TaWRKY74 participates copper tolerance through regulation of TaGST1 expression and GSH content in wheat

Transcriptome and metabolome analysis reveal key genes and metabolic pathway responses in Leersia hexandra Swartz under Cr and Ni co-stress

Phytoremediation, an eco-friendly approach for mitigating heavy metal contamination, is reliant on hyperaccumulators. This study focused on Leersia hexandra Swart, a known chromium (Cr) hyperaccumulator with demonstrated tolerance to multiple heavy metals. Our objective was to investigate its response to simultaneous Cr and nickel (Ni) stress over 12 days. Results from physiological experiments demonstrated a significant increase in the activities of antioxidant enzymes (APX, SOD, CAT) and glutathione (GSH) content under Cr and Ni stress, indicating enhanced antioxidant mechanisms. Transcriptome analysis revealed that stress resulted in the differential expression of 27 genes associated with antioxidant activity and metal binding, including APX, SOD, CAT, GSH, metallothionein (MT), and nicotinamide (NA). Among them, twenty differentially expressed genes (DEGs) related to GSH metabolic cycle were identified. Notably, GSTU6, GND1, and PGD were the top three related genes, showing upregulation with fold changes of 4.57, 6.07, and 3.76, respectively, indicating their crucial role in metal tolerance. The expression of selected DEGs was validated by quantitative real-time PCR, confirming the reliability of RNA-Seq data. Metabolomic analysis revealed changes in 1121 metabolites, with amino acids, flavonoids, and carbohydrates being the most affected. Furthermore, glucosinolate biosynthesis and amino acid biosynthesis pathways were represented in the KEGG pathway of differentially expressed metabolites (DEMs). This study provides insights into the tolerance mechanisms of L. hexandra under the co-stress of Cr and Ni, offering a new perspective for enhancing its remediation performance.

The transcriptional landscape of Populus pattern/effector-triggered immunity and how PagWRKY18 involved in it

Plants trigger a robust immune response by activating massive transcriptome reprogramming through crosstalk between PTI and ETI. However, how PTI and ETI contribute to the quantitative or/and qualitative output of immunity and how they work together when both are being activated were unclear. In this study, we performed a comprehensive overview of pathogen-triggered transcriptomic reprogramming by analyzing temporal changes in the transcriptome up to 144 h after Colletotrichum gloeosporioides inoculated in Populus. Moreover, we constructed a hierarchical gene regulatory network of PagWRKY18 and its potential target genes to explore the underlying regulatory mechanisms of PagWRKY18 that are not yet clear. Interestingly, we confirmed that PagWRKY18 protein can directly bind the W-box elements in the promoter of a transmembrane leucine-rich repeat receptor-like kinase, PagSOBIR1 gene, to trigger PTI. At the same time, PagWRKY18 functions in disease tolerance by modulation of ROS homeostasis and induction of cell death via directly targeting PagGSTU7 and PagPR4 respectively. Furthermore, PagPR4 can interact with PagWRKY18 to inhibit the expression of PagPR4 genes, forming a negative feedback loop. Taken together, these results suggest that PagWRKY18 may be involved in regulating crosstalk between PTI and ETI to activate a robust immune response and maintain intracellular homeostasis.

Decrypting Molecular Mechanisms Involved in Counteracting Copper and Nickel Toxicity in Jack Pine (Pinus banksiana) Based on Transcriptomic Analysis

