MAPK Cascades and Transcriptional Factors: Regulation of Heavy Metal Tolerance in Plants

Harnessing the interplay of protein posttranslational modifications: Enhancing plant resilience to heavy metal toxicity

Heavy metals (HMs) toxicity finds substantial plant health risk, affecting germination, growth, productivity, and survival. HMs exposure can interrupt cellular function, increase oxidative stress and affect physiological processes. Plants have developed array of adaptive responses, with proteins playing key role in detecting, signalling, and mitigating metal-induced stress. Under stress, posttranslational modifications, including phosphorylation, ubiquitination, glycosylation and acetylation, are essential regulators of protein stability, localization, and function. This review examines the comprehensive profiling of PTMs in HMs stress responses, including how PTMs regulate the signalling pathways, degradation pathways, and TFs modulation. Specifically, discuss the role of phosphorylation, ubiquitination, and sumoylation, neddylation, lipidation, and S-nitrosylation in specifically under HMs stress with PTMs regulation of antioxidant enzymes, stress proteins, metal transporters and chelators of detoxification. This review illustrates the crosstalk of PTMs to show how synergistic interactions regulate protein stability, activity, and localization upon HMs stress. In cross talk, ubiquitination often starts from phosphorylation to subsequent degradation of proteins in a timely and reversible way to trigger stress responses. However, sumoylation stabilizes key transcription factors that are rapidly dephosphorylated and integral in metal detoxification, form a synergistic combination with phosphorylation to maintain their activity. It explains the future research directions, focusing on PTM engineering to generate stress tolerant plant varieties. By studying the response of plants to HMs stress through PTMs, emphasizes the relevance of PTMs towards plant resilience and advocates for systems biology integrative approach to advancing plant stress biology.

Small-scale heterogeneity of soil properties in farmland affected fava beans growth through rhizosphere differential metabolites and microorganisms

BACKGROUND

Soil heterogeneity has been acknowledged to influence plant growth, with the small-scale soil heterogeneity always being overlooked in practice. It remains unclear how rhizosphere soil biotics and abiotics respond to soil heterogeneity and how rhizosphere interactions influence crop growth.

RESULTS

In this study, we planted fava beans in a farmland around an e-waste dismantling site, and a distinct boundary (row spacing is 30 cm) was observed in the field during the flowering stage, which divided fava beans phenotypes into two distinct groups (Big vs Little) based on the differences in biomass and height. Soil total concentrations of As, B, Co, Cr, Cu, Pb, Sr, Zn, Ni, Cd and soil pH significantly differed in the rhizosphere of fava beans in the two adjacent rows, which were located on either side of the boundary, with a row-spacing of 30 cm. Random Forest analysis demonstrated that these differentiated soil properties (soil pH, total As, B, Cd, Co, Cr, Cu, Mo, Ni and Zn) substantially influenced fava beans growth (height and biomass). Metagenomic sequencing showed that microbial taxa were significantly enriched their abundance in rhizosphere soils between the two groups of fava beans, with eukaryotic taxa being more sensitively affected. A total of 20 metabolites including coniferyl alcohol, jasmonic acid, resveratrol, and L-aspartic acid, etc. were significantly correlated with fava beans growth. These metabolites were significantly enriched in 15 metabolic pathways (nucleotide metabolism, pyrimidine metabolism, purine metabolism, biosynthesis of plant secondary metabolites, lysine biosynthesis, etc.). Furthermore, 11 microbial genera involved in these metabolic pathways, and these genera were differentially enriched between the two groups and significantly correlated with fava beans growth.

CONCLUSIONS

Overall, the integrated analysis of multi-omics revealed that soil properties heterogeneity at small-scale altered the rhizosphere differential microorganisms and metabolites, which functionally influenced fava beans growth and tolerance to environmental stress. Notably, even soil heterogeneity at such a small spatial scale can cause significant differences in plant growth, and the comprehensive explorations utilizing multi-omics techniques provide novel insights to the field management, which is crucial for the survival and sustainable development of humanity.

Unraveling tissue-specific molecular mechanisms orchestrating arsenic response processes in Pteris vittata through transcriptomic analysis

Pteris vittata remediates arsenic (As)-contaminated soils; however, the molecular mechanisms underlying the As management remain largely unknown. Therefore, in this study, we investigated As - related processes by conducting transcriptomic analysis on hydroponically grown P. vittata exposed to 500 ppb arsenate (AsV). Within 24 h, As was translocated to fronds, while As concentration among fronds differed (4.08-1323.35 µg/g-DW). Transcriptomic profiling of roots and fronds with high (PHAs) and low (PLAs) As concentrations revealed distinct As transport mechanisms. In the roots, the induction of PvPht1;3 and one PHO1 genes suggested the facilitation of AsV absorption, while ACR3 and POT genes were induced in both the roots and fronds. Notably, NRT2.5, NIP6;1, BOR2, and ABC transporter genes were specifically activated in PHAs, highlighting their potential roles in As hyperaccumulation. To our knowledge, this is the first report linking PHO1, POT, NRT2.5, NIP6;1, and BOR2 to As accumulation in P. vittata. Gene ontology enrichment analysis further emphasized a tissue-specific As response system. In the roots, differentially expressed genes (DEGs) associated with the activation of glutathione metabolic process, cell wall biogenesis, antioxidant response, and signal transduction pathways enabled a prompt response to As-derived stimuli, facilitating efficient As uptake and transport. In the fronds, DEGs related to cell wall modification, oxidative stress response, signal transduction, and active transport systems may contribute to As detoxification and hyperaccumulation. This study provides novel insights into the molecular basis of As uptake, transport, accumulation, and detoxification in P. vittata, providing valuable strategies for efficient phytoextraction via regulation of As metabolism.

A close-up of regulatory networks and signaling pathways of MKK5 in biotic and abiotic stresses

Mitogen-activated protein Kinase Kinase 5 (MKK5) is a central hub in the complex phosphorylation chain reaction of the Mitogen-activated protein kinases (MAPK) cascade, regulating plant responses to biotic and abiotic stresses. This review manuscript aims to provide a comprehensive analysis of the regulatory mechanism of the MKK5 involved in stress adaptation. This review will delve into the intricate post-transcriptional and post-translational modifications of the MKK5, discussing how they affect its expression, activity, and subcellular localization in response to stress signals. We also discuss the integration of the MKK5 into complex signaling pathways, orchestrating plant immunity against pathogens and its modulating role in regulating abiotic stresses, such as: drought, cold, heat, and salinity, through the phytohormonal signaling pathways. Furthermore, we highlight potential applications of the MKK5 for engineering stress-resilient crops and provide future perspectives that may pave the way for future studies. This review manuscript aims to provide valuable insights into the mechanisms underlying MKK5 regulation, bridge the gap from numerous previous findings, and offer a firm base in the knowledge of MKK5, its regulating roles, and its involvement in environmental stress regulation.

