Oxygen sensing and signaling

Nitric oxide mediates nitrate induced alleviation of waterlogging stress in cucumber

Effects of waterlogging (WL) stress and its mitigation by nitrate (NO3-) were investigated in a commercial cucumber hybrid line. WL resulted in a shift toward anaerobic metabolism in roots and development of adventitious roots (ARs). In WL stressed roots exodermal, extracellular H2O2 accumulation and protein nitration were detected. Shoot growth was retarded with signs of oxidative stress. Nitrate content decreased in both root and shoot. In the root WL upregulated several genes implicated in hypoxic response, including transcripts of CsRAP2.3, CsRBOHs and the CsHem3 phytoglobin genes. Nitrate supplementation restored shoot growth and mitigated oxidative stress. Fermentative metabolism was reduced in the roots. Nitrate levels increased substantially, expression of NRT1 genes was induced, supporting improved NO3- uptake and delivery. According to chemical analysis and fluorescent microscopy NO accumulated in the vascular cylinder of roots. NO depletion by cPTIO confirmed a role for NO in stress mitigation. cPTIO treatment decreased AR formation and foliar nitrate levels. It decreased protein nitration and strongly downregulated nitrate transporters' gene expression in roots. Overall, our work revealed nitrate triggered, NO mediated alleviation of WL stress in cucumber. Resolution of WL induced energy crisis in the roots by nitrate treatment was attributed to parallel effects of anaerobic respiration and AR formation. Shoot growth repression was probably alleviated by improved root functions, including elevated nitrate transport. Expression of NRT1 nitrate transporter genes was induced by nitrate, and this induction was found NO dependent in WL stressed cucumber.

Advances in plant oxygen sensing: endogenous and exogenous mechanisms

Oxygen is essential for the biochemical processes that sustain life in eukaryotic organisms. Although plants produce oxygen through photosynthesis, they often struggle to survive in low-oxygen environments, such as during flooding or submergence. To endure these conditions, they must reprogram their developmental and metabolic networks, and the adaptation process involves the continuous detection of both exogenous hypoxic signals and endogenous oxygen gradients. Recent research has significantly advanced our understanding of how plants respond to both endogenous and exogenous hypoxia signals. In this review, we explore advancements in both areas, comparing them to responses in animals, with a primary focus on how plants perceive and respond to exogenous hypoxic conditions, particularly those caused by flooding or submergence, as well as the hypoxia signaling pathways in different crops. Additionally, we discuss the interplay between endogenous and exogenous hypoxia signals in plants. Finally, we discuss future research directions aimed at improving crop resilience to flooding by integrating the perception and responses to both endogenous and exogenous signals. Through these efforts, we aspire to contribute to the development of crop varieties that are not only highly resistant but also experience minimal growth and yield penalties, thereby making substantial contributions to agricultural science.

A large-scale integrated transcriptomic atlas for soybean organ development

Soybean is one of the most important crops globally, and its production must be significantly increased to meet increasing demand. Elucidating the genetic regulatory networks underlying soybean organ development is essential for breeding elite and resilient varieties to ensure increased soybean production under climate change. An integrated transcriptomic atlas that leverages multiple types of transcriptomics data can facilitate the characterization of temporal-spatial expression patterns of most organ development-related genes and thereby help us to understand organ developmental processes. Here, we constructed a comprehensive, integrated transcriptomic atlas for soybeans, integrating bulk RNA sequencing (RNA-seq) datasets from 314 samples across the soybean life cycle, along with single-nucleus RNA-seq and spatially enhanced resolution omics sequencing datasets from five organs: root, nodule, shoot apex, leaf, and stem. Investigating genes related to organ specificity, blade development, and nodule formation, we demonstrate that the atlas has robust power for exploring key genes involved in organ formation. In addition, we developed a user-friendly panoramic database for the transcriptomic atlas, enabling easy access and queries, which will serve as a valuable resource to significantly advance future soybean functional studies.

Survival mechanisms of plants under hypoxic stress: Physiological acclimation and molecular regulation

Hypoxia (low-oxygen tension) caused by complete submergence or waterlogging is an abiotic stress factor that severely affects the yield and distribution of plants. To adapt to and survive under hypoxic conditions, plants employ several physiological and molecular strategies that integrate morphological acclimation, metabolic shifts, and signaling networks. Group VII ETHYLENE RESPONSE FACTORS (ERF-VIIs), master transcription factors, have emerged as a molecular hub for regulating plant hypoxia sensing and signaling. Several mitogen-activated protein kinases and calcium-dependent protein kinases have recently been reported to be involved in potentiating hypoxia signaling via interaction with and phosphorylation of ERF-VIIs. Here, we provide an overview of the current knowledge on the regulatory network of ERF-VIIs and their post-translational regulation in determining plant responses to hypoxia and reoxygenation, with a primary focus on recent advancements in understanding how signaling molecules, including ethylene, long-chain acyl-CoA, phosphatidic acid, and nitric oxide, are involved in the regulation of ERV-VII activities. Furthermore, we propose future directions for investigating the intricate crosstalk between plant growth and hypoxic resilience, which is central to guiding breeding and agricultural management strategies for promoting flooding and submergence stress tolerance in plants.

Waterlogging stress mechanism and membrane transporters in soybean (Glycine max (L.) Merr.)

An excess of water is more harmful to plant growth, root growth and the uniformity of the plant population than a water deficit. Water is a crucial factor in the three basic stages of soybean development: germination, emergence and flowering/seed filling. Waterlogging is one of the biggest constraints to crop production and productivity in India and can occur at any stage in soybean. However, seeds and seedlings are damaged by waterlogging resulting in a significant reduction in grain yield. Seed yield and growth are significantly correlated at the seedling stage. In addition, the plant is under constant pressure due to changing environmental conditions and has difficulty withstanding these harsh, unpredictable and difficult situations. Membrane transporters are essential and play fundamental roles during waterlogging thereby facilitating cellular homeostasis and gaseous exchange, which support plant growth and development. This review highlights the genetic basis and mechanism of waterlogging tolerance in soybean and the role of climate in influencing the genetic makeup of the crop, paving the way for further development of improved soybean varieties. Simultaneously, the article highlights membrane transporters' importance in water-mediated stress in soybeans.

Soybean tolerance to waterlogging is achieved by detoxifying root lactate via lactate dehydrogenase in leaves and metabolizing malate and succinate

Waterlogging is a significant stressor for crops, particularly in lowland regions where soil conditions exacerbate the problem. Waterlogged roots experience hypoxia, disrupting oxidative phosphorylation and triggering metabolic reorganization to sustain energy production. Here, we investigated the metabolic aspects that differentiate two soybean sister lines contrasting for waterlogging tolerance. After 11 days of waterlogging, roots of the tolerant line (PELBR15-7015C) modulated their fermentative metabolism by exporting key metabolites (lactate, malate, and succinate) to the shoot. These metabolites were metabolized in the leaves, supporting photosynthesis and facilitating sugar export to the roots, sustaining a root-shoot-root cycling process. In contrast, the sensitive line (PELBR15-7060) entered a quiescent state, depleting its carbon stock and accumulating protective metabolites. Our study reveals that long-term waterlogging tolerance is primarily achieved through lactate detoxification in the leaves, along with malate and succinate metabolism, enabling root metabolism to withstand hypoxia. This mechanism offers new insights into crop resilience under waterlogged conditions, with implications for modern agriculture as climate change intensifies the frequency and duration of such stress events.