The remediation of copper and nickel-afflicted sites is challenged by the different physiological effects imposed by each metal on a given plant system. Pinus banksiana is resilient against copper and nickel, providing an opportunity to build a valuable resource to investigate the responding gene expression toward each metal. The objectives of this study were to (1) extend the analysis of the Pinus banksiana transcriptome exposed to nickel and copper, (2) assess the differential gene expression in nickel-resistant compared to copper-resistant genotypes, and (3) identify mechanisms specific to each metal. The Illumina platform was used to sequence RNA that was extracted from seedlings treated with each of the metals. There were 449 differentially expressed genes (DEGs) between copper-resistant genotypes (RGs) and nickel-resistant genotypes (RGs) at a high stringency cut-off, indicating a distinct pattern of gene expression toward each metal. For biological processes, 19.8% of DEGs were associated with the DNA metabolic process, followed by the response to stress (13.15%) and the response to chemicals (8.59%). For metabolic function, 27.9% of DEGs were associated with nuclease activity, followed by nucleotide binding (27.64%) and kinase activity (10.16%). Overall, 21.49% of DEGs were localized to the plasma membrane, followed by the cytosol (16.26%) and chloroplast (12.43%). Annotation of the top upregulated genes in copper RG compared to nickel RG identified genes and mechanisms that were specific to copper and not to nickel. NtPDR, AtHIPP10, and YSL1 were identified as genes associated with copper resistance. Various genes related to cell wall metabolism were identified, and they included genes encoding for HCT, CslE6, MPG, and polygalacturonase. Annotation of the top downregulated genes in copper RG compared to nickel RG revealed genes and mechanisms that were specific to nickel and not copper. Various regulatory and signaling-related genes associated with the stress response were identified. They included UGT, TIFY, ACC, dirigent protein, peroxidase, and glyoxyalase I. Additional research is needed to determine the specific functions of signaling and stress response mechanisms in nickel-resistant plants.

Glutathione-dependent redox homeostasis is critical for chlorothalonil detoxification in tomato leaves

Glutathione plays a critical role in plant growth, development and response to stress. It is a major cellular antioxidant and is involved in the detoxification of xenobiotics in many organisms, including plants. However, the role of glutathione-dependent redox homeostasis and associated molecular mechanisms regulating the antioxidant system and pesticide metabolism remains unclear. In this study, endogenous glutathione levels were manipulated by pharmacological treatments with glutathione synthesis inhibitors and oxidized glutathione. The application of oxidized glutathione enriched the cellular oxidation state, reduced the activity and transcript levels of antioxidant enzymes, upregulated the expression level of nitric oxide and Ca2+ related genes and the content, and increased the residue of chlorothalonil in tomato leaves. Further experiments confirmed that glutathione-induced redox homeostasis is critical for the reduction of pesticide residues. RNA sequencing analysis revealed that miRNA156 and miRNA169 that target transcription factor SQUAMOSA-Promoter Binding Proteins (SBP) and NUCLEAR FACTOR Y (NFY) potentially participate in glutathione-mediated pesticide degradation in tomato plants. Our study provides important clues for further dissection of pesticide degradation mechanisms via miRNAs in plants.

Transcriptome analysis reveals the role of polysaccharide biosynthesis in the detoxification of Dendrobium nobile under zinc stress

Plants can bind excessive heavy metals by synthesizing compounds to alleviate the harm caused by heavy metals. To reveal the mechanism by which Dendrobium nobile alleviates zinc stress, metabolome combined transcriptome analysis was used in this research. The results showed that zinc was mainly enriched in the roots and leaves and the biomass of the roots and leaves of D. nobile decreased significantly by 18.21 % and 49.22 % (P < 0.05) compared to the control (CK), respectively. Meanwhile, the contents of nonprotein thiol(NPT), glutathione(GSH), and phytochelatins (PCs) in the roots were significantly increased by 48.8 %, 78.3 %, and 45.4 % compared to CK, respectively. Through TEM testing, it was found that D. nobile exhibited toxic symptoms. Metabolome analysis showed that the metabolites of D. nobile under zinc stress were mainly enriched in biosynthesis of other secondary metabolites and carbohydrate metabolism. Nova-seq results identified 1202 differentially expressed genes(DEGs), of which 603 were upregulated and 599 were downregulated. Through GO and KEGG annotation analysis of these DEGs, it was found that PMR6 and PECS-2.1, SS1 and GLU3 genes were significantly upregulated, leading to an increase in the biosynthesis of xylan, pectin, starch and other polysaccharides in D. nobile. These polysaccharides can form a "Polysaccharide-Zn" with excess zinc. Meanwhile, the GSTs in glutathione metabolism were significantly upregulated, leading to a significant increase in the content of NPT, GSH, and PCs. These zinc complexes were transported to vacuoles through ABC transporters for compartmentalization, effectively alleviating the damage of zinc. The results can provide new insights for phytoremediation and quality assurance of medicinal D. nobile.

