9. Flooding & hypoxia stress.pptx

# Climate change and its impact on flooding events Here is a detailed study guide section on climate change and its impact on flooding events: ## 1. Climate change and its impact on flooding events Global climate change is leading to more frequent and intense weather-related disasters, significantly impacting agricultural production and global ecosystems, with floods being a major concern. ### 1.1 The changing climate and disaster frequency The Intergovernmental Panel on Climate Change (IPCC) reports highlight a discernible increase in the frequency and intensity of both warming and precipitation events. When compared to the pre-industrial era (1850-1900), global average temperatures have risen by approximately 1.3 degrees Celsius, with temperature extremes experiencing even greater increases. Precipitation events, crucial for understanding flood risks, have also intensified, with observed increases of seven to ten percent in wetness. Projections indicate that a four-degree Celsius global temperature rise would triple the likelihood of severe flood events and increase their intensity by approximately one-third. #### 1.1.1 Relationship between global temperature rise and disaster occurrence The occurrence of climate-related disasters, such as droughts, floods, and storms, is directly correlated with changes in global temperature. * Droughts can lead to a thirty-four percent loss in production. * Floods result in a twenty-one percent loss in production. * Storms cause nineteen percent loss in production. The incidence of floods and storms, in particular, shows a much steeper incline in frequency as global temperatures rise compared to other types of disasters. This escalation in extreme weather events has profound implications for agricultural productivity and global food security. > **Tip:** Understand the concept of moving averages when analyzing temporal data of disaster occurrences, as it helps to smooth out short-term fluctuations and reveal underlying cyclical patterns and long-term trends. ### 1.2 Regional variations and extreme precipitation events The impact of climate change on flood frequency is not uniform globally. While some regions are projected to experience increased flooding, others may face greater drought conditions. Europe, for example, is experiencing a dual threat, with some areas facing increased drought and others more frequent floods. These regional impacts are influenced by microclimates, which play a significant role in how different areas respond to global climate shifts. Latin America, East Asia (particularly India and Southeast Asia), and Sub-Saharan Africa are identified as regions particularly vulnerable to increased flood events. These areas are experiencing heavy precipitation events, defined as more than 100 millimeters of rain per 24-hour period. > **Example:** A notable event occurred in Turis-Valencia in October 2024, where the region experienced 185 millimeters of rain in just one hour, illustrating the extreme intensity of some precipitation events. In Southeast Asian regions, rainfall rates can even exceed 200 millimeters per hour. Similarly, a storm in Belgium in 2021 saw some areas receive over 100 millimeters of rain in a short period, leading to widespread flooding. ### 1.3 Impacts of flooding on agriculture and ecosystems Flooding events have significant and devastating impacts on both natural and agricultural ecosystems. The primary consequences include crop losses and substantial economic costs due to water saturation. As global population growth necessitates increased agricultural production, land use intensification, unfortunately, often leads to more extensive flooding. This creates a critical challenge: meeting food demands while mitigating the environmental consequences of expanded agricultural areas. The loss of agricultural productivity extends beyond staple crops, affecting the availability of essential micronutrients. Studies subjecting crops to elevated carbon dioxide levels (approaching 600 parts per million) have shown significant reductions, at least thirty to forty percent, in certain vitamins and minerals, especially B vitamins. ### 1.4 Plant adaptations to flooding stress Plants have evolved various adaptive strategies to cope with flooding, which can manifest as waterlogging (affecting only roots) or submergence (involving aerial parts). These strategies can be categorized into morphological, biochemical, and molecular responses. #### 1.4.1 Morphological and anatomical adaptations * **Aerenchyma formation:** This involves the creation of air-filled channels within plant tissues, particularly in the cortical region of roots. These channels facilitate gas diffusion, allowing oxygen to reach submerged or waterlogged tissues. * **Pneumatophores:** These are specialized roots that grow upwards out of the water or mud to access atmospheric oxygen. They exhibit negative gravitropism, contrasting with the typical positive gravitropism of roots. * **Lenticels:** These are small pores or openings in the periderm (bark) of stems that allow for improved gas exchange with the atmosphere. * **Adventitious roots (AR):** In response to ethylene signaling, plants can form adventitious roots on their stems. The emergence of these roots involves programmed cell death (PCD) of overlying epidermal tissues, enabling the roots to pierce through. This process can be driven by mechanical pressure exerted by the growing AR primordia. * **Hypertrophic growth:** This refers to the lateral expansion of plant organs, particularly stems, which can be induced by ethylene accumulation under flooding conditions. * **Leaf morphology changes:** In some species, such as deepwater rice, leaf sheaths become longer relative to the leaf blade, and leaves may adopt an upright position (hyponastic growth) to improve gas exchange. #### 1.4.2 Metabolic and physiological adaptations Flooding leads to a significant change in the concentration of key gases, including oxygen ($O_2$), carbon dioxide ($CO_2$), ethylene ($C_2H_4$), and nitric oxide (NO). The reduced solubility and diffusion rate of gases in aqueous environments exacerbate oxygen deprivation. * **Energy crisis and carbohydrate starvation:** During submergence, plants face an "energy crisis" due to limited oxygen for aerobic respiration. This leads to carbohydrate starvation. * **Anaerobic respiration and fermentation:** Plants can switch to anaerobic respiration and fermentation pathways to regenerate $NAD^+$ and produce ATP. However, this process yields significantly less ATP (around 2 ATP molecules per glucose molecule) compared to aerobic respiration (approximately 32 ATP molecules). Common end products include ethanol, lactate, and alanine. * **Metabolic shifts for ATP production:** Plants may stimulate the breakdown of sucrose via sucrose synthase and increase amylase activity to break down starch. The resulting glucose-6-phosphate feeds into glycolysis, enabling limited ATP production. * **$NAD^+$ regeneration:** Fermentation pathways are crucial for regenerating $NAD^+$ from NADH, which is essential for sustaining glycolysis. * **Metabolic channeling (e.g., Alanine and GABA shunts):** The pyruvate produced during glycolysis can be converted to alanine, or enter the ethanol fermentation pathway. The alanine shunt, involving the conversion of glutamate to 2-oxoglutarate, can lead to increased succinate levels, which can then be used for oxidative phosphorylation to produce additional ATP and conserve the limited oxygen. The GABA shunt, involving the conversion of glutamate to GABA by glutamate decarboxylase (GAD), consumes protons, helping to stabilize intracellular pH which can drop during fermentation. #### 1.4.3 Hormonal regulation and signaling * **Ethylene ($C_2H_4$):** Ethylene plays a central role in mediating many flooding responses. Its accumulation is influenced by both increased biosynthesis and reduced diffusion/biosynthesis rates due to lower oxygen availability. Ethylene is involved in promoting adventitious root formation, hypertrophic growth, and shoot elongation. * **Abscisic acid (ABA) and Gibberellins (GA):** The balance between ABA and GA is crucial. Under flooding, ethylene can indirectly lead to a decrease in ABA levels (through downregulation of NCED and upregulation of ABA degradation) and an increase in GA levels. GA is a key hormone promoting shoot elongation. * **Nitric oxide (NO):** NO can act as a systemic signaling molecule in response to hypoxia, originating from the root transition zone. It can catalyze the upregulation of hypoxia-responsive genes and contribute to hypoxic acclimation. * **Reactive Oxygen Species (ROS):** ROS are generated during flooding, particularly through the activation of NADPH oxidases (RBOH). While ROS can contribute to programmed cell death in some contexts (e.g., enabling adventitious root emergence), they also play signaling roles and can accumulate, leading to oxidative stress upon desubmergence. #### 1.4.4 Molecular mechanisms: transcription factors and signaling pathways * **Group VII Ethylene Response Factors (ERFs):** These transcription factors are critical sensors of low oxygen conditions. In *Arabidopsis thaliana*, this group includes HRE1, HRE2, RAP2.2, RAP2.3, and RAP2.12. In rice, SUB1A, SUB1B, SUB1C, SK1, and SK2 are key members. * **N-end