Comprehensive transcriptome and proteome analysis revealed the molecular mechanisms of melatonin priming and waterlogging response in peach

Waterlogging substantially hampers the growth and development of plants. The escalating trajectory of global climate change is heightening both the frequency and intensity of waterlogging events. Peach trees are particularly vulnerable to waterlogging, with the resultant hypoxia in the rhizosphere profoundly influencing their growth and productivity. This study explored the responses of peach seedlings to waterlogging and the regulatory effects of melatonin priming. After a 24-h waterlogging treatment, a significant increase in relative electrical conductivity and an accumulation of reactive oxygen species were observed, ion permeability was markedly alleviated by melatonin priming. Transcriptomic and proteomic analyses were conducted on peach root samples to elucidate the molecular mechanisms involved in the response to waterlogging and melatonin priming. Transcriptome analysis implicated genes related to 'DNA-binding transcription factor activity', such as AP2/ERF, HSF and WRKY transcription factors, in response to waterlogging. The glycolysis/gluconeogenesis pathway was also significantly enriched, indicating its critical role in the metabolic response to waterlogging. A correlation analysis between differentially expressed genes and proteins highlighted the regulation of numerous genes at both the transcriptional and translational levels. Furthermore, core DEGs/DEPs, including heat shock proteins and stress-related proteins, were identified. Notably, ERF VII member ERF071 (Prupe.8G264900), ADH (Prupe.8G018100), and PCO (Prupe.7G011000) emerged as potential targets for genetic manipulation to enhance waterlogging tolerance in peach. This research provides targets for breeding waterlogging-tolerant varieties and strategies to mitigate waterlogging stress in peach.

Primed to persevere: Hypoxia regulation from epigenome to protein accumulation in plants

Plant cells regularly encounter hypoxia (low-oxygen conditions) as part of normal growth and development, or in response to environmental stresses such as flooding. In recent years, our understanding of the multi-layered control of hypoxia-responsive gene expression has greatly increased. In this Update, we take a broad look at the epigenetic, transcriptional, translational, and post-translational mechanisms that regulate responses to low-oxygen levels. We highlight how a network of post-translational modifications (including phosphorylation), secondary messengers, transcriptional cascades, and retrograde signals from the mitochondria and endoplasmic reticulum (ER) feed into the control of transcription factor activity and hypoxia-responsive gene transcription. We discuss epigenetic mechanisms regulating the response to reduced oxygen availability, through focussing on active and repressive chromatin modifications and DNA methylation. We also describe current knowledge of the co- and post-transcriptional mechanisms that tightly regulate mRNA translation to coordinate effective gene expression under hypoxia. Finally, we present a series of outstanding questions in the field and consider how new insights into the molecular workings of the hypoxia-triggered regulatory hierarchy could pave the way for developing flood-resilient crops.

Transcriptomics of long-term, low oxygen storage coupled with ethylene signaling interference suggests neofunctionalization of hypoxia response pathways in apple (Malus domestica)

Research on how plants respond to hypoxia has concentrated on model organisms where tissues can only survive hypoxic conditions for a few hours to a few days. In contrast, hypoxic conditions are used commercially as a method to prolong the shelf life of Malus domestica (apple) fruit for up to a year of storage without substantial changes in fruit quality, not to mention a lack of tissue death. This ability of apples to withstand protracted hypoxic conditions is an interesting adaptation that has had limited molecular investigation despite its economic importance. Here, we investigate the long-term apple hypoxia response using a time-course RNA-seq analysis of several postharvest storage conditions. We use phylogenetics, differential expression, and regulatory networks to identify genes that regulate and are regulated by the hypoxia response. We identify potential neofunctionalization of core-hypoxia response genes in apples, including novel regulation of group VII ethylene response factor (ERF VII) and plant cysteine oxidase (PCO) family members.

The chloroplast protease system degrades stromal DUF760-1 and DUF760-2 domain-containing proteins at different rates

The chloroplast chaperone CLPC1 aids to select, unfold, and deliver hundreds of proteins to the CLP protease for degradation. Through in vivo CLPC1, trapping we previously identified dozens of proteins that are (potential) substrate adaptors or substrates for the CLP chaperone-protease system. In this study, we show that two of these highly trapped proteins, DUF760-1 and DUF760-2, are substrates for the CLP protease in Arabidopsis (Arabidopsis thaliana). Loss-of-function mutants and transgenic plants were created for phenotyping, protein expression, and localization using immunoblotting and confocal microscopy. In planta BiFC, cycloheximide chase assays, and yeast 2-hybrid analyses were conducted to determine protein interactions and protein half-life. Both DUF760 proteins directly interacted with the N-domain of CLPC1 and both were highly enriched in clpc1-1 and clpr2-1 mutants. Accordingly, in vivo cycloheximide chase assays demonstrated that both DUF760 proteins are degraded by the CLP protease. The half-life of DUF760-1 was 4 to 6 h, whereas DUF760-2 was highly unstable and difficult to detect unless CLP proteolysis was inhibited. Null mutants for DUF760-1 and DUF760-2 showed weak but differential pigment phenotypes and differential sensitivity to protein translation inhibitors. This study demonstrates that DUF760-1 and DUF760-2 are substrates of the CLP chaperone-protease system and excellent candidates for the determination of CLP substrate degrons.

Short-term reoxygenation is not enough for the recovery of soybean plants exposed to saline waterlogging

The ability of plants to recover after stressful events is crucial for resuming growth and development and is a key trait when studying stress tolerance. However, there is a lack of information on the physiological responses and the time required to restore homeostasis after the stress experience. This study aimed to (i) enhance understanding of soybean photosynthesis performance during saline waterlogging and (ii) investigate the effects of this combined stress during the reoxygenation and recovery period. Soybean plants (cultivar PELBR10-6049 RR) were subjected to waterlogging, NaCl, or hypoxia + NaCl for 3 and 6 days. Afterward, plants were drained and allowed to recover for an additional two (short-term) and seven days (long-term). Compared to plants exposed to single stress, the combined hypoxia + NaCl treatment resulted in a lower net CO2 assimilation rate, ФPSII, and levels of photosynthetic pigments during the waterlogging period. Furthermore, hypoxia + NaCl increased foliar electrolyte leakage during waterlogging. In response to short-term reoxygenation, these negative effects were amplified, while prolonged reoxygenation resulted in a slight increase in biomass accumulation. In conclusion, full recovery was not achieved under any condition during the reoxygenation periods tested. Notably, the brief reoxygenation phase imposed greater stress than the initial stress conditions for plants facing combined stress. Although extended recovery increased biomass accumulation, it remained lower in plants previously subjected to saline waterlogging.

Arabidopsis VQ motif-containing proteins VQ1 and VQ10 interact with plastidial 1-deoxy-D-xylulose-5-phosphate synthase

VQ1 and VQ10 are largely unstructured homologous proteins with a significant potential for protein-protein interactions. Yeast two-hybrid (Y2H) analysis confirmed that both proteins interact not only with themselves and each other but also with other VQ and WRKY proteins. Screening an Arabidopsis Y2H library with VQ1 as bait identified 287 interacting proteins. Validation of the screening confirmed that interactions with VQ1 also occurred with VQ10, supporting their functional homology. Although VQ1 or VQ10 proteins do not localize in plastids, 47 VQ1-targets were found to be plastidial proteins. In planta interaction with the isoprenoid biosynthetic enzyme 1-deoxy-D-xylulose-5-phosphate synthase (DXS) was confirmed by co-immunoprecipitation. DXS oligomerizes through redox-regulated intermolecular disulfide bond formation, and the interaction with VQ1 or VQ10 do not involve their unique C residues. The VQ-DXS protein interaction did not alter plastid DXS localization or its oligomerization state. Although plants with enhanced or reduced VQ1 and VQ10 expression did not exhibit significantly altered levels of isoprenoids compared to wild-type plants, they did display significantly improved or diminished photosynthesis efficiency, respectively.