Cross talk between Cu excess and Fe deficiency in the roots of rice

Copper (Cu) and iron (Fe) share similar characteristics and participate as coenzymes in several physiological processes. Both Cu excess and Fe deficiency result in chlorosis, however, the crosstalk between the two is not clear in rice. In this study, we performed transcriptome analysis for Cu excess and Fe deficiency in rice. Some WRKY family members (such as WRKY26) and some bHLH family members (such as late flowering) were selected as novel potential transcription factors involved in the regulation of Cu detoxification and Fe utilization, respectively. These genes were induced under corresponding stress conditions. Many Fe uptake-related genes were induced by Cu excess, while Cu detoxification-related genes were not induced by Fe deficiency. Meanwhile, some genes, such as metallothionein 3a, gibberellin 3beta-dioxygenase 2 and WRKY11, were induced by Cu excess but repressed by Fe deficiency. Concisely, our results highlight the crosstalk between Cu excess and Fe deficiency in rice. Cu excess caused Fe deficiency response, while Fe deficiency did not lead to Cu toxicity response. Metallothionein 3a might be responsible for Cu toxicity-induced chlorosis in rice. The crosstalk between Cu excess and Fe deficiency might be regulated by gibberellic acid.

Citric acid modified ultrasmall copper peroxide nanozyme for in situ remediation of environmental sulfonylurea herbicide contamination

Herbicide residues in the environment threaten high-quality agriculture and human health. Consequently, in situ remediation of herbicide contamination is vital. We synthesized a novel self-catalyzed nanozyme, ultrasmall (2-3 nm) copper peroxide nanodots modified by citric acid (CP@CA) for this purpose, which can break down into H₂O₂ and Cu²⁺ in water or soil. Ubiquitous glutathione reduces Cu²⁺ into Cu⁺, which promotes the decomposition of H₂O₂ into •OH through a Fenton-like reaction under mild acid conditions created by the presence of citric acid. The generated •OH efficiently degrade nicosulfuron in water and soil, and the maximum degradation efficiency could be achieved at 97.58% in water at 56 min. The possible degradation mechanisms of nicosulfuron were proposed through the 25 intermediates detected. The overall ecotoxicity of the nicosulfuron system was significantly reduced after CP@CA treatment. Furthermore, CP@CA had little impact on active components of soil bacterial community. Moreover, CP@CA nanozyme could effectively remove seven other sulfonylurea herbicides from the water. In this paper, a high-efficiency method for herbicide degradation was proposed, which provides a new reference for the in situ remediation of herbicide pollution.

Migration, accumulation, and risk assessment of potentially toxic elements in soil-plant (shrub and herbage) systems at typical polymetallic mines in Northwest China

In grassland systems of the semi-arid mining area, the migration, accumulation, and bioavailability of potentially toxic elements (PTEs) are important ecological and health risk issues. Thirty-eight pairs of topsoil (0-20 cm) and plant samples were collected around Baiyin City and in Dongdagou stream valley to investigate the migration of PTEs in soils, transfer of PTEs in soil-plant (shrub and herbage) systems, and assess the risk in soils and plants. The total concentrations of PTE (Hg, As, Cu, Zn, Cd, and Pb) were analyzed following digestion in mixture acid solution, and bioavailable PTE was extracted with a strong chelating agent (DTPA-TEA-CaCl₂). The transfer factor (TF) and bioaccumulation factor (BCF) were calculated to examine the migration of PTEs in soil-plant. Hazard quotient (HQ) and total hazard index (THI) were calculated to assess the risk and migration of PTEs in soils. The results showed that PTEs in soils and plants of study area exceeded the soil background value and Hygienic Standard for Feeds. Correlation among the total Hg, As, Cu, Zn, Cd, and Pb in soils of Dongdagou stream valley was significant at p < 0.01. A good correlation was exhibited between PTEs in root/aboveground parts of plants and DTPA-soil extractable. Difference of TF and BCF was existed between Dongdagou stream valley and around Baiyin City. Hg, Cu, Zn, Cd, and Pb were mainly accumulated in soils near the mining area. The calculated THI exceeded 1, and As and Pb were the major risk factors. The ability to absorb and transfer Hg, As, Cu, and Pb of plants was lower in more serious polluted area. As had a stronger migration capacity in study area. PTEs in soils had an adverse health effect for residents, and PTEs in plants may cause toxicity to cattle and sheep.

Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information

The amount of biological data is growing at a rapid pace as many high-throughput omics technologies and data pipelines are developed. This is resulting in the growth of databases for DNA and protein sequences, gene expression, protein accumulation, structural, and localization information. The diversity and multi-omics nature of such bioinformatic data requires well-designed databases for flexible organization and presentation. Besides general-purpose online bioinformatic databases, users need narrowly focused online databases to quickly access a meaningful collection of related data for their research. Here, we describe the methodology used to implement a plant gene regulatory knowledgebase, with data, query, and tool features, as well as the ability to expand to accommodate future datasets. We exemplify this methodology for the GRASSIUS knowledgebase, but it is applicable to developing and updating similar plant gene regulatory knowledgebases. GRASSIUS organizes and presents gene regulatory data from grass species with a central focus on maize (Zea mays). The main class of data presented include not only the families of transcription factors (TFs) and co-regulators (CRs) but also protein-DNA interaction data, where available.

HvGST4 enhances tolerance to multiple abiotic stresses in barley: Evidence from integrated meta-analysis to functional verification

Extreme weather events have become more frequent, increasing crop yield fluctuations in many regions and thus the risk to global food security. Breeding crop cultivars with improved tolerance to a combination of abiotic stresses is an effective solution to counter the adverse impact of climate change. The ever-increasing genomic data and analytical tools provide unprecedented opportunities to mine genes with tolerance to multiple abiotic stresses through bioinformatics analysis. We undertook an integrated meta-analysis using 260 transcriptome data of barley related to drought, salt, heat, cold, and waterlogging stresses. A total of 223 shared differentially expressed genes (DEGs) were identified in response to five abiotic stresses, and significantly enriched in 'glutathione metabolism' and 'monoterpenoid biosynthesis' pathways. Using weighted gene co-expression network analysis (WGCNA), we further identified 15 hub genes (e.g., MYB, WRKY, NADH, and GST4) and selected the GST4 gene for functional validation. HvGST4 overexpression in Arabidopsis thaliana enhanced the tolerance to multiple abiotic stresses, likely through increasing the content of glutathione to scavenge reactive oxygen species and alleviate cell membrane peroxidation. Furthermore, we showed that virus-induced gene silencing (VIGS) of HvGST4 in barley leaves exacerbated cell membrane peroxidation under five abiotic stresses, reducing tolerance to multiple abiotic stress. Our study provides a new solution for identifying genes with tolerance to multiple abiotic stresses based on meta-analysis, which could contribute to breeding new varieties adapted genetically to adverse environmental conditions.

WRKY74 regulates cadmium tolerance through glutathione-dependent pathway in wheat

Cadmium (Cd) is a toxic heavy metal to plants and human health. Ascorbate (ASA)-glutathione (GSH) synthesis pathway plays key roles in Cd detoxification, while its molecular regulatory mechanism remains largely unknown, especially in wheat. Here, we found a WRKY transcription factor-TaWRKY74, and its function in wheat Cd stress is not clear in previous studies. The expression levels of TaWRKY74 were significantly induced by Cd stress. Compared to control, the activities of GST, GR, or APX were significantly increased by 1.55-, 1.43-, or 1.75-fold and 1.63-, 2.65-, or 2.30-fold in shoots and roots of transiently TaWRKY74-silenced wheat plants under Cd stress. Similarly, the contents of hydrogen peroxide (H₂O₂), malondialdehyde (MDA), GSH, or Cd were also significantly increased by 2.39- or 1.25-fold, 1.54- or 1.20-fold, and 1.34- or 5.94-fold in shoots or roots in transiently TaWRKY74-silenced wheat plants, while ASA content was decreased by 47.4 or 43.3% in shoots, 10.7 or 6.5% in roots in these silenced wheat plants, respectively. Moreover, the expression levels of GSH, GPX, GR, DHAR, MDHAR, and APX genes, which are involved in ASA-GSH synthesis, were separately induced by 2.42-, 2.16-, 3.28-, 2.08-, 1.92-, and 2.23-fold in shoots, or by 10.69-, 3.33-, 3.26-, 1.81-, 16.53-, and 3.57-fold in roots of the BSMV-VIGS-TaWRKY74-inoculated wheat plants, respectively. However, the expression levels of TaNramp1, TaNramp5, TaHMA2, TaHMA3, TaLCT1, and TaIRT1 metal transporters genes were decreased by 21.2-76.3% (56.6%, 59.2%, 76.3%, 53.6%, 35.8%, and 21.2%) in roots of the BSMV-VIGS-TaWRKY74-inoculated wheat plants. Taken together, our results suggested that TaWRKY74 alleviated Cd toxicity in wheat by affecting the expression of ASA-GSH synthesis genes and suppressing the expression of Cd transporter genes, and further affecting Cd uptake and translocation in wheat plants.