Rule Pathway (NERP):** This pathway regulates the stability of Group VII ERFs. Under normoxic conditions, the N-terminus of these proteins is modified, leading to their ubiquization and degradation by the proteasome. Under hypoxia, this modification is inhibited, allowing the ERFs to accumulate and bind to hypoxia-responsive elements (HREs) in the promoters of target genes. * **RAP2.12:** This ERF is a primary sensor of low oxygen in *Arabidopsis*. It can be sequestered by an ACBP (acyl-CoA-binding protein) at the plasma membrane under normoxia, preventing its translocation to the nucleus. Upon hypoxia, it dissociates from ACBP and moves to the nucleus to activate gene expression. * **Anaerobiosis Responsive Elements (AREs):** These are cis-acting elements in the promoters of anaerobically induced genes (ANP genes). Redox-sensitive transcription factors interact with AREs to promote the transcription of ANPs involved in various metabolic adjustments. * **Phytohemoglobins:** These proteins act as oxygen sensors and are involved in NO scavenging and maintaining redox balance. #### 1.4.5 Low Oxygen Escape Strategy (LOES) vs. Low Oxygen Quiescence Strategy (LOQS) Plants exhibit different primary strategies for coping with flooding: * **Low Oxygen Escape Strategy (LOES):** This strategy aims to increase gas exchange with the atmosphere. It involves enhanced shoot elongation, hyponastic growth, formation of a gas film on leaves, and specialized root structures like aerenchyma and adventitious roots. Genes like SNORKEL (SK1/SK2) are involved in promoting elongation growth via GA signaling. This strategy is particularly prominent in deepwater rice cultivars that can grow rapidly to stay above the water surface. * **Low Oxygen Quiescence Strategy (LOQS):** This strategy focuses on growth constraint and minimizing energy expenditure. It involves reducing carbohydrate consumption, relying on glycolysis, starch catabolism, and ethanolic fermentation for ATP production, and synthesizing proteins involved in metabolite transport, ROS protection, and chaperone activity. Genes like SUB1A are associated with this strategy, dampening responsiveness to GA by upregulating negative regulators of GA signaling (e.g., SLR1 and SLRL1). SUB1A also plays a role in enhancing the upregulation of genes associated with ROS amelioration and dehydration tolerance upon re-oxygenation after flooding. > **Example:** Deepwater rice cultivars like 'Plai Ngam' employ LOES, capable of growing up to one centimeter per hour to escape rising water levels. Flood-tolerant low-land varieties, such as 'FR13A', utilize LOQS and can tolerate flooding for extended periods (over two weeks). #### 1.4.6 Post-submergence stress Following the receding of floodwaters (desubmergence), plants face new challenges: * **Oxidative stress:** Rapid re-exposure to oxygen can lead to the accumulation of Reactive Oxygen Species (ROS), causing cellular damage. * **Dehydration stress:** Reduced hydraulic conductivity developed during flooding can lead to a "pseudo-drought" condition in the shoot, even when roots are still in moist soil. SUB1A plays a critical role in helping plants employing LOQS to recover from these post-submergence stresses by upregulating genes involved in ROS detoxification and ABA-mediated dehydration responses. ### 1.5 Crop development and future directions The increasing frequency and intensity of flood events underscore the urgent need to develop crops with enhanced resilience to flooding. This involves exploring the genetic variation within model, crop, and wild species to identify traits that confer flood tolerance. Understanding the ecophysiological and agronomic relevance of these traits is crucial for breeding programs aimed at securing agricultural production in a changing climate. --- # Plant responses to flooding and hypoxia Plants have evolved sophisticated mechanisms to cope with the stressful conditions imposed by flooding and the resultant hypoxia (low oxygen). These responses encompass morphological, biochemical, and metabolic adaptations aimed at survival and restoration of homeostasis. ### 2.1 The increasing relevance of flooding and hypoxia Global climate change is leading to an increased frequency and intensity of extreme weather events, including floods. This poses a significant threat to both natural and agro-ecosystems, resulting in substantial crop losses and economic costs. As global temperatures rise, the likelihood and severity of flood events are projected to increase, necessitating the development of crops with enhanced resilience. ### 2.2 Understanding flooding and hypoxia Flooding can manifest in various forms, including waterlogging (affecting only the roots) and submergence (affecting aerial parts, either partially or completely). The duration, water level, and temperature of the flood are critical factors. Flooding dramatically alters the concentration of key gases, notably oxygen ($\text{O}_2$), carbon dioxide ($\text{CO}_2$), ethylene ($\text{C}_2\text{H}_4$), and nitric oxide (NO), which have profound signaling roles. During submergence, plants face an energy crisis due to carbohydrate starvation and compromised aerobic respiration. As water recedes, they can experience oxidative stress from reactive oxygen species (ROS) accumulation and dehydration stress due to reduced hydraulic conductivity. * **Normoxia:** Refers to normal or oxygen-repleted conditions, typically around $21\%$ $\text{O}_2$ at $20^\circ\text{C}$ and $1$ atm. * **Hypoxia:** Refers to oxygen levels below normoxia but not necessarily zero. * **Anoxia:** Refers to the complete absence of oxygen. Oxygen sensing in plants can occur through two main mechanisms: * **Indirect $\text{O}_2$ sensing:** Detecting changes in homeostasis as a consequence of oxygen deprivation, such as altered levels of adenylates ($\text{AMP/ADP/ATP}$), pyruvate, $\text{pH}$, calcium ($\text{Ca}^{2+}$), ROS, and reactive nitrogen species (RNS). * **Direct $\text{O}_2$ sensing:** Involves the molecular interaction of oxygen with a specific sensor protein or chemical compound, triggering a response cascade. ### 2.3 Morphological and anatomical adaptations Plants employ a range of structural modifications to survive flooding and hypoxia. These adaptations are often tissue-specific and can be influenced by hormones like ethylene. #### 2.3.1 Root and stem adaptations * **Aerenchyma formation:** This involves the creation of air channels within the cortical tissues of roots and stems. It is a programmed cell death process that forms interconnected air spaces, facilitating faster diffusion of gases to submerged tissues. * **Pneumatophores:** These are specialized aerial roots that exhibit negative gravitropism, growing upwards out of the water or mud to access atmospheric oxygen. * **Lenticels:** These are small pores on the surface of stems, particularly prominent in plants undergoing secondary growth, that allow for enhanced gas exchange. * **Hypodermal suberization (ROL barrier):** To prevent the leakage of oxygen from aerenchyma to the surrounding soil (Radial Oxygen Loss or ROL), a barrier of suberin is deposited in the hypodermis. Suberin is a waxy substance that repels water and gases, creating a barrier that extends to the root meristem to ensure oxygen supply for growth. * **Adventitious root formation:** Ethylene plays a crucial role in the emergence of adventitious root primordia from the pericycle. The growing root exerts significant force on overlying tissues, inducing pressure-driven programmed cell death (PCD) in the epidermal layer, allowing for emergence. Ethylene also promotes ROS formation, making the outer tissues more susceptible to PCD. #### 2.3.2 Shoot adaptations * **Hypertrophic growth:** This refers to the lateral expansion of stems and other aerial organs, often induced by ethylene accumulation. * **Hyponastic growth:** In response to submergence, some plants, particularly deep-water rice, exhibit hyponastic growth where leaves are held upright, facilitating gas exchange. * **Leaf morphology changes:** Adaptations can include longer leaf sheaths relative to leaf blades, which help in gas exchange. * **Formation of a gas film on leaves:** In some species, a gas film trapped on the leaf surface can aid in gas exchange. ### 2.4 Biochemical and metabolic adaptations Flooding and hypoxia trigger significant metabolic shifts to conserve energy and maintain essential cellular functions. #### 2.4.1 Energy crisis and ATP production Under low oxygen conditions, aerobic respiration is compromised, leading to an energy crisis and carbohydrate starvation. Plants must rely on alternative pathways to generate ATP. * **Fermentation:** This process regenerates $\text{NAD}^+$ and allows for continued glycolytic flux, albeit with significantly reduced ATP yield (e.g., $2$ ATP per glucose molecule via substrate-level phosphorylation, compared to $32$ ATP from complete aerobic respiration). Common fermentation end products include ethanol, lactate, and alanine. * **Metabolic shifts to save and produce ATP:** * **Sucrose breakdown:** While direct breakdown of sucrose by invertase may be inhibited, breakdown via sucrose synthase is stimulated. The resulting products feed into glycolysis. * **Starch catabolism:** In some species, amylase activity increases to break down starch, providing glucose for