Nitric oxide, energy, and redox-dependent responses to hypoxia

Hypoxia occurs when oxygen levels fall below the levels required for mitochondria to support respiration. Regulated hypoxia is associated with quiescence, particularly in storage organs (seeds) and stem cell niches. In contrast, environmentally induced hypoxia poses significant challenges for metabolically active cells that are adapted to aerobic respiration. The perception of oxygen availability through cysteine oxidases, which function as oxygen-sensing enzymes in plants that control the N-degron pathway, and the regulation of hypoxia-responsive genes and processes is essential to survival. Functioning together with reactive oxygen species (ROS), particularly hydrogen peroxide (H2O2) and reactive nitrogen species (RNS), such as nitric oxide (·NO), nitrogen dioxide (·NO2), S-nitrosothiols (SNOs), and peroxynitrite (ONOO-), hypoxia signaling pathways trigger anatomical adaptations such as formation of aerenchyma, mobilization of sugar reserves for anaerobic germination, formation of aerial adventitious roots, and the hyponastic response. NO and H2O2 participate in local and systemic signaling pathways that facilitate acclimation to changing energetic requirements, controlling glycolytic fermentation, the γ-aminobutyric acid (GABA) shunt, and amino acid synthesis. NO enhances antioxidant capacity and contributes to the recycling of redox equivalents in energy metabolism through the phytoglobin (Pgb)-NO cycle. Here, we summarize current knowledge of the central role of NO and redox regulation in adaptive responses that prevent hypoxia-induced death in challenging conditions such as flooding.

Hypoxia reshapes Arabidopsis root architecture by integrating ERF-VII factor response and abscisic acid homoeostasis

Oxygen limitation (hypoxia), arising as a key stress factor due to flooding, negatively affects plant development. Consequently, maintaining root growth under such stress is crucial for plant survival, yet we know little about the root system's adaptions to low-oxygen conditions and its regulation by phytohormones. In this study, we examine the impact of hypoxia and, herein, the regulatory role of group VII ETHYLENE-RESPONSE FACTOR (ERFVII) transcription factors on root growth in Arabidopsis. We found lateral root (LR) elongation to be actively maintained by hypoxia via ERFVII factors, as erfVII seedlings possess hypersensitivity towards hypoxia regarding their LR growth. Pharmacological inhibition of abscisic acid (ABA) biosynthesis revealed ERFVII-driven counteraction of hypoxia-induced inhibition of LR formation in an ABA-dependent manner. However, postemergence LR growth under hypoxia mediated by ERFVIIs was independent of ABA. In roots, ERFVIIs mediate, among others, the induction of ABA-degrading ABA 8'-hydroxylases CYP707A1 expression. RAP2.12 could activate the pCYC707A1:LUC reporter gene, indicating, combined with single mutant analyses, that this transcription factor regulates ABA levels through corresponding transcript upregulation. Collectively, hypoxia-induced adaptation of the Arabidopsis root system is shaped by developmental reprogramming, whereby ERFVII-dependent promotion of LR emergence, but not elongation, is partly executed through regulation of ABA degradation.

Low-oxygen-induced root bending is altered by phytoglobin1 through mediation of ethylene response factors (ERFs) and auxin signaling

MAIN CONCLUSION

phytoglobin1 positively regulates root bending in hypoxic Arabidopsis roots through regulation of ethylene response factors and auxin transport. Hypoxia-induced root bending is known to be mediated by the redundant activity of the group VII ethylene response factors (ERFVII) RAP2.12 and HRE2, causing changes in polar auxin transport (PAT). Here, we show that phytoglobin1 (Pgb1), implicated in hypoxic adaptation through scavenging of nitric oxide (NO), can alter root direction under low oxygen. Hypoxia-induced bending is exaggerated in roots over-expressing Pgb1 and attenuated in those where the gene is suppressed. These effects were attributed to Pgb1 repressing both RAP2.12 and HRE2. Expression, immunological and genetic data place Pgb1 upstream of RAP2.12 and HRE2 in the regulation of root bending in oxygen-limiting environments. The attenuation of slanting in Pgb1-suppressing roots was associated with depletion of auxin activity at the root tip because of depression in PAT, while exaggeration of root bending in Pgb1-over-expressing roots with the retention of auxin activity. Changes in PIN2 distribution patterns, suggestive of redirection of auxin movement during hypoxia, might contribute to the differential root bending responses of the transgenic lines. In the end, Pgb1, by regulating NO levels, controls the expression of 2 ERFVIIs which, in a cascade, modulate PAT and, therefore, root bending.

Transcriptomic Insights into Molecular Response of Butter Lettuce to Different Light Wavelengths

Lettuce is a widely consumed leafy vegetable; it became popular due to its enhanced nutritional content. Recently, lettuce is also regarded as one of the model plants for vegetable production in plant factories. Light and nutrients are essential environmental factors that affect lettuce growth and morphology. To evaluate the impact of light spectra on lettuce, butter lettuce was grown under the light wavelengths of 460, 525, and 660 nm, along with white light as the control. Plant morphology, physiology, nutritional content, and transcriptomic analyses were performed to study the light response mechanisms. The results showed that the leaf fresh weight and length/width were higher when grown at 460 nm and lower when grown at 525 nm compared to the control treatment. When exposed to 460 nm light, the sugar, crude fiber, mineral, and vitamin concentrations were favorably altered; however, these levels decreased when exposed to light with a wavelength of 525 nm. The transcriptomic analysis showed that co-factor and vitamin metabolism- and secondary metabolism-related genes were specifically induced by 460 nm light exposure. Furthermore, the pathway enrichment analysis found that flavonoid biosynthesis- and vitamin B6 metabolism-related genes were significantly upregulated in response to 460 nm light exposure. Additional experiments demonstrated that the vitamin B6 and B2 content was significantly higher in leaves exposed to 460 nm light than those grown under the other conditions. Our findings suggested that the addition of 460 nm light could improve lettuce's biomass and nutritional value and help us to further understand how the light spectrum can be tuned as needed for lettuce production.

Bioinspired Supramolecular Hydrogel from Design to Applications

Nature offers a wealth of opportunities to solve scientific and technological issues based on its unique structures and function. The dynamic non-covalent interaction is considered to be the main base of living functions of creatures including humans, animals, and plants. Supramolecular hydrogels formed by non-covalent bonding interactions has become a unique platform for constructing promising materials for medicine, energy, electronic, and biological substitute. In this review, the self-assemble principle of supramolecular hydrogels is summarized. Next, the stimulation of external environment that triggers the assembly or disassembly of supramolecular hydrogels are recapitulated, including temperature, mechanics, light, pH, ions, etc. The main applications of bioinspired supramolecular hydrogels in terms of bionic objects including humans, animals, and plants are also described. Although so many efforts are done for revealing the synergized mechanism of the function and non-covalent interactions on the supramolecular hydrogel, the complexity and variability between stimulus and non-covalent bonding in the supramolecular system still require impeccable theories. As an outlook, the bioinspired supramolecular hydrogel is just beginning to exhibit its great potential in human life, offering significant opportunities in drug delivery and screening, implantable devices and substitutions, tissue engineering, micro-fluidic devices, and biosensors.