Integrative transcriptome and WGCNA analysis reveal key genes mainly in response to Alternaria alternata in Populus simonii × P. nigra

In order to explore the molecular mechanisms of Populus simonii × P. nigra response to stress and screen for genes conferring resistance to Alternaria alternata, we carried out measurements of physiological and biochemical indices and transcriptomic sequence analysis of leaves of Populus simonii × P. nigra inoculated with A. alternata. The results showed that the variation trends of multiple hormone contents and enzyme activities were broadly similar at different time points, with H2O2, SA, JA, PPO, SOD, PAL and POD showing a trend of increasing and then decrease after inoculation with the pathogen. The contents of H2O2 peaked on the second day and subsequently declined. The contents of SA and JA, as well as the enzymatic activities of SOD, PAL, and POD, reached their maxima on the third day before exhibiting a downward tendency. In contrast, the activity of PPO peaked on the fourth day. Whereas ABA content continued to increase until the fifth day and CAT content decreased and then increased. We subsequently identified 14,997 differentially expressed genes (DEGs) among the transcriptomic sequences(|log2FoldChange| > 1 and FDR value < 0.05), with genes encoding members of the ERF, MYB, bZIP, and WRKY transcription factor families being differentially expressed. Gene modules that were significantly associated with the ABA, PAL, JA, and SOD activity were identified using weighted gene co-expression network analysis (WGCNA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these genes were mainly related to biological stress, signal transduction, cell wall, and photosynthesis. Within these modules, we also identified hub genes in the regulatory network, including GLK1/2 transcriptional activators, 14-3-3 proteins, cytosine 5 methyltransferases, and a variety of proteins associated with photosynthesis and respiration. This study showed that these hub genes, which play a pivotal role in the co-expression network, which may indicate a potential role in defense process of Populus simonii × P. nigra against A. alternata. Additionally, we analyzed the gene expression regulation and defense mechanisms of Populus simonii × P. nigra adversity stress, providing new insights into how plants respond to biological stress.

Accumulation Potential of Lead and Cadmium Metals in Maize (Zea mays L.) and Effects on Physiological-Morphological Characteristics

Phytoremediation stands at the forefront of modern environmental science, offering an innovative and cost-effective solution for the remediation of heavy-metal-contaminated soils through the natural capabilities of plants. This study aims to investigate the effects of lead (Pb) and cadmium (Cd) metals on plant growth (e.g., seedling height, stem diameter, fresh and dry weight), physiological properties (e.g., tissue relative water content, tissue electrical conductivity), and biochemical parameters (e.g., chlorophyll content, superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) enzyme activities) of maize compared to the control group under greenhouse conditions at the Atatürk University Plant Production Application and Research Center. The results show that plant height decreased by 20% in the lead (Pb3000) application and by 42% in the cadmium (Cd300) application compared to the control group. The highest Pb dose (Pb3000) caused a 15% weight loss compared to the control, while the highest Cd dose (Cd300) caused a weight loss of 63%. The accumulation rates of heavy metals in soil, roots, and aboveground parts of plants indicated that maize absorbed and accumulated more Cd compared to Pb.

Novel Insights into Hg0 Oxidation in Rice Leaf: Catalase Functions and Transcriptome Responses

Rice leaves can assimilate atmospheric mercury (Hg0), which is accumulated by grains and causes health risks to rice consumers. However, the molecular mechanisms underlying Hg0 assimilation in rice leaves remain poorly understood. Here, we investigated catalase's (CAT) function in Hg0 oxidation within rice leaves, as well as the Hg speciation and transcriptomic profiles of rice leaves exposed to Hg0. The inactivation of catalase reduced Hg0 oxidation by 91% in the leaf homogenate and the Hg0 oxidation rate increased along with CAT activity, showing the CAT's function in Hg0 oxidation. Hg0 was converted to Hg(cysteine)2 complexes in the leaf. Transcriptomic results revealed that the expression levels of both OsCATA and OsCATB (catalase-encoding genes) increased with Hg concentration, suggesting the involvement of catalase-related molecular network in Hg0 oxidation. Upstream transcription factors, including NAC (NAM-no apical meristem, ATAF-Arabidopsis transcription activation factor, and CUC-cup-shaped cotyledon), and ethylene-responsive transcription factor, are likely involved in catalase expression. Genes related to cysteine metabolism and amino acid transport appeared to regulate Hg accumulation. Our findings demonstrate the important function of catalase in Hg0 oxidation within rice and are fundamental for developing genetically modified rice cultivars to minimize human Hg exposure health risks.

Chickpea defense against dual stresses of salt and Fusarium wilt is enhanced through selected bHLH transcription factors carrying the bHLH-MYC_N domain

The plant transcriptome varies between combined stresses and single stresses, and is regulated differentially by transcription factors. Therefore, understanding the complexities of plant interactions with pathogens in stressed soils is always a challenge. In chickpea, 197 CabHLH genes were newly identified. Expression of 28 defense-associated CabHLHs [individual and combined stresses of Fusarium oxysporum f. sp. ciceris (Foc) and salt (NaCl) in three chickpea cultivars (JG-315: wilt resistant, JG-36: wilt tolerant, and JG-62: wilt susceptible) in Trichoderma asperellum T42 primed and non-primed conditions] revealed upregulation of most CabHLHs at 12 h post-stress in individual stresses but decreased significantly in the combined stress (Foc and salt). However, T42 priming stimulated the transcript accumulation of most CabHLHs even earlier (6 h). Three genes (CabHLH119, 158, and 184 carrying an additional domain bHLH-MYC_N) and two additional genes (CabHLH69 and 172) belonging to the subfamilies IIIde and IIIf were upregulated significantly in all three cultivars under individual and combined stresses, and upregulated further when primed with T42. Expression of the three bHLH-MYC_N domain containing genes, and defense activities (PAL, PO activities, phenylpropanoid accumulation) in the combined stress correlated very strongly. Protein-protein interactome studies further strengthened the claim that the three bHLH-MYC_N domain carrying CabHLHs, is likely to regulate the defense signaling in chickpea under stress as they could form complexes either directly or indirectly with cis-elements of promoters of some important defense genes. The results thus showed the significance of the IIIde and IIIf subfamily genes, particularly those carrying the bHLH-MYC_N domain, in mitigating combined stresses.

Lead toxicity in plants: mechanistic insights into toxicity, physiological responses of plants and mitigation strategies

Soil toxicity is a major environmental issue that leads to numerous harmful effects on plants and human beings. Every year a huge amount of Pb is dumped into the environment either from natural sources or anthropogenically. Being a heavy metal it is highly toxic and non-biodegradable but remains in the environment for a long time. It is considered a neurotoxic and exerts harmful effects on living beings. In the present review article, investigators have emphasized the side effects of Pb on the plants. Further, the authors have focused on the various sources of Pb in the environment. Investigators have emphasized the various responses including molecular, biochemical, and morphological of plants to the toxic levels of Pb. Further emphasis was given to the effect of elevated levels of Pb on the microbial population in the rhizospheres. Further, emphasized the various remediation strategies for the Pb removal from the soil and water sources.

AaSlt2 Is Required for Vegetative Growth, Stress Adaption, Infection Structure Formation, and Virulence in Alternaria alternata

Slt2 is an important component of the Slt2-MAPK pathway and plays critical regulatory roles in growth, cell wall integrity, melanin biosynthesis, and pathogenicity of plant fungi. AaSlt2, an ortholog of the Saccharomyces cerevisiae Slt2 gene, was identified from A. alternata in this study, and its function was clarified by knockout of the gene. The ΔAaSlt2 strain of A. alternata was found to be defective in spore morphology, vegetative growth, and sporulation. Analysis of gene expression showed that expression of the AaSlt2 gene was significantly up-regulated during infection structure formation of A. alternata on hydrophobic and pear wax extract-coated surfaces. Further tests on onion epidermis confirmed that spore germination was reduced in the ΔAaSlt2 strain, together with decreased formation of appressorium and infection hyphae. Moreover, the ΔAaSlt2 strain was sensitive to cell wall inhibitors, and showed significantly reduced virulence on pear fruit. Furthermore, cell wall degradation enzyme (CWDE) activities, melanin accumulation, and toxin biosynthesis were significantly lower in the ΔAaSlt2 strain. Overall, the findings demonstrate the critical involvement of AaSlt2 in growth regulation, stress adaptation, infection structure formation, and virulence in A. alternata.