glycolysis. * **Fermentation pathways:** * **Ethanol fermentation:** Pyruvate is converted to ethanol. * **Lactic acid fermentation:** Pyruvate is converted to lactic acid. * **Alanine synthesis:** Pyruvate can be converted to alanine, coupled with the conversion of glutamate to 2-oxoglutamate. This shunt can increase succinate levels, which can enter oxidative phosphorylation to produce some ATP and conserve oxygen. * **GABA shunt:** Glutamate can be converted to gamma-aminobutyric acid (GABA) by glutamate decarboxylase (GAD). This reaction consumes protons, helping to stabilize $\text{pH}$ which can drop due to fermentation. #### 2.4.2 Anaerobic proteins (ANPs) Hypoxia and anoxia induce the expression of anaerobic proteins (ANPs). These proteins are primarily involved in the degradation of sugars and starch, glycolysis, and fermentation. The promoters of ANP genes contain anaerobiosis-responsive elements (AREs), which are thought to interact with redox-sensitive transcription factors that become activated under low oxygen conditions. #### 2.4.3 Phytohemoglobins These proteins act as oxygen sensors and are involved in nitric oxide (NO) scavenging, contributing to the maintenance of redox balance. ### 2.5 Hormonal signaling in flooding responses Several plant hormones play critical roles in mediating responses to flooding and hypoxia. #### 2.5.1 Ethylene ($\text{C}_2\text{H}_4$) Ethylene is a key signaling molecule in flooding responses. Its accumulation is partly due to reduced diffusion and biosynthesis. The conversion of its precursor, ACC (1-aminocyclopropane-1-carboxylic acid), to ethylene by ACC oxidase requires oxygen, and this reaction is slowed under hypoxic conditions. * **Ethylene's roles:** * Induces adventitious root primordia formation. * Promotes ROS formation, contributing to programmed cell death for root emergence. * Induces hypertrophic growth in shoots. * Mediates hyponastic growth in some species. * Influences the expression of genes like *SNORKEL* (SK1/SK2) involved in the escape strategy. * In some contexts, ethylene can also dampen ethylene responses itself. #### 2.5.2 Abscisic acid (ABA) and Gibberellin (GA) The balance between ABA and GA is crucial for regulating shoot elongation during submergence. * **ABA:** Its biosynthesis is downregulated (e.g., via NCED repression), and its degradation is upregulated, leading to a rapid decrease in ABA levels upon submergence. * **GA:** Its levels increase, promoting cell elongation. Ethylene can influence this balance by blocking ABA action, thus allowing GA to rise. #### 2.5.3 Expansins These cell wall-loosening proteins are upregulated, particularly under GA regulation. GA stimulates expansin expression and proton pump activity, which acidifies the cell wall. This weakens the cell wall, allowing for turgor pressure-driven elongation. ### 2.6 Strategies for flood tolerance Plants have developed distinct strategies to survive flooding: #### 2.6.1 Low oxygen escape strategy (LOES) This strategy is employed by plants that need to rapidly grow out of flooded conditions. * **Key features:** Hyponastic growth, enhanced shoot elongation, formation of a gas film on leaves, aerenchyma formation, radial oxygen loss (ROL) barrier, and adventitious root formation. * **Hormonal regulation:** Mediated by ethylene, which promotes shoot elongation through increased GA signaling (e.g., via SK1/SK2 genes). #### 2.6.2 Low oxygen quiescence strategy (LOQS) This strategy focuses on minimizing energy expenditure to conserve resources during prolonged flooding. * **Key features:** Growth constraint, ATP production via glycolysis and fermentation, starch catabolism, and synthesis of protective proteins (chaperones, ROS scavengers). * **Hormonal regulation:** Ethylene can induce genes like *SUB1A* which dampens GA responsiveness by upregulating negative regulators of GA signaling (e.g., SLR1 and SLRL1, which are DELLA proteins). * **Post-submergence recovery:** *SUB1A* also enhances the upregulation of genes involved in ROS detoxification and ABA-mediated dehydration responses, facilitating better recovery after flooding. ### 2.7 Direct low oxygen sensing mechanisms Specific transcription factors, particularly Group VII Ethylene-Response Factors (ERFs), are central to direct oxygen sensing. * **Group VII ERFs:** In *Arabidopsis thaliana*, these include *HRE1*, *HRE2*, *RAP2.2*, *RAP2.3*, and *RAP2.12*. In rice, prominent examples are *SUB1A*, *SUB1B*, *SUB1C*, *SK1*, and *SK2*. * **N-end rule pathway (NERP):** These ERFs possess a conserved N-terminal sequence that targets them for degradation under normoxic conditions via the NERP. Under hypoxia, this degradation is inhibited, allowing the ERFs to translocate to the nucleus and activate hypoxia-responsive genes. * **Normoxic degradation:** Involves cleavage of the terminal methionine by methionine amino peptidases (MAPs), oxidation of the exposed cysteine to cysteine sulfonic acid by plant cysteine oxidases (PCOs), arginylation by arginine tRNA transferases (ATE1/2), and subsequent ubiquitination and proteasomal degradation. * **Hypoxic stabilization:** The oxidation step (by PCO) is inhibited in hypoxia, preventing the degradation cascade and allowing ERFs to accumulate. * **RAP2.12:** This ERF acts as a primary sensor of low oxygen in *Arabidopsis*. It can be sequestered by an acyl-CoA-binding protein (ACBP) at the plasma membrane under normoxia, protecting it from degradation. Upon hypoxia, it dissociates from ACBP and translocates to the nucleus. ### 2.8 Systemic hypoxia signaling Hypoxia can trigger systemic signaling pathways that coordinate responses throughout the plant. * **Nitric Oxide (NO):** In maize, NO generated in the root transition zone acts as a signaling molecule, upregulating hypoxia-responsive genes and contributing to hypoxic acclimation of the entire root. NO is produced as a byproduct of mitochondrial electron transport chain under low oxygen conditions and is a catalyst for the NERP. * **1-aminocyclopropane-1-carboxylic acid (ACC):** The ethylene precursor ACC can act as a signaling molecule independently of ethylene. Its accumulation during flooding, due to insufficient oxygen for conversion to ethylene, suggests a role in systemic signaling from roots to shoots. * **Ethylene ($\text{C}_2\text{H}_4$):** While its production is hindered under hypoxia, accumulated ethylene can still play a role in systemic signaling. > **Tip:** Understanding the interplay between different hormones (ethylene, ABA, GA) and transcription factors (Group VII ERFs) is crucial for comprehending the complexity of plant responses to flooding and hypoxia. > > **Example:** The contrasting roles of *SNORKEL* (promoting escape via elongation) and *SUB1A* (promoting quiescence and recovery) in rice highlight the diverse strategies plants employ based on their genetic makeup and the environmental context. --- # Molecular mechanisms of low oxygen sensing and signaling This topic delves into how plants perceive and respond to low oxygen conditions (hypoxia), focusing on the intricate signaling pathways involving ethylene, reactive oxygen species (ROS), and specific transcription factors. ### 3.1 Sensing of low oxygen levels Plants employ both direct and indirect mechanisms to sense changes in oxygen concentration. #### 3.1.1 Indirect oxygen sensing Indirect sensing involves detecting changes in cellular homeostasis that occur as a consequence of oxygen deprivation. These changes include: * Alterations in adenylate levels ($AMP/ADP/ATP$). * Changes in pyruvate concentration. * Shifts in cellular $pH$. * Fluctuations in intracellular $Ca^{2+}$. * Accumulation of reactive oxygen species ($ROS$) and reactive nitrogen species ($RNS$). #### 3.1.2 Direct oxygen sensing Direct sensing involves the direct molecular interaction of oxygen with specific sensor proteins or chemical compounds, which then triggers a signaling cascade. ### 3.2 Key signaling molecules and pathways #### 3.2.1 Ethylene Ethylene plays a crucial role in mediating plant responses to flooding and hypoxia. Its accumulation is influenced by several factors under low oxygen conditions: * **Reduced biosynthesis:** The final step in ethylene biosynthesis, catalyzed by ACC oxidase, requires oxygen. Under hypoxia, this reaction is significantly slowed, leading to lower ethylene production rates. * **Accumulation:** While production is reduced, ethylene can also accumulate due to reduced diffusion from tissues and its increased synthesis under certain conditions, particularly in deepwater rice. * **Signaling role:** Ethylene is a central signaling molecule that triggers various adaptive responses. For instance, it is involved in the formation of adventitious roots and hyponastic growth. It also plays a role in the regulation of submergence-induced shoot elongation. #### 3.2.2 Reactive Oxygen Species (ROS) ROS are key signaling molecules in plant responses to hypoxia, particularly under waterlogging and subsequent re-oxygenation. * **Ethylene-triggered ROS:** Ethylene can activate NADPH oxidases ($RBOH$), which convert oxygen to superoxide radicals ($O_2^{\ast-}$) and subsequently to hydrogen peroxide ($H_2O_2$). * **Pressure-driven ROS:** Mechanical stress, such as that exerted by emerging adventitious roots, can also induce ROS-dependent programmed cell death ($PCD$) in surrounding tissues, making them more amenable to penetration. * **Oxidative stress:** Upon desubmergence, plants experience oxidative stress due to the rapid re-exposure to oxygen, leading to ROS accumulation. #### 3.2.3 Ethylene-Response Factor (ERF) transcription factors ERFs are a large family of transcription factors that play critical roles in plant stress responses, including those to hypoxia. * **Group VII ERFs:** A specific subfamily of ERFs (Group VII) is directly involved in sensing and responding to low oxygen conditions. Key examples include $HRE1$ and $HRE2$ in *Arabidopsis thaliana* and $SUB1A$, $SUB1B$, $SUB1C$, $SK1$, and $SK2$ in rice. * **N-end rule pathway (NERP):** The N-terminal region of Group VII ERFs is crucial for their oxygen-dependent regulation. Under normoxia, a specific N-terminal sequence is targeted for degradation via the N-end rule pathway. This involves: 1. Cleavage of the terminal methionine by methionine amino peptidases ($MAPs$). 