Spatiotemporal oxygen dynamics in young leaves reveal cyclic hypoxia in plants

Oxygen is essential for plant growth and development. Hypoxia occurs in plants due to limited oxygen availability following adverse environmental conditions as well in hypoxic niches in otherwise normoxic environments. However, the existence and functional integration of spatiotemporal oxygen dynamics with plant development remains unknown. In animal systems dynamic fluctuations in oxygen availability are known as cyclic hypoxia. In this study, we demonstrate that cyclic fluctuations in internal oxygen levels occur in young emerging leaves of Arabidopsis plants. Cyclic hypoxia in plants is based on a mechanism requiring the ETHYLENE RESPONSE FACTORS type VII (ERFVII) that are central components of the oxygen-sensing machinery in plants. The ERFVII-dependent mechanism allows precise adjustment of leaf growth in response to carbon status and oxygen availability within plant cells. This study thus establishes a functional connection between internal spatiotemporal oxygen dynamics and developmental processes of plants.

The light and hypoxia induced gene ZmPORB1 determines tocopherol content in the maize kernel

Tocopherol is an important lipid-soluble antioxidant beneficial for both human health and plant growth. Here, we fine mapped a major QTL-qVE1 affecting γ-tocopherol content in maize kernel, positionally cloned and confirmed the underlying gene ZmPORB1 (por1), as a protochlorophyllide oxidoreductase. A 13.7 kb insertion reduced the tocopherol and chlorophyll content, and the photosynthetic activity by repressing ZmPORB1 expression in embryos of NIL-K22, but did not affect the levels of the tocopherol precursors HGA (homogentisic acid) and PMP (phytyl monophosphate). Furthermore, ZmPORB1 is inducible by low oxygen and light, thereby involved in the hypoxia response in developing embryos. Concurrent with natural hypoxia in embryos, the redox state has been changed with NO increasing and H2O2 decreasing, which lowered γ-tocopherol content via scavenging reactive nitrogen species. In conclusion, we proposed that the lower light-harvesting chlorophyll content weakened embryo photosynthesis, leading to fewer oxygen supplies and consequently diverse hypoxic responses including an elevated γ-tocopherol consumption. Our findings shed light on the mechanism for fine-tuning endogenous oxygen concentration in the maize embryo through a novel feedback pathway involving the light and low oxygen regulation of ZmPORB1 expression and chlorophyll content.

OsACA9, an Autoinhibited Ca2+-ATPase, Synergically Regulates Disease Resistance and Leaf Senescence in Rice

Calcium (Ca2+) is a versatile intracellular second messenger that regulates several signaling pathways involved in growth, development, stress tolerance, and immune response in plants. Autoinhibited Ca2+-ATPases (ACAs) play an important role in the regulation of cellular Ca2+ homeostasis. Here, we systematically analyzed the putative OsACA family members in rice, and according to the phylogenetic tree of OsACAs, OsACA9 was clustered into a separated branch in which its homologous gene in Arabidopsis thaliana was reported to be involved in defense response. When the OsACA9 gene was knocked out by CRISPR/Cas9, significant accumulation of reactive oxygen species (ROS) was detected in the mutant lines. Meanwhile, the OsACA9 knock out lines showed enhanced disease resistance to both rice bacterial blight (BB) and bacterial leaf streak (BLS). In addition, compared to the wild-type (WT), the mutant lines displayed an early leaf senescence phenotype, and the agronomy traits of their plant height, panicle length, and grain yield were significantly decreased. Transcriptome analysis by RNA-Seq showed that the differentially expressed genes (DEGs) between WT and the Osaca9 mutant were mainly enriched in basal immune pathways and antibacterial metabolite synthesis pathways. Among them, multiple genes related to rice disease resistance, receptor-like cytoplasmic kinases (RLCKs) and cell wall-associated kinases (WAKs) genes were upregulated. Our results suggest that the Ca2+-ATPase OsACA9 may trigger oxidative burst in response to various pathogens and synergically regulate disease resistance and leaf senescence in rice.

Introducing the halophyte Salicornia europaea to investigate combined impact of salt and tidal submergence conditions

Tolerance mechanisms to single abiotic stress events are being investigated in different plant species, but how plants deal with multiple stress factors occurring simultaneously is still poorly understood. Here, we introduce Salicornia europaea as a species with an extraordinary tolerance level to both flooding and high salt concentrations. Plants exposed to 0.5MNaCl (mimicking sea water concentrations) grew larger than plants not exposed to salt. Adding more salt reduced growth, but concentrations up to 2.5MNaCl were not lethal. Regular tidal flooding with salt water (0.5MNaCl) did not affect growth or chlorophyll fluorescence, whereas continuous flooding stopped growth while plants survived. Quantitative polymerase chain reaction (qPCR) analysis of plants exposed to 1% oxygen in air revealed induction of selected hypoxia responsive genes, but these genes were not induced during tidal flooding, suggesting that S. europaea did not experience hypoxic stress. Indeed, plants were able to transport oxygen into waterlogged soil. Interestingly, sequential exposure to salt and hypoxic air changed the expression of several but not all genes as compared to their expression upon hypoxia only, demonstrating the potential to use S . europaea to investigate signalling-crosstalk between tolerance reactions to multiple environmental perturbations.

Identification and Characterization of a Plant Endophytic Fungus Paraphaosphaeria sp. JRF11 and Its Growth-Promoting Effects

Endophytic fungi establish mutualistic relationships with host plants and can promote the growth and development of plants. In this study, the endophytic fungus JRF11 was isolated from Carya illinoinensis. Sequence analysis of the internal transcribed spacer (ITS) region and 18S rRNA gene combined with colonial and conidial morphology identified JRF11 as a Paraphaosphaeria strain. Plant-fungus interaction assays revealed that JRF11 showed significant growth-promoting effects on plants. In particular, JRF11 significantly increased the root biomass and soluble sugar content of plants. Furthermore, transcriptome analysis demonstrated that JRF11 treatment reprogrammed a variety of genes involved in plant mitogen-activated protein kinase (MAPK) signaling and starch and sucrose metabolism pathways through Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Our research indicates that beneficial endophytic fungi are able to interact with plants and exhibit outstanding plant growth-promoting activities.

Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas

This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource (build 2023-10) providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected post-translational modifications (PTMs), and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18,267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins, and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome: the "dark" proteome. This dark proteome is highly enriched for E3 ligases, transcription factors, and for certain (e.g., CLE, IDA, PSY) but not other (e.g., THIONIN, CAP) signaling peptides families. A machine learning model trained on RNA expression data and protein properties predicts the probability that proteins will be detected. The model aids in discovery of proteins with short half-life (e.g., SIG1,3 and ERF-VII TFs) and for developing strategies to identify the missing proteins. PeptideAtlas is linked to TAIR, tracks in JBrowse, and several other community proteomics resources.

