Unveiling Molecular Mechanisms of Nitric Oxide-Induced Low-Temperature Tolerance in Cucumber by Transcriptome Profiling

Integrated transcriptomics and metabolomics reveal the role of soluble sugars and GABA in rice leaf response to Pb stress

Heavy metals as environmental pollutants pose a major threat to agroecosystems and crop quality. Among them, Pb is one of the most common heavy metal pollutants, which not only inhibits plant growth and nutrient uptake, but also disrupts the expression of genes, affects the accumulation of metabolites, and even causes plant death. We investigated a joint transcriptomics and metabolomics analysis to study the response of rice seedlings to Pb stress. Our results showed that Pb stress inhibited the growth of rice seedlings. Meanwhile, Pb stress decreased SPAD values, chlorophyll fluorescence parameters, antioxidant enzyme activities, and GSH and TGSH contents, but increased ASC and TASC contents and reactive oxygen species levels in rice leaves. Using the MetaboAnalyst website for metabolites enrichment analysis, 7 metabolic pathways involving 36 differentially expressed metabolites (DAMs) were affected. Transcriptomics analysis revealed that 1873 differentially expressed genes (DEGs) identified were mainly involved in 16 metabolic pathways. Comprehensive enrichment analysis of DAMs and DEGs showed that alanine, aspartate and glutamate metabolism as well as starch and sucrose metabolism were the co-enriched pathways and were upregulated under Pb stress. The main metabolites involving soluble sugars (cellobiose, D-glucose, trehalose and maltose) and gamma-aminobutyric acid (GABA). These findings suggest that rice leaves enhance tolerance to Pb by upregulating the expression of genes involved in carbohydrate and amino acid metabolism, increasing accumulation of soluble sugars and GABA. The results of this study will contribute to understanding the molecular mechanisms of rice response to Pb stress and provide a basis for screening rice varieties with high resistance to heavy metals.

Seasonal dynamics and molecular regulation of flavonoid biosynthesis in Cyclocarya paliurus (Batal.) Iljinsk

Introduction

Cyclocarya paliurus, an economically important species known for its high flavonoid content, has potential for industrial applications. Understanding the seasonal dynamics and molecular regulation of flavonoid biosynthesis in this species is crucial for optimizing its production.

Methods

We conducted an integrated analysis of transcriptomic and metabolomic data to identify key genes involved in flavonoid biosynthesis and regulation. Seasonal variation in flavonoid content and gene expression was examined, with a focus on the genes involved in the flavonoid synthesis pathway and their correlation with flavonoid levels.

Results

Flavonoid content peaked in August and declined towards November, with quercetin and kaempferol glycosides being the most abundant compounds. Pearson correlation analysis revealed significant relationships between the functional genes of the flavonoid synthesis pathway and flavonoid content. Seasonal variations in the expression of key biosynthetic genes (CHS, CHI, F3H, DFR, FLS) and regulatory transcription factors (MYB11, MYB12, MYB111, MYB75, MYB90, bHLH, WD40) were strongly correlated with flavonoid levels, particularly under environmental stress.

Discussion

These findings provide insights into the genetic regulation of flavonoid biosynthesis in C. paliurus and highlight the importance of seasonal and environmental factors. This knowledge has practical implications for industrial breeding and biotechnological applications, particularly in enhancing the functional properties of C. paliurus for industrial use. Our study establishes a foundation for future research aimed at optimizing flavonoid production in this species and exploring its potential for bioactive compound production.

Extracellular matrix gene set and microRNA network in intestinal ischemia-reperfusion injury: Insights from RNA sequencing for diagnosis and therapy

Intestinal ischemia-reperfusion injury (IIRI) is a complex and severe pathophysiological process characterized by oxidative stress, inflammation, and apoptosis. In recent years, the critical roles of extracellular matrix (ECM) genes and microRNAs (miRNAs) in IIRI have garnered widespread attention. This review aims to systematically summarize the diagnostic and therapeutic potential of ECM gene sets and miRNA regulatory networks in IIRI. First, we review the molecular mechanisms of IIRI, focusing on the dual role of the ECM in tissue injury and repair processes. The expression changes and functions of ECM components such as collagen, elastin, and matrix metalloproteinases during IIRI progression are deeply analyzed. Second, we systematically summarize the regulatory roles of miRNAs in IIRI, particularly the mechanisms and functions of miRNAs such as miR-125b and miR-200a in regulating inflammation, apoptosis, and ECM remodeling. Additionally, this review discusses potential diagnostic biomarkers and treatment strategies based on ECM genes and miRNAs. We extensively evaluate the prospects of miRNA-targeted therapy and ECM component modulation in preventing and treating IIRI, emphasizing the clinical translational potential of these emerging therapies. In conclusion, the diagnostic and therapeutic potential of ECM gene sets and miRNA regulatory networks in IIRI provides new directions for further research, necessitating additional clinical and basic studies to validate and expand these findings for improving clinical outcomes in IIRI patients.