GmWRKY21, a Soybean WRKY Transcription Factor Gene, Enhances the Tolerance to Aluminum Stress in Arabidopsis thaliana

The WRKY transcription factors (TFs) are one of the largest families of TFs in plants and play multiple roles in plant growth and development and stress response. In this study, GmWRKY21 encoding a WRKY transcription factor was functionally characterized in Arabidopsis and soybean. The GmWRKY21 protein containing a highly conserved WRKY domain and a C₂H₂ zinc-finger structure is located in the nucleus and has the characteristics of transcriptional activation ability. The GmWRKY21 gene presented a constitutive expression pattern rich in the roots, leaves, and flowers of soybean with over 6-fold of relative expression levels and could be substantially induced by aluminum stress. As compared to the control, overexpression of GmWRKY21 in Arabidopsis increased the root growth of seedlings in transgenic lines under the AlCl₃ concentrations of 25, 50, and 100 μM with higher proline and lower MDA accumulation. The results of quantitative real-time polymerase chain reaction (qRT-PCR) showed that the marker genes relative to aluminum stress including ALMT, ALS3, MATE, and STOP1 were induced in GmWRKY21 transgenic plants under AlCl₃ treatment. The stress-related genes, such as KIN1, COR15A, COR15B, COR47, GLOS3, and RD29A, were also upregulated in GmWRKY21 transgenic Arabidopsis under aluminum stress. Similarly, stress-related genes, such as GmCOR47, GmDREB2A, GmMYB84, GmKIN1, GmGST1, and GmLEA, were upregulated in hair roots of GmWRKY21 transgenic plants. In summary, these results suggested that the GmWRKY21 transcription factor may promote the tolerance to aluminum stress mediated by the pathways regulating the expression of the acidic aluminum stress-responsive genes and abiotic stress-responsive genes.

A WRKY transcription factor, PyWRKY75, enhanced cadmium accumulation and tolerance in poplar

Cadmium (Cd) pollution has detrimental effects on the ecological environment and human health. Currently, phytoremediation is considered an environmentally friendly way to remediate Cd pollution. The application of transgenic plants to remediate soil pollution is a new technology that has emerged in recent years. In this study, PyWRKY75 was isolated and cloned from Populus yunnanensis, and the functionality of PyWRKY75 in woody plants (poplar) under Cd stress was verified. The increase in plant height of the OE-41 line (overexpression poplar) was 33.2% higher than that of the wild type (WT). Moreover, PyWRKY75 significantly promoted the absorption and accumulation of Cd in poplar, which increased by 51.32% in the OE-41 line when compared with the WT. The chlorophyll content of transgenic poplar leaves was higher than that of the WT, which reflected a protective mechanism of PyWRKY75. Other antioxidants, such as POD, SOD, CAT, APX, AsA, GSH and PCs, also made the transgenic poplars more tolerant to Cd, and they behaved differently in roots, stems and leaves. In general, PyWRKY75 played a potential role in regulating plant tolerance to Cd stress. This study provides a scientific basis and a new type of modified poplar for Cd pollution remediation.

He-Ne laser irradiation ameliorates cadmium toxicity in wheat by modulating cadmium accumulation, nutrient uptake and antioxidant defense system