Understanding plant responses to saline waterlogging: insights from halophytes and implications for crop tolerance

MAIN CONCLUSION

Saline and wet environments stress most plants, reducing growth and yield. Halophytes adapt with ion regulation, energy maintenance, and antioxidants. Understanding these mechanisms aids in breeding resilient crops for climate change. Waterlogging and salinity are two abiotic stresses that have a major negative impact on crop growth and yield. These conditions cause osmotic, ionic, and oxidative stress, as well as energy deprivation, thus impairing plant growth and development. Although few crop species can tolerate the combination of salinity and waterlogging, halophytes are plant species that exhibit high tolerance to these conditions due to their morphological, anatomical, and metabolic adaptations. In this review, we discuss the main mechanisms employed by plants exposed to saline waterlogging, intending to understand the mechanistic basis of their ion homeostasis. We summarize the knowledge of transporters and channels involved in ion accumulation and exclusion, and how they are modulated to prevent cytosolic toxicity. In addition, we discuss how reactive oxygen species production and cell signaling enhance ion transport and aerenchyma formation, and how plants exposed to saline waterlogging can control oxidative stress. We also address the morphological and anatomical modifications that plants undergo in response to combined stress, including aerenchyma formation, root porosity, and other traits that help to mitigate stress. Furthermore, we discuss the peculiarities of halophyte plants and their features that can be leveraged to improve crop yields in areas prone to saline waterlogging. This review provides valuable insights into the mechanisms of plant adaptation to saline waterlogging thus paving the path for future research on crop breeding and management strategies.

Root damage of street trees in urban environments: An overview of its hazards, causes, and prevention and control measures

Root damage from urban street trees represents a substantial concern arising from the conflict between root growth and limited growth spaces. Nonetheless, the phenomenon of root damage, which threatens the safety of urban facilities, appears to have received little scholarly attention. Moreover, the effectiveness of some proposed measures for root damage prevention and control has not yet received consistent evaluation. Accordingly, this review aims to examine root damage, including its causes and available prevention and control measures. Urban trees are found to have a high potential to exert root damage on infrastructures when the following factors exist. These include large and mature tree, fast-growing trees, trees planted in limited soil volumes, shallow-rooted tree with buttress roots, trees whose diameter at breast height exceeds 10 cm, old and cracked road paving, high soil surface moisture content, short distances between trees and sidewalks (<2 to 3 m), and underground pipes that are already broken and made of metals or stones. The phenotypic traits of trees may be the primary factor causing root damage when there is a mismatch between the root-soil requirements of urban street trees and the actual soil environment. The poor effectiveness of root damage prevention and control measures may be attributed to the lack of connection between the development of control measures and the mechanism of root damage.

Proteomic exploration reveals a metabolic rerouting due to low oxygen during controlled germination of malting barley (Hordeum vulgare L.)

Barley (Hordeum vulgare L.) is used in malt production for brewing applications. Barley malting involves a process of controlled germination that modifies the grain by activating enzymes to solubilize starch and proteins for brewing. Initially, the grain is submerged in water to raise grain moisture, requiring large volumes of water. Achieving grain modification at reduced moisture levels can contribute to the sustainability of malting practices. This study combined proteomics, bioinformatics, and biochemical phenotypic analysis of two malting barley genotypes with observed differences in water uptake and modification efficiency. We sought to reveal the molecular mechanisms at play during controlled germination and explore the roles of protein groups at 24 h intervals across the first 72 h. Overall, 3,485 protein groups were identified with 793 significant differentially abundant (DAP) within and between genotypes, involved in various biological processes, including protein synthesis, carbohydrate metabolism, and hydrolysis. Functional integration into metabolic pathways, such as glycolysis, pyruvate, starch and sucrose metabolism, revealed a metabolic rerouting due to low oxygen enforced by submergence during controlled germination. This SWATH-MS study provides a comprehensive proteome reference, delivering new insights into the molecular mechanisms underlying the impacts of low oxygen during controlled germination. It is concluded that continued efficient modification of malting barley subjected to submergence is largely due to the capacity to reroute energy to maintain vital processes, particularly protein synthesis.

Identification of novel plant cysteine oxidase inhibitors from a yeast chemical genetic screen

Hypoxic responses in plants involve Plant Cysteine Oxidases (PCOs). They catalyze the N-terminal cysteine oxidation of Ethylene Response Factors VII (ERF-VII) in an oxygen-dependent manner, leading to their degradation via the cysteine N-degron pathway (Cys-NDP) in normoxia. In hypoxia, PCO activity drops, leading to the stabilization of ERF-VIIs and subsequent hypoxic gene upregulation. Thus far, no chemicals have been described to specifically inhibit PCO enzymes. In this work, we devised an in vivo pipeline to discover Cys-NDP effector molecules. Budding yeast expressing AtPCO4 and plant-based ERF-VII reporters was deployed to screen a library of natural-like chemical scaffolds and was further combined with an Arabidopsis Cys-NDP reporter line. This strategy allowed us to identify three PCO inhibitors, two of which were shown to affect PCO activity in vitro. Application of these molecules to Arabidopsis seedlings led to an increase in ERF-VII stability, induction of anaerobic gene expression, and improvement of tolerance to anoxia. By combining a high-throughput heterologous platform and the plant model Arabidopsis, our synthetic pipeline provides a versatile system to study how the Cys-NDP is modulated. Its first application here led to the discovery of at least two hypoxia-mimicking molecules with the potential to impact plant tolerance to low oxygen stress.

Efficient sugar utilization and transition from oxidative to substrate-level phosphorylation in high starch storage roots of African cassava genotypes

Cassava's storage roots represent one of the most important sources of nutritional carbohydrates worldwide. Particularly, smallholder farmers in sub-Saharan Africa depend on this crop plant, where resilient and yield-improved varieties are of vital importance to support steadily increasing populations. Aided by a growing understanding of the plant's metabolism and physiology, targeted improvement concepts already led to visible gains in recent years. To expand our knowledge and to contribute to these successes, we investigated storage roots of eight cassava genotypes with differential dry matter content from three successive field trials for their proteomic and metabolic profiles. At large, the metabolic focus in storage roots transitioned from cellular growth processes toward carbohydrate and nitrogen storage with increasing dry matter content. This is reflected in higher abundance of proteins related to nucleotide synthesis, protein turnover, and vacuolar energization in low starch genotypes, while proteins involved in sugar conversion and glycolysis were more prevalent in high dry matter genotypes. This shift in metabolic orientation was underlined by a clear transition from oxidative- to substrate-level phosphorylation in high dry matter genotypes. Our analyses highlight metabolic patterns that are consistently and quantitatively associated with high dry matter accumulation in cassava storage roots, providing fundamental understanding of cassava's metabolism as well as a data resource for targeted genetic improvement.

Preserving root stem cell functionality under low oxygen stress: the role of nitric oxide and phytoglobins

MAIN CONCLUSION

The preservation of quiescent center stem cell integrity in hypoxic roots by phytoglobins is exercised through their ability to scavenge nitric oxide and attenuate its effects on auxin transport and cell degradation. Under low oxygen stress, the retention or induction of phytoglobin expression maintains cell viability while loss or lack of induction of phytoglobin leads to cell degradation. Plants have evolved unique attributes to ensure survival in the environment in which they must exist. Common among the attributes is the ability to maintain stem cells in a quiescent (or low proliferation) state in unfriendly environments. From the seed embryo to meristematic regions of the plant, quiescent stem cells exist to regenerate the organism when environmental conditions are suitable to allow plant survival. Frequently, plants dispose of mature cells or organs in the process of acclimating to the stresses to ensure survival of meristems, the stem cells of which are capable of regenerating cells and organs that have been sacrificed, a feature not generally available to mammals. Most of the research on plant stress responses has dealt with how mature cells respond because of the difficulty of specifically examining plant meristem responses to stress. This raises the question as to whether quiescent stem cells behave in a similar fashion to mature cells in their response to stress and what factors within these critical cells determine whether they survive or degrade when exposed to environmental stress. This review attempts to examine this question with respect to the quiescent center (QC) stem cells of the root apical meristem. Emphasis is put on how varying levels of nitric oxide, influenced by the expression of phytoglobins, affect QC response to hypoxic stress.