Elicitors fortifies the plant resilience against metal and metalloid stress

This review addresses plant interactions with HMs, emphasizing defence mechanisms and the role of chelating agents, antioxidants and various elicitor molecules in mitigating metal toxicity in plants. To combat soil contamination with HMs, chelate assisted phytoextraction using application of natural or synthetic aminopolycarboxylic acids is an effective strategy. Plants also employ diverse signaling pathways, including hormones, calcium, reactive oxygen species, nitric oxide, and Mitogen-Activated Protein Kinases influencing gene expression and defence mechanisms to counter HM stress. Phytohormones enhance the enzymatic and non-enzymatic antioxidant defence mechanism and the level of secondary metabolites in plants when exposed to HM stress. Also it activates genes responsible for DNA repair mechanism. In addition, the plant hormones can also regulate the activity of several transporters of HMs, thereby preventing their entry into the cell. Elicitor molecules regulate metal and metalloid absorption, sequestration and transport in plants. Combining of different elicitors like jasmonic acid, calcium, salicylic acid etc. effectively mitigates metal and metalloid stress in plants. Moreover, microbes including bacteria and fungi, offer eco-friendly and efficient solution for HM remediation. Understanding these elicitors, microbes and various signaling pathways is crucial for developing strategies to enhance plant resilience to metal and metalloid stress.

Copper stress in rice: Perception, signaling, bioremediation and future prospects

Copper (Cu) is an indispensable micronutrient for plants, animals, and microorganisms and plays a vital role in different physiological processes. However, excessive Cu accumulation in agricultural soil, often through anthropogenic action, poses a potential risk to plant health and crop productivity. This review article provided a comprehensive overview of the available information regarding Cu dynamics in agricultural soils, major sources of Cu contamination, factors influencing its mobility and bioavailability, and mechanisms of Cu uptake and translocation in rice plants. This review examined the impact of Cu toxicity on the germination, growth, and photosynthesis of rice plants. It also highlighted molecular mechanisms underlying Cu stress signaling and the plant defense strategy, involving chelation, compartmentalization, and antioxidant responses. This review also identified significant areas that need further research, such as Cu uptake mechanism in rice, Cu signaling process, and the assessment of Cu-polluted paddy soil and rice toxicity under diverse environmental conditions. The development of rice varieties with reduced Cu accumulation through comprehensive breeding programs is also necessary. Regulatory measures, fungicide management, plant selection, soil and environmental investigation are recommended to prevent Cu buildup in agricultural lands to achieve sustainable agricultural goals.

Genome-wide analysis of WRKY gene family and the dynamic responses of key WRKY genes involved in cadmium stress in Brassica juncea

The WRKY transcription factors comprise one of the most extensive gene families and serve as pivotal regulators of plant responses to heavy metal stress. They contribute significantly to maintaining plant growth and development by enhancing plant tolerance. However, research on the role of WRKY genes in response to cadmium (Cd) stress in mustard is minimal. In this study, we conducted a genome-wide analysis of the mustard WRKY gene family using bioinformatics. The results revealed that 291 WRKY putative genes (BjuWRKYs) were identified in the mustard genome. These genes were categorized into seven subgroups (I, IIa-e and III) through phylogenetic analysis, with differences in motif composition between each subgroup. Homology analysis indicated that 31.62% of the genes originated from tandem duplication events. Promoter analysis revealed an abundance of abiotic stress-related elements and hormone-related elements within the BjuWRKY genes. Transcriptome analysis demonstrated that most BjuWRKY genes exhibited differential expression patterns at different Cd treatment stages in mustard. Furthermore, 10 BjuWRKY genes were confirmed to respond to Cd stress through the construction of a BjuWRKY protein interaction network, prediction of hub genes, and real-time fluorescence quantitative PCR analysis, indicating their potential involvement in Cd stress. Our findings provide a comprehensive insight into the WRKY gene family in mustard and establish a foundation for further studies of the functional roles of BjuWRKY genes in Cd stress response.

Phytoremediation of Pb-polluted soil using bermudagrass: Effect of mowing frequencies

Plant lead (Pb) tolerance and accumulation are key characteristics affecting phytoremediation efficiency. Bermudagrass is an excellent candidate for the remediation of Pb-polluted soil, and it needs to be mowed regularly. Here, we explored the effect of different mowing frequencies on the remediation of Pb-contaminated soil using bermudagrass. Mowing was found to decrease the biomass and photosynthetic efficiency of bermudagrass under Pb stress, thereby inhibiting its growth. Although mowing exacerbated membrane peroxidation, successive mowing treatments alleviated peroxidation damage by regulating enzymatic and nonenzymatic systems. A comprehensive evaluation of Pb tolerance revealed that all the mowing treatments reduced the Pb tolerance of bermudagrass, and a once-per-month mowing frequency had a less negative effect on Pb tolerance than did more frequent mowing. In terms of Pb enrichment, mowing significantly increased the Pb concentration, total Pb accumulation, translocation factor (TF), and bioenrichment factor (BCF) of bermudagrass. The total Pb accumulation was greatest under the once-a-month treatment, while the TF and BCF values were greatest under the three-times-a-month mowing treatment. Additionally, the decrease in soil pH and DOC were significantly correlated with the soil available Pb content and plant Pb accumulation parameters. The results showed that changes in the rhizosphere are crucial factors regulating Pb uptake in bermudagrass during mowing. Overall, once-a-month mowing minimally affects Pb tolerance and maximizes Pb accumulation, making it the optimal mowing frequency for soil Pb remediation by bermudagrass. This study provides a novel approach for the remediation of Pb-contaminated soil with bermudagrass based on mowing.

Micronutrient deficiency-induced oxidative stress in plants

Micronutrients like iron (Fe), zinc (Zn), copper (Cu), manganese (Mn), boron (B), nickel (Ni), and molybdenum (Mo) perform significant roles in the regulation of plant metabolism, growth, and development. Micronutrients, namely Fe, Zn, Cu, Mn, and Ni, are involved in oxidative stress and antioxidant defense as they are cofactors or activators of various antioxidant enzymes, viz., superoxide dismutase (Fe, Cu/Zn, Mn, and Ni), catalase (Fe), and ascorbate peroxidase (Fe). An effort has been made to incorporate recent advances along with classical work done on the micronutrient deficiency-induced oxidative stress and associated antioxidant responses of plants. Deficiency of a micronutrient produces ROS in the cellular compartments. Enzymatic and non-enzymatic antioxidant defense systems are often modulated by micronutrient deficiency to regulate redox balance and scavenge deleterious ROS for the safety of cellular constituents. ROS can strike cellular constituents such as lipids, proteins, and nucleic acids and can destruct cellular membranes and proteins. ROS might act as a signaling molecule and activate the antioxidant proteins by interacting with signaling partners such as respiratory burst oxidase homolog (RBOH), G-proteins, Ca2+, mitogen activated protein kinases (MAPKs), and various transcription factors (TFs). Opinions on probable ROS signaling under micronutrient deficiency have been described in this review. However, further research is required to decipher micronutrient deficiency-induced ROS generation, perception, and associated downstream signaling events, leading to the development of antioxidant responses in plants.