2. Oxidation of the exposed cysteine to cysteine sulfonic acid ($C^{\ast}$) by plant cysteine oxidases ($PCO$). This step is inhibited under hypoxia. 3. Addition of an arginine residue by arginyl-tRNA transferases ($ATE1/2$) to the oxidized cysteine. 4. Recognition of the arginylated protein by E3 ligases (e.g., $PRT6$), leading to polyubiquitination. 5. Degradation of the ubiquitinated ERF by the 26S proteasome. * **Hypoxia-induced stabilization:** Under hypoxia, the oxidation of cysteine to $C^{\ast}$ is inhibited, preventing the subsequent steps of the NERP. This leads to the stabilization of Group VII ERFs, allowing them to translocate to the nucleus and bind to hypoxia-responsive elements ($HREs$) in the promoters of target genes, thereby activating the transcription of hypoxia-responsive genes. * **Role in adaptive strategies:** * In deepwater rice, ethylene-induced ERFs like $SK1/2$ (SNORKEL) promote shoot elongation for escape from submergence by increasing gibberellin ($GA$) accumulation. * In submergence-tolerant rice, ethylene-induced $SUB1A$ dampens responsiveness to $GA$ by upregulating negative regulators of $GA$ signaling, such as $SLR1$ and $SLRL1$. $SUB1A$ also enhances the expression of genes involved in ROS detoxification and dehydration tolerance, aiding in recovery after submergence. * **RAP2.12:** This Group VII ERF in *Arabidopsis* is considered a primary sensor of low oxygen. It can be protected from degradation under normoxia by binding to an acyl-CoA-binding protein ($ACBP$) at the plasma membrane. Upon hypoxia, it dissociates from $ACBP$ and translocates to the nucleus. ### 3.3 Metabolic adjustments under low oxygen Plants undergo significant metabolic changes to conserve energy and produce ATP under hypoxic conditions. * **ATP conservation:** Reduced $ATP$ production due to inhibited photosynthesis and aerobic respiration necessitates strategies to minimize energy expenditure. * **Alternative metabolic pathways:** * **Glycolysis and fermentation:** Increased flux through glycolysis leads to pyruvate production. Pyruvate can then be converted to lactic acid, ethanol, or alanine. Ethanolic fermentation and alanine production are crucial for sustaining some energy generation, with $ATP$ production being significantly lower than in aerobic respiration (e.g., 2 $ATP$ molecules per glucose molecule compared to 32). * **Sucrose metabolism:** Instead of regular breakdown via invertase, sucrose is broken down via sucrose synthase, leading to products that feed into glycolysis. * **Starch catabolism:** Amylase activity increases in some species, breaking down starch into glucose, which then enters glycolysis. * **GABA shunt:** The conversion of glutamate to $GABA$ by glutamate decarboxylase ($GAD$) consumes protons, helping to stabilize intracellular $pH$ which can drop due to fermentation. This pathway also contributes to $ATP$ production and oxygen conservation. * **Anaerobic proteins (ANPs):** The expression of specific anaerobic proteins is induced under hypoxia and anoxia. These proteins are involved in sugar and starch degradation, glycolysis, and fermentation, as well as chaperone activity. Their promoters often contain anaerobiosis-responsive elements ($AREs$), which are targeted by redox-sensitive transcription factors. ### 3.4 Systemic hypoxia signaling Hypoxia can trigger signals that are transmitted throughout the plant, coordinating responses across different tissues. * **Nitric oxide (NO):** In *Zea mays*, $NO$ generated in the root apex, particularly in the transition zone, acts as a systemic signal. $NO$ can be a byproduct of mitochondrial electron transport under hypoxia and is a catalyst for the upregulation of hypoxia-responsive genes through the $NERP$. * **1-aminocyclopropane-1-carboxylic acid (ACC):** The precursor to ethylene, $ACC$, can act as a signaling molecule itself, independently of ethylene. Under flooding conditions where ethylene biosynthesis is impaired, significant accumulation of $ACC$ occurs. As $ACC$ is soluble and readily transported, it can act as a systemic signal from waterlogged roots to shoots. ### 3.5 Morphological and physiological adaptations Plants have developed various morphological and physiological adaptations to survive flooding and hypoxia. #### 3.5.1 Root adaptations * **Aerenchyma formation:** The development of air channels within the root cortex facilitates gas diffusion to oxygen-deprived tissues. * **Pneumatophores:** Specialized roots that grow upwards out of the water or mud to access atmospheric oxygen. * **Lenticels:** Small pores on stems and roots that improve gas exchange. * **Radial oxygen loss (ROL) barrier:** The deposition of suberin in the hypodermis and outer root tissues acts as a barrier to prevent the loss of oxygen from aerenchyma to the surrounding soil, ensuring it reaches the root tip. * **Adventitious root (AR) formation:** Ethylene-mediated induction of adventitious root primordia, coupled with pressure-driven programmed cell death in overlying tissues, allows for the emergence of new roots to access oxygen. #### 3.5.2 Shoot adaptations * **Hyponastic growth:** Upward orientation of leaves, which can increase gas exchange with the atmosphere. * **Enhanced shoot elongation (Low Oxygen Escape Strategy - LOES):** Rapid elongation of shoots, often mediated by hormones like ethylene and gibberellins, allows plants to reach the water surface and access atmospheric oxygen. This is observed in deepwater rice varieties. * **Growth constraint (Low Oxygen Quiescence Strategy - LOQS):** In flood-tolerant varieties, growth is suppressed to minimize energy expenditure. This strategy relies on metabolic adjustments and the expression of tolerance genes. * **Hypertrophic growth:** Lateral expansion of stems and shoots. * **Epinasty:** Downward bending of leaves due to ethylene-induced asymmetrical growth. * **Stomatal closure:** While potentially leading to reduced photosynthesis, it can help conserve water and reduce oxygen demand. * **Leaf senescence and abscission:** In severe cases, the plant may shed leaves to reduce metabolic load. #### 3.5.3 Hydraulic alterations * **Reduced hydraulic conductance:** Flooding can impair water transport through the xylem due to factors like xylem embolism and impaired aquaporin function, leading to a state of "pseudo-drought" in the shoot. * **Post-submergence stress:** Upon re-oxygenation, plants face oxidative stress and dehydration stress due to reduced hydraulic conductivity. $SUB1A$ plays a role in enhancing recovery from these stresses. > **Tip:** Understanding the distinction between LOES and LOQS in rice is crucial for grasping the different adaptive strategies plants employ under flooding. LOES prioritizes escape through rapid growth, while LOQS focuses on survival through energy conservation and stress tolerance. > **Example:** Deepwater rice cultivars that exhibit rapid shoot elongation (LOES) to escape submergence often show increased ethylene production and elevated gibberellin levels, facilitated by specific ERF transcription factors like SNORKEL. In contrast, submergence-tolerant varieties using LOQS, like those expressing SUB1A, prioritize suppressing growth and enhancing stress resilience mechanisms. --- # Flood adaptation strategies in rice cultivars Rice cultivars employ distinct strategies to survive submergence, primarily categorized as the 'low oxygen escape strategy' (LOES) and the 'low oxygen quiescence strategy' (LOQS), each with a unique genetic basis and physiological response to low oxygen conditions. ### 4.1 The challenge of flooding for plants Flooding events, characterized by waterlogging (roots submerged) or complete submergence (aerial parts submerged), are increasing in frequency and intensity due to global climate change. These conditions drastically alter the soil gas composition, leading to decreased oxygen ($O_2$), increased carbon dioxide ($CO_2$), and altered levels of ethylene ($C_2H_4$) and nitric oxide (NO). The reduced solubility and diffusion rate of gases in water, approximately ten thousand times lower than in air, are primary issues. Flooding impacts plants by: * Compromising aerobic respiration, leading to an energy crisis and carbohydrate starvation. * Reducing photosynthesis due to limited $CO_2$ availability. * Disrupting aerobic respiration, which impairs the plant's ability to maintain energy levels. * Inducing