Assessment of cold resistance in tobacco varieties using JIP-test parameters and seedling growth

Cold stress (CS) is a significant natural hazard, and distinguishing between plant cold resistance and sensitivity is critical for cultivar breeding and the development of germplasm resources. This study used 205 tobacco (Nicotiana tabacum L.) varieties from around the world to investigate the changes in the chlorophyll a fluorescence (OJIP) transients, JIP-test parameters, and seedling growth caused by seven days of CS (5°C) treatment. Their cold resistance was assessed using the cold-resistant coefficient, derived from the relative growth rate of shoots, damage scores, and JIP-test parameters. The results showed that total electron carriers per reaction center (Sm) and relative variable fluorescence at the I-step (VI) were better indicators of cold resistance than maximum quantum yield of photochemistry at t = 0 (Fv/Fm), which was widely used to assess plant cold resistance. Next, the study examined the effects of CS and subsequent recovery on OJIP transients, JIP-test parameters, and seedling growth in two highly resistant (HR) and two highly sensitive (HS) varieties to confirm the reliability of the assessment methods. The results indicated that HR varieties experienced less photoinhibitory damage to photosystem II, exhibited lower growth inhibition during CS, and showed better recovery during the recovery period compared to HS varieties. These findings suggested that the JIP-test parameters could serve as a reliable tool for assessing tobacco cold resistance and aid in selecting varieties with enhanced resilience to CS.

Glutathione is required for nitric oxide-induced chilling tolerance by synergistically regulating antioxidant system, polyamine synthesis, and mitochondrial function in cucumber (Cucumis sativus L.)

In this paper, we discussed the physiological mechanism of enhanced chilling tolerance with combined treatment of nitric oxide (NO) and reduced glutathione (GSH) in cucumber seedlings. With prolonged low temperature (10 °C/6 °C), oxidative stress improved, which was manifested as an increase the hydrogen peroxide (H2O2) and malondialdehyde (MDA), causing cell membrane damage, particularly after 48 h of chilling stress. Exogenous sodium nitroprusside (SNP, NO donor) enhanced the activity of nitric oxide synthase NOS-like, the contents of GSH and polyamines (PAs), and the cellular redox state, thus regulating the activities of mitochondrial oxidative phosphorylation components (CI, CII, CIV, CV). However, buthionine sulfoximine (BSO, a GSH synthase inhibitor) treatment drastically reversed or attenuated the effects of NO. Importantly, the combination of SNP and GSH treatment had the best effect in alleviating chilling-induced oxidative stress by upregulating the activities of antioxidant enzyme, including superoxidase dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and peroxidase (POD) and improved the PAs content, thereby increased activities of CI, CII, CIII, CIV, and CV. This potentially contributes to the maintenance of oxidative phosphorylation originating from mitochondria. In addition, the high activity of S-nitrosoglutathione reductase (GSNOR) in the combined treatment of SNP and GSH possibly mediates the conversion of NO and GSH to S-nitrosoglutathione. Our study revealed that the combined treatment with NO and GSH to synergistically improve the cold tolerance of cucumber seedlings under prolonged low-temperature stress.

Transcriptome analysis revealed enrichment pathways and regulation of gene expression associated with somatic embryogenesis in Camellia sinensis

The high frequency, stable somatic embryo system of tea has still not been established due to the limitations of its own characteristics and therefore severely restricts the genetic research and breeding process of tea plants. In this study, the transcriptome was used to illustrate the mechanisms of gene expression regulation in the somatic embryogenesis of tea plants. The number of DEGs for the (IS intermediate stage)_PS (preliminary stage), ES (embryoid stage)_IS and ES_PS stages were 109, 2848 and 1697, respectively. The enrichment analysis showed that carbohydrate metabolic processes were considerably enriched at the ES_IS stage and performed a key role in somatic embryogenesis, while enhanced light capture in photosystem I could provide the material basis for carbohydrates. The pathway analysis showed that the enriched pathways in IS_PS process were far less than those in ES_IS or ES_PS, and the photosynthesis and photosynthetic antenna protein pathway of DEGs in ES_IS or ES_PS stage were notably enriched and up-regulated. The key photosynthesis and photosynthesis antenna protein pathways and the Lhcb1 gene were discovered in tea plants somatic embryogenesis. These results were of great significance to clarify the mechanism of somatic embryogenesis and the breeding research of tea plants.