ERFVII transcription factors and their role in the adaptation to hypoxia in Arabidopsis and crops

In this review, we focus on ethylene transcription factors (ERFs), which are a crucial family of transcription factors that regulate plant development and stress responses. ERFVII transcription factors have been identified and studied in several crop species, including rice, wheat, maize, barley, and soybean. These transcription factors are known to be involved in regulating the plant's response to low oxygen stress-hypoxia and could thus improve crop yields under suboptimal growing conditions. In rice (Oryza sativa) several ERFVII genes have been identified and characterized, including SUBMERGENCE 1A (SUB1A), which enables rice to tolerate submergence. The SUB1A gene was used in the development of SUB1 rice varieties, which are now widely grown in flood-prone areas and have been shown to improve yields and farmer livelihoods. The oxygen sensor in plants was discovered using the model plant Arabidopsis. The mechanism is based on the destabilization of ERFVII protein via the N-degron pathway under aerobic conditions. During hypoxia, the stabilized ERFVIIs translocate to the nucleus where they activate the transcription of hypoxia-responsive genes (HRGs). In summary, the identification and characterization of ERFVII transcription factors and their mechanism of action could lead to the development of new crop varieties with improved tolerance to low oxygen stress, which could have important implications for global food security.

Waterlogging Tolerance of Actinidia valvata Dunn Is Associated with High Activities of Pyruvate Decarboxylase, Alcohol Dehydrogenase and Antioxidant Enzymes

Kiwifruit (Actinidia spp.) is susceptible to waterlogging stress. Although abundant wild germplasm resources exist among Actinidia plants for improving the waterlogging tolerance of kiwifruit cultivars, the underlying mechanisms remain largely unknown. Here, a comparative study was undertaken using one wild germplasm, Maorenshen (A. valvata Dunn, MRS), and one cultivar, Miliang-1 (A. chinensis var. deliciosa (A.Chev.) A.Chev. cv. Miliang-1, ML). Under stress, the ML plantlets were seriously damaged with wilted chlorotic leaves and blackened rotten roots, whereas the symptoms of injury in the MRS plantlets were much fewer, along with higher photosynthetic rates, chlorophyll fluorescence characteristics and root activity under stress conditions. However, neither aerenchyma in the root nor adventitious roots appeared in both germplasms upon stress exposure. The activities of pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH), as well as their transcript levels, were constitutively higher in MRS than those in ML under both normal and stress conditions. Waterlogging stress significantly enhanced the PDC and ADH enzyme activities in both germplasms, which were 60.8% and 22.4% higher in the MRS roots than those in the ML roots under waterlogging stress, respectively. Moreover, MRS displayed higher activities of antioxidant enzymes, including SOD, CAT, and APX, as well as DPPH-radical scavenging ability, and decreased H2O2 and MDA accumulation under both normal and stress conditions. Our findings suggest that the waterlogging tolerance of the wild A. valvata germplasm was associated with high PDC and ADH, as well as antioxidant ability.

Mapping the Arabidopsis thaliana proteome in PeptideAtlas and the nature of the unobserved (dark) proteome; strategies towards a complete proteome

This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected PTMs, and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for building the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome - the 'dark' proteome. This dark proteome is highly enriched for certain ( e.g. CLE, CEP, IDA, PSY) but not other ( e.g. THIONIN, CAP,) signaling peptides families, E3 ligases, TFs, and other proteins with unfavorable physicochemical properties. A machine learning model trained on RNA expression data and protein properties predicts the probability for proteins to be detected. The model aids in discovery of proteins with short-half life ( e.g. SIG1,3 and ERF-VII TFs) and completing the proteome. PeptideAtlas is linked to TAIR, JBrowse, PPDB, SUBA, UniProtKB and Plant PTM Viewer.

Causes and consequences of endogenous hypoxia on growth and metabolism of developing maize kernels

Maize (Zea mays) kernels are the largest cereal grains, and their endosperm is severely oxygen deficient during grain fill. The causes, dynamics, and mechanisms of acclimation to hypoxia are minimally understood. Here, we demonstrate that hypoxia develops in the small, growing endosperm, but not the nucellus, and becomes the standard state, regardless of diverse structural and genetic perturbations in modern maize (B73, popcorn, sweet corn), mutants (sweet4c, glossy6, waxy), and non-domesticated wild relatives (teosintes and Tripsacum species). We also uncovered an interconnected void space at the chalazal pericarp, providing superior oxygen supply to the placental tissues and basal endosperm transfer layer. Modeling indicated a very high diffusion resistance inside the endosperm, which, together with internal oxygen consumption, could generate steep oxygen gradients at the endosperm surface. Manipulation of oxygen supply induced reciprocal shifts in gene expression implicated in controlling mitochondrial functions (23.6 kDa Heat-Shock Protein, Voltage-Dependent Anion Channel 2) and multiple signaling pathways (core hypoxia genes, cyclic nucleotide metabolism, ethylene synthesis). Metabolite profiling revealed oxygen-dependent shifts in mitochondrial pathways, ascorbate metabolism, starch synthesis, and auxin degradation. Long-term elevated oxygen supply enhanced the rate of kernel development. Altogether, evidence here supports a mechanistic framework for the establishment of and acclimation to hypoxia in the maize endosperm.

Plant responses to limited aeration: Advances and future challenges

Limited aeration that is caused by tissue geometry, diffusion barriers, high elevation, or a flooding event poses major challenges to plants and is often, but not exclusively, associated with low oxygen. These processes span a broad interest in the research community ranging from whole plant and crop responses, post-harvest physiology, plant morphology and anatomy, fermentative metabolism, plant developmental processes, oxygen sensing by ERF-VIIs, gene expression profiles, the gaseous hormone ethylene, and O2 dynamics at cellular resolution. The International Society for Plant Anaerobiosis (ISPA) gathers researchers from all over the world contributing to understand the causes, responses, and consequences of limited aeration in plants. During the 14th ISPA meeting, major research progress was related to the evolution of O2 sensing mechanisms and the intricate network that balances low O2 signaling. Here, the work moved beyond flooding stress and emphasized novel underexplored roles of low O2 and limited aeration in altitude adaptation, fruit development and storage, and the vegetative development of growth apices. Regarding tolerance towards flooding, the meeting stressed the relevance and regulation of developmental plasticity, aerenchyma, and barrier formation to improve internal aeration. Additional newly explored flood tolerance traits concerned resource balance, senescence, and the exploration of natural genetic variation for novel tolerance loci. In this report, we summarize and synthesize the major progress and future challenges for low O2 and aeration research presented at the conference.