Heavy metal stress and mitogen activated kinase transcription factors in plants: Exploring heavy metal-ROS influences on plant signalling pathways

Due to their stationary nature, plants are exposed to a diverse range of biotic and abiotic stresses, of which heavy metal (HM) stress poses one of the most detrimental abiotic stresses, targeting diverse plant processes. HMs instigate the overproduction of reactive oxygen species (ROS), and to mitigate the adverse effects of ROS, plants induce multiple defence mechanisms. Besides the negative implications of overproduction of ROS, these molecules play a multitude of signalling roles in plants, acting as a central player in the complex signalling network of cells. One of the ROS-associated signalling mechanisms is the mitogen-activated protein kinase (MAPK) cascade, a signalling pathway which transduces extracellular stimuli into intracellular responses. Plant MAPKs have been implicated in signalling involved in stress response, phytohormone regulation, and cell cycle cues. However, the influence of various HMs on MAPK activation has not been well documented. In this review, we address and summarise several aspects related to various HM-induced ROS signalling. Additionally, we touch on how these signals activate the MAPK cascade and the downstream transcription factors that influence plant responses to HMs. Moreover, we propose a workflow that could characterise genes associated with MAPKs and their roles during plant HM stress responses.

A review of amendments for simultaneously reducing Cd and As availability in paddy soils and rice grain based on meta-analysis

Arsenic (As) and cadmium (Cd) accumulation in rice grains is a global food safety issue, and various methods and materials have been used to remove or reduce As and Cd in agricultural soils and rice grains. Despite the availability of synthesized materials capable of simultaneous As and Cd reduction from soil and rice grains, the contributions, efficiency, and main ingredients of the materials for As and Cd immobilization remain unclear. The present study first summarized the biogeochemistry of As and Cd in paddy soils and their transfer in the soil-food-human continuum. We also reviewed a series of reported inorganic and organic materials for simultaneous immobilization of As and Cd in paddy soils, and their reduction efficiency of As and Cd bioavailability were listed and compared. Based on the abovementioned materials, the study conducted a meta-analysis of 38 articles with 2565 observations to quantify the impacts of materials on simultaneous As and Cd reduction from soil and rice grains. Meta-analysis results showed that combining organic and inorganic amendments corresponded to effect sizes of -62.3% and -67.8% on As and Cd accumulation in rice grains, while the effect sizes on As and Cd reduction in paddy soils were -44.2% and -46.2%, respectively. Application of Fe based materials significantly (P < 0.05) reduced As (-54.2%) and Cd (-74.9%), accounting for the highest immobilization efficiency of As and Cd in rice grain among all the reviewed materials, outweighing S, Mn, P, Si, and Ca based materials. Moreover, precipitation, surface complexation, ion exchange, and electrostatic attraction mechanisms were involved in the co-immobilization tactics. The present study underlines the application of combined organic and inorganic amendments in simultaneous As and Cd immobilization. It also highlighted that employing Fe-incorporated biochar material may be a potential strategy for co-mitigating As and Cd pollution in paddy soils and accumulation in rice grains.

Promising New Methods Based on the SOD Enzyme and SAUR36 Gene to Screen for Canola Materials with Heavy Metal Resistance

Canola is the largest self-produced vegetable oil source in China, although excessive levels of cadmium, lead, and arsenic seriously affect its yield. Therefore, developing methods to identify canola materials with good heavy metal tolerance is a hot topic for canola breeding. In this study, canola near-isogenic lines with different oil contents (F338 (40.62%) and F335 (46.68%) as the control) and heavy metal tolerances were used as raw materials. In an experiment with 100 times the safe standard values, the superoxide dismutase (SOD) and peroxidase (POD) activities of F335 were 32.02 mmol/mg and 71.84 mmol/mg, while the activities of F338 were 24.85 mmol/mg and 63.86 mmol/mg, exhibiting significant differences. The DEGs and DAPs in the MAPK signaling pathway of the plant hormone signal transduction pathway and other related pathways were analyzed and verified using RT-qPCR. SAUR36 and SAUR32 were identified as the key differential genes. The expression of the SAUR36 gene in canola materials planted in the experimental field was significantly higher than in the control, and FY958 exhibited the largest difference (27.82 times). In this study, SOD and SAUR36 were found to be closely related to heavy metal stress tolerance. Therefore, they may be used to screen for new canola materials with good heavy metal stress tolerance for canola breeding.

Tomato SlWRKY3 Negatively Regulates Botrytis cinerea Resistance via TPK1b

Botrytis cinerea is considered the second most important fungal plant pathogen, and can cause serious disease, especially on tomato. The TPK1b gene encodes a receptor-like kinase that can positively regulate plant resistance to B. cinerea. Here, we identified a tomato WRKY transcription factor SlWRKY3 that binds to the W-box on the TPK1b promoter. It can negatively regulate TPK1b transcription, then regulate downstream signaling pathways, and ultimately negatively regulate tomato resistance to B. cinerea. SlWRKY3 interference can enhance resistance to B. cinerea, and SlWRKY3 overexpression leads to susceptibility to B. cinerea. Additionally, we found that B. cinerea can significantly, and rapidly, induce the upregulation of SlWRKY3 expression. In SlWRKY3 transgenic plants, the TPK1b expression level was negatively correlated with SlWRKY3 expression. Compared with the control, the expression of the SA pathway marker gene PR1 was downregulated in W3-OE plants and upregulated in W3-Ri plants when inoculated with B. cinerea for 48 h. Moreover, SlWRKY3 positively regulated ROS production. Overall, SlWRKY3 can inhibit TPK1b transcription in tomato, and negatively regulate resistance to B. cinerea by modulating the downstream SA and ROS pathways.

Arsenic and cadmium availability and its removal in paddy farming areas

Arsenic (As) and cadmium (Cd) accumulation in rice grain is a global concern threatening food security and safety to the growing population. As and Cd are toxic non-essential elements poisonous to animal and human at higher levels. Its accumulation in agro-ecosystems pose a public health risk to consumers of agro-ecosystem products. Due to their hazards, As and Cd sources should be cleared, avoiding entering plants and the human body. As and Cd removal in soils and grains in agro-ecosystems has been conducted by various materials (natural and synthesized), however, there are little documentation on their contribution on As and Cd removal or reduction in rice grains. This identified knowledge gap necessitate a systematically review to understand efficiency and mechanisms of As and Cd availability reduction and removal in paddy farming areas through utilization of various synthetic and modified materials. To achieve this, published peer reviewed articles between 2010 and 2024 were collected from various database i.e., Science Direct, Web of Science, Google Scholar, and Research Gate and analyzed its content in respect to As and Cd reduction and removal. Furthermore, collected data were re-analyzed to determine standardized mean differences (SMD) with 95% confidence intervals (CI). Based on 96 studies with 228 observations involving Fe, Ca, Si, and Se-based materials were identified, it was found that application of Fe, Ca, Si, and Se-based materials potentially reduced As and Cd in rice grains among various study sites and across studies. Among the studied materials, Fe-based materials observed to be more efficient compared to other utilized materials. However, there little or no information on performance of materials when used in combination and how they can improve crop productivity and soil health, thus requiring further studies. Thus, this study confirm Fe, Ca, Si, and Se modified materials have significant potential to reduce As and Cd availability in paddy farming areas and rice grains, thus necessary effort must be made to ensure materials access and availability for farmers utilization in paddy fields to reduce As and Cd accumulation.