Transcriptome Analyses Revealed the Wax and Phenylpropanoid Biosynthesis Pathways Related to Disease Resistance in Rootstock-Grafted Cucumber

Cucumbers (Cucumis sativus L.) are a global popular vegetable and are widely planted worldwide. However, cucumbers are susceptible to various infectious diseases such as Fusarium and Verticillium wilt, downy and powdery mildew, and bacterial soft rot, which results in substantial economic losses. Grafting is an effective approach widely used to control these diseases. The present study investigated the role of wax and the phenylpropanoid biosynthesis pathway in black-seed pumpkin rootstock-grafted cucumbers. Our results showed that grafted cucumbers had a significantly higher cuticular wax contents on the fruit surface than that of self-rooted cucumbers at all stages observed. A total of 1132 differently expressed genes (DEGs) were detected in grafted cucumbers compared with self-rooted cucumbers. Pathway enrichment analysis revealed that phenylpropanoid biosynthesis, phenylalanine metabolism, plant circadian rhythm, zeatin biosynthesis, and diterpenoid biosynthesis were significantly enriched. In this study, 1 and 13 genes involved in wax biosynthesis and the phenylpropanoid biosynthesis pathway, respectively, were up-regulated in grafted cucumbers. Our data indicated that the up-regulated genes in the wax and phenylpropanoid biosynthesis pathways may contribute to disease resistance in rootstock-grafted cucumbers, which provides promising targets for enhancing disease resistance in cucumbers by genetic manipulation.

Transcriptomic analysis of Cucumis sativus uncovers putative genes related to hormone signaling under low temperature (LT) and high humidity (HH) stress

Climate change has caused changes in environmental conditions, leading to both low temperature (LT) and high humidity (HH) stress on crops worldwide. Therefore, there is a growing need to enhance our understanding of the physiological and molecular mechanisms underlying LT and HH stress tolerance in cucumbers, given the significance of climate change. The findings of this study offer a comprehensive understanding of how the transcriptome and hormone profiles of cucumbers respond to LT and HH stress. In this study, cucumber seedlings were subjected to LT and HH stress (9/5 °C day/night temperature, 95% humidity) as well as control (CK) conditions (25/18 °C day/night temperature, 80% humidity) for 24, 48, and 72 h. It was observed that the LT and HH stress caused severe damage to the morphometric traits of the plants compared to the control treatment. The concentrations of phytohormones IAA, ethylene, and GA were lower, while ABA and JA were higher during LT and HH stress at most time points. To gain insights into the molecular mechanisms underlying this stress response, RNA-sequencing was performed. The analysis revealed a total of 10,459 differentially expressed genes (DEGs) with annotated pathways. These pathways included plant hormone signal transduction, protein processing in the endoplasmic reticulum, MAPK signaling pathway, carbon fixation in photosynthetic organisms, and glycerolipid metabolism. Furthermore, 123 DEGs associated with hormone signaling pathways were identified, and their responses to LT and HH stress were thoroughly discussed. Overall, this study sheds light on the LT and HH tolerance mechanisms in cucumbers, particularly focusing on the genes involved in the LT and HH response and the signaling pathways of endogenous phytohormones.

Nitric oxide and hydrogen peroxide mediated regulation of chromium (VI) toxicity in wheat seedlings involves alterations in antioxidants and high affinity sulfate transporter

Chromium contamination of the soil is a major scientific concern with reference to crop productivity and human health. In recent years, several approaches are being employed in managing metal toxicity in crop plants. Here, we have investigated about potential and probable crosstalk of nitric oxide (NO) and hydrogen peroxide (H₂O₂) in mitigating hexavalent chromium [Cr(VI)] toxicity in wheat seedlings. Cr(VI) toxicity reduced the fresh mass and overall growth due to accumulation of reactive oxygen species (ROS) and decreased efficiency of AsA-GSH cycle and downregulation of high affinity sulfate transporter. However, exogenous treatment of NO and H₂O₂ significantly alleviated Cr toxicity. Application of NO and ROS scavengers reversed stress mitigating effects of NO and H₂O₂, respectively suggesting that endogenous NO and H₂O₂ are necessary for rendering Cr toxicity tolerance. Furthermore, NO rescued negative effect of diphenylene iodonium (DPI, NADPH oxidase inhibitor) and H₂O₂ reversed the negative effect of c-PTIO suggesting that they exhibit independent signalling in mitigating Cr stress. Altogether, data indicated that NO and H₂O₂ rendered mitigation of Cr stress by up-regulating enzymes (activity and relative gene expression) and metabolites of AsA-GSH cycle, high affinity sulfate transporter (relative gene expression) and glutathione biosynthesis which collectively controlled occurrence of oxidative stress.