oxidative stress and dehydration stress upon water recession. ### 4.2 General plant responses to hypoxia and submergence Plants have evolved adaptive responses to low oxygen (hypoxia) and submergence, involving both morphological and biochemical changes in roots and shoots. #### 4.2.1 Morphological and anatomical adaptations * **Aerenchyma formation:** Development of air channels within cortical tissues, facilitating gas diffusion to submerged tissues. This often involves programmed cell death (PCD) in cortical parenchyma. * **Pneumatophores:** Specialized aerial roots that grow upwards from the mud to reach atmospheric oxygen, exhibiting negative gravitropism. * **Lenticels:** Small pores on stems that enhance gas exchange. * **Adventitious root (AR) formation:** Roots that develop from non-root organs, such as stems. Ethylene plays a crucial role in the emergence of ARs through the cortex and overlying epidermal layers via a process involving pressure-driven PCD. * **Hypertrophic growth:** Lateral expansion of organs, often induced by ethylene. * **Hyponastic growth:** Upright orientation of leaves, contrasting with epinasty (downward bending) which occurs due to ethylene accumulation and asymmetrical growth. #### 4.2.2 Biochemical and metabolic adaptations * **Anaerobic respiration and fermentation:** When aerobic respiration is compromised, plants shift to glycolysis and fermentation to regenerate $NAD^+$ and produce limited ATP. This yields end products such as ethanol, lactate, and alanine. Substrate-level phosphorylation produces significantly less ATP per glucose molecule (typically 2 ATP) compared to aerobic respiration (32 ATP). * **Metabolic flux adjustments:** Under hypoxia, glucose breakdown through sucrose synthase is stimulated, feeding into glycolysis. Starch catabolism via amylase also increases to provide glucose. * **GABA shunt:** The conversion of glutamate to $\gamma$-aminobutyric acid (GABA) by glutamate decarboxylase (GAD) consumes protons, helping to stabilize intracellular pH, which tends to decrease due to fermentation. This pathway also contributes to oxygen conservation and ATP production. * **Anaerobic proteins (ANPs):** Induced under hypoxia/anoxia, these proteins are involved in sugar and starch degradation, glycolysis, and fermentation, alongside chaperones. Their transcription is regulated by anaerobiosis-responsive elements (AREs) in their promoters, often involving redox-sensitive transcription factors. * **Phytohemoglobins:** Act as oxygen sensors, scavenge nitric oxide (NO), and help maintain redox balance. #### 4.2.3 Signaling pathways * **Ethylene ($C_2H_4$) signaling:** Ethylene accumulation is a key response to flooding. Its biosynthesis can be affected by reduced oxygen availability, particularly the final ACC oxidase step. Ethylene triggers various adaptive responses, including adventitious root formation, hypertrophic growth, and hyponasty. * **Reactive oxygen species (ROS):** ROS play a dual role, being involved in signaling pathways that promote adaptation (e.g., triggering PCD for organ emergence) but also contributing to oxidative stress upon re-oxygenation. * **Nitric oxide (NO):** Involved in systemic hypoxia signaling, NO can be generated in roots and catalyze the upregulation of hypoxia-responsive genes and NERP (N-end rule pathway). * **1-aminocyclopropane-1-carboxylic acid (ACC):** The precursor to ethylene, ACC can act as a signaling molecule independently of ethylene, transported from roots to shoots. ### 4.3 Ethylene-induced flooding adaptation strategies in rice Rice, particularly deepwater rice varieties, exhibits remarkable flood tolerance, allowing for the study of distinct adaptation strategies. These strategies are often associated with specific ethylene-induced responses. #### 4.3.1 Low oxygen escape strategy (LOES) LOES aims to increase gas exchange with the atmosphere by enhancing shoot elongation. This strategy is characteristic of deepwater rice cultivars that can survive prolonged submergence by rapidly growing upwards to reach the water surface. * **Mechanism:** * **Hyponastic growth and enhanced shoot elongation:** This is a primary response to escape submergence. * **Hormonal regulation:** * **Ethylene accumulation:** Increased ethylene levels, both newly synthesized and accumulated, promote shoot elongation. * **ABA and GA balance:** Ethylene acts by inhibiting abscisic acid (ABA) synthesis and degradation, leading to increased gibberellin (GA) levels. GA is a major hormone promoting elongation. * **Expansin regulation:** GA stimulates the expression of expansins, cell wall loosening proteins, which are crucial for cell expansion and elongation growth. * **SNORKEL (SK) genes:** These genes, belonging to Group VII Ethylene-Response Factors (ERFs), are upregulated by ethylene and are critical for promoting GA-mediated elongation growth, allowing rice to escape submergence. * **Trapped gas film:** Formation of a gas film on leaves can aid in gas exchange. * **Leaf morphology changes:** Development of longer leaf sheaths relative to leaf blades. * **Root adaptations:** Aerenchyma formation and the development of a barrier to radial oxygen loss (ROL barrier) in roots, along with adventitious root formation, further support survival. #### 4.3.2 Low oxygen quiescence strategy (LOQS) LOQS focuses on minimizing energy expenditure by constraining growth and relying on efficient ATP production through alternative metabolic pathways. This strategy is employed by flood-tolerant low-land rice varieties to survive flash floods or shorter periods of submergence. * **Mechanism:** * **Growth constraint:** Plants enter a resting state to conserve energy. * **Metabolic adjustments for ATP production:** * **Glycolysis and fermentation:** Efficient ATP production via substrate-level phosphorylation, including ethanolic fermentation. * **Starch catabolism:** Breakdown of stored starch to glucose, feeding into glycolysis. * **Protein synthesis:** Upregulation of proteins involved in metabolite transport, ROS protection (chaperones), and stress response. * **SUB1A gene:** This gene, also belonging to Group VII ERFs, is induced by ethylene. However, unlike SK genes, SUB1A dampens responsiveness to GA by upregulating genes like SLENDER RICE 1 (SLR1) and SLRL1, which are negative regulators of GA signaling (DELLA proteins). This inhibition of elongation prevents excessive energy expenditure. * **Post-submergence recovery:** SUB1A also enhances the upregulation of genes involved in ROS detoxification and ABA-mediated dehydration responses, facilitating better recovery after flooding recedes. ### 4.4 Genetic basis and direct low oxygen sensing Group VII ERF transcription factors (TFs) play a central role in sensing and responding to low oxygen conditions in both Arabidopsis and rice. * **Group VII ERFs:** In Arabidopsis, genes like HRE1, HRE2, RAP2.2, RAP2.3, and RAP2.12 are hypoxia-responsive. In rice, SUB1A, SUB1B, SUB1C, SK1, and SK2 are key members. * **N-end rule pathway (NERP):** These ERF proteins possess a characteristic conserved N-terminus containing methionine and cysteine. Under normoxia, this N-terminus undergoes oxygen-dependent post-translational modifications (PTMs) via NERP, leading to their degradation by the proteasome. * **Normoxic degradation:** Terminal methionine is cleaved by methionine amino peptidases (MAPs). The exposed cysteine is oxidized to cysteine sulfonic acid ($C^*$) by plant cysteine oxidase (PCO). An arginine residue is added by arginine tRNA transferases (ATE1/2), targeting the protein for ubiquitination and degradation by the 26S proteasome. * **Hypoxic stabilization:** Under hypoxia, the oxidation of cysteine is inhibited, preventing the formation of $C^*$. This stabilizes the ERF proteins, allowing them to translocate to the nucleus and bind to hypoxia-responsive elements (HRPEs) in the promoters of target genes, thereby activating hypoxia-responsive transcription. * **RAP2.12:** In Arabidopsis, RAP2.12 is considered a primary sensor of low oxygen. It can be protected from degradation under normoxia by binding to acyl-CoA binding protein (ACBP) at the plasma membrane, allowing for a rapid response upon hypoxia by dissociating and translocating to the nucleus. * **Functional significance:** Loss-of-function mutants for ERFVII in plants demonstrate their critical importance in waterlogging responses. Modifications to the N-terminus of RAP2.12 can reduce plant vigor and submergence tolerance, highlighting the significance of this regulatory mechanism. > **Tip:** Understanding the differential roles of SNORKEL (SK) genes versus SUB1A in regulating GA responses under ethylene signaling is crucial for comprehending the divergence between the escape and quiescence strategies in rice. > **Example:** Overexpression of SUB1A in submergence-sensitive rice cultivars has been shown to confer significant tolerance to prolonged submergence, demonstrating its critical role in the quiescence strategy and minimizing injury. --- ## Common mistakes to avoid - Review all topics thoroughly before exams - Pay attention to formulas and key definitions - Practice with examples provided in each section - Don't memorize without understanding the underlying concepts

| Term | Definition | |------|------------| | Climate Change | A long-term shift in global or regional