Subsurface aeration mitigates organic material mulching-induced anaerobic stress via regulating hormone signaling in Phyllostachys praecox roots

Organic material mulching has been used extensively to allow Phyllostachys praecox to promote growth and development of shoots. However, the bamboo forest always showed a significant degradation, probably due to anaerobic damage caused by the mulching after several years. Therefore, we have innovatively proposed an improvement measure to aerate the underground pipes for the first time. We investigated the role of subsurface pipe aeration in regulating root hypoxia to reduce the stress and to identify the degradation mechanism. Results showed that aeration increased oxygen concentration, shoot yield and root growth compared with mulching, and the aeration enhanced the concentration of indole-3-acetic acid (IAA) and the expression of Aux/IAAs (Aux1, Aux2, Aux3, and Aux4). Aeration reduced gibberellin (GA), ethylene (ETH), and abscisic acid (ABA) contents as well as anaerobic enzyme activities (alanine transaminase, AlaAT; alcohol dehydrogenase, ADH; pyruvate decarboxylase, PDC; and lactate dehydrogenase, LDH), which alleviated root damage in anoxic conditions. Furthermore, correlation showed that the activities of ADH, LDH, PDC, and AlaAT showed significant linear correlations with soil oxygen levels. RDA analyses showed that ABA, IAA, and ETH were found as the key driving hormones of Aux/IAAs in the root of the forest mulched with organic material. Here we show that subsurface aeration increases soil oxygen concentration, shoot yield, root growth and regulates phytohormone concentrations and Aux/IAAs expression, which reduces anaerobic enzyme activities. Consequently, subsurface pipe aeration is an effective measure to mitigate the degradation of bamboo forests caused by soil hypoxia that results from organic material mulching.

Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress

We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.

Integrating UV-Vis Spectroscopy and Oxygen Optode for Accurate Determination of Oxygen Affinity of Proteins

Protein-based oxygen sensors exhibit a wide range of affinity values ranging from low nanomolar to high micromolar. How proteins utilize different metals, cofactors, and macromolecular structure to regulate their oxygen affinity (K_d) to a value that is appropriate for their biological function is an important question in biochemistry and microbiology. In this chapter, we describe a simple setup that integrates a UV-Vis spectrometer with an oxygen optode for direct determination of K_d of heme-containing oxygen sensors. We provide details on how to set up the assay, acquire and fit data for accurate K_d determination using Cs H-NOX (K_d = 23 ± 2 nM) as an example, and also discuss tips and tricks to make the assay work for other oxygen-binding proteins.

Kinetic Measurements to Investigate the Oxygen-Sensing Properties of Plant Cysteine Oxidases

Enzymatic O₂ sensors transduce the availability of O₂ within the cell into a physiological, typically adaptive response. One such O₂-sensing enzymatic family is the N-terminal cysteine dioxygenases in plants (plant cysteine oxidases [PCOs]). In vitro kinetic studies have determined the O₂-sensing capacity of PCOs. Here we describe the rationale and experimental protocol for an assay with which the O₂ sensitivity of Arabidopsis thaliana PCOs (AtPCOs) can be measured. We explain each step from the recombinant protein synthesis of AtPCOs to the steady-state kinetic assays of AtPCOs for primary substrate and O₂ from which kinetic parameters can be derived. The same techniques can be applied to other N-terminal cysteine thiol dioxygenases, e.g. 2-aminoethanethiol dioxygenase (ADO), and similar principles can be applied to determine kinetic characteristics of other oxygenase enzymes towards O₂.

Acquisition of hypoxia inducibility by oxygen sensing N-terminal cysteine oxidase in spermatophytes

N-terminal cysteine oxidases (NCOs) use molecular oxygen to oxidise the amino-terminal cysteine of specific proteins, thereby initiating the proteolytic N-degron pathway. To expand the characterisation of the plant family of NCOs (plant cysteine oxidases [PCOs]), we performed a phylogenetic analysis across different taxa in terms of sequence similarity and transcriptional regulation. Based on this survey, we propose a distinction of PCOs into two main groups. A-type PCOs are conserved across all plant species and are generally unaffected at the messenger RNA level by oxygen availability. Instead, B-type PCOs appeared in spermatophytes to acquire transcriptional regulation in response to hypoxia. The inactivation of two A-type PCOs in Arabidopsis thaliana, PCO4 and PCO5, is sufficient to activate the anaerobic response in young seedlings, whereas the additional removal of B-type PCOs leads to a stronger induction of anaerobic genes and impairs plant growth and development. Our results show that both PCO types are required to regulate the anaerobic response in angiosperms. Therefore, while it is possible to distinguish two clades within the PCO family, we conclude that they all contribute to restrain the anaerobic transcriptional programme in normoxic conditions and together generate a molecular switch to toggle the hypoxic response.

Proteasome Dysfunction Leads to Suppression of the Hypoxic Response Pathway in Arabidopsis

Proteasome is a large proteolytic complex that consists of a 20S core particle (20SP) and 19S regulatory particle (19SP) in eukaryotes. The proteasome degrades most cellular proteins, thereby controlling many key processes, including gene expression and protein quality control. Proteasome dysfunction in plants leads to abnormal development and reduced adaptability to environmental stresses. Previous studies have shown that proteasome dysfunction upregulates the gene expression of proteasome subunits, which is known as the proteasome bounce-back response. However, the proteasome bounce-back response cannot explain the damaging effect of proteasome dysfunction on plant growth and stress adaptation. To address this question, we focused on downregulated genes caused by proteasome dysfunction. We first confirmed that the 20SP subunit PBE is an essential proteasome subunit in Arabidopsis and that PBE1 mutation impaired the function of the proteasome. Transcriptome analyses showed that hypoxia-responsive genes were greatly enriched in the downregulated genes in pbe1 mutants. Furthermore, we found that the pbe1 mutant is hypersensitive to waterlogging stress, a typical hypoxic condition, and hypoxia-related developments are impaired in the pbe1 mutant. Meanwhile, the 19SP subunit rpn1a mutant seedlings are also hypersensitive to waterlogging stress. In summary, our results suggested that proteasome dysfunction downregulated the hypoxia-responsive pathway and impaired plant growth and adaptability to hypoxia stress.

ERF subfamily transcription factors and their function in plant responses to abiotic stresses

Ethylene Responsive Factor (ERF) subfamily comprise the largest number of proteins in the plant AP2/ERF superfamily, and have been most extensively studied on the biological functions. Members of this subfamily have been proven to regulate plant resistances to various abiotic stresses, such as drought, salinity, chilling and some other adversities. Under these stresses, ERFs are usually activated by mitogen-activated protein kinase induced phosphorylation or escape from ubiquitin-ligase enzymes, and then form complex with nucleic proteins before binding to cis-element in promoter regions of stress responsive genes. In this review, we will discuss the phylogenetic relationships among the ERF subfamily proteins, summarize molecular mechanism how the transcriptional activity of ERFs been regulated and how ERFs of different subgroup regulate the transcription of stress responsive genes, such as high-affinity K⁺ transporter gene PalHKT1;2, reactive oxygen species related genes LcLTP, LcPrx, and LcRP, flavonoids synthesis related genes FtF3H and LhMYBSPLATTER, etc. Though increasing researches demonstrate that ERFs are involved in various abiotic stresses, very few interact proteins and target genes of them have been comprehensively annotated. Hence, future research prospects are described on the mechanisms of how stress signals been transited to ERFs and how ERFs regulate the transcriptional expression of stress responsive genes.

