arabidopsis thaliana) that is specifically induced during hypoxia. We show that under normoxic conditions, the expression of AtERF73/HRE1 can be induced by exogenous addition of 1-aminocyclopropane-1-carboxylic acid and that a combination of hypoxia and 1-aminocyclopropane-1-carboxylic acid results in hyperinduction of AtERF73/HRE1 expression. In addition, hypoxic induction of AtERF73/HRE1 is reduced but not completely abolished in ethylene-insensitive mutants and in the presence of inhibitors of ethylene biosynthesis and responses. These results suggest that, in addition to ethylene, an ethylene-independent signal is also required to mediate hypoxic induction of AtERF73/HRE1. To assess the role of AtERF73/HRE1, we generated three independent RNA interference (RNAi) knockdown lines of AtERF73/HRE1. Under normoxic conditions, the AtERF73/HRE1-RNAi seedlings displayed increased ethylene sensitivity and exaggerated triple responses, indicating that AtERF73/HRE1 might play a negative regulatory role in modulating ethylene responses. Gas chromatography analyses showed that the production of ethylene was similar between wild-type and RNAi lines under hypoxia. Quantitative reverse transcription-polymerase chain reaction analyses showed that hypoxia-inducible genes could be affected by AtERF73/HRE1-RNAi lines in two different ways: hypoxic induction of glycolytic and fermentative genes was reduced, whereas induction of a number of peroxidase and cytochrome P450 genes was increased. Taken together, our results show that AtERF73/HRE1 is involved in modulating ethylene responses under both normoxia and hypoxia.

Regulation of the molecular response to oxygen limitations in plants

The oxygen availability to plant tissues can vary strongly in time and space. To endure short- or long-term oxygen deprivation, plants evolved a series of metabolic and morphological adaptations that have been extensively studied. However, our knowledge of the molecular regulation of these processes is not as well understood. In this review, the recent findings on the molecular effectors that regulate the response of higher plants to oxygen deficiency are discussed. Although no direct oxygen sensor has been discovered in plants so far, mechanisms that perceive low-oxygen derived signals have been reported, involving different sets of transcription factors (TFs). The ERF (Ethylene Responsive Factor) family especially appears to play a crucial role in the determination of survival to reduced oxygen availability in Arabidopsis and rice. This class of TFs displays a broad range of targets, being involved in both the metabolic reprogramming and the morphological adaptations exploited by plants when subjected to low-oxygen conditions.

Arabidopsis RAP2.2: an ethylene response transcription factor that is important for hypoxia survival

Arabidopsis (Arabidopsis thaliana) RAP2.2 (At3g14230) is an APETALA2/ethylene response factor-type transcription factor that belongs to the same subfamily as the rice (Oryza sativa) submergence tolerance gene SUB1A. RAP2.2 is expressed at constitutively high levels in the roots and at lower levels in the shoots, where it is induced by darkness. Effector studies and analysis of ethylene signal transduction mutants indicate that RAP2.2 is induced in shoots by ethylene and functions in an ethylene-controlled signal transduction pathway. Overexpression of RAP2.2 resulted in improved plant survival under hypoxia (low-oxygen) stress, whereas lines containing T-DNA knockouts of the gene had poorer survival rates than the wild type. This indicates that RAP2.2 is important in a plant's ability to resist hypoxia stress. Observation of the expression pattern of 32 low-oxygen and ethylene-associated genes showed that RAP2.2 affects only part of the low-oxygen response, particularly the induction of genes encoding sugar metabolism and fermentation pathway enzymes, as well as ethylene biosynthesis genes. Our results provide a new insight on the regulation of gene expression under low-oxygen conditions. Lighting plays an important regulatory role and is intertwined with hypoxia conditions; both stimuli may act collaboratively to regulate the hypoxic response.

Physiological and biochemical changes in plants under waterlogging

Waterlogging usually results from overuse and/or poor management of irrigation water and is a serious constraint with damaging effects. The rapidly depleting oxygen from submerged root zone is sensed and plant adjusts expressing anaerobic proteins. Plant cells shift their metabolism towards low energy yielding anaerobic fermentation pathways in the absence of oxygen. Structural modifications are also induced as aerenchyma formation and adventitious rootings, etc. Studies at molecular and biochemical levels to facilitate early perception and subsequent responses have also been worked out to produce resistant transgenic plants. This review explores the sequential changes of plant responses at different levels regarding their defense strategies and efforts made to enhance them, tailoring crucial regulators so that they can withstand waterlogging stress.