Physiological and molecular mechanisms of ZnO quantum dots mitigating cadmium stress in Salvia miltiorrhiza

This study delved into the physiological and molecular mechanisms underlying the mitigation of cadmium (Cd) stress in the model medicinal plant Salvia miltiorrhiza through the application of ZnO quantum dots (ZnO QDs, 3.84 nm). A pot experiment was conducted, wherein S. miltiorrhiza was subjected to Cd stress for six weeks with foliar application of 100 mg/L ZnO QDs. Physiological analyses demonstrated that compared to Cd stress alone, ZnO QDs improved biomass, reduced Cd accumulation, increased the content of photosynthetic pigments (chlorophyll and carotenoids), and enhanced the levels of essential nutrient elements (Ca, Mn, and Cu) under Cd stress. Furthermore, ZnO QDs significantly lowered Cd-induced reactive oxygen species (ROS) content, including H2O2, O2-, and MDA, while enhancing the activity of antioxidant enzymes (SOD, POD, APX, and GSH-PX). Additionally, ZnO QDs promoted the biosynthesis of primary and secondary metabolites, such as total protein, soluble sugars, terpenoids, and phenols, thereby mitigating Cd stress in S. miltiorrhiza. At the molecular level, ZnO QDs were found to activate the expression of stress signal transduction-related genes, subsequently regulating the expression of downstream target genes associated with metal transport, cell wall synthesis, and secondary metabolite synthesis via transcription factors. This activation mechanism contributed to enhancing Cd tolerance in S. miltiorrhiza. In summary, these findings shed light on the mechanisms underlying the mitigation of Cd stress by ZnO QDs, offering a potential nanomaterial-based strategy for enhancing Cd tolerance in medicinal plants.

Deciphering the regulation of transporters and mitogen-activated protein kinase in arsenic and iron exposed rice

This study investigates the influence of arsenic (As) and iron (Fe) on the molecular aspects of rice plants. The mRNA-abundance of As (OsLsi, OsPHT, OsNRAMP1, OsABCC1) and Fe (OsIRT, OsNRAMP1, OsYSL, OsFRDL1, OsVIT2, OsSAMS1, OsNAS, OsNAAT1, OsDMAS1, OsTOM1, OsFER) related genes has been observed in 12-d old As and Fe impacted rice varieties. Analyses of phytosiderophores synthesis and Fe-uptake genes affirm the existence of specialized Fe-uptake strategies in rice with varieties PB-1 and Varsha favouring strategy I and II, respectively. Expression of OsNAS3, OsVIT2, OsFER and OsABCC1 indicated PB-1's tolerance towards Fe and As. Analysis of mitogen-activated protein kinase cascade members (OsMKK3, OsMKK4, OsMKK6, OsMPK3, OsMPK4, OsMPK7, and OsMPK14) revealed their importance in the fine adjustment of As/Fe in the rice system. A conditional network map was generated based on the gene expression pattern that unfolded the differential dynamics of both rice varieties. The mating based split ubiquitin system determined the interaction of OsIRT1 with OsMPK3, and OsLsi1 with both OsMPK3 and OsMPK4. In-silico tools also confirmed the binding affinities of OsARM1 with OsLsi1, OsMPK3 and OsMPK4, and of OsIDEF1/OsIRO2 with OsIRT1 and OsMPK3, supporting our hypothesis that OsARM1, OsIDEF1, OsIRO2 were active in the connections discovered by mbSUS.

Unveiling Innovative Approaches to Mitigate Metals/Metalloids Toxicity for Sustainable Agriculture

Due to anthropogenic activities, environmental pollution of heavy metals/metalloids (HMs) has increased and received growing attention in recent decades. Plants growing in HM-contaminated soils have slower growth and development, resulting in lower agricultural yield. Exposure to HMs leads to the generation of free radicals (oxidative stress), which alters plant morpho-physiological and biochemical pathways at the cellular and tissue levels. Plants have evolved complex defense mechanisms to avoid or tolerate the toxic effects of HMs, including HMs absorption and accumulation in cell organelles, immobilization by forming complexes with organic chelates, extraction via numerous transporters, ion channels, signaling cascades, and transcription elements, among others. Nonetheless, these internal defensive mechanisms are insufficient to overcome HMs toxicity. Therefore, unveiling HMs adaptation and tolerance mechanisms is necessary for sustainable agriculture. Recent breakthroughs in cutting-edge approaches such as phytohormone and gasotransmitters application, nanotechnology, omics, and genetic engineering tools have identified molecular regulators linked to HMs tolerance, which may be applied to generate HMs-tolerant future plants. This review summarizes numerous systems that plants have adapted to resist HMs toxicity, such as physiological, biochemical, and molecular responses. Diverse adaptation strategies have also been comprehensively presented to advance plant resilience to HMs toxicity that could enable sustainable agricultural production.

Transcriptome analysis reveals cadmium exposure enhanced the isoquinoline alkaloid biosynthesis and disease resistance in Coptis chinensis

Coptis chinensis Franch is a perennial herb from the Ranunculaceae family with a long history of medicinal use. As the medicinal part, the rhizome of coptis often accumulates excessive cadmium (Cd) even at low concentrations in the soil, which not only compromises its medicinal safety but also raises concerns about adverse effects on human health. Therefore, effective strategies are needed to mitigate this accumulation and ensure its safe use in traditional medicine. This study utilized transcriptome profiling and physiological analysis to explore molecular mechanisms associated with ecological significance and the active accumulation of Cd in C. chinensis. The response to Cd in C. chinensis was assessed through RNA sequencing, Cd determination and isoquinoline alkaloid measurement using its roots, stems, and leaves. The transcriptome revealed, a total of 2667, 2998, or 2815 up-regulated deferentially expressed genes in roots, stems or leaves in response to Cd exposure. Furthermore, we identified phenylpropanoid and isoquinoline alkaloid biosynthesis as the key pathways response to Cd exposure, which suggests that C. chinensis may improve its tolerance to Cd through regulating the phenylpropanoid biosynthesis pathway. Under Cd exposure, plant-pathogen interaction in leaves was identified as the key pathway, which indicates that upregulation of genes involved in plant-pathogen interaction could enhance disease resistance in C. chinensis. WGCNA analysis identified WRKY8 (Cluster-55763.31419) and WRKY47 (Cluster-55763.221590) as potential regulators of secondary metabolic synthesis and plant-pathogen interaction pathway in C. chinensis triggered by Cd. The measurement of berberine, coptisine, palmatine, and epiberberine also demonstrated that Cd simulated the four isoquinoline alkaloids in roots. Therefore, our study not only presented a transcriptome expression profiles that revealed significant upregulation of genes involved in metal transport and detoxification pathways but also suggested a possible mechanism to cope with Cd accumulation. This knowledge provides a new insight into gene manipulation for controlling Cd accumulation, enhancing resistance and promoting synthesis of secondary metabolites with potential medicinal properties in other medicinal plant species.