climate patterns, primarily attributed to the increase in greenhouse gas concentrations in the atmosphere, leading to rising global temperatures and altered weather patterns. | | Flooding Events | An overflow of water that submerges land that is usually dry, characterized by increased frequency and intensity due to climate change, with significant impacts on agriculture and ecosystems. | | Extreme Weather Events | Weather phenomena that are at the extremes of the historical distribution, such as severe floods, droughts, storms, and heatwaves, which are becoming more frequent and intense with climate change. | | Global Temperature Increase | The observed rise in the average temperature of Earth's climate system, currently around 1.3°C above pre-industrial levels, leading to various climatic shifts and an increase in extreme weather. | | Agricultural Production Losses | Reductions in the yield and output of crops and livestock due to climate-related disasters such as floods, droughts, and storms, impacting global food security and economic stability. | | Waterlogging | A condition where soil remains saturated with water, preventing adequate aeration of plant roots and negatively affecting plant growth and survival by limiting oxygen availability. | | Submergence | A type of flooding where aerial plant parts, such as stems and leaves, are covered by water, leading to an "energy crisis" for the plant due to carbohydrate starvation and limited respiration. | | Hypoxia | A condition in which an organism, tissue, or cell experiences a lower level of oxygen than is required, often occurring in waterlogged or submerged plant tissues, leading to adaptive responses. | | Normoxia | The normal or oxygen-repleted condition, typically considered to be around 21% oxygen at standard temperature and atmospheric pressure, as opposed to hypoxic or anoxic conditions. | | Anaerobic Respiration | A metabolic process that produces ATP energy in the absence or near-absence of oxygen, often involving fermentation pathways that result in end products like ethanol or lactic acid. | | Fermentation | A metabolic process that converts sugar to acids, gases, or alcohol, occurring in yeast and bacteria, or in muscle cells during strenuous exercise. In plants, it's a key process under low oxygen. | | Ethylene | A plant hormone that plays a crucial role in various growth and developmental processes, including responses to environmental stresses like flooding, where its accumulation triggers adaptation strategies. | | ROS (Reactive Oxygen Species) | Chemically reactive molecules containing oxygen that can damage cells, but also act as signaling molecules in plants, especially in response to stress, including the oxidative stress that can occur after flooding. | | Acclimation | The physiological or behavioral adjustments made by an organism in response to a change in its environment, such as plants developing morphological and biochemical changes to tolerate flooding. | | Low Oxygen Escape Strategy (LOES) | A plant's adaptive response to low oxygen conditions, aiming to increase gas exchange with the atmosphere through mechanisms like shoot elongation and hyponastic growth. | | Low Oxygen Quiescence Strategy (LOQS) | A plant's adaptive strategy to survive low oxygen conditions by minimizing energy expenditure, involving growth constraint and efficient ATP production through anaerobic pathways. | | Aerenchyma | Specialized tissues in some plants that contain large intercellular air spaces, facilitating gas exchange and oxygen transport to submerged or waterlogged roots. | | Pneumatophores | Modified root structures that grow upward from the soil or water surface, typically in mangrove trees, to facilitate gas exchange for submerged root systems. | | Lenticels | Small pores on the surface of stems and roots of woody plants that allow for gas exchange between the internal tissues and the atmosphere. | | Adventitious Roots | Roots that arise from any plant organ other than the primary root, often forming in response to environmental cues like flooding as an escape strategy. | | Programmed Cell Death (PCD) | An evolutionarily conserved process of cell suicide, which plays vital roles in development and in removing damaged or infected cells, and can be involved in plant adaptation to stress. | | Hydraulic Conductance | A measure of the ease with which water can move through a plant's vascular system (xylem) from the soil to the leaves, which can be impaired by flooding leading to a "pseudo-drought" effect. | | ABA (Abscisic Acid) | A plant hormone involved in various physiological processes, including stress responses such as stomatal closure and growth inhibition, and its levels are often affected by flooding. | | GA (Gibberellin) | A class of plant hormones that promote stem elongation and seed germination, and are involved in plant responses to flooding, particularly in escape strategies. | | Expansins | Proteins that play a critical role in cell wall loosening, enabling cell expansion and growth. Their activity is often regulated by plant hormones like GA during plant responses to submergence. | | ERFs (Ethylene-Response Factors) | A large family of transcription factors that play key roles in plant responses to various stresses, including hypoxia and flooding, often by regulating the expression of specific genes. | | N-end Rule Pathway (NERP) | A protein degradation pathway that targets proteins for degradation based on the identity of their amino-terminal residue, and plays a role in regulating plant responses to low oxygen conditions. | | Phytohemoglobins | Proteins found in some plants that are involved in oxygen sensing, scavenging of nitric oxide, and maintaining redox balance, particularly important in adapting to hypoxic environments. | | Systemic Hypoxia Signaling | The communication of low oxygen stress throughout a plant, involving signaling molecules like nitric oxide (NO) and ethylene precursors, to coordinate adaptive responses in different tissues. | | ACC (1-aminocyclopropane-1-carboxylic acid) | The immediate precursor to ethylene in plant biosynthesis, which can accumulate significantly under flooding conditions and act as a signaling molecule itself. | | Global Climate Change | Long-term shifts in temperatures and weather patterns, driven by human activities, leading to an increased frequency and intensity of extreme events like floods, impacting global agriculture. | | IPCC (Intergovernmental Panel on Climate Change) | An international body that assesses the science related to climate change, providing comprehensive reports on its causes, impacts, and future risks, including changes in precipitation and temperature extremes. | | :-------------------------------------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Anoxia | A complete absence of oxygen in an environment, representing the most extreme low-oxygen condition that plants may encounter, posing significant challenges to cellular respiration and energy production. | | Flooding | An environmental condition characterized by the inundation of plant tissues with water, leading to reduced oxygen availability and impacting various physiological processes. | | Heavy Precipitation | Rainfall exceeding 100 mm within a 24-hour period, often leading to flash floods and significant disruption to natural and agricultural ecosystems. | | Hyponastic Growth | A type of plant growth where leaves or organs are oriented upwards or outwards, often observed as a response to flooding to maximize light capture and gas exchange with the atmosphere. | | Hypertrophic Growth | Increased lateral expansion of plant organs, such as stems, often induced by ethylene under flooding conditions, contributing to buoyancy and improved access to atmospheric oxygen. | | Indirect O2 Sensing | A mechanism where plants detect a change in cellular homeostasis, such as altered levels of adenylates or pH, as a consequence of oxygen deprivation, rather than directly sensing oxygen molecules. | | Metabolic Acclimation | The physiological and biochemical adjustments plants make to survive low oxygen stress, including changes in glycolysis, fermentation pathways, and substrate utilization to optimize ATP production. | | Quiescence | A resting state adopted by plants under stress, characterized by reduced growth and metabolic activity to conserve energy and survive unfavorable conditions like flooding. | | Radial Oxygen Loss (ROL) Barrier | A physiological adaptation in plant roots, often involving suberin deposition, that prevents the leakage of oxygen from the root tissues into the surrounding soil, thus conserving oxygen internally. | | Reactive Oxygen Species (ROS) | Chemically reactive molecules containing oxygen, such as superoxide radicals and hydrogen peroxide, which can be signaling molecules or cause oxidative stress and cellular damage under certain conditions. | | Acclimation to hypoxia | The process involving morphological and biochemical changes in plant organs and tissues that enable adaptation to conditions of low oxygen availability. | | Aerobic respiration | A metabolic process that requires oxygen to generate energy (ATP) from glucose and other organic molecules, yielding carbon dioxide and water as byproducts. | | Alanine | An amino acid produced as an end-product of fermentation, which plays a role in sustaining