G proteins as regulators in ethylene-mediated hypoxia signaling

Waterlogging or flooding are frequently or constitutively encountered by many plant species. The resulting reduction in endogenous O2 concentration poses a severe threat. Numerous adaptations at the anatomical, morphological and metabolic level help plants to either escape low oxygen conditions or to endure them. Formation of aerenchyma or rapid shoot elongation are escape responses, as is the formation of adventitious roots. The metabolic shift from aerobic respiration to anaerobic fermentation contributes to a basal energy supply at low oxygen conditions. Ethylene plays a central role in hypoxic stress signaling, and G proteins have been recognized as crucial signal transducers in various hypoxic signaling pathways. The programmed death of parenchyma cells that results in hypoxia-induced aerenchyma formation is an ethylene response. In maize, aerenchyma are induced in the absence of ethylene when G proteins are constitutively activated. Similarly, ethylene induced death of epidermal cells that cover adventitious roots at the stem node of rice is strictly dependent on heterotrimeric G protein activity. Knock down of the unique Gα gene RGA1 in rice prevents epidermal cell death. Finally, in Arabidopsis, induction of alcohol dehydrogenase with resulting increased plant survival relies on the balanced activities of a small Rop G protein and its deactivating protein RopGAP4. Identifying the general mechanisms of G protein signaling in hypoxia adaptation of plants is one of the tasks ahead.

Preparation of ethylene gas and comparison of ethylene responses induced by ethylene, ACC, and ethephon

Ethylene is a gaseous plant hormone used in many physiological studies examining its role in plant growth and development. However, ethylene gas may not be conveniently available to many laboratories for occasional use, and therefore several chemicals can be used as replacements. Here we report that the kinetics of the ethylene response induced by ethylene and two widely-used ethylene replacements are different. ACC failed to efficiently replace prolonged ethylene treatments, while the decomposition products of ethephon may cause non-specific responses and the efficiency of ethephon conversion to ethylene was relatively low. A cost-effective method to prepare ethylene gas was developed. Analyzed by gas chromatography, the chemically produced ethylene exhibited an identical chromatogram to that from the commercial source. Our synthetic ethylene gave the same dose-response curve in Arabidopsis as gaseous ethylene. Our study shows that the use of the ethylene gas is essential to experiments that are sensitive to treatment duration and dosage. When ACC and ethephon are used as replacements, caution should be taken in the experimental design. For laboratories that do not have an ethylene tank, ethylene gas can be easily prepared by a chemical approach without further purification.

VERNALIZATION INSENSITIVE 3 (VIN3) is required for the response of Arabidopsis thaliana seedlings exposed to low oxygen conditions

VERNALIZATION INSENSITIVE 3 (VIN3), which is required for the vernalization-mediated epigenetic repression of FLOWERING LOCUS C (FLC) in Arabidopsis thaliana, is quantitatively induced in response to low temperatures. We found that hypoxic conditions also induce VIN3 in a quantitative manner but high salt, high temperatures and osmotic stress do not. Inhibition of mitochondrial respiration did not induce VIN3 expression, consistent with the lack of VIN3 induction in response to other stresses that affect the rate of mitochondrial respiration. De novo protein synthesis is required for VIN3 induction during hypoxic conditions; this situation is not the case for VIN3 induction by low temperatures, indicating that different mechanisms act to induce VIN3 expression in response to cold and hypoxic conditions. Without VIN3 activity, fewer seedlings survived following a 72-h period of hypoxic treatment, indicating that VIN3 is required for the survival of Arabidopsis thaliana in response to hypoxic stress. Complementation of the vin3 mutant with a VIN3 transgene restored the wild-type response to low oxygen and confirmed the role of VIN3 in protecting both shoots and roots during low oxygen conditions. Loss of VIN3 protein did not affect the transcriptional regulation of genes known to be important in the response to low oxygen stress, which suggests that there is a novel mechanism to combat hypoxia that involves VIN3. This mechanism is likely to involve chromatin remodelling and may be similar to the role of VIN3 in the epigenetic repression of FLC during the vernalization response.