Integrative Physiological and Transcriptome Analysis Reveals the Mechanism of Cd Tolerance in Sinapis alba

Recently, pollution caused by the heavy metal Cd has seriously affected the environment and agricultural crops. While Sinapis alba is known for its edible and medicinal value, its tolerance to Cd and molecular response mechanism remain unknown. This study aimed to analyze the tolerance of S. alba to Cd and investigate its molecular response mechanism through transcriptomic and physiological indicators. To achieve this, S. alba seedlings were treated with different concentrations of CdCl2 (0.25 mmol/L, 0.5 mmol/L, and 1.0 mmol/L) for three days. Based on seedling performance, S. alba exhibited some tolerance to a low concentration of Cd stress (0.25 mmol/L CdCl2) and a strong Cd accumulation ability in its roots. The activities and contents of several antioxidant enzymes generally exhibited an increase under the treatment of 0.25 mmol/L CdCl2 but decreased under the treatment of higher CdCl2 concentrations. In particular, the proline (Pro) content was extremely elevated under the 0.25 and 0.5 mmol/L CdCl2 treatments but sharply declined under the 1.0 mmol/L CdCl2 treatment, suggesting that Pro is involved in the tolerance of S. alba to low concentration of Cd stress. In addition, RNA sequencing was utilized to analyze the gene expression profiles of S. alba exposed to Cd (under the treatment of 0.25 mmol/L CdCl2). The results indicate that roots were more susceptible to disturbance from Cd stress, as evidenced by the detection of 542 differentially expressed genes (DEGs) in roots compared to only 37 DEGs in leaves. GO and KEGG analyses found that the DEGs induced by Cd stress were primarily enriched in metabolic pathways, plant hormone signal transduction, and the biosynthesis of secondary metabolites. The key pathway hub genes were mainly associated with intracellular ion transport and cell wall synthesis. These findings suggest that S. alba is tolerant to a degree of Cd stress, but is also susceptible to the toxic effects of Cd. Furthermore, these results provide a theoretical basis for understanding Cd tolerance in S. alba.

Toxic effects of lead on plants: integrating multi-omics with bioinformatics to develop Pb-tolerant crops

MAIN CONCLUSION

Lead disrupts plant metabolic homeostasis and key structural elements. Utilizing modern biotechnology tools, it's feasible to develop Pb-tolerant varieties by discovering biological players regulating plant metabolic pathways under stress. Lead (Pb) has been used for a variety of purposes since antiquity despite its toxic nature. After arsenic, lead is the most hazardous heavy metal without any known beneficial role in the biological system. It is a crucial inorganic pollutant that affects plant biochemical and morpho-physiological attributes. Lead toxicity harms plants throughout their life cycle and the extent of damage depends on the concentration and duration of exposure. Higher levels of lead exposure disrupt numerous key metabolic activities of plants including oxygen-evolving complex, organelles integrity, photosystem II connectivity, and electron transport chain. This review summarizes the detrimental effects of lead toxicity on seed germination, crop growth, and yield, oxidative and ultra-structural alterations, as well as nutrient absorption, transport, and assimilation. Further, it discusses the Pb-induced toxic modulation of stomatal conductance, photosynthesis, respiration, metabolic-enzymatic activity, osmolytes accumulation, and antioxidant activity. It is a comprehensive review that reports on omics-based studies along with morpho-physiological and biochemical modifications caused by lead stress. With advances in DNA sequencing technologies, genomics and transcriptomics are gradually becoming popular for studying Pb stress effects in plants. Proteomics and metabolomics are still underrated and there is a scarcity of published data, and this review highlights both their technical and research gaps. Besides, there is also a discussion on how the integration of omics with bioinformatics and the use of the latest biotechnological tools can aid in developing Pb-tolerant crops. The review concludes with core challenges and research directions that need to be addressed soon.

Genome-wide identification of the mitogen-activated kinase gene family from Limonium bicolor and functional characterization of LbMAPK2 under salt stress

BACKGROUND

Mitogen-activated protein kinases (MAPKs) are ubiquitous signal transduction components in eukaryotes. In plants, MAPKs play an essential role in growth and development, phytohormone regulation, and abiotic stress responses. The typical recretohalophyte Limonium bicolor (Bunge) Kuntze has multicellular salt glands on its stems and leaves; these glands secrete excess salt ions from its cells to mitigate salt damage. The number, type, and biological function of L. bicolor MAPK genes are unknown.

RESULTS

We identified 20 candidate L. bicolor MAPK genes, which can be divided into four groups. Of these 20 genes, 17 were anchored to 7 chromosomes, while LbMAPK18, LbMAPK19, and LbMAPK20 mapped to distinct scaffolds. Structure analysis showed that the predicted protein LbMAPK19 contains the special structural motif TNY in its activation loop, whereas the other LbMAPK members harbor the conserved TEY or TDY motif. The promoters of most LbMAPK genes carry cis-acting elements related to growth and development, phytohormones, and abiotic stress. LbMAPK1, LbMAPK2, LbMAPK16, and LbMAPK20 are highly expressed in the early stages of salt gland development, whereas LbMAPK4, LbMAPK5, LbMAPK6, LbMAPK7, LbMAPK11, LbMAPK14, and LbMAPK15 are highly expressed during the late stages. These 20 LbMAPK genes all responded to salt, drought and ABA stress. We explored the function of LbMAPK2 via virus-induced gene silencing: knocking down LbMAPK2 transcript levels in L. bicolor resulted in fewer salt glands, lower salt secretion ability from leaves, and decreased salt tolerance. The expression of several genes [LbTTG1 (TRANSPARENT TESTA OF GL1), LbCPC (CAPRICE), and LbGL2 (GLABRA2)] related to salt gland development was significantly upregulated in LbMAPK2 knockdown lines, while the expression of LbEGL3 (ENHANCER OF GL3) was significantly downregulated.

CONCLUSION

These findings increase our understanding of the LbMAPK gene family and will be useful for in-depth studies of the molecular mechanisms behind salt gland development and salt secretion in L. bicolor. In addition, our analysis lays the foundation for exploring the biological functions of MAPKs in an extreme halophyte.

Reactive oxygen species- and nitric oxide-dependent regulation of ion and metal homeostasis in plants

Deterioration and impoverishment of soil, caused by environmental pollution and climate change, result in reduced crop productivity. To adapt to hostile soils, plants have developed a complex network of factors involved in stress sensing, signal transduction, and adaptive responses. The chemical properties of reactive oxygen species (ROS) and reactive nitrogen species (RNS) allow them to participate in integrating the perception of external signals by fine-tuning protein redox regulation and signal transduction, triggering specific gene expression. Here, we update and summarize progress in understanding the mechanistic basis of ROS and RNS production at the subcellular level in plants and their role in the regulation of ion channels/transporters at both transcriptional and post-translational levels. We have also carried out an in silico analysis of different redox-dependent modifications of ion channels/transporters and identified cysteine and tyrosine targets of nitric oxide in metal transporters. Further, we summarize possible ROS- and RNS-dependent sensors involved in metal stress sensing, such as kinases and phosphatases, as well as some ROS/RNS-regulated transcription factors that could be involved in metal homeostasis. Understanding ROS- and RNS-dependent signaling events is crucial to designing new strategies to fortify crops and improve plant tolerance of nutritional imbalance and metal toxicity.

Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses

The present day's ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant's innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the 'omics' toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant's genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence 'multi-omics') integrated-omics approaches can decipher the plant's abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop's variable abiotic stress tolerance to ensure food security under changing environmental circumstances.