Nitric Oxide, a Key Modulator in the Alleviation of Environmental Stress-Mediated Damage in Crop Plants: A Meta-Analysis

Nitric oxide (NO) is a small, diatomic, gaseous, free radicle, lipophilic, diffusible, and highly reactive molecule with unique properties that make it a crucial signaling molecule with important physiological, biochemical, and molecular implications for plants under normal and stressful conditions. NO regulates plant growth and developmental processes, such as seed germination, root growth, shoot development, and flowering. It is also a signaling molecule in various plant growth processes, such as cell elongation, differentiation, and proliferation. NO also regulates the expression of genes encoding hormones and signaling molecules associated with plant development. Abiotic stresses induce NO production in plants, which can regulate various biological processes, such as stomatal closure, antioxidant defense, ion homeostasis, and the induction of stress-responsive genes. Moreover, NO can activate plant defense response mechanisms, such as the production of pathogenesis-related proteins, phytohormones, and metabolites against biotic and oxidative stressors. NO can also directly inhibit pathogen growth by damaging their DNA and proteins. Overall, NO exhibits diverse regulatory roles in plant growth, development, and defense responses through complex molecular mechanisms that still require further studies. Understanding NO's role in plant biology is essential for developing strategies for improved plant growth and stress tolerance in agriculture and environmental management.

Ethylene Renders Silver Nanoparticles Stress Tolerance in Rice Seedlings by Regulating Endogenous Nitric Oxide Accumulation

Developments in the field of nanotechnology over the past few years have increased the prevalence of silver nanoparticles (AgNPs) in the environment, resulting in increased exposure of plants to AgNPs. Recently, various studies have reported the effect of AgNPs on plant growth at different concentrations. However, identifying the mechanisms and signaling molecules involved in plant responses against AgNPs stress is crucial to find an effective way to deal with the phytotoxic impacts of AgNPs on plant growth and development. Therefore, this study was envisaged to investigate the participation of ethylene in mediating the activation of AgNPs stress tolerance in rice (Oryza sativa L.) through a switch that regulates endogenous nitric oxide (NO) accumulation. Treatment of AgNPs alone hampered the growth of rice seedlings due to severe oxidative stress as a result of decline in sulfur assimilation, glutathione (GSH) biosynthesis and alteration in the redox status of GSH. These results are also accompanied by the higher endogenous NO level. However, addition of ethephon (a donor of ethylene) reversed the AgNP-induced effects. Though the application of silicon nanoparticles (SiNPs) alone promoted the growth of rice seedlings but, interestingly their application in combination with AgNPs enhanced the AgNP-induced toxicity in the seedlings through the same routes as exhibited in the case of AgNPs alone treatment. Interestingly, addition of ethephon reversed the negative effects of SiNPs under AgNPs stress. These results suggest that ethylene might act as a switch to regulate the level of endogenous NO, which in turn could be associated with AgNPs stress tolerance in rice. Furthermore, the results also indicated that addition of l-NG-nitro arginine methyl ester (l-NAME) (an inhibitor of endogenous NO synthesis) also reversed the toxic effects of SiNPs together with AgNPs, further suggesting that the low level of endogenous NO was associated with AgNPs stress tolerance. Overall, the results indicate that the low level of endogenous NO triggers AgNPs stress tolerance, while high level leads to AgNPs toxicity by regulating sulfur assimilation, GSH biosynthesis, redox status of GSH and oxidative stress markers. The results revealed that ethylene might act as a switch for regulating AgNPs stress in rice seedlings by controlling endogenous NO accumulation.