some level of energy production in plants under low oxygen stress. | | Anaerobic proteins (ANPs) | Proteins synthesized in response to hypoxia or anoxia, primarily involved in the degradation of sugars and starches, glycolysis, and fermentation pathways, often including chaperones. | | Adventitious roots (AR) | Roots that develop from any plant organ other than the primary root, often formed on stems or leaves, and are involved in flooding adaptation strategies. | | Ascorbate | A molecule that can act as an antioxidant and is involved in the mitigation of oxidative stress. | | ATP (Adenosine Triphosphate) | The primary energy currency of cells, produced through cellular respiration and fermentation. | | ATP synthesis | The process by which ATP is generated, including substrate-level phosphorylation during glycolysis and fermentation, and oxidative phosphorylation in mitochondria. | | ABA-8'ox | An enzyme involved in the degradation of Abscisic Acid (ABA). | | ABCG exporting long chain FA | A type of ATP-binding cassette transporter involved in exporting long-chain fatty acids, which are components of suberin. | | ACC oxidase | An enzyme that catalyzes the conversion of ACC to ethylene, requiring oxygen for its activity. | | ACC synthase | Enzymes involved in the biosynthesis of ACC. | | Cell death | The termination of a cell's life, which can be programmed and play a role in plant development and adaptation, such as in adventitious root emergence. | | Chlorophyll fluorescence | A technique used to assess photosynthetic efficiency and plant stress levels by measuring the light re-emitted by chlorophyll molecules. | | CO2 (Carbon Dioxide) | A gas involved in photosynthesis and respiration, whose concentration can change during flooding. | | Cortical parenchyma | The tissue layer in plant roots located between the epidermis and the endodermis, which can be modified to form aerenchyma. | | Cytosolic pH | The acidity or alkalinity of the cytoplasm within a cell, which can be affected by metabolic processes like fermentation. | | Deepwater rice | A specialized cultivar of rice adapted to survive prolonged and deep flooding conditions by employing escape strategies. | | DELLA proteins | A family of proteins that act as negative regulators of Gibberellic Acid (GA) signaling, thereby inhibiting elongation growth. | | Desubmergence | The process of a plant emerging from a submerged state, which can lead to oxidative stress and dehydration. | | Direct O2 sensing | The mechanism by which a cell directly perceives oxygen levels through molecular interaction with a sensor protein or chemical compound, initiating a response cascade. | | Drought | A prolonged period of abnormally low rainfall, leading to a shortage of water. | | Elongation growth | The process by which plant organs increase in length, often regulated by hormones like Gibberellic Acid (GA) and influenced by ethylene. | | Embrio | Embryo. | | Embryonic | Relating to or forming an embryo. | | Endogenous | Originating from within the plant. | | ERF (Ethylene-Response Factor) | A family of transcription factors that play crucial roles in plant development and stress responses, particularly in mediating ethylene signaling and hypoxia responses. | | Ethane | A simple alkane gas, sometimes found in plant tissues. | | Ethanol | An alcohol produced as an end-product of alcoholic fermentation. | | Ethylene (C2H4) | A plant hormone involved in various developmental processes and stress responses, including flooding adaptation and shoot elongation. | | Ethylene biosynthesis | The metabolic pathway by which ethylene is produced in plants, involving precursors like ACC. | | Ethylene signaling | The complex network of molecular events initiated by ethylene perception, leading to downstream physiological responses. | | Exosmosis | The movement of water out of a cell or tissue. | | Gas film | A layer of gas that can form on plant surfaces, such as leaves, during submergence to facilitate gas exchange. | | GABA (Gamma-aminobutyric acid) | An amino acid that can be produced via the GABA shunt, contributing to pH stabilization and stress response. | | GA (Gibberellic Acid) | A plant hormone promoting cell elongation and growth, often interacting with ABA in a balanced manner. | | GA signaling | The cascade of molecular events triggered by Gibberellic Acid perception, leading to specific cellular responses. | | GAD (Glutamate decarboxylase) | An enzyme that catalyzes the conversion of glutamate to GABA, consuming protons and helping to stabilize pH. | | Glc-6-P (Glucose-6-phosphate) | A key intermediate in glycolysis, formed from glucose. | | Glucose-UDP | A sugar nucleotide intermediate. | | Glutamate | An amino acid involved in various metabolic pathways, including the GABA shunt. | | Glycolysis | The initial metabolic pathway in carbohydrate breakdown, converting glucose into pyruvate and generating a small amount of ATP. | | Growth control | The regulation of plant development and increase in size, influenced by hormones and environmental factors. | | H2O2 (Hydrogen Peroxide) | A reactive oxygen species (ROS) that can be produced during oxidative stress and plays signaling roles. | | Heterotrophic | Organisms that cannot produce their own food and rely on consuming other organisms. | | Hijau | Green (Indonesian/Malay, not relevant to the academic context). | | Hormonal interactions | The complex interplay between different plant hormones in regulating physiological processes. | | HRPE (Hypoxia Responsive Element) | A DNA sequence found in the promoter region of hypoxia-responsive genes that binds to transcription factors to regulate gene expression. | | Hydraulic conductivity | The ability of a plant's vascular system (xylem) to conduct water. | | Hydrolic conductance | Synonym for hydraulic conductivity. | | Hypobiosis | A state of reduced metabolic activity, similar to quiescence. | | Ion transport | The movement of ions across cell membranes, crucial for maintaining cell potential and turgor. | | Invertase | An enzyme that breaks down sucrose into glucose and fructose. | | IPPC (Intergovernmental Panel on Climate Change) | An international body that assesses the science related to climate change. | | Lactate | Lactic acid, an end-product of lactic acid fermentation. | | Ligand | A molecule that binds to a receptor or sensor protein. | | Low oxygen sensing | The physiological process by which plants detect and respond to reduced oxygen concentrations. | | L-threonine | An amino acid. | | MAPs (Methionine amino peptidases) | Enzymes that cleave methionine from the N-terminus of proteins, a step in the N-end rule pathway. | | Metabolic changes | Alterations in the biochemical reactions occurring within cells. | | Metabolic flux | The rate at which metabolites are processed through a metabolic pathway. | | Metabolite | A substance formed or used during metabolism. | | Metallothioneins | Proteins that bind to metal ions and play a role in mitigating oxidative stress by scavenging reactive oxygen species. | | Microclimates | Localized variations in climate conditions. | | Mitochondria | Organelles within eukaryotic cells responsible for cellular respiration and ATP production. | | Mitochondrial ETC (Electron Transport Chain) | A series of protein complexes in the inner mitochondrial membrane that generate ATP through oxidative phosphorylation. | | Morphological adaptations | Changes in the physical structure or form of plant organs to suit environmental conditions. | | NAD+ | Nicotinamide adenine dinucleotide, a coenzyme involved in redox reactions, regenerated during fermentation. | | NERP (N-end rule pathway) | A protein degradation pathway regulated by the N-terminal amino acid of a protein, significantly influenced by oxygen levels and involved in hypoxia responses. | | Nitrite | A polyatomic ion with the formula NO2−. | | Nitrogen (N) | An essential nutrient for plant growth. | | NO (Nitric Oxide) | A signaling molecule in plants, involved in systemic hypoxia signaling and regulating gene expression. | | NO scavenging | The process of removing or neutralizing nitric oxide. | | Non-circular TCA flux | A modified flux through the tricarboxylic acid cycle, where intermediates may not fully cycle back. | | O2•- (Superoxide radical) | A highly reactive oxygen species formed during oxidative stress. | | O2 saturation | The degree to which oxygen is dissolved in a liquid. | | Osmosis | The movement of water across a semipermeable membrane from an area of high water concentration to an area of low water concentration. | | Oxidative stress | Cellular damage caused by an imbalance between the production of reactive oxygen species (ROS) and the body's ability to detoxify them. | | Oxygen conservation | Mechanisms employed by plants to reduce oxygen consumption or utilize available oxygen more efficiently. | | Oxygen deprivation | A reduction in the availability of oxygen. | | Oxygen levels | The concentration of oxygen in a given environment. | | Oxygen sensing | The process by which organisms detect and respond to changes in oxygen concentration. | | Oxygen signaling | The molecular pathways activated by oxygen levels, influencing cellular processes. | | Partial submergence | A type of flooding where only a portion of the plant's aerial parts are submerged. | | Pentuple mutant | A mutant organism lacking