Detoxifying the heavy metals: a multipronged study of tolerance strategies against heavy metals toxicity in plants

Heavy metal concentrations exceeding permissible limits threaten human life, plant life, and all other life forms. Different natural and anthropogenic activities emit toxic heavy metals in the soil, air, and water. Plants consume toxic heavy metals from their roots and foliar part inside the plant. Heavy metals may interfere with various aspects of the plants, such as biochemistry, bio-molecules, and physiological processes, which usually translate into morphological and anatomical changes. They use various strategies to deal with the toxic effects of heavy metal contamination. Some of these strategies include restricting heavy metals to the cell wall, vascular sequestration, and synthesis of various biochemical compounds, such as phyto-chelators and organic acids, to bind the free moving heavy metal ions so that the toxic effects are minimized. This review focuses on several aspects of genetics, molecular, and cell signaling levels, which integrate to produce a coordinated response to heavy metal toxicity and interpret the exact strategies behind the tolerance of heavy metals stress. It is suggested that various aspects of some model plant species must be thoroughly studied to comprehend the approaches of heavy metal tolerance to put that knowledge into practical use.

Heavy Metals, Their Phytotoxicity, and the Role of Phenolic Antioxidants in Plant Stress Responses with Focus on Cadmium: Review

The current state of heavy metal (HM) environmental pollution problems was considered in the review: the effects of HMs on the vital activity of plants and the functioning of their antioxidant system, including phenolic antioxidants. The latter performs an important function in the distribution and binding of metals, as well as HM detoxification in the plant organism. Much attention was focused on cadmium (Cd) ions as one of the most toxic elements for plants. The data on the accumulation of HMs, including Cd in the soil, the entry into plants, and the effect on their various physiological and biochemical processes (photosynthesis, respiration, transpiration, and water regime) were analyzed. Some aspects of HMs, including Cd, inactivation in plant tissues, and cell compartments, are considered, as well as the functioning of various metabolic pathways at the stage of the stress reaction of plant cells under the action of pollutants. The data on the effect of HMs on the antioxidant system of plants, the accumulation of low molecular weight phenolic bioantioxidants, and their role as ligand inactivators were summarized. The issues of polyphenol biosynthesis regulation under cadmium stress were considered. Understanding the physiological and biochemical role of low molecular antioxidants of phenolic nature under metal-induced stress is important in assessing the effect/aftereffect of Cd on various plant objects-the producers of these secondary metabolites are widely used for the health saving of the world's population. This review reflects the latest achievements in the field of studying the influence of HMs, including Cd, on various physiological and biochemical processes of the plant organism and enriches our knowledge about the multifunctional role of polyphenols, as one of the most common secondary metabolites, in the formation of plant resistance and adaptation.

Cadmium exposure-triggered growth retardation in Hyphantria cunea larvae involves disturbances in food utilization and energy metabolism

Serious environmental pollution in the ecosystem makes phytophagous insects face a great risk of exposure to pollutants, especially heavy metals. This study aims to understand the effects of Cd exposure on the growth and development of Hyphantria cunea and to elucidate the mechanism of growth toxicity induced by Cd from the perspective of food utilization and energy metabolism. Our results showed that the larval basal growth data, growth index, fitness index, and standard growth index were significantly decreased after feeding on Cd-containing artificial diets. The Cd-treated larvae had significantly higher digestibility than the untreated larvae. However, the food consumption, efficiency of conversion of digested food, and efficiency of conversion of ingested food were significantly lower than those of untreated larvae. Eight key metabolites in the glycolysis pathway and six key metabolites in the tricarboxylic acid cycle pathway were significantly reduced in Cd-treated larvae. The mRNA expression levels of two regulatory genes (6-phosphofructokinase 1 and hexokinase-1) belonging to two key enzymes in the glycolysis pathway and four regulatory genes (isocitrate dehydrogenase-1, isocitrate dehydrogenase-3, citrate synthase, and oxoglutarate dehydrogenase) belonging to three key enzymes in the tricarboxylic acid cycle pathway were significantly lower in the Cd-treated group than in the control group. Furthermore, most fitness-related traits were significantly and positively correlated with food utilization (except approximate digestibility) or energy metabolism parameters. Taken together, Cd exposure-triggered growth retardation of H. cunea larvae is a consequence of disturbances in food utilization and energy metabolism, thereby emphasizing the toxicity of heavy metals.

The Effect of Cadmium on Plants in Terms of the Response of Gene Expression Level and Activity

Cadmium (Cd) is a heavy metal that can cause damage to living organisms at different levels. Even at low concentrations, Cd can be toxic to plants, causing harm at multiple levels. As they are unable to move away from areas contaminated by Cd, plants have developed various defence mechanisms to protect themselves. Hyperaccumulators, which can accumulate and detoxify heavy metals more efficiently, are highly valued by scientists studying plant accumulation and detoxification mechanisms, as they provide a promising source of genes for developing plants suitable for phytoremediation techniques. So far, several genes have been identified as being upregulated when plants are exposed to Cd. These genes include genes encoding transcription factors such as iron-regulated transporter-like protein (ZIP), natural resistance associated macrophage protein (NRAMP) gene family, genes encoding phytochelatin synthases (PCs), superoxide dismutase (SOD) genes, heavy metal ATPase (HMA), cation diffusion facilitator gene family (CDF), Cd resistance gene family (PCR), ATP-binding cassette transporter gene family (ABC), the precursor 1-aminocyclopropane-1-carboxylic acid synthase (ACS) and precursor 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) multigene family are also influenced. Thanks to advances in omics sciences and transcriptome analysis, we are gaining more insights into the genes involved in Cd stress response. Recent studies have also shown that Cd can affect the expression of genes related to antioxidant enzymes, hormonal pathways, and energy metabolism.

Transcriptome Analysis Reveals Differentially Expressed Genes Involved in Cadmium and Arsenic Accumulation in Tea Plant (Camellia sinensis)

Tea (Camellia sinensis) is the second most consumed drink in the world. Rapid industrialization has caused various impacts on nature and increased pollution by heavy metals. However, the molecular mechanisms of cadmium (Cd) and arsenic (As) tolerance and accumulation in tea plants are poorly understood. The present study focused on the effects of heavy metals Cd and As on tea plants. Transcriptomic regulation of tea roots after Cd and As exposure was analyzed to explore the candidate genes involved in Cd and As tolerance and accumulation. In total, 2087, 1029, 1707, and 366 differentially expressed genes (DEGs) were obtained in Cd1 (with Cd treatment for 10 days) vs. CK (without Cd treatment), Cd2 (with Cd treatment for 15 days) vs. CK, As1 (with As treatment for 10 days) vs. CK (without Cd treatment), and As2 (with As treatment for 15 days) vs. CK, respectively. Analysis of DEGs showed that a total of 45 DEGs with the same expression patterns were identified in four pairwise comparison groups. One ERF transcription factor (CSS0000647) and six structural genes (CSS0033791, CSS0050491, CSS0001107, CSS0019367, CSS0006162, and CSS0035212) were only increased at 15 d of Cd and As treatments. Using weighted gene co-expression network analysis (WGCNA) revealed that the transcription factor (CSS0000647) was positively correlated with five structural genes (CSS0001107, CSS0019367, CSS0006162, CSS0033791, and CSS0035212). Moreover, one gene (CSS0004428) was significantly upregulated in both Cd and As treatments, suggesting that these genes might play important roles in enhancing the tolerance to Cd and As stresses. These results provide candidate genes to enhance multi-metal tolerance through the genetic engineering technology.