Endoplasmic reticulum oxidoreductin provides resilience against reductive stress and hypoxic conditions by mediating luminal redox dynamics

Oxidative protein folding in the endoplasmic reticulum (ER) depends on the coordinated action of protein disulfide isomerases and ER oxidoreductins (EROs). Strict dependence of ERO activity on molecular oxygen as the final electron acceptor implies that oxidative protein folding and other ER processes are severely compromised under hypoxia. Here, we isolated viable Arabidopsis thaliana ero1 ero2 double mutants that are highly sensitive to reductive stress and hypoxia. To elucidate the specific redox dynamics in the ER in vivo, we expressed the glutathione redox potential (EGSH) sensor Grx1-roGFP2iL-HDEL with a midpoint potential of -240 mV in the ER of Arabidopsis plants. We found EGSH values of -241 mV in wild-type plants, which is less oxidizing than previously estimated. In the ero1 ero2 mutants, luminal EGSH was reduced further to -253 mV. Recovery to reductive ER stress induced by dithiothreitol was delayed in ero1 ero2. The characteristic signature of EGSH dynamics in the ER lumen triggered by hypoxia was affected in ero1 ero2 reflecting a disrupted balance of reductive and oxidizing inputs, including nascent polypeptides and glutathione entry. The ER redox dynamics can now be dissected in vivo, revealing a central role of EROs as major redox integrators to promote luminal redox homeostasis.

The Role of Aquaporins in Plant Growth under Conditions of Oxygen Deficiency

Plants frequently experience hypoxia due to flooding caused by intensive rainfall or irrigation, when they are partially or completely submerged under a layer of water. In the latter case, some resistant plants implement a hypoxia avoidance strategy by accelerating shoot elongation, which allows lifting their leaves above the water surface. This strategy is achieved due to increased water uptake by shoot cells through water channels (aquaporins, AQPs). It remains a puzzle how an increased flow of water through aquaporins into the cells of submerged shoots can be achieved, while it is well known that hypoxia inhibits the activity of aquaporins. In this review, we summarize the literature data on the mechanisms that are likely to compensate for the decline in aquaporin activity under hypoxic conditions, providing increased water entry into cells and accelerated shoot elongation. These mechanisms include changes in the expression of genes encoding aquaporins, as well as processes that occur at the post-transcriptional level. We also discuss the involvement of hormones, whose concentration changes in submerged plants, in the control of aquaporin activity.

Function of Cajal Bodies in Nuclear RNA Retention in A. thaliana Leaves Subjected to Hypoxia

Retention of RNA in the nucleus precisely regulates the time and rate of translation and controls transcriptional bursts that can generate profound variability in mRNA levels among identical cells in tissues. In this study, we investigated the function of Cajal bodies (CBs) in RNA retention in A. thaliana leaf nuclei during hypoxia stress was investigated. It was observed that in ncb-1 mutants with a complete absence of CBs, the accumulation of poly(A⁺) RNA in the leaf nuclei was lower than that in wt under stress. Moreover, unlike in root cells, CBs store less RNA, and RNA retention in the nuclei is much less intense. Our results reveal that the function of CBs in the accumulation of RNA in nuclei under stress depends on the plant organ. Additionally, in ncb-1, retention of introns of mRNA RPB1 (largest subunit of RNA polymerase II) mRNA was observed. However, this isoform is highly accumulated in the nucleus. It thus follows that intron retention in transcripts is more important than CBs for the accumulation of RNA in nuclei. Accumulated mRNAs with introns in the nucleus could escape transcript degradation by NMD (nonsense-mediated mRNA decay). From non-fully spliced mRNAs in ncb-1 nuclei, whose levels increase during hypoxia, introns are removed during reoxygenation. Then, the mRNA is transferred to the cytoplasm, and the RPB1 protein is translated. Despite the accumulation of isoforms in nuclei with retention of introns in reoxygenation, ncb-1 coped much worse with long hypoxia, and manifested faster yellowing and shrinkage of leaves.

Integrated Transcriptomic and Proteomic Analyses Uncover the Regulatory Mechanisms of Myricaria laxiflora Under Flooding Stress

Flooding is one of the major environmental stresses that severely influence plant survival and development. However, the regulatory mechanisms underlying flooding stress remain largely unknown in Myricaria laxiflora, an endangered plant mainly distributed in the flood zone of the Yangtze River, China. In this work, transcriptome and proteome were performed in parallel in roots of M. laxiflora during nine time-points under the flooding and post-flooding recovery treatments. Overall, highly dynamic and stage-specific expression profiles of genes/proteins were observed during flooding and post-flooding recovery treatment. Genes related to auxin, cell wall, calcium signaling, and MAP kinase signaling were greatly down-regulated exclusively at the transcriptomic level during the early stages of flooding. Glycolysis and major CHO metabolism genes, which were regulated at the transcriptomic and/or proteomic levels with low expression correlations, mainly functioned during the late stages of flooding. Genes involved in reactive oxygen species (ROS) scavenging, mitochondrial metabolism, and development were also regulated exclusively at the transcriptomic level, but their expression levels were highly up-regulated upon post-flooding recovery. Moreover, the comprehensive expression profiles of genes/proteins related to redox, hormones, and transcriptional factors were also investigated. Finally, the regulatory networks of M. laxiflora in response to flooding and post-flooding recovery were discussed. The findings deepen our understanding of the molecular mechanisms of flooding stress and shed light on the genes and pathways for the preservation of M. laxiflora and other endangered plants in the flood zone.

The Intersection of Non-Coding RNAs Contributes to Forest Trees' Response to Abiotic Stress

Non-coding RNAs (ncRNAs) play essential roles in plants by modulating the expression of genes at the transcriptional or post-transcriptional level. In recent years, ncRNAs have been recognized as crucial regulators for growth and development in forest trees, and ncRNAs that respond to various abiotic stresses are now under intense study. In this review, we summarized recent advances in the understanding of abiotic stress-responsive microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in forest trees. Furthermore, we analyzed the intersection of miRNAs, and epigenetic modified ncRNAs of forest trees in response to abiotic stress. In particular, the abiotic stress-related lncRNA/circRNA-miRNA-mRNA regulatory network of forest trees was explored.

Transcriptome Analysis of Endogenous Hormone Response Mechanism in Roots of Styrax tonkinensis Under Waterlogging

As a promising oil species, Styrax tonkinensis has great potential as a biofuel due to an excellent fatty acid composition. However, frequent flooding caused by global warming and the low tolerance of the species to waterlogging largely halted its expansion in waterlogged areas. To explore endogenous hormones and phytohormone-related molecular response mechanism of S. tonkinensis under waterlogging, we determined 1-aminocyclopropane-1-carboxylic acid (ACC) and three phytohormone content (ABA, abscisic acid; SA, salicylic acid; IAA, indole-3-acetic acid) and analyzed the transcriptome of its seedlings under waterlogged condition of 3-5 cm. The sample collecting time was 0, 9, 24, and 72 h, respectively. It was concluded that ACC presented an upward trend, but other plant hormones showed a downward trend from 0 to 72 h under waterlogging stress. A total of 84,601 unigenes were assembled with a total length of 81,389,823 bp through transcriptome analysis. The GO enrichment analysis of total differentially expressed genes (DEGs) revealed that 4,637 DEGs, 8,238 DEGs, and 7,146 DEGs were assigned into three main GO functional categories in 9 vs. 0 h, 24 vs. 0 h, and 72 vs. 0 h, respectively. We also discovered several DEGs involved in phytohormone synthesis pathway and plant hormone signaling pathway. It was concluded that the decreased transcription of PYL resulted in the weak ABA signal transduction pathway. Moreover, decreased SA content caused by the low-expressed PAL might impact the resistance of S. tonkinensis seedlings under waterlogging stress. Our research may provide a scientific basis for the understanding of the endogenous hormone response mechanism of S. tonkinensis to waterlogging and lay a foundation for further exploration of the waterlogging defect resistance genes of S. tonkinensis and improving its resistance to waterlogging stress.