five specific genes. | | Plant biotechnology | The application of biological principles and techniques to modify plants for specific purposes. | | Plant development | The series of changes a plant undergoes from germination to maturity. | | Plant physiology | The study of the functions and mechanisms of living plants. | | Plant responses | The physiological and biochemical reactions of plants to environmental stimuli. | | Plant vigor | The overall health and strength of a plant. | | PM (Plasma Membrane) | The outer boundary of the cytoplasm of a cell, enclosing the protoplasm. | | Post-translational modification (PTM) | Chemical modifications that occur to a protein after its synthesis, affecting its function and stability. | | Precursor | A substance from which another substance is formed. | | Pressure-driven PCD | Programmed cell death that is induced by mechanical pressure. | | Primary sensor | The initial molecule or receptor that detects a stimulus. | | Production loss | Reduction in yield or output, particularly in agriculture. | | Protective mechanisms | Biological strategies employed to defend against harm or damage. | | Protein synthesis | The process by which cells build proteins. | | Proteasome (26S proteasome) | A large protein complex in cells that degrades unwanted or damaged proteins. | | Pseudodrought | A state of water deficit in shoots that mimics drought conditions, occurring even when roots are in waterlogged soil. | | Pyruvate | A key intermediate molecule in glycolysis and fermentation. | | Pyruvate decarboxylase (PDC) | An enzyme involved in alcoholic fermentation. | | RCN1 | A gene (reduced culm number) related to ABCG transporters involved in suberin formation. | | Reactive nitrogen species (RNS) | Molecules derived from nitrogen, such as nitric oxide and peroxynitrite, that can cause cellular damage. | | Receding water | The withdrawal of floodwaters. | | Redox balance | The equilibrium between the processes of oxidation and reduction within a cell. | | Related to AP2 (RAP) | A classification for certain transcription factors related to the APETALA2 (AP2) family. | | Relative leaf water content | A measure of the amount of water in a leaf relative to its full hydration capacity. | | Respiratory burst NADPH-oxidase homolog (RBOH) | Enzymes that produce reactive oxygen species (ROS) through the oxidation of NADPH. | | Rice (Oryza sativa) | A staple food crop widely cultivated globally, serving as a model for flood tolerance studies. | | Root apex | The tip of a plant root, containing the root meristem. | | Root meristem | The actively dividing tissue at the tip of a plant root responsible for root growth. | | Root-shoot communication | The signaling and transport of substances between the root and shoot systems of a plant. | | ROS accumulation | The buildup of reactive oxygen species in cells. | | ROS-dependent PCD | Programmed cell death that is triggered or mediated by reactive oxygen species. | | ROS detoxification | The process of neutralizing or removing reactive oxygen species from cells. | | ROL barrier (Radial Oxygen Loss barrier) | A layer, typically composed of suberin, deposited in plant roots to prevent the leakage of oxygen to the surrounding soil. | | Rumex sp. | A genus of plants in the family Polygonaceae. | | Rumex acetosa | Sorrel, a species within the Rumex genus. | | Salinity | The salt content of soil or water. | | Seasonal events | Events that occur at specific times of the year, such as monsoons. | | Secondary growth | The increase in girth of plant stems and roots due to cell division in the vascular cambium and cork cambium. | | Shoot elongation | The increase in length of the aerial parts of a plant. | | Shoot morphology | The form and structure of a plant's shoots. | | Shunts | Metabolic pathways that deviate from the main metabolic route. | | Signaling cascades | A series of biochemical reactions in response to a stimulus that amplify and transmit the signal. | | SLR1 (SLENDER RICE 1) | A negative regulator of GA signaling in rice, belonging to the DELLA protein family. | | SLR1/SLRL1 | Genes encoding DELLA proteins that inhibit GA responses. | | SNORKEL (SK1/SK2) | Genes in rice that promote shoot elongation and escape from submergence by increasing GA accumulation. | | Solanum lycopersicum | The scientific name for the tomato plant. | | Sorrel | Common name for plants in the Rumex genus. | | Spatial signal | A signal that indicates location or position. | | Starch catabolism | The breakdown of starch into smaller sugars. | | Stomatal closure | The closing of stomata, pores on the leaf surface that regulate gas exchange, often triggered by water deficit or stress. | | Suberization | The deposition of suberin, a waxy substance, in cell walls, contributing to barrier formation. | | Substrate-level phosphorylation | The direct transfer of a phosphate group from a substrate molecule to ADP to form ATP, occurring during glycolysis and fermentation. | | Sucrose synthase | An enzyme that breaks down sucrose, providing substrates for glycolysis. | | Sugars | Simple carbohydrates that serve as energy sources. | | Sulfonic acid | An organic compound containing a C-SO3H group. | | Superoxide dismutase (SOD) | An enzyme that catalyzes the conversion of superoxide radicals into oxygen and hydrogen peroxide, playing a crucial role in antioxidant defense. | | Systemic signaling | Signaling that occurs throughout the entire plant, coordinating responses across different tissues and organs. | | T carbohydrates | Carbohydrates. | | Terminal electron acceptor | The final molecule in an electron transport chain that accepts electrons. | | Tissue specificity | The characteristic localization of a physiological process or response within particular plant tissues. | | Tomato | A common garden plant and its edible fruit. | | Transcription factor (TF) | A protein that binds to specific DNA sequences to control the rate of transcription of genetic information from DNA to messenger RNA. | | Transition zone | A region in the root between the root meristem and the elongation zone, involved in systemic signaling. | | Translocation | The movement of substances within a plant. | | Turgor pressure | The pressure exerted by the contents of a plant cell against its cell wall. | | Twinset | A hormonal balance where two hormones (e.g., GA and ABA) regulate each other. | | Ubi promotor | A promoter derived from the ubiquitin gene, commonly used for ubiquitous gene expression in plants. | | UDP (Uridine diphosphate) | A nucleotide that serves as a coenzyme in various metabolic pathways. | | UP-regulates | Increases the activity or expression of something. | | Water replacement | The process of refilling tissues or cells with water. | | Wild species | Species of plants that grow in natural environments without human cultivation. | | Xylem | The vascular tissue in plants that conducts water and dissolved nutrients from the roots to the rest of the plant. | | Xylem embolism | The formation of air bubbles within xylem vessels, which can block water transport. | | Zea mays | The scientific name for corn or maize. | | Ethylene-Response Factors (ERFs) | A large family of transcription factors that regulate gene expression in response to ethylene signaling. Certain ERFs, particularly Group VII ERFs, are critically involved in mediating plant responses to hypoxia and submergence, influencing strategies like elongation or quiescence. | | SUB1A | A key Group VII Ethylene-Response Factor (ERF) gene in rice that confers submergence tolerance. It plays a crucial role in the Low Oxygen Quiescence Strategy (LOQS) by dampening the plant's responsiveness to gibberellins (GAs) and enhancing tolerance to post-submergence stress. | | Gibberellin (GA) | A class of plant hormones that promote stem elongation and are crucial for growth and development. In flood adaptation, GA levels are often modulated; increased GA promotes elongation in escape strategies, while repression of GA is associated with quiescence strategies. | | Abscisic Acid (ABA) | A plant hormone involved in stress responses, including drought and osmotic stress. During submergence, ABA levels typically decrease in deepwater rice varieties employing escape strategies, while its role in quiescence strategies is linked to dehydration tolerance post-submergence. | | Nitric Oxide (NO) | A signaling molecule that can be generated during mitochondrial respiration under hypoxic conditions and plays a role in systemic hypoxia signaling, potentially by catalyzing the N-end rule pathway and upregulating hypoxia-responsive genes. | | 1-aminocyclopropane-1-carboxylic acid (ACC) | The immediate precursor to ethylene in plant biosynthesis. Under flooding conditions, reduced oxygen can limit the conversion of ACC to ethylene, leading to ACC accumulation, which may also act as a signaling molecule itself. | | Dehydration Stress | A stress experienced by plants when they lose water faster than they can absorb it. In post-flooding scenarios, reduced hydraulic conductance can contribute to a form of dehydration stress even when roots are still wet. | | Lowland Rice | Rice cultivars typically grown in fields that can be intermittently flooded but are not adapted to deep or prolonged submergence. They exhibit varying degrees of flood tolerance, with some employing quiescence strategies. |