Genome-wide annotation and expression analysis of WRKY and bHLH transcriptional factor families reveal their involvement under cadmium stress in tomato (Solanum lycopersicum L.)

The WRKY and bHLH transcription factors have been implicated in the regulation of gene expression during various physiological processes in plants, especially in plant stress responses. However, little information about the heavy metal-responsive SlWRKY and SlbHLH in tomato (Solanum lycopersicum) is available. We performed a genome-wide investigation for these two TF families in S. lycopersicum and determined their role in cadmium (Cd) stress tolerance. Furthermore, ortholog analysis with the Arabidopsis genome led to classifying WRKY and bHLH ortholog genes into nine and 11 clusters, respectively. The comparative phylogenetic analysis revealed duplication events and gene loss in Arabidopsis and S. lycopersicum, which occurred during evolution both before and after the last common ancestor of the two species. Orthologous relationships are also supported by additional evidence, such as gene structure, conserved motif compositions, and protein-protein interaction networks for the majority of genes, suggesting their similar functions. A comprehensive transcriptomics analysis revealed that both WRKY and bHLH genes were differentially expressed in response to cadmium stress as compared with control plants. A gene ontology analysis revealed that most WRKYs and bHLHs are DNA-binding essential proteins that regulate gene expression positively and negatively. Analyses of interaction networks revealed that both WRKYs and bHLHs mediate networks implicated in several stress-signaling pathways. The findings of this work may help us to comprehend the intricate transcriptional control of WRKY and bHLH genes and identify potential stress-responsive genes relevant to tomato genetic improvement. Moreover, identifying heavy metal stress-responsive WRKY and bHLH genes in S. lycopersicum will provide fundamental insights for developing new heavy metal stress-tolerant varieties of tomato crops.

Rhizospheric microbiomics integrated with plant transcriptomics provides insight into the Cd response mechanisms of the newly identified Cd accumulator Dahlia pinnata

Phytoremediation that depends on excellent plant resources and effective enhancing measures is important for remediating heavy metal-contaminated soils. This study investigated the cadmium (Cd) tolerance and accumulation characteristics of Dahlia pinnata Cav. to evaluate its Cd phytoremediation potential. Testing in soils spiked with 5-45 mg kg-1 Cd showed that D. pinnata has a strong Cd tolerance capacity and appreciable shoot Cd bioconcentration factors (0.80-1.32) and translocation factors (0.81-1.59), indicating that D. pinnata can be defined as a Cd accumulator. In the rhizosphere, Cd stress (45 mg kg-1 Cd) did not change the soil physicochemical properties but influenced the bacterial community composition compared to control conditions. Notably, the increased abundance of the bacterial phylum Patescibacteria and the dominance of several Cd-tolerant plant growth-promoting rhizobacteria (e.g., Sphingomonas, Gemmatimonas, Bryobacter, Flavisolibacter, Nocardioides, and Bradyrhizobium) likely facilitated Cd tolerance and accumulation in D. pinnata. Comparative transcriptomic analysis showed that Cd significantly induced (P < 0.001) the expression of genes involved in lignin synthesis in D. pinnata roots and leaves, which are likely to fix Cd2+ to the cell wall and inhibit Cd entry into the cytoplasm. Moreover, Cd induced a sophisticated signal transduction network that initiated detoxification processes in roots as well as ethylene synthesis from methionine metabolism to regulate Cd responses in leaves. This study suggests that D. pinnata can be potentially used for phytoextraction and improves our understanding of Cd-response mechanisms in plants from rhizospheric and molecular perspectives.

Reprisal of Schima superba to Mn stress and exploration of its defense mechanism through transcriptomic analysis

One of the most diverse protein families, ATP-binding cassette (ABC) transporters, play a role in disease resistance, heavy metal tolerance, and food absorption.Differentially expressed genes contribute in the investigation of plant defense mechanisms under varying stress conditions. To elucidate the molecular mechanisms involved in Mn metal stress, we performed a transcriptomic analysis to explore the differential gene expression in Schima superba with the comparison of control. A total of 79.84 G clean data was generated and 6558 DEGs were identified in response to Mn metal stress. Differentially expressed genes were found to be involved in defense, signaling pathways, oxidative burst, transcription factors and stress responses. Genes important in metal transport were more expressive in Mn stress than control plants. The investigation of cis-acting regions in the ABC family indicated that these genes might be targeted by a large variety of trans-acting elements to control a variety of stress circumstances. Moreover, genes involved in defense responses, the mitogen-activated protein kinase (MAPK) signaling and signal transduction in S. superba were highly induced in Mn stress. Twenty ABC transporters were variably expressed on 1st, 5th, and 10th day of Mn treatment, according to the qRT PCR data. Inclusively, our findings provide an indispensable foundation for an advanced understanding of the metal resistance mechanisms. Our study will enrich the sequence information of S. superba in a public database and would provide a new understanding of the molecular mechanisms of heavy metal tolerance and detoxification.

Transcriptome analysis of the response of Hypomyces chrysospermus to cadmium stress

Hypomyces chrysospermus is a fungal parasite that grows on Boletus species. One isolated strain of H. chrysospermus from B. griseus was obtained and proved of strong ability to tolerate and absorb cadmium (Cd) by previous research. However, the molecular mechanisms of underlying the resistance of H. chrysospermus to Cd stress have not been investigated. This study aimed to assess the effect of Cd stress on the global transcriptional regulation of H. chrysospermus. A total of 1,839 differentially expressed genes (DEGs) were identified under 120 mg/l Cd stress. Gene ontology (GO) enrichment analysis revealed that large amounts of DEGs were associated with cell membrane components, oxidoreductase activity, and transport activity. KEGG enrichment analysis revealed that these DEGs were mainly involved in the translation, amino acid metabolism, transport and catabolism, carbohydrate metabolism, and folding/sorting and degradation pathways under Cd stress. Moreover, the expression of DEGs encoding transporter proteins, antioxidant enzymes, nonenzymatic antioxidant proteins, detoxification enzymes, and transcription factors was associated with the Cd stress response. These results provide insights into the molecular mechanisms underlying Cd tolerance in H. chrysospermus and serve as a valuable reference for further studies on the detoxification mechanisms of heavy metal-tolerant fungi. Our findings may also facilitate the development of new and improved fungal bioremediation strategies.

Role of phytomelatonin responsive to metal stresses: An omics perspective and future scenario

A pervasive melatonin (N-acetyl-5-methoxytryptamine) reveals a crucial role in stress tolerance and plant development. Melatonin (MT) is a unique molecule with multiple phenotypic expressions and numerous actions within the plants. It has been extensively studied in crop plants under different abiotic stresses such as drought, salinity, heat, cold, and heavy metals. Mainly, MT role is appraised as an antioxidant molecule that deals with oxidative stress by scavenging reactive oxygen species (ROS) and modulating stress related genes. It improves the contents of different antioxidant enzyme activities and thus, regulates the redox hemostasis in crop plants. In this comprehensive review, regulatory effects of melatonin in plants as melatonin biosynthesis, signaling pathway, modulation of stress related genes and physiological role of melatonin under different heavy metal stress have been reviewed in detail. Further, this review has discussed how MT regulates different genes/enzymes to mediate defense responses and overviewed the context of transcriptomics and phenomics followed by the metabolomics pathways in crop plants.