Cadmium (Cd) is one of the most hazardous heavy metals that negatively affect the growth and yield of wheat. He-Ne laser irradiation is known to ameliorate cadmium (Cd) stress in wheat. However, the underlying mechanism of He-Ne laser irradiation on protecting wheat against Cd stress is not well recognized. In present study, Cd-treated wheat showed significant reduction in growth, root morphology and total chlorophyll content, but notably increase of Cd accumulation in both roots and shoots. However, He-Ne laser irradiation dramatically reduced concentrations of malondialdehyde (MDA) and hydrogen peroxide (H₂O₂), and increased total chlorophyll content and activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX) in roots of wheat plants under Cd stress. Further, He-Ne laser irradiation significantly upregulated the transcripts of TaGR (glutathione reductase) and TaGST (glutathione-S-transferase) genes along with the increased activities of GR and GST and glutathione (GSH) concentration in roots of wheat seedlings under Cd stress. In addition, He-Ne laser irradiation enhanced the uptake of mineral elements (N, P, Mg, Fe, Zn and Cu), and significantly decreased Cd uptake and transport mainly through down-regulating the expressions of Cd transport genes (TaHMA2 and TaHMA3) in roots of wheat seedlings under Cd stress. Overall, these findings suggested that He-Ne laser irradiation alleviated the adverse effects of Cd on wheat growth by enhancing antioxidant defense system, improving mineral nutrient status, and decreasing the Cd uptake and transport. This study provides new insights into the roles of He-Ne laser irradiation in the amelioration of Cd stress in wheat and indicates the potential application of this irradiation in crop breeding and growth under Cd stress conditions.

BcGR1.1, a Cytoplasmic Localized Glutathione Reductase, Enhanced Tolerance to Copper Stress in Arabidopsis thaliana

Copper is a mineral element, which is necessary for the normal growth and development of plants, but high levels of copper will seriously damage plants. Studies have shown that AtGR1 improves the tolerance of Arabidopsis to aluminum and cadmium stress. However, the role of GR in the copper stress response of plants is still unclear. Here, we identified four genes (named BcGR1.1, BcGR1.2, BcGR2.1 and BcGR2.2, respectively) encoding glutathione reductase (GR) in non-heading Chinese cabbage (Brassica campestris (syn. Brassica rapa) ssp. chinensis), which could be divided into two types based on the subcellular localization. Among them, BcGR1.1, which belonged to the cytoplasmic localization type, was significantly upregulated under copper stress. Compared to WT (the wild type), Arabidopsis thaliana heterologously overexpressed BcGR1.1 had longer roots, higher fresh weight, higher GSH levels and GSH/GSSG (oxidized form of GSH) ratio, and accumulated more superoxide dismutase and peroxidase under copper stress. However, in the AsA-GSH cycle under copper stress, the contents of AsA and AsA/DHA were significantly downregulated, and the contents of DHA and T-AsA (total AsA) were upregulated, in the BcGR1.1-overexpressing Arabidopsis. Therefore, BcGR1.1 could improve the scavenging ability of reactive oxygen species (ROS) by increasing the activity of GR, antioxidant enzymes and the utilization of AsA, and then enhance the copper stress tolerance of plants.

Magnesium hydride confers copper tolerance in alfalfa via regulating nitric oxide signaling

Magnesium hydride (MgH₂) as a solid-state hydrogen source might be potentially applied in industry and medicine. However, its biological function in plants has not yet been fully discovered. In this report, it was observed that MgH₂ administration could relieve copper (Cu) toxicity in alfalfa that was confirmed by a reduction in root growth inhibition. By using old MgH₂ as a negative control, it was concluded that above MgH₂ function was primarily derived from the releasing of molecular hydrogen (H₂), but not caused by either magnesium metabolites or pH alteration. Further results revealed that Cu-triggered nitric oxide (NO) production was intensified by MgH₂. Subsequent pharmacological and biochemical experiments suggested that nitrate reductase might be mainly responsible for NO production during above processes. Cu accumulation in the root tissues was also obviously reduced in the presence of MgH₂. Meanwhile, increased non-protein thiols (NPTs) content and the deposition of Cu in cell wall of seedling roots could be used to explain the mechanism underlying MgH₂-alleviated Cu toxicity via NO signaling. Further, the plant redox balance was reestablished since the Cu stress-modulated antioxidant enzymes activities, reactive oxygen species (ROS) accumulation, and oxidative injury detected by in vivo histochemical and biochemical analyses, were differentially abolished by MgH₂. The above responses could be blocked by the removal of endogenous NO after the addition of its scavenger. Taken together, these results clearly suggested that MgH₂ control of plant tolerance against Cu toxicity might be mediated by NO signaling, which might open a new window for the application of solid-state hydrogen materials in agriculture.