Say "NO" to plant stresses: Unravelling the role of nitric oxide under abiotic and biotic stress

Nitric oxide (NO) is a diatomic gaseous molecule, which plays different roles in different strata of organisms. Discovered as a neurotransmitter in animals, NO has now gained a significant place in plant signaling cascade. NO regulates plant growth and several developmental processes including germination, root formation, stomatal movement, maturation and defense in plants. Due to its gaseous state, it is unchallenging for NO to reach different parts of cell and counterpoise antioxidant pool. Various abiotic and biotic stresses act on plants and affect their growth and development. NO plays a pivotal role in alleviating toxic effects caused by various stressors by modulating oxidative stress, antioxidant defense mechanism, metal transport and ion homeostasis. It also modulates the activity of some transcriptional factors during stress conditions in plants. Besides its role during stress conditions, interaction of NO with other signaling molecules such as other gasotransmitters (hydrogen sulfide), phytohormones (abscisic acid, salicylic acid, jasmonic acid, gibberellin, ethylene, brassinosteroids, cytokinins and auxin), ions, polyamines, etc. has been demonstrated. These interactions play vital role in alleviating plant stress by modulating defense mechanisms in plants. Taking all these aspects into consideration, the current review focuses on the role of NO and its interaction with other signaling molecules in regulating plant growth and development, particularly under stressed conditions.

The participation of nitric oxide in hydrogen sulphide-mediated chromium tolerance in pepper (Capsicum annuum L) plants by modulating subcellular distribution of chromium and the ascorbate-glutathione cycle

The promising response of chromium-stressed (Cr(VI)-S) plants to hydrogen sulphide (H₂S) has been observed, but the participation of nitric oxide (NO) synthesis in H₂S-induced Cr(VI)-S tolerance in plants remains to be elucidated. It was aimed to assess the participation of NO in H₂S-mediated Cr(VI)-S tolerance by modulating subcellular distribution of Cr and the ascorbate-glutathione (AsA-GSH) cycle in the pepper seedlings. Two weeks following germination, plants were exposed to control (no Cr) or Cr(VI)-S (50 μM K₂Cr₂O₇) for further two weeks. The Cr(VI)-S-plants grown in nutrient solution were supplied with 200 μM sodium hydrosulphide (NaHS, donor of H₂S), or NaHS plus 100 μM sodium nitroprusside (SNP, a donor of NO). Chromium stress suppressed plant growth and leaf water status, while elevated proline content, oxidative stress, and the activities of AsA-GSH related enzymes, as well as endogenous H₂S and NO contents. The supplementation of NaHS increased Cr accumulation at root cell walls and vacuoles of leaves as soluble fraction to reduce its toxicity. Furthermore it limited oxidative stress, improved plant growth, modulated leaf water status, and the AsA-GSH cycle-associated enzymes' activities, as well as it further improved H₂S and NO contents. The positive effect of NaHS was found to be augmented on those parameters in the CrS-plants by the SNP supplementation. However, 0.1 mM cPTIO, the scavenger of NO, inverted the prominent effect of NaHS by decreasing NO content. The supplementation of SNP along with NaHS + cPTIO reinstalled the positive effect of NaHS by restoring NO content, which suggested that NO might have a potential role in H₂S-induced tolerance to Cr(VI)-S in pepper plants by stepping up the AsA-GSH cycle.

Involvement of NO and Ca2+ in the enhancement of cold tolerance induced by melatonin in winter turnip rape (Brassica rapa L.)

As a multifunctional phytohormone, melatonin (Mel) plays pivotal roles in plant responses to multiple stresses. However, its mechanism of action remains elusive. In the present study, we evaluated the role of NO and Ca²⁺ signaling in Mel enhanced cold tolerance in winter turnip rape. The results showed that the NO content and concentration of intracellular free Ca²⁺ ([Ca²⁺]_cyt) increased by 35.42% and 30.87%, respectively, in the leaves of rape seedlings exposed to cold stress. Compared with those of the seedlings in cold stress alone, the NO content and concentration of [Ca²⁺]_cyt in rape seedlings pretreated with Mel increased further. In addition, the Mel-mediated improvement of cold tolerance was inhibited by L-NAME (a NO synthase inhibitor), tungstate (a nitrate reductase inhibitor), LaCl₃ (a Ca²⁺ channel blocker), and EGTA (a Ca²⁺ chelator), and this finding was mainly reflected in the increase in ROS content and the decrease in osmoregulatory capacity, photosynthetic efficiency and antioxidant enzyme activities, and expression levels of antioxidant enzyme genes. These findings suggest that NO and Ca²⁺ are necessary for Mel to improve cold tolerance and function synergistically downstream of Mel. Notably, the co-treatment of Mel with L-NAME, tungstate, LaCl₃, or EGTA also inhibited the Mel-induced expression of MAPK3/6 under cold stress. In conclusion, NO and Ca²⁺ are involved in the enhancement of cold tolerance induced by Mel through activating the MAPK cascades in rape seedlings, and a crosstalk may exist between NO and Ca²⁺ signaling.