Ethylene, free radicals and the transition between stable states in plant morphology

Treatment with hydrogen peroxide has notable effects in the morphology of the root apex in Arabidopsis seedlings. The result was described as consisting in two aspects: first, a reduction in curvature values in the root profile. Second, alterations in size and shape of the cells in the root cap. Cells of the root cap were smaller and had higher circularity index (Fig. 1). The results of peroxide treatment were similar to alterations in the root apex of ethylene insensitive mutants and wild-type seedlings treated with ethylene inhibitors. This brings new evidence in favour of the association between ethylene and hydrogen peroxide signalling that was recently demonstrated in stomatal cells. Notable changes in morphology under peroxide treatment were previously reported in other biological systems (Fig. 2). In the following paragraphs we make emphasis on the need of an accurate analysis of morphology. This aspect has not received the attention required in biology, a discipline dominated by functional analysis. We suggest that the observed morphological characteristics in the root apex treated with peroxide may be the manifestation of global processes of adaptation in the organism. Alternative forms of roots grown in water or in peroxide are stable situations representing different global configurations that may have other (genomic, physiological) traits associated. Each form represents a different mode of adaptation to environmental change. The accurate description of morphology in organisms, with particular emphasis in model systems, and their variations under stress, is needed to identify and understand the basis of genomic organization and plasticity.

Hydrogen peroxide treatment results in reduced curvature values in the Arabidopsis root apex

Curvature of a plane curve is a measurement related to its shape. A Mathematica code was developed [Cervantes E, Tocino A. J Plant Physiol 2005;162:1038-1045] to obtain parametric equations from microscopic images of the Arabidopsis thaliana root apex. In addition, curvature values for these curves were given. It was shown that ethylene-insensitive mutants (etr1-1 and ein2-1) have reduced curvature values in the root apex. It has also been shown that blocking ethylene action by norbornadiene, an ethylene inhibitor, results in reduced curvature values in the two outer cell layers of the root apex [Noriega A, Cervantes E, Tocino A. J Plant Physiol 2008, in press]. Because ethylene action has been related with hydrogen peroxide [Desikan R, Hancock JT, Bright J, Harrison J, Weir I, Hooley R, Neill SJ. Plant Physiol 2005;137:831-834], the effect of a treatment with hydrogen peroxide in the curvature values of three successive layers of the root apex in Arabidopsis thaliana was investigated by confocal microscopy. Treatment with 10mM hydrogen peroxide resulted in reduced curvature values in the three layers. The effect was associated with smaller cells having higher circularity indices. The results are discussed in the context of the role of ethylene in development.

Response of jujube fruits to exogenous oxalic acid treatment based on proteomic analysis

In this study, we found that oxalic acid (OA) at the concentration of 5 mM could delay jujube fruit sene-scence by reducing ethylene production, repressing fruit reddening and reducing alcohol content, which consequently increased fruit resistance against blue mold caused by Penicillium expansum. In order to gain a further understanding of the mechanism by which OA delays senescence and increases disease resistance of jujube fruit, we used a proteomics approach to compare soluble proteome of jujube fruits treated with water or 5 mM OA for 10 min. A total of 25 differentially expressed proteins were identified by using electrospray ionization quadrupole time-of-flight tandem mass spectrometry (ESI-Q-TOF-MS/MS). Among these proteins, alcohol dehydrogenase 1, which plays a direct role in ethanol metabolism, was repressed, and the abundances of three photosynthesis-related proteins was enhanced in jujube fruit after OA treatment. The protein identified as a cystathionine beta-synthase domain-containing protein, which can regulate ethylene precursors, was also induced by OA treatment. The activity of 1-aminocyclopropane-1-carboxylic acid synthase was significantly suppressed in OA-treated jujube fruit. In addition, three proteins related to the defense/stress response were up-regulated by OA, and contributed to the establishment of systemic resistance induced by OA in jujube fruits. These results indicated that OA treatment might affect ethanol and ethylene metabolism, resulting in delaying senescence, and increase resistance of jujube fruits against fungal pathogens.